bluuebunny/crossref_metadata_2025_split huggingface dataset:
Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS): basics and clinical applications
Authors: Israr Muhammad Zubair , Bernieh Dennis , Salzano Andrea , Cassambai Shabana , Yazaki Yoshiyuki , Suzuki Toru 
Published: April 2020

Abstract

Background
Matrix-assisted laser desorption ionisation (MALDI) mass spectrometry (MS) has been used for more than 30 years. Compared with other analytical techniques, it offers ease of use, high throughput, robustness, cost-effectiveness, rapid analysis and sensitivity. As advantages, current clinical techniques (e.g. immunoassays) are unable to directly measure the biomarker; rather, they measure secondary signals. MALDI-MS has been extensively researched for clinical applications, and it is set for a breakthrough as a routine tool for clinical diagnostics.

Content
This review reports on the principles of MALDI-MS and discusses current clinical applications and the future clinical prospects for MALDI-MS. Furthermore, the review assesses the limitations currently experienced in clinical assays, the advantages and the impact of MALDI-MS to transform clinical laboratories.

Summary
MALDI-MS is widely used in clinical microbiology for the screening of microbial isolates; however, there is scope to apply MALDI-MS in the diagnosis, prognosis, therapeutic drug monitoring and biopsy imaging in many diseases.

Outlook
There is considerable potential for MALDI-MS in clinic as a tool for screening, profiling and imaging because of its high sensitivity and specificity over alternative techniques.
Isotope dilution-LC-MS/MS method for quantification of the urinary cotinine-to-creatinine ratio
Authors: Habler Katharina , Paal Michael , Vogeser Michael 
Published: April 2020

Abstract

Background
Appropriate monitoring of tobacco smoking is extremely important in several areas of medicine, e.g. management of chronic obstructive pulmonary disease (COPD), epidemiological surveys, and allocation of heart or lung transplants. The major metabolite of nicotine is cotinine that is increasingly used as a laboratory parameter for assessing tobacco smoke exposure.

Methods
Creatinine and cotinine were analyzed simultaneously in urine by ultra-high-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) in one run within 3 min using a biphenyl column. For quantification, the respective stable-isotope-labeled standards were used.

Results
Detuning and measuring a natural isotope of creatinine as precursor and product ion allowed a simultaneous quantification of creatinine and cotinine. The method revealed robust validation results. For both analytes, inaccuracy and imprecision of the quality control and external quality assessment (EQA) samples were ≤−11.1%.

Conclusions
One essential novelty of the method presented here is the simultaneous quantification of creatinine and cotinine covered by one analytical method. Despite the very different natural concentrations of creatinine and cotinine, this allows the immediate reporting of the cotinine-to-creatinine ratio without the need for a separate creatinine analysis.
Hematologic, biochemical and immune biomarker abnormalities associated with severe illness and mortality in coronavirus disease 2019 (COVID-19): a meta-analysis
Authors: Henry Brandon Michael , de Oliveira Maria Helena Santos , Benoit Stefanie , Plebani Mario , Lippi Giuseppe 
Published: April 2020

Abstract

Background
As coronavirus disease 2019 (COVID-19) pandemic rages on, there is urgent need for identification of clinical and laboratory predictors for progression towards severe and fatal forms of this illness. In this study we aimed to evaluate the discriminative ability of hematologic, biochemical and immunologic biomarkers in patients with and without the severe or fatal forms of COVID-19.

Methods
An electronic search in Medline (PubMed interface), Scopus, Web of Science and China National Knowledge Infrastructure (CNKI) was performed, to identify studies reporting on laboratory abnormalities in patients with COVID-19. Studies were divided into two separate cohorts for analysis: severity (severe vs. non-severe and mortality, i.e. non-survivors vs. survivors). Data was pooled into a meta-analysis to estimate weighted mean difference (WMD) with 95% confidence interval (95% CI) for each laboratory parameter.

Results
A total number of 21 studies was included, totaling 3377 patients and 33 laboratory parameters. While 18 studies (n = 2984) compared laboratory findings between patients with severe and non-severe COVID-19, the other three (n = 393) compared survivors and non-survivors of the disease and were thus analyzed separately. Patients with severe and fatal disease had significantly increased white blood cell (WBC) count, and decreased lymphocyte and platelet counts compared to non-severe disease and survivors. Biomarkers of inflammation, cardiac and muscle injury, liver and kidney function and coagulation measures were also significantly elevated in patients with both severe and fatal COVID-19. Interleukins 6 (IL-6) and 10 (IL-10) and serum ferritin were strong discriminators for severe disease.

