bluuebunny/crossref_metadata_2025 huggingface dataset:
Deciphering Historical Water-Quality Changes Recorded in Sediments Using eDNA
Authors: Sun Jing , Chen Xueping , Yu Juan , Chen Zheng , Liu Lihua , Yue Yihong , Fu Zhiwei , Yang Ming , Wang Fushun
Published: June 2021

Reservoir sediments harbor abundant bacterial communities that are sensitive to substances transferred from the water column and might record historic water quality in environmental DNA (eDNA). The unique bacterial community along the sediment profile were retrieved based on eDNA in a reservoir to investigate potential links between water quality and the microbial population on a long-time scale. Bacterial communities in sediment samples gathered into three clusters along the depth (depths of 18–38, 8–18, and 1–7 cm). These three sections accumulated during three periods in which water quality was recorded in history (the pristine stage, degraded stage and remediated stage). Sediment samples from the degraded stage had lower microbial community evenness and diversity and higher microgAMBI indices than the other two sections, suggesting that poor water quality during that period was recorded in sedimental eDNA. After decades of biogeochemical cycles, statistical analysis revealed that the main factors affecting the microbial community were bromine, chlorine, and high molecular-weight PAHs in sediments from the degraded stage. The relevant functional groups Dehalococcoidia, Gemmatimonadales, Sva0485, Burkholderiales and Xanthomonadales might be indicators of the historical loading of these pollutants. Amending the microgAMBI index with our functional group of pollution can better illustrate the significant long-term environmental changes caused by historic anthropogenic activities. In sediments from the pristine stage with less pollution input, DIC (dissolved inorganic carbon) from the karst landform was the dominant factor controlling microbial communities. Whereas, the surface sediments, which accumulated during the remediated stage, had more correlation with chemistry, such as sulfate and heavy metals, in the overlying water. Our research revealed that historical changes in the water condition, that can be affected by anthropogenic activities, can be depicted by changes in the bacterial communities stored in the sediment using sedimental eDNA. Assessments of the bacterial communities in the sediments, either by describing their biodiversity or using particular species as indicators, would be potential proxies to describe historical environmental development of microbial communities.
Prediction of Cadmium Transfer From Soil to Potato in Karst Soils, China
Authors: Liu Ke , Liu Hongyan , Zhou Xianyong , Chen Zhu , Wang Xulian
Published: June 2021

Contamination of food with the heavy metal Cd is a significant global concern. In this study, a field survey was performed to investigate the characteristics of Cd transfer from soil to potato tubers (n = 105). The results showed that the bioaccumulation factor of the potato tuber ranged from about 0.1 to 1. The soil threshold of Cd derived from the cumulative probability distribution was 0.15 mg kg−1 in order to protect 95% of potatoes. Additionally, prediction models for Cd transfer were constructed based on soil properties and the concentration of CaCl2-extractable soil Cd. The results of the analysis showed that pH was the critical factor affecting Cd uptake by potatoes. Additionally, the R2 of different empirical models increased from 0.354 to 0.715 as the number of soil parameters was increased, and the predicted soil Cd concentration approached the measured values at values of about 0–15 mg kg−1. The results of this study suggest that the probability distribution method was stricter than the empirical prediction models for estimating the ecological risk of Cd contamination of potatoes in karst soils.
Does Phenological Plasticity Help or Hinder Range Shifts Under Climate Change?
Authors: Zettlemoyer Meredith A. , Peterson Megan L.
Published: June 2021

Climate warming is predicted to shift species’ ranges as previously uninhabitable environments just beyond the leading range edges become suitable habitat and trailing range edges become increasingly unsuitable. Understanding which aspects of the environment and species traits mediate these range shifts is critical for understanding species’ possible redistributions under global change, yet we have a limited understanding of the ecological and evolutionary responses underlying population spread or extinction at species’ range edges. Within plant populations, shifts in flowering phenology have been one of the strongest and most consistent responses to climate change, and are likely to play an important role in mediating population dynamics within and beyond species’ ranges. However, the role of phenological shifts, and particularly phenological plasticity, in species’ range shifts remains relatively unstudied. Here, we synthesize literature on phenology, plasticity, and adaptation to suggest ways in which phenological responses to climate may vary across species’ ranges and review the empirical evidence for and against these hypotheses. We then outline how phenological plasticity could facilitate or hinder persistence and potential consequences of phenological plasticity in range expansions, including phenological cues, shifts in correlated traits, altered species interactions, and effects on gene flow. Finally, we suggest future avenues for research, such as characterizing reaction norms for phenology across a species’ range and in beyond-the-range transplant experiments. Given the prevalence and magnitude of phenological shifts, future work should carefully dissect its costs and benefits for population persistence, and incorporate phenological plasticity into models predicting species’ persistence and geographic range shifts under climate change.
Further Evidence That OPG rs2073618 Is Associated With Increased Risk of Musculoskeletal Symptoms in Patients Receiving Aromatase Inhibitors for Early Breast Cancer
Authors: Hertz Daniel L. , Smith Karen Lisa , Zong Yuhua , Gersch Christina L. , Pesch Andrea M. , Lehman Jennifer , Blackford Amanda L. , Henry N. Lynn , Kidwell Kelley M. , Rae James M. , Stearns Vered
Published: June 2021

Background

Aromatase inhibitors (AI) reduce recurrence and death in patients with early-stage hormone receptor-positive (HR +) breast cancer. Treatment-related toxicities, including AI-induced musculoskeletal symptoms (AIMSS), are common and may lead to early AI discontinuation. The objective of this study was to replicate previously reported associations for candidate germline genetic polymorphisms with AIMSS.

