bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction of a web-based nanomaterial database by big data curation and modeling friendly nanostructure annotations
Authors: Yan Xiliang , Sedykh Alexander , Wang Wenyi , Yan Bing , Zhu Hao 
Published: May 2020

AbstractModern nanotechnology research has generated numerous experimental data for various nanomaterials. However, the few nanomaterial databases available are not suitable for modeling studies due to the way they are curated. Here, we report the construction of a large nanomaterial database containing annotated nanostructures suited for modeling research. The database, which is publicly available throughhttp://www.pubvinas.com/, contains 705 unique nanomaterials covering 11 material types. Each nanomaterial has up to six physicochemical properties and/or bioactivities, resulting in more than ten endpoints in the database. All the nanostructures are annotated and transformed into protein data bank files, which are downloadable by researchers worldwide. Furthermore, the nanostructure annotation procedure generates 2142 nanodescriptors for all nanomaterials for machine learning purposes, which are also available through the portal. This database provides a public resource for data-driven nanoinformatics modeling research aimed at rational nanomaterial design and other areas of modern computational nanotechnology.
Immunogenicity of a DNA vaccine candidate for COVID-19
Authors: Smith Trevor R. F. , Patel Ami , Ramos Stephanie , Elwood Dustin , Zhu Xizhou , Yan Jian , Gary Ebony N. , Walker Susanne N. , Schultheis Katherine , Purwar Mansi , Xu Ziyang , Walters Jewell , Bhojnagarwala Pratik , Yang Maria , Chokkalingam Neethu , Pezzoli Patrick , Parzych Elizabeth , Reuschel Emma L. , Doan Arthur , Tursi Nicholas , Vasquez Miguel , Choi Jihae , Tello-Ruiz Edgar , Maricic Igor , Bah Mamadou A. , Wu Yuanhan , Amante Dinah , Park Daniel H. , Dia Yaya , Ali Ali Raza , Zaidi Faraz I. , Generotti Alison , Kim Kevin Y. , Herring Timothy A. , Reeder Sophia , Andrade Viviane M. , Buttigieg Karen , Zhao Gan , Wu Jiun-Ming , Li Dan , Bao Linlin , Liu Jiangning , Deng Wei , Qin Chuan , Brown Ami Shah , Khoshnejad Makan , Wang Nianshuang , Chu Jacqueline , Wrapp Daniel , McLellan Jason S. , Muthumani Kar , Wang Bin , Carroll Miles W. , Kim J. Joseph , Boyer Jean , Kulp Daniel W. , Humeau Laurent M. P. F. , Weiner David B. , Broderick Kate E. 
Published: May 2020

AbstractThe coronavirus family member, SARS-CoV-2 has been identified as the causal agent for the pandemic viral pneumonia disease, COVID-19. At this time, no vaccine is available to control further dissemination of the disease. We have previously engineered a synthetic DNA vaccine targeting the MERS coronavirus Spike (S) protein, the major surface antigen of coronaviruses, which is currently in clinical study. Here we build on this prior experience to generate a synthetic DNA-based vaccine candidate targeting SARS-CoV-2 S protein. The engineered construct, INO-4800, results in robust expression of the S protein in vitro. Following immunization of mice and guinea pigs with INO-4800 we measure antigen-specific T cell responses, functional antibodies which neutralize the SARS-CoV-2 infection and block Spike protein binding to the ACE2 receptor, and biodistribution of SARS-CoV-2 targeting antibodies to the lungs. This preliminary dataset identifies INO-4800 as a potential COVID-19 vaccine candidate, supporting further translational study.
IolR, a negative regulator of the myo-inositol metabolic pathway, inhibits cell autoaggregation and biofilm formation by downregulating RpmA in Aeromonas hydrophila
Authors: Dong Yuhao , Li Shougang , Zhao Dan , Liu Jin , Ma Shuiyan , Geng Jinzhu , Lu Chengping , Liu Yongjie 
Published: May 2020