Conclusions
Several biomarkers which may potentially aid in risk stratification models for predicting severe and fatal COVID-19 were identified. In hospitalized patients with respiratory distress, we recommend clinicians closely monitor WBC count, lymphocyte count, platelet count, IL-6 and serum ferritin as markers for potential progression to critical illness.
Analytical performances of a chemiluminescence immunoassay for SARS-CoV-2 IgM/IgG and antibody kinetics
Authors: Padoan Andrea , Cosma Chiara , Sciacovelli Laura , Faggian Diego , Plebani Mario 
Published: April 2020

Abstract

Background
Coronavirus disease 2019, abbreviated to COVID-19, represents an emerging health threat worldwide as, after initial reports in China, it has continued to spread rapidly. The clinical spectrum of the disease varies from mild to severe acute respiratory distress syndrome (ARDS). Moreover, many patients can be asymptomatic, thus increasing the uncertainty of the diagnostic work-up. Laboratory tests play a pivotal role in the diagnosis and management of COVID-19, the current gold standard being real-time reverse transcription polymerase chain reaction (rRT-PCR) on respiratory tract specimens. However, the diagnostic accuracy of rRT-PCR depends on many pre-analytical and analytical variables. The measurement of specific COVID-19 antibodies (both IgG and IgM) should serve as an additional, non-invasive tool for disease detection and management.

Methods
The imprecision of the MAGLUMI™ 2000 Plus 2019-nCov IgM and IgG assays (Snibe, Shenzhen, China) was assessed by adopting the Clinical and Laboratory Standards Institute (CLSI) EP15-A3 protocol. Linearity of dilution and recovery was evaluated by means of mixes of high-level pools and low-level pools of serum samples. Immunoglobulin time kinetics were evaluated using a series of serum samples, repeatedly collected from COVID-19-positive patients at different times, from <5 days up to 26–30 days.

Results
Findings at the analytical validation of the assay carried out according to the CLSI EP15-A3 guideline demonstrated that imprecision and repeatability were acceptable (repeatability was <4% and <6% for IgM and IgG, respectively, whilst intermediate imprecision was <6%). In addition, results of dilution and recovery studies were satisfactory. The kinetics of COVID-19 antibodies confirmed previously reported findings, showing a rapid increase of both IgM and IgG after 6–7 days from the symptom onset. IgG had 100% sensitivity on day 12, whilst 88% was the higher positive rate achieved for IgM after the same time interval.

Conclusions
The findings of this study demonstrate the validity of the MAGLUMI 2000 Plus CLIA assay for the measurement of specific IgM and IgG in sera of COVID-19 patients, and for obtaining valuable data on the kinetics of both (IgM and IgG) COVID-19 antibodies. These data represent a pre-requisite for the appropriate utilization of specific antibodies for the diagnosis and management of COVID-19 patients.
Checkerboard copula defined by sums of random variables
Authors: Kuzmenko Viktor , Salam Romel , Uryasev Stan 
Published: April 2020

Abstract
We consider the problem of finding checkerboard copulas for modeling multivariate distributions. A checkerboard copula is a distribution with a corresponding density defined almost everywhere by a step function on an m-uniform subdivision of the unit hyper-cube. We develop optimization procedures for finding copulas defined by multiply-stochastic matrices matching available information. Two types of information are used for building copulas: 1) Spearman Rho rank correlation coefficients; 2) Empirical distributions of sums of random variables combined with empirical marginal probability distributions. To construct checkerboard copulas we solved optimization problems. The first problem maximizes entropy with constraints on Spearman Rho coefficients. The second problem minimizes some error function to match available data. We conducted a case study illustrating the application of the developed methodology using property and casualty insurance data. The optimization problems were numerically solved with the AORDA Portfolio Safeguard (PSG) package, which has precoded entropy and error functions. Case study data, codes, and results are posted at the web.
Resistance Mechanisms ofSaccharomyces cerevisiaeto Commercial Formulations of Glyphosate Involve DNA Damage Repair, the Cell Cycle, and the Cell Wall Structure
Authors: Ravishankar Apoorva , Pupo Amaury , Gallagher Jennifer E G 
Published: April 2020