Methods

Women with stage 0-III HR + breast cancer initiating adjuvant AI were enrolled in a prospective clinic-based observational cohort. AIMSS were assessed by patient-reported outcomes (PRO) including the PROMIS pain interference and physical function measures plus the FACT-ES joint pain question at baseline and after 3 and 6 months. For the primary analysis, AIMSS were defined as ≥ 4-point increase in the pain interference T-score from baseline. Secondary AIMSS endpoints were defined as ≥ 4-point decrease in the physical function T-score from baseline and as ≥ 1-point increase on the FACT-ES joint pain question from baseline. The primary hypothesis was that TCL1A rs11849538 would be associated with AIMSS. Twelve other germline variants in CYP19A1, VDR, PIRC66, OPG, ESR1, CYP27B1, CYP17A1, and RANKL were also analyzed assuming a dominant genetic effect and prespecified direction of effect on AIMSS using univariate logistic regression with an unadjusted α = 0.05. Significant univariate associations in the expected direction were adjusted for age, race, body mass index (BMI), prior taxane, and the type of AI using multivariable logistic regression.

Results

A total of 143 participants with PRO and genetic data were included in this analysis, most of whom were treated with anastrozole (78%) or letrozole (20%). On primary analysis, participants carrying TCL1A rs11849538 were not more likely to develop AIMSS (odds ratio = 1.29, 95% confidence interval: 0.55–3.07, p = 0.56). In the statistically uncorrected secondary analysis, OPG rs2073618 was associated with AIMSS defined by worsening on the FACT-ES joint pain question (OR = 3.33, p = 0.004), and this association maintained significance after covariate adjustment (OR = 3.98, p = 0.003).

Conclusion

Carriers of OPG rs2073618 may be at increased risk of AIMSS. If confirmed in other cohorts, OPG genotyping can be used to identify individuals with HR + early breast cancer in whom alternate endocrine therapy or interventions to enhance symptom detection and implement strategies to reduce musculoskeletal symptoms may be needed.
Characterizing Promoter and Enhancer Sequences by a Deep Learning Method
Authors: Zeng Xin , Park Sung-Joon , Nakai Kenta
Published: June 2021

Promoters and enhancers are well-known regulatory elements modulating gene expression. As confirmed by high-throughput sequencing technologies, these regulatory elements are bidirectionally transcribed. That is, promoters produce stable mRNA in the sense direction and unstable RNA in the antisense direction, while enhancers transcribe unstable RNA in both directions. Although it is thought that enhancers and promoters share a similar architecture of transcription start sites (TSSs), how the transcriptional machinery distinctly uses these genomic regions as promoters or enhancers remains unclear. To address this issue, we developed a deep learning (DL) method by utilizing a convolutional neural network (CNN) and the saliency algorithm. In comparison with other classifiers, our CNN presented higher predictive performance, suggesting the overarching importance of the high-order sequence features, captured by the CNN. Moreover, our method revealed that there are substantial sequence differences between the enhancers and promoters. Remarkably, the 20–120 bp downstream regions from the center of bidirectional TSSs seemed to contribute to the RNA stability. These regions in promoters tend to have a larger number of guanines and cytosines compared to those in enhancers, and this feature contributed to the classification of the regulatory elements. Our CNN-based method can capture the complex TSS architectures. We found that the genomic regions around TSSs for promoters and enhancers contribute to RNA stability and show GC-biased characteristics as a critical determinant for promoter TSSs.
Increase of Neutrophil Extracellular Traps, Mitochondrial DNA and Nuclear DNA in Newly Diagnosed Type 1 Diabetes Children but Not in High-Risk Children
Authors: Skoglund Camilla , Appelgren Daniel , Johansson Ingela , Casas Rosaura , Ludvigsson Johnny
Published: June 2021

Neutrophil extracellular traps (NETs) and mitochondrial DNA (mtDNA) are inflammatory mediators involved in the development of type 1 diabetes (T1D). Pancreas-infiltrating neutrophils can release NETs, contributing to the inflammatory process. Levels of NETs are increased in serum from patients with T1D and mtDNA is increased in adult T1D patients. Our aim was to investigate extracellular DNA (NETs, mtDNA and nuclear DNA) in children with newly diagnosed T1D and in children at high risk of the disease. We also elucidated if extracellular DNA short after diagnosis could predict loss of endogenous insulin production. Samples were analysed for mtDNA and nuclear DNA using droplet digital PCR and NETs were assessed by a NET-remnants ELISA. In addition, in vitro assays for induction and degradation of NETs, as well as analyses of neutrophil elastase, HLA genotypes, levels of c-peptide, IL-1beta, IFN and autoantibodies (GADA, IA-2A, IAA and ZnT8A) were performed. In serum from children 10 days after T1D onset there was an increase in NETs (p=0.007), mtDNA (p<0.001) and nuclear DNA (p<0.001) compared to healthy children. The elevated levels were found only in younger children. In addition, mtDNA increased in consecutive samples short after onset (p=0.017). However, levels of extracellular DNA short after onset did not reflect future loss of endogenous insulin production. T1D serum induced NETs in vitro and did not deviate in the ability to degrade NETs. HLA genotypes and autoantibodies, except for ZnT8A, were not associated with extracellular DNA in T1D children. Serum from children with high risk of T1D showed fluctuating levels of extracellular DNA, sometimes increased compared to healthy children. Therefore, extracellular DNA in serum from autoantibody positive high-risk children does not seem to be a suitable biomarker candidate for prediction of T1D. In conclusion, we found increased levels of extracellular DNA in children with newly diagnosed T1D, which might be explained by an ongoing systemic inflammation.
Enhanced IL-1β Release Following NLRP3 and AIM2 Inflammasome Stimulation Is Linked to mtROS in Airway Macrophages in Pulmonary Fibrosis
Authors: Trachalaki Athina , Tsitoura Eliza , Mastrodimou Semeli , Invernizzi Rachele , Vasarmidi Eirini , Bibaki Eleni , Tzanakis Nikolaos , Molyneaux Philip L. , Maher Toby M. , Antoniou Katerina
Published: June 2021