AbstractAeromonas hydrophila is the causative agent of motile Aeromonad septicemia in fish. Previous studies have shown that the myo-inositol metabolism is essential for the virulence of this bacterium. IolR is a transcription inhibitor that negatively regulates myo-inositol metabolic activity. While in the process of studying the inositol catabolism in A. hydrophila Chinese epidemic strain NJ-35, we incidentally found that ΔiolR mutant exhibited obvious autoaggregation and increased biofilm formation compared to the wild type. The role of surface proteins in A. hydrophila autoaggregation was confirmed by different degradation treatments. Furthermore, calcium promotes the formation of aggregates, which disappear in the presence of the calcium chelator EGTA. Transcriptome analysis, followed by targeted gene deletion, demonstrated that biofilm formation and autoaggregation caused by the inactivation of iolR was due to the increased transcription of a RTX-family adhesion gene, rmpA. Further, IolR was determined to directly regulate the transcription of rmpA. These results indicated that iolR is negatively involved in autoaggregation and biofilm formation in A. hydrophila, and this involvement was associated with its inhibition on the expression of rmpA.
Global high-resolution emissions of soil NOx, sea salt aerosols, and biogenic volatile organic compounds
Authors: Weng Hongjian , Lin Jintai , Martin Randall , Millet Dylan B. , Jaeglé Lyatt , Ridley David , Keller Christoph , Li Chi , Du Mingxi , Meng Jun 
Published: May 2020

AbstractNatural emissions of air pollutants from the surface play major roles in air quality and climate change. In particular, nitrogen oxides (NOx) emitted from soils contribute ~15% of global NOx emissions, sea salt aerosols are a major player in the climate and chemistry of the marine atmosphere, and biogenic emissions are the dominant source of non-methane volatile organic compounds at the global scale. These natural emissions are often estimated using nonlinear parameterizations, which are sensitive to the horizontal resolutions of inputted meteorological and ancillary data. Here we use the HEMCO model to compute these emissions worldwide at horizontal resolutions of 0.5° lat. × 0.625° lon. for 1980–2017 and 0.25° lat. × 0.3125° lon. for 2014–2017. We further offer the respective emissions at lower resolutions, which can be used to evaluate the impacts of resolution on estimated global and regional emissions. Our long-term high-resolution emission datasets offer useful information to study natural pollution sources and their impacts on air quality, climate, and the carbon cycle.
In vitro passage alters virulence, immune activation and proteomic profiles of Burkholderia pseudomallei
Authors: Duangurai Taksaon , Reamtong Onrapak , Rungruengkitkun Amporn , Srinon Varintip , Boonyuen Usa , Limmathurotsakul Direk , Chantratita Narisara , Pumirat Pornpan 
Published: May 2020

AbstractSerial passage is a problem among many bacterial species, especially those where strains have been stored (banked) for several decades. Prior to banking with an organization such as ATCC, many bacterial strains were passaged for many years, so the characteristics of each strain may be extremely different. This is in addition to any differences in the original host environment. For Burkholderia pseudomallei, the number of serial passages should be carefully defined for each experiment because it undergoes adaptation during the course of serial passages. In the present study, we found that passaged B. pseudomallei fresh clinical isolates and reference strain in Luria-Bertani broth exhibited increased plaque formation, invasion, intracellular replication, Galleria mellonella killing abilities, and cytokine production of host cells. These bacteria also modulated proteomic profiles during in vitro passage. We presume that the modulation of protein expression during in vitro passage caused changes in virulence and immunogenicity phenotypes. Therefore, we emphasize the need for caution regarding the use of data from passaged B. pseudomallei. These findings of phenotypic adaptation during in vitro serial passage can help researchers working on B. pseudomallei and on other species to better understand disparate findings among strains that have been reported for many years.
Clinical validation of urinary indole-reacted calcium oxalate crystallization index (iCOCI) test for diagnosing calcium oxalate urolithiasis
Authors: More-krong Pimkanya , Tubsaeng Praween , Madared Natcha , Srisa-Art Monpichar , Insin Numpon , Leeladee Pannee , Boonla Chanchai 
Published: May 2020