AbstractThe use of glyphosate-based herbicides is widespread and despite their extensive use, their effects are yet to be deciphered completely. The additives in commercial formulations of glyphosate, though labeled inert when used individually, have adverse effects when used in combination with other additives along with the active ingredient. As a species, Saccharomyces cerevisiae has a wide range of resistance to glyphosate-based herbicides. To investigate the underlying genetic differences between sensitive and resistant strains, global changes in gene expression were measured, when yeast were exposed to a glyphosate-based herbicide (GBH). Expression of genes involved in numerous pathways crucial to the cell’s functioning, such as DNA replication, MAPK signaling, meiosis, and cell wall synthesis changed. Because so many diverse pathways were affected, these strains were then subjected to in-lab-evolutions (ILE) to select mutations that confer increased resistance. Common fragile sites were found to play a role in adaptation to resistance to long-term exposure of GBHs. Copy number increased in approximately 100 genes associated with cell wall proteins, mitochondria, and sterol transport. Taking ILE and transcriptomic data into account it is evident that GBHs affect multiple biological processes in the cell. One such component is the cell wall structure which acts as a protective barrier in alleviating the stress caused by exposure to inert additives in GBHs. Sed1, a GPI-cell wall protein, plays an important role in tolerance of a GBH. Hence, a detailed study of the changes occurring at the genome and transcriptome levels is essential to better understand the effects of an environmental stressor such as a GBH, on the cell as a whole.
Genetic Selection Based on a Ste6*C-HA-Ura3 Substrate Identifies New Cytosolic Quality Control Alleles in Saccharomyces cerevisiae
Authors: Chan Shu Ning , Prasad Rupali , Matsudaira Paul 
Published: April 2020

Abstract
Protein quality control in the cytosol (CytoQC) is an important cellular pathway consisting of a network of components which monitor the folding of cytosolic proteins and ensure the efficient removal of aberrant ones. Our understanding of CytoQC mechanisms is limited in part by the ability of current approaches to identify new genes in the pathway. In this study, we developed a CytoQC reporter substrate, Ste6*C-HA-Ura3, for a new genetic selection of spontaneous CytoQC mutations in the yeast Saccharomyces cerevisiae. In addition to UBR1, which encodes for a known CytoQC E3 ligase, we identified six new CytoQC candidates. In the preliminary characterization of two mutants, we found that Doa4 is involved in the degradation of misfolded substrates while Pup2 functions in the selectivity of CytoQC and ERAD substrates. Overall, the strategy demonstrates the potential to identify novel genes and advance our understanding of CytoQC.
The Yeast Hsp70 Cochaperone Ydj1 Regulates Functional Distinction of Ssa Hsp70s in the Hsp90 Chaperoning Pathway
Authors: Gaur Deepika , Singh Prashant , Guleria Jyoti , Gupta Arpit , Kaur Satinderdeep , Sharma Deepak 
Published: April 2020

Abstract
Heat-shock protein (Hsp) 90 assists in the folding of diverse sets of client proteins including kinases and growth hormone receptors. Hsp70 plays a major role in many Hsp90 functions by interacting and modulating conformation of its substrates before being transferred to Hsp90s for final maturation. Each eukaryote contains multiple members of the Hsp70 family. However, the role of different Hsp70 isoforms in Hsp90 chaperoning actions remains unknown. Using v-Src as an Hsp90 substrate, we examined the role of each of the four yeast cytosolic Ssa Hsp70s in regulating Hsp90 functions. We show that the strain expressing stress-inducible Ssa3 or Ssa4, and the not constitutively expressed Ssa1 or Ssa2, as the sole Ssa Hsp70 isoform reduces v-Src-mediated growth defects. The study shows that although different Hsp70 isoforms interact similarly with Hsp90s, v-Src maturation is less efficient in strains expressing Ssa4 as the sole Hsp70. We further show that the functional distinction between Ssa2 and Ssa4 is regulated by its C-terminal domain. Further studies reveal that Ydj1, which is known to assist substrate transfer to Hsp70s, interacts relatively weakly with Ssa4 compared with Ssa2, which could be the basis for poor maturation of the Hsp90 client in cells expressing stress-inducible Ssa4 as the sole Ssa Hsp70. The study thus reveals a novel role of Ydj1 in determining the functional distinction among Hsp70 isoforms with respect to the Hsp90 chaperoning action.
Chromatographic fingerprinting and quantitative analysis for the quality evaluation of Xinfeng capsule
Authors: Gao Leilei , Wang Fang , Meng Mei 
Published: April 2020