Fibrotic Interstitial lung diseases (ILDs) are complex disorders of variable clinical behaviour. The majority of them cause significant morbidity, whilst Idiopathic Pulmonary Fibrosis (IPF) is recognised as the most relentless. NLRP3, AIM2, and NLRC4 inflammasomes are multiprotein complexes driving IL-1β release; a proinflammatory and profibrotic cytokine. Several pathogenetic factors associated with IPF are identified as inflammasome activators, including increases in mtROS and bacterial burden. Mitochondrial oxidation and alterations in bacterial burden in IPF and other ILDs may lead to augmented inflammasome activity in airway macrophages (AMs). IPF (n=14), non-IPF-ILDs (n=12) patients and healthy subjects (n=12) were prospectively recruited and AMs were isolated from bronchoalveolar lavage. IL-1β release resulting from NLRP3, AIM2 and NLRC4 inflammasomes stimulation in AMs were determined and baseline levels of mitochondrial ROS and microbial burden were also measured. Our results showed that NLRP3 was more inducible in IPF and other ILDs compared to controls. Additionally, following AIM2 activation IL-1β release was significantly higher in IPF compared to controls, whereas similar trends were observed in Non-IPF-ILDs. NLRC4 activation was similar across groups. mtROS was significantly associated with heightened NLRP3 and AIM2 activation, and mitochondrial antioxidant treatment limited inflammasome activation. Importantly, microbial burden was linked to baseline IL-1β release and AIM2 and IL-18 relative expression independently of mtROS. In conclusion, the above findings suggested a link between the overactivation of NLRP3 and AIM2 inflammasomes, driven by mitochondrial oxidation, in the pathogenesis of lung fibrosis while changes in the microbiota may prime the inflammasome in the lungs.
Plasma Metabolomics Reveals Dysregulated Metabolic Signatures in HIV-Associated Immune Reconstitution Inflammatory Syndrome
Authors: Pei Luxin , Fukutani Kiyoshi F. , Tibúrcio Rafael , Rupert Adam , Dahlstrom Eric W. , Galindo Frances , Laidlaw Elizabeth , Lisco Andrea , Manion Maura , Andrade Bruno B. , Sereti Irini
Published: June 2021

Immune reconstitution inflammatory syndrome (IRIS) is an inflammatory complication associated with an underlying opportunistic infection that can be observed in HIV-infected individuals shortly after the initiation of antiretroviral therapy, despite successful suppression of HIV viral load and CD4+ T cell recovery. Better understanding of IRIS pathogenesis would allow for targeted prevention and therapeutic approaches. In this study, we sought to evaluate the metabolic perturbations in IRIS across longitudinal time points using an unbiased plasma metabolomics approach as well as integrated analyses to include plasma inflammatory biomarker profile and whole blood transcriptome. We found that many lipid and amino acid metabolites differentiated IRIS from non-IRIS conditions prior to antiretroviral therapy and during the IRIS event, implicating the association between oxidative stress, tryptophan pathway, and lipid mediated signaling and the development of IRIS. Lipid and amino acid metabolic pathways also significantly correlated with inflammatory biomarkers such as IL-12p70 and IL-8 at the IRIS event, indicating the role of cellular metabolism on cell type specific immune activation during the IRIS episode and in turn the impact of immune activation on cellular metabolism. In conclusion, we defined the metabolic profile of IRIS and revealed that perturbations in metabolism may predispose HIV-infected individuals to IRIS development and contribute to the inflammatory manifestations during the IRIS event. Furthermore, our findings expanded our current understanding IRIS pathogenesis and highlighted the significance of lipid and amino acid metabolism in inflammatory complications.
Porous Titanium Dioxide Spheres for Drug Delivery and Sustained Release
Authors: Cui Xin-gang , Chen Hua , Ye Qing-bang , Cui Xin-yu , Cui Xiao-jing , Cui Hong-jing , Shen Guang-zhi , Li Miao-jing , Lin Jian-tao , Sun Ya-xin
Published: June 2021

By hydrothermal method, porous TiO2 spheres with pompon morphology are successfully synthesized in the tetrabutyl titanate (TBT)–acetic acid (HAc) system with no other additives. The morphological, structural and textural properties of the specimen are figured out by transmission electron microscopy (TEM), scanning electron microscopy (SEM), Fourier Transform Infrared Spectroscopy (FT-IR), X-ray powder diffraction (XRD), N2 adsorption/desorption, and fluorescence microscope. The results show the pompon-like morphology of porous TiO2 with high specific surface area and large pore volume, which can be used as a drug carrier. In this paper, doxorubicin hydrochloride (DOX) is chosen as drug model to understand the process of drug release. And results indicate that the porous TiO2 is biocompatible and can be used for continuing drug-release, which shows lots of possibilities in medical fields.
Risk Factors for Developing Rheumatoid Arthritis in Patients With Undifferentiated Arthritis and Inflammatory Arthralgia
Authors: Novella-Navarro Marta , Plasencia-Rodríguez Chamaida , Nuño Laura , Balsa Alejandro
Published: June 2021

