bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel class of sulfur-containing aminolipids widespread in marine roseobacters
Authors: Smith Alastair F , Silvano Eleonora , Päuker Orsola , Guillonneau Richard , Quareshy Mussa , Murphy Andrew , Mausz Michaela A , Stirrup Rachel , Rihtman Branko , Aguilo-Ferretjans Maria , Brandsma Joost , Petersen Jörn , Scanlan David J , Chen Yin 
Published: March 2021

Abstract
Marine roseobacter group bacteria are numerically abundant and ecologically important players in ocean ecosystems. These bacteria are capable of modifying their membrane lipid composition in response to environmental change. Remarkably, a variety of lipids are produced in these bacteria, including phosphorus-containing glycerophospholipids and several amino acid-containing aminolipids such as ornithine lipids and glutamine lipids. Here, we present the identification and characterization of a novel sulfur-containing aminolipid (SAL) in roseobacters. Using high resolution accurate mass spectrometry, a SAL was found in the lipid extract of Ruegeria pomeroyi DSS-3 and Phaeobacter inhibens DSM 17395. Using comparative genomics, transposon mutagenesis and targeted gene knockout, we identified a gene encoding a putative lyso-lipid acyltransferase, designated salA, which is essential for the biosynthesis of this SAL. Multiple sequence analysis and structural modeling suggest that SalA is a novel member of the lysophosphatidic acid acyltransferase (LPAAT) family, the prototype of which is the PlsC acyltransferase responsible for the biosynthesis of the phospholipid phosphatidic acid. SAL appears to play a key role in biofilm formation in roseobacters. salA is widely distributed in Tara Oceans metagenomes and actively expressed in Tara Oceans metatranscriptomes. Our results raise the importance of sulfur-containing membrane aminolipids in marine bacteria.
Infectivity, susceptibility, and risk factors associated with SARS-CoV-2 transmission under intensive contact tracing in Hunan, China
Authors: Hu Shixiong , Wang Wei , Wang Yan , Litvinova Maria , Luo Kaiwei , Ren Lingshuang , Sun Qianlai , Chen Xinghui , Zeng Ge , Li Jing , Liang Lu , Deng Zhihong , Zheng Wen , Li Mei , Yang Hao , Guo Jinxin , Wang Kai , Chen Xinhua , Liu Ziyan , Yan Han , Shi Huilin , Chen Zhiyuan , Zhou Yonghong , Sun Kaiyuan , Vespignani Alessandro , Viboud Cécile , Gao Lidong , Ajelli Marco , Yu Hongjie 
Published: March 2021

AbstractSeveral mechanisms driving SARS-CoV-2 transmission remain unclear. Based on individual records of 1178 potential SARS-CoV-2 infectors and their 15,648 contacts in Hunan, China, we estimated key transmission parameters. The mean generation time was estimated to be 5.7 (median: 5.5, IQR: 4.5, 6.8) days, with infectiousness peaking 1.8 days before symptom onset, with 95% of transmission events occurring between 8.8 days before and 9.5 days after symptom onset. Most transmission events occurred during the pre-symptomatic phase (59.2%). SARS-CoV-2 susceptibility to infection increases with age, while transmissibility is not significantly different between age groups and between symptomatic and asymptomatic individuals. Contacts in households and exposure to first-generation cases are associated with higher odds of transmission. Our findings support the hypothesis that children can effectively transmit SARS-CoV-2 and highlight how pre-symptomatic and asymptomatic transmission can hinder control efforts.
Evaluating the effect of spaceflight on the host–pathogen interaction between human intestinal epithelial cells and Salmonella Typhimurium
Authors: Barrila Jennifer , Sarker Shameema F. , Hansmeier Nicole , Yang Shanshan , Buss Kristina , Briones Natalia , Park Jin , Davis Richard R. , Forsyth Rebecca J. , Ott C. Mark , Sato Kevin , Kosnik Cristine , Yang Anthony , Shimoda Cheryl , Rayl Nicole , Ly Diana , Landenberger Aaron , Wilson Stephanie D. , Yamazaki Naoko , Steel Jason , Montano Camila , Halden Rolf U. , Cannon Tom , Castro-Wallace Sarah L. , Nickerson Cheryl A. 
Published: March 2021