AbstractA simple, accurate and sensitive method of high performance liquid chromatography (HPLC) with diode array detector was established to identify Xinfeng capsules and systematically evaluated its quality, based on chromatographic fingerprint integrated with the similarity analysis, hierarchical cluster analysis and the quantitative analysis of multi-components by single marker (QAMS). In this study, 18 peaks were selected as the common peaks to evaluate the similarities among different batches (S1–S10) of Xinfeng capsules samples, which were manufactured in the First Affiliated Hospital of Anhui University of Chinese Medicine with a three-year span. Compared to control fingerprint, the similarities values for 10 batches of samples were more than 0.90. Moreover, by analyzing the reference of astragalus, the chromatogram of astragalus was developed, and 10 common peaks of astragalus were identified. More importantly, simultaneous quantification of three markers in Xinfeng capsule, including Calycosin-7-glucoside, calycosin and Formononetinaldehyde was performed, the three constituents showed good regression (R > 0.999) within linear ranges, and their recoveries were within the range of 97.6–101.5%. The validation results showed that the developed method was specific, accurate, precise and robust. This study demonstrated that the developed method offers an efficient, reliable and practical approach for systematic quality evaluation of Xinfeng capsule.
MONTE AMIATA VOLCANO (TUSCANY, ITALY) IN THE HISTORY OF VOLCANOLOGY, PART 1: ITS ROLE IN THE DEBATES ON EXTINCT VOLCANOES, SOURCES OF MAGMA, AND ERUPTIVE MECHANISMS (1733–1935)
Authors: VEZZOLI LUIGINA , PRINCIPE CLAUDIA 
Published: April 2020

A review of the main contributions to the scientific literature between the eighteenth and twentieth centuries concerning the geology and volcanology of Monte Amiata volcano (Tuscany, central Italy) is presented. Monte Amiata, and the nearby volcano of Radicofani, are of great interest for the history of volcanology because they have the primacy of being the first to be recognized of volcanic origin in a region (Tuscany) which was not volcanically active, thirty years before Guettard's studies on the Auvergne region in France. Indeed, the Florentine botanist Pier Antonio Micheli identified as extinct volcanoes Radicofani in 1722 and Monte Amiata in 1733. Moreover, the merit of Micheli's work resides in interpreting Monte Amiata as an extinct volcano despite the absence of a conventional cone-shaped volcano morphology, and in his recognizing its rocks as lavas despite their marked differences to those produced by the known active volcanoes of its times, such as the iconic Vesuvius.
During the eighteenth century and until the first half of the nineteenth century, Monte Amiata was a destination for scientific journeys by Tuscan and foreign scholars (e.g. Micheli, Baldassarri, Arduino, Fortis, Ferber, Dolomieu, Santi, Repetti, Hoffmann). In addition, its rocks were part of important collections throughout Europe visited by illustrious mineralogists. Furthermore, samples from Monte Amiata were used to illustrate the general discussions on the nature and origin of rocks such as basalt and granite.
In the nineteenth century, Monte Amiata was included in the lists of known volcanoes recorded in the early treatises on volcanology made by Scrope, Daubeny, and Hoffmann, and its ‘trachyte’ was the subject of early essays on microscope petrography and chemical analysis of rocks, performed by vom Rath, Rosenbusch, Williams, Lacroix, and Washington. Between the end of the nineteenth century and the first quarter of the twentieth century, the volcano geologists of the Comitato Geologico Italiano, especially Verri, Lotti, and Sabatini, carried out field-surveys on Monte Amiata resulting in geological maps and volcano-stratigraphies. Moreover, modern petrographic (Novarese, Artini, Rodolico) and geographical (Dainelli and Olinto Marinelli) scientific studies were carried out on this volcano. Nevertheless, up to the middle part of the twentieth century, the major interest in Monte Amiata was related not to its volcanological aspects but to its natural resources: drinking waters, diatomaceous earths, earth pigments, and mercury ore-minerals.
Degradação de ecossistemas marinhos: análises a partir do caso do descarte de efluentes de estações de tratamento offshore à luz dos princípios da prevenção e da precaução
Authors: Mafort Antonio Vinicius Lamblet , Ferreira Maria Inês Paes , Pinto Augusto Eduardo Miranda 
Published: April 2020

Acompanhando o crescimento das atividades navais, a degradação dos oceanos surge como uma grande preocupação e motivo de alerta às ações conservacionistas desses ambientes. Os objetivos de desenvolvimento sustentável (ODS) propostos pela Organização das Nações Unidas corroboram esses fatos e ratificam a importância ambiental dos oceanos. Por meio de revisão bibliográfica, este artigo busca analisar as regulamentações acerca da suficiência de políticas públicas que preencham lacunas relativas aos descartes de efluentes sanitários de embarcações e que ratifiquem a importância de se empregarem os princípios da precaução e prevenção para que abordagens, por meio de novas regulamentações, estabeleçam parâmetros, até então inexistentes, de controle de qualidade de efluentes condizentes com as proposições de sustentabilidade ambiental abordadas nos ODS e aplicáveis ao caso brasileiro.
SIFAT KIMIAWI MENTEGA KETAPANG (Catappa butter) (Pengaruh Lama Sangrai Dan Lama Rendam)
Authors: Wijonarko Gunawan , Erminawati Erminawati , Handayani Isti 
Published: April 2020