Currently, there is an increasing interest in treating patients at risk of rheumatoid arthritis (RA) to prevent the development of this chronic disease. In this sense, research has focused attention on the early identification of predictive factors of this disease. Autoantibodies and markers of systemic inflammation can be present before clinical arthritis and RA development. So, the phase of inflammatory arthralgia preceding clinical arthritis is an important part of the window of opportunity and, starting treatment might prevent progression to chronic arthritis. Additionally, the early diagnosis and treatment initiation, in patients with inflammatory arthritis at risk of persistence and/or erosive progression, are fundamental because may allow optimal clinical responses, better chances of achieving sustained remission, preventing irreversible organ damage and optimizing long-term outcomes. This review aims to give an overview of clinical risk factors for developing RA, both in suspected arthralgia and in undifferentiated arthritis. Besides taking into consideration the role of serological markers (immunological and acute phase reactants) and clinical features assessed at consultation such as: articular affection and patient's clinical perception. Other features as sociodemographic and environmental factors (lifestyle habits, microbiota, periodontal disease among others), have been included in this revision to give an insight on strategies to prevent development of RA and/or to treat it in early stages.
Dynamics of Bacterial and Fungal Communities and Metabolites During Aerobic Exposure in Whole-Plant Corn Silages With Two Different Moisture Levels
Authors: Bai Chunsheng , Wang Chao , Sun Lin , Xu Haiwen , Jiang Yun , Na Na , Yin Guomei , Liu Sibo , Xue Yanlin
Published: June 2021

The study was aimed to investigate the effect of moisture content on microbial communities, metabolites, fermentation quality, and aerobic stability during aerobic exposure in whole-plant corn silages preserved long time to improve the quality and aerobic stability of the silage during feed-out. Corn plants with two different moisture levels (high-moisture content, 680 g/kg; low-moisture content, 620 g/kg) were harvested at one-third and two-thirds milk-line stages, respectively, ensiled in laboratory-scale silos, and then sampled at 350 day after ensiling and at 2 and 5 day after opening to investigate bacterial and fungal communities, metabolites, and aerobic stability. High-moisture content increased aerobic stability and pH and decreased lactic acid and microbial counts in silages (P < 0.05). During aerobic exposure, the low-moisture silages had higher pH and lactic acid bacterial count and lower lactic acid than the high-moisture silages (P < 0.05); Acinetobacter sp. was the most main bacterial species in the silages; Candida glabrata and unclassified Candida had an increasing abundance and negatively correlation with aerobic stability of high-moisture silages (P < 0.05), while C. glabrata, Candida xylopsoci, unclassified Saccharomycetaceae, and unclassified Saccharomycetales negative correlated with aerobic stability of low-moisture silages (P < 0.05) with a rising Saccharomycetaceae; the silages had a reducing concentration of total metabolites (P < 0.05). Moreover, the high-moisture silages contained greater total metabolites, saturated fatty acids (palmitic and stearic acid), essential fatty acids (linoleic acid), essential amino acids (phenylalanine), and non-essential amino acids (alanine, beta-alanine, and asparagine) than the low-moisture silages at 5 day of opening (P < 0.05). Thus, the high-moisture content improved the aerobic stability. Acinetobacter sp. and Candida sp. dominated the bacterial and fungal communities, respectively; Candida sp. resulted in the aerobic deterioration in high-moisture silages, while the combined activities of Candida sp. and Saccharomycetaceae sp. caused the aerobic deterioration in low-moisture silages. The greater aerobic stability contributed to preserve the palmitic acid, stearic acid, linoleic acid, phenylalanine, alanine, beta-alanine, and asparagine during aerobic exposure.
Respiratory Heme A-Containing Oxidases Originated in the Ancestors of Iron-Oxidizing Bacteria
Authors: Degli Esposti Mauro , Moya-Beltrán Ana , Quatrini Raquel , Hederstedt Lars
Published: June 2021

Respiration is a major trait shaping the biology of many environments. Cytochrome oxidase containing heme A (COX) is a common terminal oxidase in aerobic bacteria and is the only one in mammalian mitochondria. The synthesis of heme A is catalyzed by heme A synthase (CtaA/Cox15), an enzyme that most likely coevolved with COX. The evolutionary origin of COX in bacteria has remained unknown. Using extensive sequence and phylogenetic analysis, we show that the ancestral type of heme A synthases is present in iron-oxidizing Proteobacteria such as Acidithiobacillus spp. These bacteria also contain a deep branching form of the major COX subunit (COX1) and an ancestral variant of CtaG, a protein that is specifically required for COX biogenesis. Our work thus suggests that the ancestors of extant iron-oxidizers were the first to evolve COX. Consistent with this conclusion, acidophilic iron-oxidizing prokaryotes lived on emerged land around the time for which there is the earliest geochemical evidence of aerobic respiration on earth. Hence, ecological niches of iron oxidation have apparently promoted the evolution of aerobic respiration.
PCV2 Triggers PK-15 Cell Apoptosis Through the PLC–IP3R–Ca2+ Signaling Pathway
Authors: Wang Shuo , Li Chen , Sun Panpan , Shi Jianli , Wu Xiaoyan , Liu Chang , Peng Zhe , Han Hong , Xu Shaojian , Yang Ying , Tian Yao , Li Jiaxin , He Hongbin , Li Jun , Wang Zhao
Published: June 2021

