bluuebunny/crossref_metadata_2025_split huggingface dataset:
High pressure acid leaching: a newly introduced technology in Indonesia
Authors: Gultom T , Sianipar A 
Published: January 2020

Abstract
PT Halmahera Persada Lygend (PTHPL) plans to construct new technology for nickel laterite ore processing in Obi Island, North Maluku Province. The facility is expected to produce 247,000 tonnes of NiSO4.7H2O and 32,000 tonnes of CoSO4.7H2O to be sold for the raw material of electric vehicle battery. Indonesia is one of world largest nickel laterite resources and currently only nickel ore saprolite has been exploited while nickel limonite is abandoned as waste due to the lack of technology. In the last decade, nickel smelter is booming in Indonesia to process nickel saprolite to become Ferro Nickel, Nickel Pig Iron, Nickel Matte. This study is aimed to assess the potential implementation of High-Pressure Acid Leaching (HPAL). HPAL is a proven technology but not utilized in Indonesia due to the high investment, and it requires a large media for waste disposal. Nickel limonite ore with grade 1.1 – 1.4 % can be processed using HPAL technology to produce more than 37% nickel and another beneficial product, which is cobalt. Nickel world demand shifts to support electric vehicle battery even though stainless steel demand is still high. The Government of Indonesia is currently starting to support the electric vehicle market program. Therefore HPAL project in Indonesia is a high opportunity and a good investment for investors.
One-pot biosynthesis of CdS quantum dots through in vitro regeneration of hairy roots of Rhaphanus sativus L. And their apoptosis effect on MCF-7 and AGS cancerous human cell lines
Authors: Gholami Zahra , Dadmehr Mehdi , Babaeian Jelodar Nadali , Hosseini Morteza , oroojalian Fatemeh , Pakdin Parizi Ali 
Published: January 2020

Abstract
Development of green based synthesis of nanoparticles has been regarded as a novel and safe alternative method compared to conventional methods. Semiconductor cadmium sulfide quantum dots (CdS QDs) possess unique biological and medical applications includes labeling cells, diagnosing of diseases and imaging intercellular events. The present paper reports the biosynthesis of CdS QDs through aqueous extracts of the regenerated hairy roots of Rhaphanus sativus L. as the organic source for both reducing and stabilizing of Cd and S precursor ions. The characterization of synthesized QDs showed maximum absorbance peak of 460 nm and fluorescence spectrum of cadmium sulfide at 530 nm. The results of Transmission Electron Microscope (TEM) and EDS analysis demonstrated that the particles were morphologically spherical with size distribution between 2–7 nm and confirmed presence of CdS QDs. Fourier transform infrared spectroscopy (FT-IR) also showed the active presence of aromatic, amino, and carboxyl groups on the surface of quantum dots. Cytotoxicity effect of the synthesized CdS QDs on two cell lines include MCF-7 breast cancer and AGS gastric cancer were assayed through MTT assay. The results showed significant inhibitory effects of synthesized QDs on treated cells in a dose dependent manner. It was also concluded that CdS QDs had more apoptosis effect on MCF-7 cells rather than AGS cell lines. The obtained results clearly illustrated that the synthesis of CdS quantum dots with standard features would be possible through cost-effective, reliable, environmentally friendly and less toxic alternative method compared to chemical and physical processes and the MTT toxicity assay also illustrated the significant apoptotic effects of synthesized CdS QDs on carcinogenesis.
Optimization of WEDM parameters for Mg-Zn-RE-Zr alloy using Passing Vehicle Search algorithm
Authors: Sheth Mohak , Sheth Nisarg , Radadia Nishil , Parsana Sohil , Savsani Vimal , Mishra R K , Arivarasu M , Prabhu T Ram 
Published: January 2020