AbstractSpaceflight uniquely alters the physiology of both human cells and microbial pathogens, stimulating cellular and molecular changes directly relevant to infectious disease. However, the influence of this environment on host–pathogen interactions remains poorly understood. Here we report our results from the STL-IMMUNE study flown aboard Space Shuttle mission STS-131, which investigated multi-omic responses (transcriptomic, proteomic) of human intestinal epithelial cells to infection withSalmonellaTyphimurium when both host and pathogen were simultaneously exposed to spaceflight. To our knowledge, this was the first in-flight infection and dual RNA-seq analysis using human cells.
Benchmarking surface tension measurement method using two oscillation modes in levitated liquid metals
Authors: Brosius Nevin , Ward Kevin , Wilson Evan , Karpinsky Zachary , SanSoucie Michael , Ishikawa Takehiko , Matsumoto Satoshi , Narayanan Ranga 
Published: March 2021

AbstractThe Faraday forcing method in levitated liquid droplets has recently been introduced as a method for measuring surface tension using resonance. By subjecting an electrostatically levitated liquid metal droplet to a continuous, oscillatory, electric field, at a frequency nearing that of the droplet’s first principal mode of oscillation (known as mode 2), the method was previously shown to determine surface tension of materials that would be particularly difficult to process by other means, e.g., liquid metals and alloys. It also offers distinct advantages in future work involving high viscosity samples because of the continuous forcing approach. This work presents (1) a benchmarking experimental method to measure surface tension by excitation of the second principal mode of oscillation (known as mode 3) in a levitated liquid droplet and (2) a more rigorous quantification of droplet excitation using a projection method. Surface tension measurements compare favorably to literature values for Zirconium, Inconel 625, and Rhodium, using both modes 2 and 3. Thus, this new method serves as a credible, self-consistent benchmarking technique for the measurement of surface tension.
Performance characteristics and costs of serological tests for brucellosis in a pastoralist community of northern Tanzania
Authors: Lukambagire AbdulHamid S. , Mendes Ângelo J. , Bodenham Rebecca F. , McGiven John A. , Mkenda Nestory A. , Mathew Coletha , Rubach Matthew P. , Sakasaka Philoteus , Shayo Davis D. , Maro Venance P. , Shirima Gabriel M. , Thomas Kate M. , Kasanga Christopher J. , Kazwala Rudovick R. , Halliday Jo E. B. , Mmbaga Blandina T. 
Published: March 2021

AbstractThe control of brucellosis across sub-Saharan Africa is hampered by the lack of standardized testing and the use of tests with poor performance. This study evaluated the performance and costs of serological assays for human brucellosis in a pastoralist community in northern Tanzania. Serum collected from 218 febrile hospital patients was used to evaluate the performance of seven index tests, selected based on international recommendation or current use. We evaluated the Rose Bengal test (RBT) using two protocols, four commercial agglutination tests and a competitive enzyme-linked immunosorbent assay (cELISA). The sensitivity, specificity, positive predictive value, negative predictive value, Youden’s index, diagnostic accuracy, and per-sample cost of each index test were estimated. The diagnostic accuracy estimates ranged from 95.9 to 97.7% for the RBT, 55.0 to 72.0% for the commercial plate tests, and 89.4% for the cELISA. The per-sample cost range was $0.69–$0.79 for the RBT, $1.03–$1.14 for the commercial plate tests, and $2.51 for the cELISA. The widely used commercial plate tests performed poorly and cost more than the RBT. These findings provide evidence for the public health value of discontinuing the use of commercial agglutination tests for human brucellosis in Tanzania.
Metallothionein-3 promotes cisplatin chemoresistance remodelling in neuroblastoma
Authors: Rodrigo Miguel Angel Merlos , Michalkova Hana , Strmiska Vladislav , Casar Berta , Crespo Piero , de los Rios Vivian , Ignacio Casal J. , Haddad Yazan , Guran Roman , Eckschlager Tomas , Pokorna Petra , Heger Zbynek , Adam Vojtech 
Published: March 2021