The endoplasmic reticulum (ER) plays an essential role in Ca2+ concentration balance and protein biosynthesis. During infection, the virus needs to complete its life process with the help of ER. At the same time, ER also produces ER stress (ERS), which induces apoptosis to resist virus infection. Our study explored the Ca2+ concentration, ERS, and the apoptosis mechanism after porcine circovirus 2 (PCV2) infection. We show here that PCV2 infection induces the increased cytoplasmic Ca2+ level and PK-15 cell ER swelling. The colocalization of phospholipase C (PLC) and inositol 1,4,5-trisphosphate receptor (IP3R) in the cytoplasm was observed by laser confocal microscopy. Western blot and quantitative polymerase chain reaction experiments confirmed that PLC and IP3R expression levels increased after PCV2 infection, and Ca2+ concentration in the cytoplasm increased after virus infection. These results suggest that PCV2 infection triggers ERS of PK-15 cells via the PLC–IP3R–Ca2+ signaling pathway to promote the release of intracellular Ca2+ and led to cell apoptosis.
Cyanobacterial Akinete Distribution, Viability, and Cyanotoxin Records in Sediment Archives From the Northern Baltic Sea
Authors: Wood Steffaney M. , Kremp Anke , Savela Henna , Akter Sultana , Vartti Vesa-Pekka , Saarni Saija , Suikkanen Sanna
Published: June 2021

Cyanobacteria of the order Nostocales, including Baltic Sea bloom-forming taxaNodularia spumigena, Aphanizomenon flosaquae, andDolichospermumspp., produce resting stages, known as akinetes, under unfavorable conditions. These akinetes can persist in the sediment and germinate if favorable conditions return, simultaneously representing past blooms and possibly contributing to future bloom formation. The present study characterized cyanobacterial akinete survival, germination, and potential cyanotoxin production in brackish water sediment archives from coastal and open Gulf of Finland in order to understand recent bloom expansion, akinete persistence, and cyanobacteria life cycles in the northern Baltic Sea. Results showed that cyanobacterial akinetes can persist in and germinate from Northern Baltic Sea sediment up to >40 and >400 years old, at coastal and open-sea locations, respectively. Akinete abundance and viability decreased with age and depth of vertical sediment layers. The detection of potential microcystin and nodularin production from akinetes was minimal and restricted to the surface sediment layers. Phylogenetic analysis of culturable cyanobacteria from the coastal sediment core indicated that most strains likely belonged to the benthic genusAnabaena. Potentially planktonic species ofDolichospermumcould only be revived from the near-surface layers of the sediment, corresponding to an estimated age of 1–3 years. Results of germination experiments supported the notion that akinetes do not play an equally significant role in the life cycles of all bloom-forming cyanobacteria in the Baltic Sea. Overall, there was minimal congruence between akinete abundance, cyanotoxin concentration, and the presence of cyanotoxin biosynthetic genes in either sediment core. Further research is recommended to accurately detect and quantify akinetes and cyanotoxin genes from brackish water sediment samples in order to further describe species-specific benthic archives of cyanobacteria.
Urine NMR Metabolomics Profile of Preterm Infants With Necrotizing Enterocolitis Over the First Two Months of Life: A Pilot Longitudinal Case-Control Study
Authors: Picaud Jean-Charles , De Magistris Anna , Mussap Michele , Corbu Sara , Dessì Angelica , Noto Antonio , Fanos Vassilios , Cesare Marincola Flaminia
Published: June 2021

Objective: To investigate changes in the urine metabolome of very low birth weight preterm newborns with necrotizing enterocolitis (NEC) and feed intolerance, we conducted a longitudinal study over the first 2 months of life. The metabolome of NEC newborns was compared with two control groups that did not develop NEC: the first one included preterm babies with feed intolerance, while the second one preterm babies with good feed tolerance.

Methods: Newborns developing NEC within the 3 weeks of life were identified as early onset NEC, while the remaining as late onset NEC. Case-control matching was done according to the gestational age (±1 week), birth weight (± 200 g), and postnatal age. A total of 96 urine samples were collected and analyzed. In newborns with NEC, samples were collected before, during and after the diagnosis over the first 2 months of life, while in controls samples were collected as close as possible to the postnatal age of newborns with NEC. Proton nuclear magnetic resonance (1H NMR) spectroscopy was used for metabolomic analysis. Data were analyzed by univariate and multivariate statistical analysis.

Results: In all the preterm newborns, urine levels of betaine, glycine, succinate, and citrate positively correlated with postnatal age. Suberate and lactate correlated with postnatal age in preterms with NEC and in controls with food intolerance, while N,N-dimethylglycine (N,N-DMG) correlated only in controls with good digestive tolerance. Preterm controls with feed intolerance showed a progressive significant decrease of N-methylnicotinamide and carnitine. Lactate, betaine, myo-inositol, urea, creatinine, and N,N-dimethylglycine discriminated late-onset NEC from controls with good feed tolerance.

