bluuebunny/crossref_metadata_2025_split huggingface dataset:
The challenges of containing SARS-CoV-2 via test-trace-and-isolate
Authors: Contreras Sebastian , Dehning Jonas , Loidolt Matthias , Zierenberg Johannes , Spitzner F. Paul , Urrea-Quintero Jorge H. , Mohr Sebastian B. , Wilczek Michael , Wibral Michael , Priesemann Viola 
Published: January 2021

AbstractWithout a cure, vaccine, or proven long-term immunity against SARS-CoV-2, test-trace-and-isolate (TTI) strategies present a promising tool to contain its spread. For any TTI strategy, however, mitigation is challenged by pre- and asymptomatic transmission, TTI-avoiders, and undetected spreaders, which strongly contribute to ”hidden" infection chains. Here, we study a semi-analytical model and identify two tipping points between controlled and uncontrolled spread: (1) the behavior-driven reproduction number$${R}_{t}^{H}$$RtHof the hidden chains becomes too large to be compensated by the TTI capabilities, and (2) the number of new infections exceeds the tracing capacity. Both trigger a self-accelerating spread. We investigate how these tipping points depend on challenges like limited cooperation, missing contacts, and imperfect isolation. Our results suggest that TTI alone is insufficient to contain an otherwise unhindered spread of SARS-CoV-2, implying that complementary measures like social distancing and improved hygiene remain necessary.
Comparison of two fluorescent probes in preclinical non-invasive imaging and image-guided debridement surgery of Staphylococcal biofilm implant infections
Authors: Park Howard Y. , Zoller Stephen D. , Hegde Vishal , Sheppard William , Burke Zachary , Blumstein Gideon , Hamad Christopher , Sprague Marina , Hoang John , Smith Ryan , Romero Pastrana Francisco , Czupryna Julie , Miller Lloyd S. , López-Álvarez Marina , Bispo Mafalda , van Oosten Marleen , van Dijl Jan Maarten , Francis Kevin P. , Bernthal Nicholas M. 
Published: January 2021

AbstractImplant-associated infections are challenging to diagnose and treat. Fluorescent probes have been heralded as a technologic advancement that can improve our ability to non-invasively identify infecting organisms, as well as guide the inexact procedure of surgical debridement. This study’s purpose was to compare two fluorescent probes for their ability to localize Staphylococcus aureus biofilm infections on spinal implants utilizing noninvasive optical imaging, then assessing the broader applicability of the more successful probe in other infection animal models. This was followed by real-time, fluorescence image-guided surgery to facilitate debridement of infected tissue. The two probe candidates, a labelled antibiotic that targets peptidoglycan (Vanco-800CW), and the other, a labelled antibody targeting the immunodominant Staphylococcal antigen A (1D9-680), were injected into mice with spine implant infections. Mice were then imaged noninvasively with near infrared fluorescent imaging at wavelengths corresponding to the two probe candidates. Both probes localized to the infection, with the 1D9-680 probe showing greater fidelity over time. The 1D9-680 probe was then tested in mouse models of shoulder implant and allograft infection, demonstrating its broader applicability. Finally, an image-guided surgery system which superimposes fluorescent signals over analog, real-time, tissue images was employed to facilitate debridement of fluorescent-labelled bacteria.
Inhibition of mitochondrial complex II in neuronal cells triggers unique pathways culminating in autophagy with implications for neurodegeneration
Authors: Ranganayaki Sathyanarayanan , Jamshidi Neema , Aiyaz Mohamad , Rashmi Santhosh-Kumar , Gayathri Narayanappa , Harsha Pulleri Kandi , Padmanabhan Balasundaram , Srinivas Bharath Muchukunte Mukunda 
Published: January 2021