AbstractMetallothionein-3 has poorly characterized functions in neuroblastoma. Cisplatin-based chemotherapy is a major regimen to treat neuroblastoma, but its clinical efficacy is limited by chemoresistance. We investigated the impact of human metallothionein-3 (hMT3) up-regulation in neuroblastoma cells and the mechanisms underlying the cisplatin-resistance. We confirmed the cisplatin-metallothionein complex formation using mass spectrometry. Overexpression of hMT3 decreased the sensitivity of neuroblastoma UKF-NB-4 cells to cisplatin. We report, for the first time, cisplatin-sensitive human UKF-NB-4 cells remodelled into cisplatin-resistant cells via high and constitutive hMT3 expression in an in vivo model using chick chorioallantoic membrane assay. Comparative proteomic analysis demonstrated that several biological pathways related to apoptosis, transport, proteasome, and cellular stress were involved in cisplatin-resistance in hMT3 overexpressing UKF-NB-4 cells. Overall, our data confirmed that up-regulation of hMT3 positively correlated with increased cisplatin-chemoresistance in neuroblastoma, and a high level of hMT3 could be one of the causes of frequent tumour relapses.
Eltrombopag for the treatment of refractory thrombocytopenia associated with connective tissue disease
Authors: Wang Juan , Dai Min , Fu Qiong , Chen Sheng 
Published: March 2021

AbstractTo assess the efficacy and safety of eltrombopag in connective tissue disease (CTD)-immune thrombocytopenia (ITP), we conducted this single-center retrospective observational study, including patients with refractory CTD-ITP who were treated with eltrombopag between January 2018 and August 2019. The characteristics of patients at baseline, and the efficacy and safety of the drug were analyzed. The predictors for a response were analyzed using a univariate analysis such as Chi-square or nonparametric test and a multiple correspondence analysis (MCA) method. A total of 15 patients with refractory CTD-ITP were included in the study. Their median age at the time of inclusion was 40.6 years. The median platelet count at initiation of eltrombopag was 11.53 × 109/L. The median remission time was 3.42 weeks. The complete remission (CR) and overall response rate decreased with time. The factors that associated with response to eltrombopag in patients with CTD-ITP were protopathy, WBC counts, levels of hemoglobin, and characteristics of bone marrow findings in univariate analysis. In addition, MCA indicated that a poor response to eltrombopag in patients with refractory CTD-ITP was closely associated with a protopathy with SS, medium to severe degree of anemia, leukopenia, and bone marrow aspiration showing aplastic anemia, an absence of megakaryocytes or macrophage activation syndrome (MAS). In conclusion, eltrombopag was effective and well-tolerated in patients with CTD-associated thrombocytopenia. Some factors should be considered in the use of eltrombopag, including the protopathy, blood test, and bone marrow histology.
Removing auto-activators from yeast-two-hybrid assays by conditional negative selection
Authors: Shivhare Devendra , Musialak-Lange Magdalena , Julca Irene , Gluza Pawel , Mutwil Marek 
Published: March 2021

AbstractYeast-two-hybrid (Y2H) is widely used as a strategy to detect protein–protein interactions (PPIs). Recent advancements have made it possible to generate and analyse genome-wide PPI networks en masse by coupling Y2H with next-generation sequencing technology. However, one of the major challenges of yeast two-hybrid assay is the large amount of false-positive hits caused by auto-activators (AAs), which are proteins that activate the reporter genes without the presence of an interacting protein partner. Here, we have developed a negative selection to minimize these auto-activators by integrating the pGAL2-URA3 fragment into the yeast genome. Upon activation of the pGAL2 promoter by an AA, yeast cells expressing URA3 cannot grow in media supplemented with 5-Fluoroorotic acid (5-FOA). Hence, we selectively inhibit the growth of yeast cells expressing auto-activators and thus minimizing the amount of false-positive hits. Here, we have demonstrated that auto-activators can be successfully removed from a Marchantia polymorpha cDNA library using pGAL2-URA3 and 5-FOA treatment, in liquid and solid-grown cultures. Furthermore, since URA3 can also serve as a marker for uracil autotrophy, we propose that our approach is a valuable addition to any large-scale Y2H screen.
Deep learning classification of lung cancer histology using CT images
Authors: Chaunzwa Tafadzwa L. , Hosny Ahmed , Xu Yiwen , Shafer Andrea , Diao Nancy , Lanuti Michael , Christiani David C. , Mak Raymond H. , Aerts Hugo J. W. L. 
Published: March 2021