Conclusion: Our findings are discussed in terms of contributions from nutritional and clinical managements of patients and gut microbiota.
Double-Layer Flexible Neural Probe With Closely Spaced Electrodes for High-Density in vivo Brain Recordings
Authors: Pimenta Sara , Rodrigues José A. , Machado Francisca , Ribeiro João F. , Maciel Marino J. , Bondarchuk Oleksandr , Monteiro Patricia , Gaspar João , Correia José H. , Jacinto Luis
Published: June 2021

Flexible polymer neural probes are an attractive emerging approach for invasive brain recordings, given that they can minimize the risks of brain damage or glial scaring. However, densely packed electrode sites, which can facilitate neuronal data analysis, are not widely available in flexible probes. Here, we present a new flexible polyimide neural probe, based on standard and low-cost lithography processes, which has 32 closely spaced 10 μm diameter gold electrode sites at two different depths from the probe surface arranged in a matrix, with inter-site distances of only 5 μm. The double-layer design and fabrication approach implemented also provides additional stiffening just sufficient to prevent probe buckling during brain insertion. This approach avoids typical laborious augmentation strategies used to increase flexible probes’ mechanical rigidity while allowing a small brain insertion footprint. Chemical composition analysis and metrology of structural, mechanical, and electrical properties demonstrated the viability of this fabrication approach. Finally, in vivo functional assessment tests in the mouse cortex were performed as well as histological assessment of the insertion footprint, validating the biological applicability of this flexible neural probe for acquiring high quality neuronal recordings with high signal to noise ratio (SNR) and reduced acute trauma.
Identification of Novel Genomic Regions for Biofortification Traits Using an SNP Marker-Enriched Linkage Map in Wheat (Triticum aestivum L.)
Authors: Krishnappa Gopalareddy , Rathan Nagenahalli Dharmegowda , Sehgal Deepmala , Ahlawat Arvind Kumar , Singh Santosh Kumar , Singh Sumit Kumar , Shukla Ram Bihari , Jaiswal Jai Prakash , Solanki Ishwar Singh , Singh Gyanendra Pratap , Singh Anju Mahendru
Published: June 2021

Micronutrient and protein malnutrition is recognized among the major global health issues. Genetic biofortification is a cost-effective and sustainable strategy to tackle malnutrition. Genomic regions governing grain iron concentration (GFeC), grain zinc concentration (GZnC), grain protein content (GPC), and thousand kernel weight (TKW) were investigated in a set of 163 recombinant inbred lines (RILs) derived from a cross between cultivated wheat variety WH542 and a synthetic derivative (Triticum dicoccon PI94624/Aegilops tauschii [409]//BCN). The RIL population was genotyped using 100 simple-sequence repeat (SSR) and 736 single nucleotide polymorphism (SNP) markers and phenotyped in six environments. The constructed genetic map had a total genetic length of 7,057 cM. A total of 21 novel quantitative trait loci (QTL) were identified in 13 chromosomes representing all three genomes of wheat. The trait-wise highest number of QTL was identified for GPC (10 QTL), followed by GZnC (six QTL), GFeC (three QTL), and TKW (two QTL). Four novel stable QTL (QGFe.iari-7D.1, QGFe.iari-7D.2, QGPC.iari-7D.2, and QTkw.iari-7D) were identified in two or more environments. Two novel pleiotropic genomic regions falling between Xgwm350–AX-94958668 and Xwmc550–Xgwm350 in chromosome 7D harboring co-localized QTL governing two or more traits were also identified. The identified novel QTL, particularly stable and co-localized QTL, will be validated to estimate their effects on different genetic backgrounds for subsequent use in marker-assisted selection (MAS). Best QTL combinations were identified by the estimation of additive effects of the stable QTL for GFeC, GZnC, and GPC. A total of 11 RILs (eight for GZnC and three for GPC) having favorable QTL combinations identified in this study can be used as potential donors to develop bread wheat varieties with enhanced micronutrients and protein.
Hippocampal PPARα Plays a Role in the Pharmacological Mechanism of Vortioxetine, a Multimodal-Acting Antidepressant
Authors: Wang Yuan , Gu Jiang-Hong , Liu Ling , Liu Yue , Tang Wen-Qian , Ji Chun-Hui , Guan Wei , Zhao Xin-Yi , Sun Ying-Fang , Xu Da-Wei , Jiang Bo
Published: June 2021

As a well-known multimodal-acting antidepressant, vortioxetine is thought to aim at several serotonin (5-HT) receptors and the 5-HT transporter. However, recently more and more proteins besides 5-HT are being reported to participate in the antidepressant mechanism of vortioxetine. As a widely known nuclear hormone receptor, peroxisome proliferator activated receptor α (PPARα) possesses transcriptional activity and is very important in the brain. Several reports have suggested that hippocampal PPARα is implicated in antidepressant responses. Here we speculate that hippocampal PPARα may participate in the antidepressant mechanism of vortioxetine. In this study, chronic unpredictable mild stress (CUMS), chronic social defeat stress (CSDS), behavioral tests, the western blotting and adenovirus associated virus (AAV)-mediated gene knockdown methods were used together. It was found that vortioxetine administration significantly reversed the inhibitory actions of both CUMS and CSDS on the hippocampal PPARα expression. Pharmacological blockade of PPARα notably prevented the antidepressant actions of vortioxetine in the CUMS and CSDS models. Moreover, genetic knockdown of PPARα in the hippocampus also significantly blocked the protecting effects of vortioxetine against both CUMS and CSDS. Therefore, the antidepressant effects of vortioxetine in mice require hippocampal PPARα.
The Effects of Asymmetrical Guanxi Perception on Job Burnout: Task Conflict, Relationship Conflict, and Process Conflict as Mediators
Authors: Hung Hao-Kai
Published: June 2021