Abstract
Wire Electric Discharge Machining (WEDM) is a high precision spark machining capable of cutting electrically conductive materials of varying hardness and/or having complex shapes. Since the last decade, focus has increased on magnesium alloys because of their high specific strength and inelasticity, excellent damping properties. The addition of Rare Earth (RE) improves creep and corrosion resistant properties thus rendering them highly useful for several aerospace applications. In the present study, parametric optimization of WEDM on Mg-Zn-RE-Zr alloy is performed using a novel meta-heuristic algorithm-Passing Vehicle Search (PVS). The control parameters considered are current, pulse-on time, pulse-off time and wire feed rate. Response Surface Methodology (RSM) philosophy is implemented through Central Composite Design (CCD) to formulate the mathematical model of Average Surface Roughness (Ra). The adequacy of obtained quadratic model is established using Analysis of Variance (ANOVA). The PVS algorithm employs a population based search method by emulating the algebraic characteristics of vehicles over-taking on a two-lane highway from an initial solution set. Results of optimization through PVS are compared against standard real coded Genetic Algorithm. A remarkable improvement was observed which is critical while considering aerospace standards. This kind of analysis could be useful for production process planning in the aerospace industry.
Wavelength-stabilized DBR high-power diode laser
Authors: Paoletti R , Coriasso C , Meneghini G , Gaziano F , Gotta P , Codato S , Maina A , Morello G , De Melchiorre P , Pippione G , Riva E , Rosso M , Stano A , Gattiglio M 
Published: January 2020

Abstract
This paper reports a wavelength-stabilized high-power diode laser emitting up to 14 W CW in the 9xx nm range. Wavelength stabilization is achieved by a distributed Bragg reflector (DBR) monolithically integrated in the diode laser chip. Key features are identical layer epitaxy (ILE) and the use of a multiple-order electron beam lithography (EBL) optical confining grating. ILE avoids any regrowth or complex technology processes, while EBL multiple-order grating allows narrow-band back reflection and effective lateral optical confinement, and makes it possible to stabilize multiple wavelengths on the same wafer using a manufacturable and reliable technology. DBR diode lasers with different pitches, whose wavelengths were 3 nm spaced, were fabricated and high spectral purity (95% optical power within about 0.6 nm) and wavelength stability were measured. Moreover, the high uniformity of performances across the wafer with different emitted wavelengths demonstrates the maturity of the proposed technology for high-yield, high-volume laser diode production for wavelength-stabilized applications. A multi-emitter module, including ten DBR diode lasers, collimating and focusing optics, showed 100 W CW wavelength-stabilized output power at 14 A in a 135 μm core optical fiber within 0.17 NA. Single diode lasers, or multi-emitter modules, can be used to combine high-power optical beams by wavelength division multiplexing (WDM) using dichroic optics, scaling up beam power to the kW range and maintaining optical beam quality.
The domestication syndrome in vegetatively propagated field crops
Authors: Denham Tim , Barton Huw , Castillo Cristina , Crowther Alison , Dotte-Sarout Emilie , Florin S Anna , Pritchard Jenifer , Barron Aleese , Zhang Yekun , Fuller Dorian Q 
Published: January 2020

AbstractBackgroundVegetatively propagated crops are globally significant in terms of current agricultural production, as well as for understanding the long-term history of early agriculture and plant domestication. Today, significant field crops include sugarcane (Saccharum officinarum), potato (Solanum tuberosum), manioc (Manihot esculenta), bananas and plantains (Musa cvs), sweet potato (Ipomoea batatas), yams (Dioscorea spp.) and taro (Colocasia esculenta). In comparison with sexually reproduced crops, especially cereals and legumes, the domestication syndrome in vegetatively propagated field crops is poorly defined.Aims and ScopeHere, a range of phenotypic traits potentially comprising a syndrome associated with early domestication of vegetatively propagated field crops is proposed, including: mode of reproduction, yield of edible portion, ease of harvesting, defensive adaptations, timing of production and plant architecture. The archaeobotanical visibility of these syndrome traits is considered with a view to the reconstruction of the geographical and historical pathways of domestication for vegetatively propagated field crops in the past.ConclusionsAlthough convergent phenotypic traits are identified, none of them are ubiquitous and some are divergent. In contrast to cereals and legumes, several traits seem to represent varying degrees of plastic response to growth environment and practices of cultivation, as opposed to solely morphogenetic ‘fixation’.
A novel methodSEPromfor prokaryotic promoter prediction based on DNA structure and energetics
Authors: Mishra Akhilesh , Dhanda Sahil , Siwach Priyanka , Aggarwal Shruti , Jayaram B 
Published: January 2020