AbstractTumor histology is an important predictor of therapeutic response and outcomes in lung cancer. Tissue sampling for pathologist review is the most reliable method for histology classification, however, recent advances in deep learning for medical image analysis allude to the utility of radiologic data in further describing disease characteristics and for risk stratification. In this study, we propose a radiomics approach to predicting non-small cell lung cancer (NSCLC) tumor histology from non-invasive standard-of-care computed tomography (CT) data. We trained and validated convolutional neural networks (CNNs) on a dataset comprising 311 early-stage NSCLC patients receiving surgical treatment at Massachusetts General Hospital (MGH), with a focus on the two most common histological types: adenocarcinoma (ADC) and Squamous Cell Carcinoma (SCC). The CNNs were able to predict tumor histology with an AUC of 0.71(p = 0.018). We also found that using machine learning classifiers such as k-nearest neighbors (kNN) and support vector machine (SVM) on CNN-derived quantitative radiomics features yielded comparable discriminative performance, with AUC of up to 0.71 (p = 0.017). Our best performing CNN functioned as a robust probabilistic classifier in heterogeneous test sets, with qualitatively interpretable visual explanations to its predictions. Deep learning based radiomics can identify histological phenotypes in lung cancer. It has the potential to augment existing approaches and serve as a corrective aid for diagnosticians.
A multicenter, prospective, observational study to determine association of mesangial C1q deposition with renal outcomes in IgA nephropathy
Authors: Tan Li , Tang Yi , Pei Gaiqin , Zhong Zhengxia , Tan Jiaxing , Zhou Ling , Wen Dongmei , Sheikh-Hamad David , Qin Wei 
Published: March 2021

AbstractIt was reported that histopathologic lesions are risk factors for the progression of IgA Nephropathy (IgAN). The aim of this study was to investigate the relationships between mesangial deposition of C1q and renal outcomes in IgAN. 1071 patients with primary IgAN diagnosed by renal biopsy were enrolled in multiple study centers form January 2013 to January 2017. Patients were divided into two groups: C1q-positive and C1q-negative. Using a 1: 4 propensity score matching (PSM) method identifying age, gender, and treatment modality to minimize confounding factors, 580 matched (out of 926) C1q-negative patients were compared with 145 C1q-positive patients to evaluate severity of baseline clinicopathological features and renal outcome. Kaplan–Meier and Cox proportional hazards analyses were performed to determine whether mesangial C1q deposition is associated with renal outcomes in IgAN. During the follow-up period (41.89 ± 22.85 months), 54 (9.31%) patients in the C1q negative group and 23 (15.86%) patients in C1q positive group reached the endpoint (50% decline of eGFR and/or ESRD or death) respectively (p = 0.01) in the matched cohort. Significantly more patients in C1q negative group achieved complete or partial remission during the follow up period (P = 0.003) both before and after PSM. Three, 5 and 7-year renal survival rates in C1q-positive patients were significantly lower than C1q-negative patients in either unmatched cohort or matched cohort (all p < 0.05). Furthermore, multivariate Cox regression analysis showed that independent risk factors influencing renal survival included Scr, urinary protein, T1-T2 lesion and C1q deposition. Mesangial C1q deposition is a predictor of poor renal survival in IgA nephropathy.Trial registration TCTR, TCTR20140515001. Registered May 15, 2014, http://www.clinicaltrials.in.th/index.php?tp=regtrials&menu=trialsearch&smenu=fulltext&task=search&task2=view1&id=1074.
Swine growth promotion with antibiotics or alternatives can increase antibiotic resistance gene mobility potential
Authors: Muurinen Johanna , Richert Jacob , Wickware Carmen L. , Richert Brian , Johnson Timothy A. 
Published: March 2021

AbstractEven though the use of antibiotics for food-producing animals may contribute to the emergence of antimicrobial resistance, antibiotics are still used as growth promoters. Due to consumer and regulatory pressures, the use of alternatives to antibiotics as growth promoters is increasing, thus more information is needed on their capability to disseminate antimicrobial resistance compared to antibiotics. We investigated the impacts of carbadox (antibiotic), copper sulfate and zinc oxide (metals) and mushroom powder (natural product) on the pig fecal resistome and microbiome. Antibiotic resistance gene (ARG) and mobile genetic element (MGE) abundances were measured using a high-throughput qPCR array with 382 primer pairs. Bacterial community composition was determined by 16S rRNA gene sequencing. More ARGs co-occurred with MGEs in the growth promoter group samples than in the control group samples. Community composition could not be linked to resistome in the growth promoter group samples, indicating a potential decoupling of ARGs and phylogeny. Additionally, machine-learning methods aided in defining the community and resistome differences in response to treatments. Since increased ARG mobility potential was the primary response to the dietary additives used in this study, we suggest that ARG mobility should be considered when designing antimicrobial use policies and antimicrobial resistance surveillances.
Development of sensitive and accurate solid-phase microextraction procedure for preconcentration of As(III) ions in real samples
Authors: Elik Adil , Tuzen Mustafa , Hazer Baki , Kaya Savaş , Katin K. P. , Altunay Nail 
Published: March 2021