In Chinese organizations, individuals benefit in many ways from having good guanxi. For employees, however, guanxi also comes with well-documented negative effects. Until recently, the guanxi investigated in these studies was always of a substantial nature. The negative effects of non-substantial guanxi (in effect, the absence of real guanxi), such as the guanxi of misunderstandings for those who lack good guanxi, have not been examined. This study investigates how the existence of asymmetrical guanxi perception for an employee (i.e., when other people believe that good guanxi exists between a manager and an employee, but the employee disagrees with the belief that he/she has good guanxi with his/her supervisors) contributes to job burnout for that employee due to task conflict, relationship conflict, and process conflict. A cross-sectional data sample was collected from 363 employees of 10 hotels in Taiwan. Structural equation modeling results suggest that relationship conflict is the most powerful mediator affecting the relationship between asymmetrical guanxi perception and job burnout. The results provide insights for researchers interested in the mechanism of how asymmetrical guanxi perception induces employee job burnout while generating useful implications for managers charged with reducing such burnout.
Radiomics Is Effective for Distinguishing Coronavirus Disease 2019 Pneumonia From Influenza Virus Pneumonia
Authors: Lin Liaoyi , Liu Jinjin , Deng Qingshan , Li Na , Pan Jingye , Sun Houzhang , Quan Shichao
Published: June 2021

Objectives: To develop and validate a radiomics model for distinguishing coronavirus disease 2019 (COVID-19) pneumonia from influenza virus pneumonia.

Materials and Methods: A radiomics model was developed on the basis of 56 patients with COVID-19 pneumonia and 90 patients with influenza virus pneumonia in this retrospective study. Radiomics features were extracted from CT images. The radiomics features were reduced by the Max-Relevance and Min-Redundancy algorithm and the least absolute shrinkage and selection operator method. The radiomics model was built using the multivariate backward stepwise logistic regression. A nomogram of the radiomics model was established, and the decision curve showed the clinical usefulness of the radiomics nomogram.

Results: The radiomics features, consisting of nine selected features, were significantly different between COVID-19 pneumonia and influenza virus pneumonia in both training and validation data sets. The receiver operator characteristic curve of the radiomics model showed good discrimination in the training sample [area under the receiver operating characteristic curve (AUC), 0.909; 95% confidence interval (CI), 0.859–0.958] and in the validation sample (AUC, 0.911; 95% CI, 0.753–1.000). The nomogram was established and had good calibration. Decision curve analysis showed that the radiomics nomogram was clinically useful.

Conclusions: The radiomics model has good performance for distinguishing COVID-19 pneumonia from influenza virus pneumonia and may aid in the diagnosis of COVID-19 pneumonia.
From the Soil to the Club in the Roots: Clubroot
Authors: Pérez-López Edel
Published: June 2021

Among the millions of microorganisms inhabiting the soils, some can be plant pathogens, meaning they can become a disease to plants. Some diseases are more well-known than others. This is the case of clubroot, a very atypical microorganism that infects cruciferous plants, such as cabbage, kale, canola, and the common research plant thale cress. In this article, I will tell you more about clubroot and clubroot disease because there is still a lot to discover about the pathogen and the disease. Maybe you will be part of our lab in the future and investigate a fascinating soil-borne pathogen.
Prevalence and Factors Associated With Suicidal Ideation Among Children and Adolescents Attending a Pediatric HIV Clinic in Uganda
Authors: Namuli Justine Diana , Nalugya Joyce Sserunjogi , Bangirana Paul , Nakimuli-Mpungu Etheldreda
Published: June 2021

Background: Suicidal behavior and HIV/AIDS are vital public health challenges especially in low and middle-income countries. As suicide in adults is perturbing for those closest to them, this sentiment is much more intense and generalized in the case of a child or adolescent. Knowledge of factors associated with suicidal ideation in HIV infected children and adolescents may inform suicide prevention strategies needed to improve their quality of life. This study aimed to assess the prevalence and factors associated with suicidal ideation among HIV infected children and adolescents attending a pediatric HIV clinic in Uganda.

Methods: Data from a sample of 271 children and adolescents aged 6–18 years living with HIV/AIDS attending a pediatric HIV clinic was analyzed. Child characteristics and clinical variables were assessed using a socio-demographic questionnaire and medical records respectively. Suicidal ideation and depression were assessed using the Child Depression Inventory. The types of behavioral problems and the parent–child relationship were assessed using Child Behavioral Check List (6–18 years) and the Parent Child Relationship Scale respectively. Child exposure to different stressful life events was assessed with a series of standardized questions. Logistic regression models were used to explore factors independently associated with suicidal ideation.

Results: The prevalence of suicidal ideation was 17%. In the multivariate analysis; Child exposure to family or friend’s death (prevalence rate ratio (PRR = 2.02; 95% CI, 1.01–4.03), p = 0.046), HIV wasting syndrome (PRR = 0.39; 95% CI, 0.21–0.75, p = 0.04), Depression (PRR = 1.08; 95% CI, 1.03–1.12, p = 0.001), Anxiety symptoms (PRR = 1.10; 95% CI, 1.01–1.20, p = 0.024) and Rule breaking behavior (PRR = 1.06; 95% CI, 0.99–1.13, p = 0.051) were independently associated with suicidal ideations.