AbstractMitochondrial dysfunction and neurodegeneration underlie movement disorders such as Parkinson’s disease, Huntington’s disease and Manganism among others. As a corollary, inhibition of mitochondrial complex I (CI) and complex II (CII) by toxins 1-methyl-4-phenylpyridinium (MPP+) and 3-nitropropionic acid (3-NPA) respectively, induced degenerative changes noted in such neurodegenerative diseases. We aimed to unravel the down-stream pathways associated with CII inhibition and compared with CI inhibition and the Manganese (Mn) neurotoxicity. Genome-wide transcriptomics of N27 neuronal cells exposed to 3-NPA, compared with MPP+ and Mn revealed varied transcriptomic profile. Along with mitochondrial and synaptic pathways, Autophagy was the predominant pathway differentially regulated in the 3-NPA model with implications for neuronal survival. This pathway was unique to 3-NPA, as substantiated by in silico modelling of the three toxins. Morphological and biochemical validation of autophagy markers in the cell model of 3-NPA revealed incomplete autophagy mediated by mechanistic Target of Rapamycin Complex 2 (mTORC2) pathway. Interestingly, Brain Derived Neurotrophic Factor (BDNF), which was elevated in the 3-NPA model could confer neuroprotection against 3-NPA. We propose that, different downstream events are activated upon neurotoxin-dependent CII inhibition compared to other neurotoxins, with implications for movement disorders and regulation of autophagy could potentially offer neuroprotection.
Tryptophan-derived metabolites and BAK1 separately contribute to Arabidopsis postinvasive immunity against Alternaria brassicicola
Authors: Kosaka Ayumi , Pastorczyk Marta , Piślewska-Bednarek Mariola , Nishiuchi Takumi , Ono Erika , Suemoto Haruka , Ishikawa Atsushi , Frerigmann Henning , Kaido Masanori , Mise Kazuyuki , Bednarek Paweł , Takano Yoshitaka 
Published: January 2021

AbstractNonhost resistance of Arabidopsis thaliana against the hemibiotrophic fungus Colletotrichum tropicale requires PEN2-dependent preinvasive resistance and CYP71A12 and CYP71A13-dependent postinvasive resistance, which both rely on tryptophan (Trp) metabolism. We here revealed that CYP71A12, CYP71A13 and PAD3 are critical for Arabidopsis’ postinvasive basal resistance toward the necrotrophic Alternaria brassicicola. Consistent with this, gene expression and metabolite analyses suggested that the invasion by A. brassicicola triggered the CYP71A12-dependent production of indole-3-carboxylic acid derivatives and the PAD3 and CYP71A13-dependent production of camalexin. We next addressed the activation of the CYP71A12 and PAD3-dependent postinvasive resistance. We found that bak1-5 mutation significantly reduced postinvasive resistance against A. brassicicola, indicating that pattern recognition contributes to activation of this second defense-layer. However, the bak1-5 mutation had no detectable effects on the Trp-metabolism triggered by the fungal penetration. Together with this, further comparative gene expression analyses suggested that pathogen invasion in Arabidopsis activates (1) CYP71A12 and PAD3-related antifungal metabolism that is not hampered by bak1-5, and (2) a bak1-5 sensitive immune pathway that activates the expression of antimicrobial proteins.
Prevalence of different comorbidities in chronic obstructive pulmonary disease among Shahrekord PERSIAN cohort study in southwest Iran
Authors: Kiani Fatemeh Zeynab , Ahmadi Ali 
Published: January 2021

AbstractComorbidities are common in chronic obstructive pulmonary disease (COPD) patients. This study was conducted to determine the prevalence of common comorbidities in patients with COPD compared with people without COPD. This cross-sectional, population-based study was performed on 6961 adults aged 35–70 years enrolled in the Shahrekord PERSIAN cohort study. Data (demographic and clinical characteristics, comorbidities, anthropometric and blood pressure measurements, laboratory, and spirometry tests) collection was performed according to the cohort protocol from 2015 to 2019. In the present study, 215 (3.1%) patients were diagnosed with COPD and 1753 (25.18%) ones with restrictive lung patterns. The mean age of COPD patients was 52.5 ± 9.76 years. 55.8% of patients were male, 17.7% were current smokers and 12.1% had a history of smoking or were former smokers. 5.6% of patients had no comorbidity and 94.5% had at least one comorbidity. The most common comorbidities in COPD patients were dyslipidemia (70.2%), hypertension (30.2%), metabolic syndrome (22.8%), and diabetes (16.7%). The most common comorbidities in individuals with a restrictive spirometry pattern were dyslipidemia (68.9%), metabolic syndrome (27.2%), hypertension (26.1%), depression (17.6%), and fatty liver (15.5%). The logistic regression analysis with 95% confidence interval (95%CI) of odds ratio (OR) showed that comorbidities of chronic lung diseases (OR = 2.12, 95% CI 1.30–3.44), diabetes (OR = 1.54, 95%CI 1.03–2.29), cardiovascular disease (OR = 1.52, 95%CI 1.17–2.43), and hypertension (OR = 1.4, 95%CI 1.02–1.99) were more likely to occur in COPD patients than in healthy individuals. Knowing these prevalence rates and related information provides new insights on comorbidities to reduce disease burden and develop preventive interventions and to regulate health care resources to meet the needs of patients in primary health care.
Crop nutrient management using Nutrient Expert improves yield, increases farmers’ income and reduces greenhouse gas emissions
Authors: Sapkota Tek B. , Jat Mangi L. , Rana Dharamvir S. , Khatri-Chhetri Arun , Jat Hanuman S. , Bijarniya Deepak , Sutaliya Jhabar M. , Kumar Manish , Singh Love K. , Jat Raj K. , Kalvaniya Kailash , Prasad Gokul , Sidhu Harminder S. , Rai Munmun , Satyanarayana T. , Majumdar Kaushik 
Published: January 2021