AbstractAn indole-reacted calcium oxalate crystallization index (iCOCI) test was developed to quantify the total competence of urine to precipitate calcium oxalate (CaOx) crystals. We conducted the prospective cohort study in accordance with the STARD guideline to evaluate the accuracy of urinary iCOCI test (index test) for diagnosing urolithiasis. A total of 281 participants were recruited for the study. Levels of urinary iCOCI were determined in the pre-diagnostic 24-h urine samples. Positive urinary iCOCI (≥ 0.6 COM eqv., g/L) was accounted for 51% (144/281), and the rest of 49% (137/281) were negative. Non-contrast CT imaging (reference standard) was subsequently performed for the definite diagnosis of urolithiasis to divide the participants into two groups, non-stone subjects (NSS, n = 122) and stone-forming subjects (SFS, n = 159). It should be noted that only subjects who currently had urinary stone at the time of study were classified as SFS. Urinary iCOCI levels in the SFS were significantly higher than the NSS. ROC analysis revealed an area under curve (AUC) of 0.893 (95% CI: 0.855–0.932) in separating NSS from all SFS. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), accuracy, positive likelihood ratio (LH+) and negative likelihood ratio (LH−) of urinary iCOCI test for diagnosis of all urolithiasis were 87%, 80%, 84%, 84%, 83%, 4.44 and 0.16, respectively. Of 159 SFS, 38 were confirmed to have CaOx stones. Among these 38 CaOx SFS, only 2 had negative urinary iCOCI test. The AUC of urinary iCOCI test for separating CaOx SFS from NSS was markedly high (0.946, 95% CI: 0.914–0.978). Sensitivity, specificity, PPV, NPV, accuracy, LH+ and LH− of urinary iCOCI test for diagnosing CaOx urolithiasis were 95%, 86%, 68%, 98%, 88%, 6.80 and 0.06, respectively. Conclusion, we clinically validated that an innovative non-invasive urinary iCOCI test was highly accurate to diagnose urolithiasis, especially CaOx stone. With its high sensitivity and NPV, urinary iCOCI test is clinically intended to use as a screening test for CaOx urolithiasis. LH− of 0.06 indicates that negative result of urinary iCOCI test is highly accurate to rule out the CaOx stone formation. It is noted that urinary iCOCI level is expressed as arbitrary unit, and it is not directly related to the actual physiological level of urinary oxalate.
PolyRad – Protection Against Free Radical Damage
Authors: Kim Hannah , Tse Yin , Webb Andrew , Mudd Ethan , Abedin Muhammad Raisul , Mormile Melanie , Dutta Subhadeep , Rege Kaushal , Barua Sutapa 
Published: May 2020

AbstractThe effects of elevated levels of radiation contribute to the instability of pharmaceutical formulations in space compared to those on earth. Existing technologies are ineffective at maintaining the therapeutic efficacies of drugs in space. Thus, there is an urgent need to develop novel space-hardy formulations for preserving the stability and efficacy of drug formulations. This work aims to develop a novel approach for the protection of space pharmaceutical drug molecules from the radiation-induced damage to help extend or at least preserve their structural integrity and potency. To achieve this, free radical scavenging antioxidant, Trolox was conjugated on the surface of poly-lactic-co-glycolic acid (PLGA) nanoparticles for the protection of a candidate drug, melatonin that is used as a sleep aid medication in International Space Station (ISS). Melatonin-PLGA-PLL-Trolox nanoparticle as named as PolyRad was synthesized employing single oil in water (o/w) emulsion solvent evaporation method. PolyRad is spherical in shape and has an average diameter of ~600 nm with a low polydispersity index of 0.2. PolyRad and free melatonin (control) were irradiated by UV light after being exposed to a strong oxidant, hydrogen peroxide (H2O2). Bare melatonin lost ~80% of the active structure of the drug following irradiation with UV light or treatment with H2O2. In contrast, PolyRad protected >80% of the active structure of melatonin. The ability of PolyRad to protect melatonin structure was also carried out using 0, 1, 5 and 10 Gy gamma radiation. Gamma irradiation showed >98% active structures of melatonin encapsulated in PolyRads. Drug release and effectiveness of melatonin using PolyRad were evaluated on human umbilical vein endothelial cells (HUVEC) in vitro. Non-irradiated PolyRad demonstrated maximum drug release of ~70% after 72 h, while UV-irradiated and H2O2-treated PolyRad showed a maximum drug release of ~85%. Cytotoxicity of melatonin was carried out using both live/dead and MTT assays. Melatonin, non-radiated PolyRad and irradiated PolyRad inhibited the viability of HUVEC in a dose-dependent manner. Cell viability of melatonin, PolyRad alone without melatonin (PolyRad carrier control), non-radiated PolyRad, and irradiated PolyRad were ~98, 87, 75 and 70%, respectively at a concentration $$ \sim $$
~
0.01 $${mg}/{ml}$$
mg
/
ml
($$10\mu g/{ml}$$
10
μ
g
/
ml
). Taken together, PolyRad nanoparticle provides an attractive formulation platform for preventing damage to pharmaceutical drugs in potential space mission applications.
Histone H3K27M Mutation Overrides Histological Grading in Pediatric Gliomas
Authors: Mosaab Amal , El-Ayadi Moatasem , Khorshed Eman N. , Amer Nada , Refaat Amal , El-Beltagy Mohamed , Hassan Zeinab , Soror Sameh H. , Zaghloul Mohamed Saad , El-Naggar Shahenda 
Published: May 2020