AbstractMotivationDespite conservation in general architecture of promoters and protein–DNA interaction interface of RNA polymerases among various prokaryotes, identification of promoter regions in the whole genome sequences remains a daunting challenge. The available tools for promoter prediction do not seem to address the problem satisfactorily, apparently because the biochemical nature of promoter signals is yet to be understood fully. Using 28 structural and 3 energetic parameters, we found that prokaryotic promoter regions have a unique structural and energy state, quite distinct from that of coding regions and the information for this signature state is in-built in their sequences. We developed a novel promoter prediction tool from these 31 parameters using various statistical techniques.ResultsHere, we introduce SEProm, a novel tool that is developed by studying and utilizing the in-built structural and energy information of DNA sequences, which is applicable to all prokaryotes including archaea. Compared to five most recent, diverged and current best available tools, SEProm performs much better, predicting promoters with an ‘F-value’ of 82.04 and ‘Precision’ of 81.08. The next best ‘F-value’ was obtained with PromPredict (72.14) followed by BProm (68.37). On the basis of ‘Precision’ value, the next best ‘Precision’ was observed for Pepper (75.39) followed by PromPredict (72.01). SEProm maintained the lead even when comparison was done on two test organisms (not involved in training for SEProm).Availability and implementationThe software is freely available with easy to follow instructions (www.scfbio-iitd.res.in/software/TSS_Predict.jsp).Supplementary informationSupplementary data are available at Bioinformatics online.
Lep-Anchor: automated construction of linkage map anchored haploid genomes
Authors: Rastas Pasi 
Published: January 2020

Abstract

Motivation
Linkage mapping provides a practical way to anchor de novo genome assemblies into chromosomes and to detect chimeric or otherwise erroneous contigs. Such anchoring improves with higher number of markers and individuals, as long as the mapping software can handle all the information. Recent software Lep-MAP3 can robustly construct linkage maps for millions of genotyped markers and on thousands of individuals, providing optimal maps for genome anchoring. For such large datasets, automated and robust genome anchoring tool is especially valuable and can significantly reduce intensive computational and manual work involved.

Results
Here, we present a software Lep-Anchor (LA) to anchor genome assemblies automatically using dense linkage maps. As the main novelty, it takes into account the uncertainty of the linkage map positions caused by low recombination regions, cross type or poor mapping data quality. Furthermore, it can automatically detect and cut chimeric contigs, and use contig–contig, single read or alternative genome assembly alignments as additional information on contig order and orientations and to collapse haplotype contigs. We demonstrate the performance of LA using real data and show that it outperforms ALLMAPS on anchoring completeness and speed. Accuracy-wise LA and ALLMAPS are about equal, but at the expense of lower completeness of ALLMAPS. The software Chromonomer was faster than the other two methods but has major limitations and is lower in accuracy. We also show that with additional information, such as contig–contig and read alignments, the anchoring completeness can be improved by up to 70% without significant loss in accuracy. Based on simulated data, we conclude that the anchoring accuracy can be improved by utilizing information about map position uncertainty. Accuracy is the rate of contigs in correct orientation and completeness is the number contigs with inferred orientation.

Availability and implementation
Lep-Anchor is available with the source code under GNU general public license from http://sourceforge.net/projects/lep-anchor. All the scripts and code used to produce the reported results are included with Lep-Anchor.
Treatment of Human Plague: A Systematic Review of Published Aggregate Data on Antimicrobial Efficacy, 1939–2019
Authors: Godfred-Cato Shana , Cooley Katharine M , Fleck-Derderian Shannon , Becksted Heidi A , Russell Zachary , Meaney-Delman Dana , Mead Paul S , Nelson Christina A 
Published: January 2020