AbstractReduction of excess nutrient application and balanced fertilizer use are the key mitigation options in agriculture. We evaluated Nutrient Expert (NE) tool-based site-specific nutrient management (SSNM) in rice and wheat crops by establishing 1594 side-by-side comparison trials with farmers’ fertilization practices (FFP) across the Indo-Gangetic Plains (IGP) of India. We found that NE-based fertilizer management can lower global warming potential (GWP) by about 2.5% in rice, and between 12 and 20% in wheat over FFP. More than 80% of the participating farmers increased their crop yield and farm income by applying the NE-based fertilizer recommendation. We also observed that increased crop yield and reduced fertilizer consumption and associated greenhouse gas (GHG) emissions by using NE was significantly influenced by the crop type, agro-ecology, soil properties and farmers’ current level of fertilization. Adoption of NE-based fertilizer recommendation practice in all rice and wheat acreage in India would translate into 13.92 million tonnes (Mt) more rice and wheat production with 1.44 Mt less N fertilizer use, and a reduction in GHG of 5.34 Mt CO2e per year over farmers’ current practice. Our study establishes the utility of NE to help implement SSNM in smallholder production systems for increasing crop yields and farmers’ income while reducing GHG emissions.
Isolation of the South China Sea from the North Pacific Subtropical Gyre since the latest Miocene due to formation of the Luzon Strait
Authors: Yin Shaoru , Hernández-Molina F. Javier , Lin Lin , Chen Jiangxin , Ding Weifeng , Li Jiabiao 
Published: January 2021

AbstractThe North Pacific subtropical gyre (NPSG) plays a major role in present global ocean circulation. At times, the gyre has coursed through the South China Sea, but its role in the evolutionary development of that Sea remains uncertain. This work systematically describes a major shift in NPSG paleo-circulation evident from sedimentary features observed in seismic and bathymetric data. These data outline two contourite depositional systems—a buried one formed in the late Miocene, and a latest Miocene to present-day system. The two are divided by a prominent regional discontinuity that represents a major shift in paleo-circulation during the latest Miocene (~ 6.5 Ma). The shift coincides with the further restriction of the South China Sea with respect to the North Pacific due to the formation of the Luzon Strait as a consequence of further northwest movement of the Philippine Sea plate. Before that restriction, data indicate vigorous NPSG circulation in the South China Sea. Semi-closure, however, established a new oceanographic circulation regime in the latest Miocene. This work demonstrates the significant role of recent plate tectonics, gateway development, and marginal seas in the establishment of modern global ocean circulation.
Benchtop micro-mashing: high-throughput, robust, experimental beer brewing
Authors: Kerr Edward D. , Caboche Christopher H. , Josh Peter , Schulz Benjamin L. 
Published: January 2021

AbstractBrewing science is undergoing a renaissance with the use of modern analytical chemistry and microbiology techniques. However, these modern analytical tools and techniques are not necessarily aligned with the scale and scope of brewing science. In particular, brewing processes can be time consuming, ingredient intensive, and require specialised technical equipment. These drawbacks compound with the need for appropriate numbers of replicates for adequately powered experimental design. Here, we describe a micro-scale mash method that can be performed using a common laboratory benchtop shaker/incubator, allowing for high throughput mashing and easy sample replication for statistical analysis. Proteomic profiles at both the protein and peptide levels were consistent between the 1 mL micro-mash and a 23 L Braumeister mash, and both mash scales produced wort with equivalent fermentable sugar and free amino acid profiles. The experimental flexibility offered by our micro-mash method allowed us to investigate the effects of altered mash parameters on the beer brewing proteome.
Biodiversity response to forest management intensity, carbon stocks and net primary production in temperate montane forests
Authors: Asbeck Thomas , Sabatini Francesco , Augustynczik Andrey L. D. , Basile Marco , Helbach Jan , Jonker Marlotte , Knuff Anna , Bauhus Jürgen 
Published: January 2021