Conclusion: The prevalence of suicidal ideation among children and adolescents living with HIV/AIDS is substantial. Children and adolescents with exposure to family or friend’s death, those with higher depression scores, anxiety symptoms and rule breaking behavior are more likely to report suicidal ideation. Those with HIV wasting syndrome were less likely to report suicidal ideation. There is urgent need for HIV care providers to screen for suicide and link to mental health services.
A Field-Tested Harvesting Robot for Oyster Mushroom in Greenhouse
Authors: Rong Jiacheng , Wang Pengbo , Yang Qian , Huang Feng
Published: June 2021

The fully autonomous harvesting of oyster mushrooms in the greenhouse requires the development of a reliable and robust harvesting robot. In this paper, we propose an oyster-mushroom-harvesting robot, which can realize harvesting operations in the entire greenhouse. The two crucial components of the harvesting robot are the perception module and the end-effector. Intel RealSense D435i is adopted to collect RGB images and point cloud images in real time; an improved SSD algorithm is proposed to detect mushrooms, and finally, the existing soft gripper is manipulated to grasp oyster mushrooms. Field experiments exhibit the feasibility and robustness of the proposed robot system, in which the success rate of the mushroom recognition success rate reaches 95%, the harvesting success rate reaches 86.8% (without considering mushroom damage), and the harvesting time for a single mushroom is 8.85 s.
A Framework for Identification of Stable Genotypes Basedon MTSI and MGDII Indexes: An Example in Guar (Cymopsis tetragonoloba L.)
Authors: Benakanahalli Niranjana Kumara , Sridhara Shankarappa , Ramesh Nandini , Olivoto Tiago , Sreekantappa Gangaprasad , Tamam Nissren , Abdelbacki Ashraf M. M. , Elansary Hosam O. , Abdelmohsen Shaimaa A. M.
Published: June 2021

Guar, the most popular vegetable, is tolerant of drought and is a valuable industrial crop enormously grown across India, Pakistan, USA, and South Africa for pharmaceutically and cosmetically usable galactomannan (gum) content present in seed endosperm. Guar genotypes with productive traits which could perform better in differential environmental conditions are of utmost priority for genotype selection. This could be achieved by employing multivariate trait analysis. In this context, Multi-Trait Stability Index (MTSI) and Multi-Trait Genotype-Ideotype Distance Index (MGIDI) were employed for identifying high-performing genotypes exhibiting multiple traits. In the current investigation, 85 guar accessions growing in different seasons were assessed for 15 morphological traits. The results obtained by MTSI and MGIDI indexes revealed that, out of 85, only 13 genotypes performed better across and within the seasons, and, based on the coincidence index, only three genotypes (IC-415106, IC-420320, and IC-402301) were found stable with high seed production in multi-environmental conditions. View on strengths and weakness as described by the MGIDI reveals that breeders concentrated on developing genotype with desired traits, such as quality of the gum and seed yield. The strength of the ideal genotypes in the present work is mainly focused on high gum content, short crop cycle, and high seed yield possessing good biochemical traits. Thus, MTSI and MGIDI serve as a novel tool for desired genotype selection process simultaneously in plant breeding programs across multi-environments due to uniqueness and ease in interpreting data with minimal multicollinearity issues.
Pointing Out Some Issues Regarding Reproduction Management in Murciano-Granadina Goats
Authors: Fernández Nemesio , Beltrán M. Carmen , Romero Gema , Roca M. Amparo , Rodríguez Martín , Balasch Sebastián
Published: June 2021

Two of the most important problems in high-yielding dairy goat farms are early and accurate pregnancy diagnosis and the appropriate dry off of lactating does before the next kidding. The hypothesis posits that it could be possible to identify pregnant does through maximum progesterone milk levels at any time during the pregnancy, and that there is an optimal time to apply a lactation inhibitor to help dry off lactating does. Therefore, 114 Murciano-Granadina breed goats were used, from which 74 goats were inseminated at week 20 of lactation and samples of milk from pregnant and non-pregnant goats were taken at two-week intervals. The average maximum progesterone milk levels were higher outside the natural breeding season (40° latitude) than in the breeding season (11.6 ± 1.13 vs. 8.6 ± 1.02 ng/mL), although the levels from pregnant and non-pregnant goats were similar (10.85 ± 1.3 vs. 9.74 ± 1.6 ng/mL), except in the case of pregnancy with four foetuses (12.5 ± 1.3 ng/mL). Milk yield at mating does not affect fertility until a value of at least 3250 mL/day. Pregnancy started to affect milk yield up to the +7th week and was 59.9% lower in the +10th week after mating, so the use of lactation inhibitors could be more effective from this latter week. In conclusion, the results show that it is not possible to detect gestation in goats reliably through the maximum concentration of progesterone in milk at any time during lactation, except in the case of goats gestating four foetuses, that the milk yield of goats at mating does not affect fertility until a value of at least 3250 mL/day, and that from the 10th week post-mating, the application of lactation inhibitors would be optimal.
Mycoplasma agalactiae: The Sole Cause of Classical Contagious Agalactia?
Authors: Migliore Sergio , Puleio Roberto , Nicholas Robin A. J. , Loria Guido R.
Published: June 2021

Contagious agalactia (CA) is suspected when small ruminants show all or several of the following clinical signs: mastitis, arthritis, keratoconjunctivitis and occasionally abortion. It is confirmed following mycoplasma isolation or detection. The historical and major cause is Mycoplasma agalactiae which was first isolated from sheep in 1923. Over the last thirty years, three other mycoplasmas (Mycoplasma mycoides subsp. capri, Mycoplasma capricolum subsp. capricolum and Mycoplasma putrefaciens) have been added to the etiology of CA because they can occasionally cause clinically similar outcomes though nearly always in goats. However, only M. agalactiae is subject to animal disease regulations nationally and internationally. Consequently, it makes little sense to list mycoplasmas other than M. agalactiae as causes of the OIE-listed CA when they are not officially reported by the veterinary authorities and unlikely to be so in the future. Indeed, encouraging countries just to report M. agalactiae may bring about a better understanding of the importance of CA. In conclusion, we recommend that CA should only be diagnosed and confirmed when M. agalactiae is detected either by isolation or molecular methods, and that the other three mycoplasmas be removed from the OIE Manual of Diagnostic Tests and Vaccines in Terrestrial Animals and associated sources.