AbstractWe synthesized the poly(methyl methacrylate-co-2-aminoethyl methacrylate (PMaema) amphiphilic copolymer in a form of solid phase adsorbent. Then it was used for separation, preconcentration and determination of trace amount of As(III) ions from foods and waters with hydride generation atomic absorption spectrometry. The PMaema was characterized by fourier transform infrared spectrometer and nuclear magnetic resonance spectrometer. The adsorption of As(III) to the PMaema was also supported using computational chemistry studies. The experimental parameters (pH, PMaema amount, adsorption time and ethanol volume) were optimized using a three-level Box–Behnken design with four experimental factors. We observed linear calibration curve for the PMaema amount in the 10–500 ng L−1 range (R2 = 0.9956). Limit of detection, preconcentration factor and sorbent capacity of PMaema were equal to 3.3 ng L−1, 100 and 75.8 mg g−1, respectively. The average recoveries (spiked at 50 ng L−1) changes in the range of 91.5–98.6% with acceptable relative standard deviation less than 4.3%. After validation studies, the method was successfully applied for separation, preconcentration and determination of trace amount of As(III) from foods and waters.
East Antarctica magnetically linked to its ancient neighbours in Gondwana
Authors: Ebbing Jörg , Dilixiati Yixiati , Haas Peter , Ferraccioli Fausto , Scheiber-Enslin Stephanie 
Published: March 2021

AbstractWe present a new magnetic compilation for Central Gondwana conformed to a recent satellite magnetic model (LCS-1) with the help of an equivalent layer approach, resulting in consistent levels, corrections that have not previously been applied. Additionally, we use the satellite data to its full spectral content, which helps to include India, where high resolution aeromagnetic data are not publically available. As India is located north of the magnetic equator, we also performed a variable reduction to the pole to the satellite data by applying an equivalent source method. The conformed aeromagnetic and satellite data are superimposed on a recent deformable Gondwana plate reconstruction that links the Kaapvaal Craton in Southern Africa with the Grunehogna Craton in East Antarctica in a tight fit. Aeromagnetic anomalies unveil, however, wider orogenic belts that preserve remnants of accreted Meso- to Neoproterozoic crust in interior East Antarctica, compared to adjacent sectors of Southern Africa and India. Satellite and aeromagnetic anomaly datasets help to portray the extent and architecture of older Precambrian cratons, re-enforcing their linkages in East Antarctica, Australia, India and Africa.
Corneal proteome and differentially expressed corneal proteins in highly myopic chicks using a label-free SWATH-MS quantification approach
Authors: Kang Byung Soo , Lam Thomas Chuen , Cheung Jimmy Ka-wai , Li King Kit , Kee Chea-su 
Published: March 2021

AbstractMyopia, or short-sightedness, is a highly prevalent refractive disorder in which the eye’s focal length is too short for its axial dimension in its relaxed state. High myopia is associated with increased risks of blinding ocular complications and abnormal eye shape. In addition to consistent findings on posterior segment anomalies in high myopia (e.g., scleral remodeling), more recent biometric and biomechanical data in myopic humans and animal models also indicate anterior segment anomalies (e.g., corneal biomechanical properties). Because the cornea is the anterior-most ocular tissue, providing essential refractive power and physiological stability, it is important to understand the biochemical signaling pathway during myopia development. This study first aimed to establish the entire chicken corneal proteome. Then, using the classical form deprivation paradigm to induce high myopia in chicks, state-of-the-art bioinformatics technologies were applied to identify eight differentially expressed proteins in the highly myopic cornea. These results provide strong foundation for future corneal research, especially those using chicken as an animal model for myopia development.