AbstractManaged forests are a key component of strategies aimed at tackling the climate and biodiversity crises. Tapping this potential requires a better understanding of the complex, simultaneous effects of forest management on biodiversity, carbon stocks and productivity. Here, we used data of 135 one-hectare plots from southwestern Germany to disentangle the relative influence of gradients of management intensity, carbon stocks and forest productivity on different components of forest biodiversity (birds, bats, insects, plants) and tree-related microhabitats. We tested whether the composition of taxonomic groups varies gradually or abruptly along these gradients. The richness of taxonomic groups was rather insensitive to management intensity, carbon stocks and forest productivity. Despite the low explanatory power of the main predictor variables, forest management had the greatest relative influence on richness of insects and tree-related microhabitats, while carbon stocks influenced richness of bats, birds, vascular plants and pooled taxa. Species composition changed relatively abruptly along the management intensity gradient, while changes along carbon and productivity gradients were more gradual. We conclude that moderate increases in forest management intensity and carbon stocks, within the range of variation observed in our study system, might be compatible with biodiversity and climate mitigation objectives in managed forests.
A pilot study: effectiveness of local injection of autologous platelet-rich plasma in treating women with stress urinary incontinence
Authors: Long Cheng-Yu , Lin Kun-Ling , Shen Chin-Ru , Ker Chin-Ru , Liu Yi-Yin , Loo Zi-Xi , Hsiao Hui-Hua , Lee Yung-Chin 
Published: January 2021

AbstractThe study aims to evaluate the effectiveness of local injection of autologous platelet rich plasma (A-PRP) as a treatment for women suffering from stress urinary incontinence (SUI). In a prospective intervention study, twenty consecutive women suffering from SUI were treated with A-PRP injection at anterior vaginal wall where mid-urethra locates. Self-reported questionnaires were used to measure pre-treatment, 1 month and 6 months post-treatment symptom severity. Secondary outcomes of sexual function and treatment effect sorted by age were analyzed with valid statistical methods. A-PRP is effective in relieving SUI symptoms at both 1 month and 6 months post-treatment without significant adverse reactions reported. It seems to have a trend that treatment success rate with cured and improved symptoms was slightly higher in the younger group, although it did not reach statistical significance (P = 0.07). No significant changes in sexual function before and after the treatment were reported by the patients. This pilot study is the first to report A-PRP treatment effect for SUI in women. The result suggested that A-PRP is a considerable treatment option for mild to moderate SUI cases. It also opens up further research opportunities for A-PRP’s clinical applications.
Thiamethoxam exposure deregulates short ORF gene expression in the honey bee and compromises immune response to bacteria
Authors: Decio Pâmela , Ustaoglu Pinar , Derecka Kamila , Hardy Ian C. W. , Roat Thaisa C. , Malaspina Osmar , Mongan Nigel , Stöger Reinhard , Soller Matthias 
Published: January 2021

AbstractMaximizing crop yields relies on the use of agrochemicals to control insect pests. One of the most widely used classes of insecticides are neonicotinoids that interfere with signalling of the neurotransmitter acetylcholine, but these can also disrupt crop-pollination services provided by bees. Here, we analysed whether chronic low dose long-term exposure to the neonicotinoid thiamethoxam alters gene expression and alternative splicing in brains of Africanized honey bees, Apis mellifera, as adaptation to altered neuronal signalling. We find differentially regulated genes that show concentration-dependent responses to thiamethoxam, but no changes in alternative splicing. Most differentially expressed genes have no annotated function but encode short Open Reading Frames, a characteristic feature of anti-microbial peptides. As this suggested that immune responses may be compromised by thiamethoxam exposure, we tested the impact of thiamethoxam on bee immunity by injecting bacteria. We show that intrinsically sub-lethal thiamethoxam exposure makes bees more vulnerable to normally non-pathogenic bacteria. Our findings imply a synergistic mechanism for the observed bee population declines that concern agriculturists, conservation ecologists and the public.
Baseline local hemodynamics as predictor of lumen remodeling at 1-year follow-up in stented superficial femoral arteries
Authors: Colombo Monika , He Yong , Corti Anna , Gallo Diego , Casarin Stefano , Rozowsky Jared M. , Migliavacca Francesco , Berceli Scott , Chiastra Claudio 
Published: January 2021