AbstractPediatric high-grade gliomas (HGG) are rare aggressive tumors that present a prognostic and therapeutic challenge. Diffuse midline glioma, H3K27M–mutant is a new entity introduced to HGG in the latest WHO classification. In this study we evaluated the presence of H3K27M mutation in 105 tumor samples histologically classified into low-grade gliomas (LGG) (n = 45), and HGG (n = 60). Samples were screened for the mutation in histone H3.3 and H3.1 variants to examine its prevalence, prognostic impact, and assess its potential clinical value in limited resource settings. H3K27M mutation was detected in 28 of 105 (26.7%) samples, and its distribution was significantly associated with midline locations (p-value < 0.0001) and HGG (p-value = 0.003). Overall and event- free survival (OS and EFS, respectively) of patients with mutant tumors did not differ significantly, neither according to histologic grade (OSp-value = 0.736, EFSp-value = 0.75) nor across anatomical sites (OSp-value = 0.068, EFSp-value = 0.153). Detection of H3K27M mutation in pediatric gliomas provides more precise risk stratification compared to traditional histopathological techniques. Hence, mutation detection should be pursued in all pediatric gliomas. Meanwhile, focusing on midline LGG can be an alternative in lower-middle-income countries to maximally optimize patients’ treatment options.
Transforming growth factor-beta stimulates human bone marrow-derived mesenchymal stem/stromal cell chondrogenesis more so than kartogenin
Authors: Music E. , Klein T. J. , Lott W. B. , Doran M. R. 
Published: May 2020

AbstractA previous study identified kartogenin (KGN) as a potent modulator of bone marrow mesenchymal stem/stromal cell (BMSC) chondrogenesis. This initial report did not contrast KGN directly against transforming growth factor-beta 1 (TGF-β1), the most common growth factor used in chondrogenic induction medium. Herein, we directly compared the in vitro chondrogenic potency of TGF-β1 and KGN using a high resolution micropellet model system. Micropellets were cultured for 7–14 days in medium supplemented with TGF-β1, KGN, or both TGF-β1 + KGN. Following 14 days of induction, micropellets exposed to TGF-β1 alone or TGF-β1 + KGN in combination were larger and produced more glycosominoglycan (GAG) than KGN-only cultures. When TGF-β1 + KGN was used, GAG quantities were similar or slightly greater than the TGF-β1-only cultures, depending on the BMSC donor. BMSC micropellet cultures supplemented with KGN alone contracted in size over the culture period and produced minimal GAG. Indicators of hypertrophy were not mitigated in TGF-β1 + KGN cultures, suggesting that KGN does not obstruct BMSC hypertrophy. KGN appears to have weak chondrogenic potency in human BMSC cultures relative to TGF-β1, does not obstruct hypertrophy, and may not be a viable alternative to growth factors in cartilage tissue engineering.
No correlation between microbiota composition and blood parameters in nesting flatback turtles (Natator depressus)
Authors: Scheelings T. Franciscus , Moore Robert J. , Van Thi Thu Hao , Klaassen Marcel , Reina Richard D. 
Published: May 2020

AbstractThe microbiota is considered critical for normal vertebrate homeostasis and it may exert its effects at a local level within the gastrointestinal tract, or systemically through the production of bacterial metabolites. To date, investigations into the role that the microbiota plays in reptile physiology are rare. To address this knowledge gap, we explored the relationship between differences in microbial communities to see if they accounted for differences in haematology and biochemistry values, in different populations of nesting flatback turtles (Natator depressus). We found that microbiota composition was not correlated to any of the blood analytes we measured in flatbacks. This study is the first of its kind in reptiles and highlights the need for further investigations to determine mechanisms by which the microbiota influences the physiology and health of reptiles.
Establishment of rat liver cancer cell lines with different metastatic potential
Authors: Song Lei , Zhang Jian-gang , Zheng Long , Feng Xu , Hou Jie , Zhang Huan-ling , Liu Shu-feng 
Published: May 2020