AbstractBackgroundPlague, caused by the bacterium Yersinia pestis, has killed millions in historic pandemics and continues to cause sporadic outbreaks. Numerous antimicrobials are considered effective for treating plague; however, well-defined information on the relative efficacy of various treatments is lacking. We conducted a systematic review of published data on antimicrobial treatment of plague reported in aggregate.MethodsWe searched databases including Embase, Medline, CINAHL, Cochrane Library, and others for publications with terms related to plague and antimicrobials. Articles were included if they contained 1) a group of patients treated for plague, with outcomes reported by antimicrobial regimen, and 2) laboratory evidence of Y. pestis infection or an epidemiologic link to patients with laboratory evidence of Y. pestis. Case fatality rate by antimicrobial regimen was calculated.ResultsIn total, 5837 articles were identified; among these, 26 articles published between 1939 and 2008 met inclusion criteria. A total of 2631 cases of human plague reported within these articles were included. Among cases classified by primary clinical form of plague, 93.6% were bubonic, 5.9% pneumonic, and 0.5% septicemic with associated case fatalities of 14.2%, 31.1%, and 20.0%, respectively. Case fatality rate among patients who received monotherapy with tetracyclines, chloramphenicol, aminoglycosides, or sulfonamides was 1.3%, 1.4%, 7.5%, and 20.2%, respectively. Fluoroquinolones were only given as part of combination therapy. Penicillin was associated with a case fatality rate of 75%.ConclusionsTetracyclines, chloramphenicol, and aminoglycosides were associated with the lowest case fatality rates of all antimicrobials used for treatment of plague. Additional research is needed to determine the efficacy of fluoroquinolones as monotherapy.
The Silence Speaks, but We Do Not Listen: Synonymous c.1824C&gt;T Gene Variant in the Last Exon of the Prothrombin Gene as a New Prothrombotic Risk Factor
Authors: Pruner Iva , Farm Maria , Tomic Branko , Gvozdenov Maja , Kovac Mirjana , Miljic Predrag , Soutari Nida Mahmoud Hourani , Antovic Aleksandra , Radojkovic Dragica , Antovic Jovan , Djordjevic Valentina 
Published: January 2020

AbstractBackgroundThrombosis is a major global disease burden with almost 60% of cases related to underlying heredity and most cases still idiopathic. Synonymous single nucleotide polymorphisms (sSNPs) are considered silent and phenotypically neutral. Our previous study revealed a novel synonymous FII c.1824C&gt;T variant as a potential risk factor for pregnancy loss, but it has not yet been associated with thrombotic diseases.MethodsTo determine the frequency of the FII c.1824C&gt;T variant we have sequenced patients’ DNA. Prothrombin RNA expression was measured by quantitative PCR. Functional analyses included routine hemostasis tests, western blotting and ELISA to determine prothrombin levels in plasma, and global hemostasis assays for thrombin and fibrin generation in carriers of the FII c.1824C&gt;T variant. Scanning electron microscopy was used to examine the structure of fibrin clots.ResultsFrequency of the FII c.1824C&gt;T variant was significantly increased in patients with venous thromboembolism and cerebrovascular insult. Examination in vitro demonstrated increased expression of prothrombin mRNA in FII c.1824T transfected cells. Our ex vivo study of FII c.1824C&gt;T carriers showed that the presence of this variant was associated with hyperprothrombinemia, hypofibrinolysis, and formation of densely packed fibrin clots resistant to fibrinolysis.ConclusionOur data indicate that FII c.1824C&gt;T, although a synonymous variant, leads to the development of a prothrombotic phenotype and could represent a new prothrombotic risk factor. As a silent variant, FII c.1824C&gt;T would probably be overlooked during genetic screening, and our results show that it could not be detected in routine laboratory tests.
miR-TV: an interactive microRNA Target Viewer for microRNA and target gene expression interrogation for human cancer studies
Authors: Pan Chao-Yu , Lin Wen-Chang 
Published: January 2020