AbstractIn-stent restenosis (ISR) is the major drawback of superficial femoral artery (SFA) stenting. Abnormal hemodynamics after stent implantation seems to promote the development of ISR. Accordingly, this study aims to investigate the impact of local hemodynamics on lumen remodeling in human stented SFA lesions. Ten SFA models were reconstructed at 1-week and 1-year follow-up from computed tomography images. Patient-specific computational fluid dynamics simulations were performed to relate the local hemodynamics at 1-week, expressed in terms of time-averaged wall shear stress (TAWSS), oscillatory shear index and relative residence time, with the lumen remodeling at 1-year, quantified as the change of lumen area between 1-week and 1-year. The TAWSS was negatively associated with the lumen area change (ρ = − 0.75, p = 0.013). The surface area exposed to low TAWSS was positively correlated with the lumen area change (ρ = 0.69, p = 0.026). No significant correlations were present between the other hemodynamic descriptors and lumen area change. The low TAWSS was the best predictive marker of lumen remodeling (positive predictive value of 44.8%). Moreover, stent length and overlapping were predictor of ISR at follow-up. Despite the limited number of analyzed lesions, the overall findings suggest an association between abnormal patterns of WSS after stenting and lumen remodeling.
Identification and genetic diversity analysis of a male-sterile gene (MS1) in Japanese cedar (Cryptomeria japonica D. Don)
Authors: Hasegawa Yoichi , Ueno Saneyoshi , Wei Fu-Jin , Matsumoto Asako , Uchiyama Kentaro , Ujino-Ihara Tokuko , Hakamata Tetsuji , Fujino Takeshi , Kasahara Masahiro , Bino Takahiro , Yamaguchi Katsushi , Shigenobu Shuji , Tsumura Yoshihiko , Moriguchi Yoshinari 
Published: January 2021

AbstractIdentifying causative genes for a target trait in conifer reproduction is challenging for species lacking whole-genome sequences. In this study, we searched for the male-sterility gene (MS1) inCryptomeria japonica, aiming to promote marker-assisted selection (MAS) of male-sterileC. japonicato reduce the pollinosis caused by pollen dispersal from artificialC. japonicaforests in Japan. We searched for mRNA sequences expressed in male strobili and found the gene CJt020762, coding for a lipid transfer protein containing a 4-bp deletion specific to male-sterile individuals. We also found a 30-bp deletion by sequencing the entire gene of another individual with thems1. All nine breeding materials with the allelems1had either a 4-bp or 30-bp deletion in gene CJt020762, both of which are expected to result in faulty gene transcription and function. Furthermore, the 30-bp deletion was detected from three of five individuals in the Ishinomaki natural forest. From our findings, CJt020762 was considered to be the causative gene ofMS1. Thus, by performing MAS using two deletion mutations as a DNA marker, it will be possible to find novel breeding materials ofC. japonicawith the allelems1adapted to the unique environment of each region of the Japanese archipelago.
Generation of highly amenable cellulose-Iβ via selective delignification of rice straw using a reusable cyclic ether-assisted deep eutectic solvent system
Authors: Thulluri Chiranjeevi , Balasubramaniam Ravi , Velankar Harshad Ravindra 
Published: January 2021

AbstractCellulolytic enzymes can readily access the cellulosic component of lignocellulosic biomass after the removal of lignin during biomass pretreatment. The enzymatic hydrolysis of cellulose is necessary for generating monomeric sugars, which are then fermented into ethanol. In our study, a combination of a deep eutectic (DE) mixture (of 2-aminoethanol and tetra-n-butyl ammonium bromide) and a cyclic ether (tetrahydrofuran) was used for selective delignification of rice straw (RS) under mild conditions (100 °C). Pretreatment with DE-THF solvent system caused ~ 46% delignification whereas cellulose (~ 91%) and hemicellulose (~ 67%) recoveries remained higher. The new solvent system could be reused upto 10 subsequent cycles with the same effectivity. Interestingly, the DE-THF pretreated cellulose showed remarkable enzymatic hydrolysability, despite an increase in its crystallinity to 72.3%. Contrary to conventional pretreatments, we report for the first time that the enzymatic hydrolysis of pretreated cellulose is enhanced by the removal of lignin during DE-THF pretreatment, notwithstanding an increase in its crystallinity. The current study paves way for the development of newer strategies for biomass depolymerization with DES based solvents.