AbstractThe gloomy outcome of liver cancer is mainly due to the high rates of metastasis and recurrence, even after curative resection for early stage liver cancer. Our study was conducted to find the animal model suitable for the study of liver cancer metastasis. In our study, two liver cancer cells were obtained from N-nitrosodiethylamine (DEN) and N-nitrosomorpholine (NMOR) induced rats, and they were cultivated, screened and cloning cultivated. Bionomics of cells was analyzed. The results show that 2 cells had different metastatic potentiality. They were named Wrh-f2 and Wrh-s2, and they have the characteristics of Hepatocellular carcinoma cells. The bionomics of 2 cells showed: (1) The chromosome karyotype analysis showed that the mode of Wrh-f2 was 80–83 and Wrh-s2 was 55–57; (2) AFP positive cytoplasmic staining was observed in Wrh-f2 and Wrh-s2. Cytokeratin (CK) 7 and CK8 positive staining was present in Wrh-f2. CK8 positive staining was present in Wrh-s2; (3) The numbers of Wrh-f2 and Wrh-s2 that passed through the Transwells were 98 ± 12 and 55 ± 15;(4) Wrh-f2 had the significant higher colony formation (78%) than Wrh-s2(8%) (P < 0.01). (5) The animal models generated solid tumours when 2 cells were inoculated to nude mouse and rat. And Wrh-f2 developed stable pulmonary metastasis. The established cell lines with different metastatic potential showed obvious advantages over liver cancer in mimicking the biological properties of malignant liver cancer tumors. It provided a suitable model for the mechanism of liver cancer metastasis in vivo and in vitro.
Differences Between School-Age Children With Apraxia of Speech and Other Speech Sound Disorders on Multisyllable Repetition
Authors: Benway Nina R. , Preston Jonathan L. 
Published: May 2020

Purpose
The aim of the study was to evaluate whether features of childhood apraxia of speech (CAS) identified in previous literature could be replicated in a sample of school-age children.

Method

A literature review was conducted to identify candidate speech features that have been previously considered when differentiating CAS from other types of speech sound disorders (SSDs). The candidate features recoverable from blinded transcriptions of multisyllable word repetitions (MSWRs) were applied to a cohort of 61 children aged 7–17 years, previously classified as having CAS (
n
= 21) or non-CAS SSD (
n
= 40).

Results
One hundred and ninety-four features had been explored in previous literature to assess their ability to differentiate CAS from other SSDs. Fifteen perceptual features were selected from this list to be applied to performance on the MSWR. In this sample, children with CAS differed from children with SSD on the prevalence of voicing changes, percentage of structurally correct words, correct lexical stress, and syllable deletions within a speech corpus derived from the MSWR task.

Conclusion
Although previous literature points to numerous features as differentiating CAS from other SSDs, only a portion of those features were replicated in this sample of school-age children. Features of CAS that affect segmental accuracy, prosody, and word structure may be likely to persist into late childhood and early adolescence.
Efficient implementation and performance improvement of three‐phase EPLL under non‐ideal grid conditions
Authors: Sevilmiş Fehmi , Karaca Hulusi 
Published: May 2020

In this study, an advanced phase‐locked‐loop (PLL), which has a simple structure and a low computational burden is proposed. The proposed PLL also improves the dynamic performance and the filtering capability of the conventional three‐phase enhanced‐PLL (3pEPLL) significantly. The conventional 3pEPLL operates three individual EPLL blocks for each phase voltage and a fourth EPLL for estimation of the magnitude, frequency, and phase angle, which considerably increases the structural complexity and computational burden. However, the proposed PLL called enhanced‐3pEPLL (E2 PLL) employs only two single‐phase EPLL modules in its pre‐filtering stage. A moving‐average‐filter (MAF) is also supplemented on the error signal path of these EPLL modules, which allows smoother estimation of the magnitude, frequency, and phase angle, and improves the filtering capability of the EPLLs. Unlike the conventional 3pEPLL, the proposed E2 PLL employs a quasi‐type‐1 PLL (QT1‐PLL) to estimate the magnitude, frequency, and phase information of the fundamental grid voltage. The structure of QT1‐PLL is similar to a type‐1 PLL, which offers a low transient response time. The small‐signal model of the proposed PLL is derived for stability analysis and parameter design procedure. The effectiveness of the E2 PLL is verified owing to experimental results and comparison with the conventional 3pEPLL and QT1‐PLL.