bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiplex PCR assay for the identification of eight Anopheles species belonging to the Hyrcanus, Barbirostris and Lindesayi groups
Authors: Bang Woo Jun , Kim Heung Chul , Ryu Jihun , Lee Hyeon Seung , Lee So Youn , Kim Myung Soon , Chong Sung Tae , Klein Terry A. , Choi Kwang Shik 
Published: June 2021

Abstract
Background
Genus Anopheles mosquitoes are the primary vectors of human malaria, which is a serious threat to public health worldwide. To reduce the spread of malaria and identify the malaria infection rates in mosquitoes, accurate species identification is needed. Malaria re-emerged in 1993 in the Republic of Korea (ROK), with numbers peaking in 2004 before decreasing to current levels. Eight Anopheles species (Anopheles sinensis, Anopheles pullus, Anopheles belenrae, Anopheles lesteri, Anopheles kleini, Anopheles sineroides, Anopheles koreicus, Anopheles lindesayi) are distributed throughout Korea. Members of the Anopheles Hyrcanus group currently cannot be identified morphologically. The other species of Anopheles can be identified morphologically, except when specimens are damaged in traps. The purpose of this study was to develop a rapid and accurate method for simultaneous molecular identification of the eight Anopheles species present in the ROK.

Methods
Anopheles spp. used in this study were collected near/in the demilitarized zone in ROK, where most malaria cases are reported. DNA from 165 of the Anopheles specimens was used to develop a multiplex PCR assay. The internal transcribed spacer 2 (ITS2) region of each species was sequenced and analysed for molecular identification.

Results
DNA from a total of 165 Anopheles specimens was identified to species using a multiplex diagnostic system. These included: 20 An. sinensis, 21 An. koreicus, 17 An. lindesayi, 25 An. kleini, 11 An. lesteri, 22 An. sineroides, 23 An. belenrae, and 26 An. pullus. Each species was clearly distinguished by electrophoresis as follows: 1,112 bp for An. sinensis; 925 bp for An. koreicus; 650 bp for An. lindesayi; 527 bp for An. kleini; 436 bp for An. lesteri; 315 bp for An. sineroides; 260 bp for An. belenrae; and, 157 bp for An. pullus.

Conclusion
A multiplex PCR assay was developed to identify Anopheles spp. distributed in ROK. This method can be used to accurately identify Anopheles species that are difficult to identify morphologically to determine species distributions and malaria infection rates.
mbImpute: an accurate and robust imputation method for microbiome data
Authors: Jiang Ruochen , Li Wei Vivian , Li Jingyi Jessica 
Published: June 2021

AbstractA critical challenge in microbiome data analysis is the existence of many non-biological zeros, which distort taxon abundance distributions, complicate data analysis, and jeopardize the reliability of scientific discoveries. To address this issue, we propose the first imputation method for microbiome data—mbImpute—to identify and recover likely non-biological zeros by borrowing information jointly from similar samples, similar taxa, and optional metadata including sample covariates and taxon phylogeny. We demonstrate that mbImpute improves the power of identifying disease-related taxa from microbiome data of type 2 diabetes and colorectal cancer, and mbImpute preserves non-zero distributions of taxa abundances.
The glycosyltransferase ST3GAL2 is regulated by miR-615-3p in the intestinal tract of Campylobacter jejuni infected mice
Authors: Xi De , Hofmann Lukas , Alter Thomas , Einspanier Ralf , Bereswill Stefan , Heimesaat Markus M. , Gölz Greta , Sharbati Soroush 
Published: June 2021

Abstract
Background
Campylobacter jejuni (C. jejuni) infections are of increasing importance worldwide. As a typical mucosal pathogen, the interaction of C. jejuni with mucins is a prominent step in the colonisation of mucosal surfaces. Despite recent advances in understanding the interaction between bacterial pathogens and host mucins, the mechanisms of mucin glycosylation during intestinal C. jejuni infection remain largely unclear. This prompted us to identify relevant regulatory networks that are concerted by miRNAs and could play a role in the mucin modification and interaction.

Results
We firstly used a human intestinal in vitro model, in which we observed altered transcription of MUC2 and TFF3 upon C. jejuni NCTC 11168 infection. Using a combined approach consisting of in silico analysis together with in vitro expression analysis, we identified the conserved miRNAs miR-125a-5p and miR-615-3p associated with MUC2 and TFF3. Further pathway analyses showed that both miRNAs appear to regulate glycosyltransferases, which are related to the KEGG pathway ‘Mucin type O-glycan biosynthesis’. To validate the proposed interactions, we applied an in vivo approach utilising a well-established secondary abiotic IL-10−/− mouse model for infection with C. jejuni 81-176. In colonic tissue samples, we confirmed infection-dependent aberrant transcription of MUC2 and TFF3. Moreover, two predicted glycosyltransferases, the sialyltransferases ST3GAL1 and ST3GAL2, exhibited inversely correlated transcriptional levels compared to the expression of the identified miRNAs miR-125a-5p and miR-615-3p, respectively. In this study, we mainly focused on the interaction between miR-615-3p and ST3GAL2 and were able to demonstrate their molecular interaction using luciferase reporter assays and RNAi. Detection of ST3GAL2 in murine colonic tissue by immunofluorescence demonstrated reduced intensity after C. jejuni 81-176 infection and was thus consistent with the observations made above.