Biji ketapang mempunyaicita rasa yang enak dan komposisi kimia yang mirip dengan kacang tanah. Oleh karena itu biji ketapang mempunyai potensi yang sangat besar untuk dibuat menjadi produk pangan baru. Salah satu produk pangan tersebut adalah mentega ketapang (Catapa butter). Berdasarkan hal tersebut maka perlu dilakukan penelitian yang bertujuan untukmengevaluasi sifat kmiawi mentega ketapang yang dibuat pada berbagai : (1) lama penyangraian (2) lama perendaman (3) lama penyangraian dan perendaman.Rancangan yang digunakan dalam peneltian ini adalah Rancangan Acak Lengkap. Faktor yang dicoba adalah lama penyangraian (4 ; 8 ; dan 12 menit) dan lama prendaman (0 dan 12 jam). Perlakuan disusun secara faktorial sehingga diperoleh 6 kombinasi perlakuan. Percobaan diulang 4 kali dengan 24 unit percobaan. Variabel yang diamati adalah kadar air, abu, serat kasar, lemak dan protein. Data hasil pengamatan dianalisis menggunakan Uji F. Jika terdapat perbedaan nyata antar perlakuan maka dilanjutkan dengan Uji Rentang Jamak Duncan (DMRT) untuk menentukan perlakuan terbaik. Perlakuan terbaik kemudian dibandingakn dengan selai kacang tanah non komersial. Hasil penelitian menunjukkan lama penyangraian berpengaruh nyata terhadap kadar air dan abu sedangkan perendaman berpengaruh nyata terhadap kadar air, abu dan protein. Kombinasi keduanya memberikan pengaruh yang nyata hanya terhadap kadar protein. Penyangraian 8 menit menghasilkan mentega ketapang dengan kadar air 2,8% dan abu 2,6% sedangkan perendaman 0 jam menghasilkan mentega ketapang dengan kadar air 2,5%, abu 2,7% dan protein 26,5%. Kombinasi kedua perlakuan berpengaruh terhadap kadar air, abu dan protein mentega ketapang. Dibandingkan dengan SNI selai kacang tanah, mentega ketapang mempunyai karakter kimiawi yang mirip kecuali pada kadar abu yang cenderung lebih tinggi yaitu sebesar 2,7%. Penyangraian 8 menit dan perendaman 0 jam menghasilkan mentega ketapang dengan kadar air 2,7%, abu 2,5%, serat kasar 1,8%, lemak 50,6% dan protein 27,6%.
Study of Local Herb Potency as Rumen Modifier: Red Ginger (Zingiber Officinale Var. Rubrum) Addition Effect on In Vitro Ruminal Nutrient Digestibility
Authors: Kurniawati Asih , Yusiati Lies Mira , Widodo Widodo , Artama Wayan Tunas 
Published: April 2020

Red ginger is herb that commonly used as part of traditional medicine due to its essential oil content. Some essential oil have proven as rumen fermentation modifier. Addition of red ginger in ruminant diet was studied using in vitro gas production technique to evaluate its effect on nutrient digestibility. Red ginger meal was added to meet essential oil level in fermentation medium of 0 mg/l as control, 25, 50, 75 and 100 mg/l. The diet consisted of Penisetum hybride, rice bran, wheat pollard in ratio 60:20:20 DM basis. Feed fermentation was incubated for 24 h at 39°C. At the end of incubation data of gas production volume was taken, and residual feed were collected for further nutrient analysis to calculate the digestibility of dry matter (DM), organic matter (OM), crude protein (CP) and crude fiber (CF). Variance analysis was used to analysis collected data, followed by DMRT analysis. Addition of red ginger increase total volume of gas production at level 50 mg/L and above. DM and OM digestibility did not affected by red ginger addition whereas CP digestibility were significantly decreased start at level 50 mg/l. In contrast, CF digestibility of treatment level of 50 mg/l significantly higher than control. In conclusion, addition of red ginger correspond to level essential oil of 50 to 100 mg/l improve ruminal nutrient fermentation.