Abstract
MicroRNAs (miRNAs) have been identified in many organisms, and they are essential for gene expression regulation in many critical cellular processes. The expression levels of these genes and miRNAs are closely associated with the progression of diseases such as cancers. Furthermore, survival analysis is a significant indicator for evaluating the criticality of these cellular processes in cancer progression. We established a web tool, miRNA Target Viewer (miR-TV), which integrates 5p-arm and 3p-arm miRNA expression profiles, mRNA target gene expression levels in healthy and cancer populations, and clinical data of cancer patients and their survival information. The developed miR-TV obtained miRNA-seq, mRNA-seq and clinical data from the Cancer Genome Atlas and potential miRNA target gene predictions from miRDB, targetScan and miRanda. The data presentation was implemented using the D3 javascript toolkit. The D3 toolkit is frequently used to provide an easy-to-use interactive interface. Our miR-TV provides a user-friendly and interactive interface, which can be beneficial for biomedical researchers to freely interrogate miRNA expression information and their potential target genes. We believe that such a data visualization bioinformatics tool is excellent for obtaining information from massive biological data.
Database URL: http://mirtv.ibms.sinica.edu.tw
Risk of perioperative coronary stent stenosis or occlusion in patients with previous percutaneous coronary intervention undergoing coronary artery bypass grafting surgery
Authors: Grieshaber Philippe , Oswald Irina , Albert Marc , Reents Wilko , Zacher Michael , Roth Peter , Niemann Bernd , Dörr Oliver , Krüger Tobias , Nef Holger , Sodah Ayman , Hamm Christian , Schlensak Christian , Diegeler Anno , Sedding Daniel , Franke Ulrich , Boening Andreas 
Published: January 2020

Abstract

OBJECTIVES
There is an ongoing discussion about how to treat coronary stents during bypass surgery: Should patent stents be left alone and the stented vessels be ungrafted, or should every stented coronary artery receive a bypass graft? This study aims to determine the relevance of perioperative stent stenosis or occlusion on postoperative outcomes up to 3 years postoperatively.

METHODS
Patients undergoing coronary artery bypass grafting surgery (CABG) (±concomitant procedures) with previous percutaneous coronary intervention from 4 centres were prospectively included in this observatory study between April 2015 and June 2017. A coronary angiography was conducted between the fifth and seventh postoperative days. The preoperative and postoperative angiograms were assessed in a core laboratory, assessing the patencies of coronary stents and bypass grafts. The core lab investigators were blinded to the patients’ characteristics and perioperative course.

RESULTS
A total of 107 patients were included in the study. In the postoperative coronary angiography, 265 bypass grafts and 189 coronary stents were examined angiographically. Ninety-seven percent of preoperatively patent stents remained patent. New coronary stent stenoses were observed in 5 patients (4.7%). All 5 patients were asymptomatic and managed conservatively. Bypass stenoses were observed in 12 patients (11%), of whom were managed conservatively, 4 underwent percutaneous coronary intervention and 1 underwent redo-CABG. Two years postoperatively, 97% of patients were alive. Patients with new stent stenosis tended to have a better survival compared with patients with bypass stenosis (100% vs 73%; P = 0.09) up to 3 years postoperatively.

CONCLUSIONS
Perioperative coronary stent stenosis occurs rarely. It is safe to leave a patently stented coronary vessel without bypass grafting.
Stool Reducing Sugars and Stool pH Are Poor Screening Tests for Intestinal Disaccharidase Deficiencies in Children
Authors: Erickson J Alan , Case Kristin , Neider Cole , Johnson Lisa M 
Published: January 2020

AbstractBackgroundTests for stool reducing sugars and stool pH are ordered for children with osmotic diarrhea to screen for carbohydrate malabsorption.MethodsWe compared the results of the two screening tests, stool reducing sugars and stool pH, with a more definitive result from an intestinal tissue disaccharidase activity assay ordered for pediatric patients (&lt;18 years old). Overall, 159 patients had results for tissue disaccharidase and stool reducing sugars, but only 115 had additional results of stool pH. Forty-six of the 159 patients had mild, moderate, or severe disaccharidase deficiencies. The sensitivity and specificity of the screening tests were calculated for individual disaccharidase deficiencies. In addition, trends of abnormal tissue disaccharidase, stool reducing sugars, and stool pH results were examined in different age groups.ResultsThe sensitivities for stool reducing sugars and stool pH were 9% to 28% and specificities were 74% to 81% for individual disaccharidase deficiencies. Infants (0 years of age) had the highest percentage of abnormal results across all three tests; however, the positive predicative values were 54% and 50% for stool reducing sugars and stool pH, respectively.ConclusionsThe screening tests, stool reducing sugars and stool pH, had low sensitivity compared with results of measured tissue disaccharidase activity in pediatric patients. Infants had the highest percentage of abnormal results for all three tests, but the screening tests still performed poorly in that age group. This study suggests that stool reducing sugars and stool pH should not be used as screening tests for carbohydrate malabsorption due to disaccharidase deficiencies in pediatric patients.