Conclusions
We report here for the first time the regulation of glycosyltransferases by miRNAs during murine infection with C. jejuni 81-176. Our data suggest that mucin type O-glycan biosynthesis is concerted by the interplay of miRNAs and glycosyltransferases, which could determine the shape of intestinal glycosylated proteins during infection.
The penicillin binding protein 1A of Helicobacter pylori, its amoxicillin binding site and access routes
Authors: Attaran Bahareh , Salehi Najmeh , Ghadiri Bahareh , Esmaeili Maryam , Kalateh Shadi , Tashakoripour Mohammad , Eshagh Hosseini Mahmoud , Mohammadi Marjan 
Published: June 2021

AbstractBackgroundAmoxicillin-resistantH. pyloristrains are increasing worldwide. To explore the potential resistance mechanisms involved, the 3D structure modeling and access tunnel prediction for penicillin-binding proteins (PBP1A) was performed, based on theStreptococcus pneumoniae, PBP 3D structure. Molecular covalent docking was used to determine the interactions between amoxicillin (AMX) and PBP1A.ResultsThe AMX-Ser368 covalent complex interacts with the binding site residues (Gly367, Ala369, ILE370, Lys371, Tyr416, Ser433, Thr541, Thr556, Gly557, Thr558, and Asn560) of PBP1A, non-covalently. Six tunnel-like structures, accessing the PBP1A binding site, were characterized, using the CAVER algorithm. Tunnel-1 was the ultimate access route, leading to the drug catalytic binding residue (Ser368). This tunnel comprises of eighteen amino acid residues, 8 of which are shared with the drug binding site. Subsequently, to screen the presence of PBP1A mutations, in the binding site and tunnel residues, in our clinical strains, in vitro assays were performed.H. pyloristrains, isolated under gastroscopy, underwent AMX susceptibility testing by E-test. Of the 100 clinical strains tested, 4 were AMX-resistant. The transpeptidase domain of thepbp1agene of these resistant, plus 10 randomly selected AMX-susceptible strains, were amplified and sequenced. Of the amino acids lining the tunnel-1 and binding site residues, three (Ser414Arg, Val469Met and Thr556Ser) substitutions, were detected in 2 of the 4 resistant and none of the sequenced susceptible strains, respectively.ConclusionsWe hypothesize that mutations in amino acid residues lining the binding site and/or tunnel-1, resulting in conformational/spatial changes, may block drug binding to PBP1A and cause AMX resistance.
SINE jumping contributes to large-scale polymorphisms in the pig genomes
Authors: Chen Cai , D’Alessandro Enrico , Murani Eduard , Zheng Yao , Giosa Domenico , Yang Naisu , Wang Xiaoyan , Gao Bo , Li Kui , Wimmers Klaus , Song Chengyi 
Published: June 2021

Abstract
Background
Molecular markers based on retrotransposon insertion polymorphisms (RIPs) have been developed and are widely used in plants and animals. Short interspersed nuclear elements (SINEs) exert wide impacts on gene activity and even on phenotypes. However, SINE RIP profiles in livestock remain largely unknown, and not be revealed in pigs.

Results
Our data revealed that SINEA1 displayed the most polymorphic insertions (22.5 % intragenic and 26.5 % intergenic), followed by SINEA2 (10.5 % intragenic and 9 % intergenic) and SINEA3 (12.5 % intragenic and 5.0 % intergenic). We developed a genome-wide SINE RIP mining protocol and obtained a large number of SINE RIPs (36,284), with over 80 % accuracy and an even distribution in chromosomes (14.5/Mb), and 74.34 % of SINE RIPs generated by SINEA1 element. Over 65 % of pig SINE RIPs overlap with genes, most of them (> 95 %) are in introns. Overall, about one forth (23.09 %) of the total genes contain SINE RIPs. Significant biases of SINE RIPs in the transcripts of protein coding genes were observed. Nearly half of the RIPs are common in these pig breeds. Sixteen SINE RIPs were applied for population genetic analysis in 23 pig breeds, the phylogeny tree and cluster analysis were generally consistent with the geographical distributions of native pig breeds in China.

Conclusions
Our analysis revealed that SINEA1–3 elements, particularly SINEA1, are high polymorphic across different pig breeds, and generate large-scale structural variations in the pig genomes. And over 35,000 SINE RIP markers were obtained. These data indicate that young SINE elements play important roles in creating new genetic variations and shaping the evolution of pig genome, and also provide strong evidences to support the great potential of SINE RIPs as genetic markers, which can be used for population genetic analysis and quantitative trait locus (QTL) mapping in pig.
Oxygen concentration affects de novo DNA methylation and transcription in in vitro cultured oocytes
Authors: Naillat Florence , Saadeh Heba , Nowacka-Woszuk Joanna , Gahurova Lenka , Santos Fatima , Tomizawa Shin-ichi , Kelsey Gavin 
Published: June 2021

Abstract
Background
Reproductive biology methods rely on in vitro follicle cultures from mature follicles obtained by hormonal stimulation for generating metaphase II oocytes to be fertilised and developed into a healthy embryo. Such techniques are used routinely in both rodent and human species. DNA methylation is a dynamic process that plays a role in epigenetic regulation of gametogenesis and development. In mammalian oocytes, DNA methylation establishment regulates gene expression in the embryos. This regulation is particularly important for a class of genes, imprinted genes, whose expression patterns are crucial for the next generation. The aim of this work was to establish an in vitro culture system for immature mouse oocytes that will allow manipulation of specific factors for a deeper analysis of regulatory mechanisms for establishing transcription regulation-associated methylation patterns.

Results
An in vitro culture system was developed from immature mouse oocytes that were grown to germinal vesicles (GV) under two different conditions: normoxia (20% oxygen, 20% O2) and hypoxia (5% oxygen, 5% O2). The cultured oocytes were sorted based on their sizes. Reduced representative bisulphite sequencing (RRBS) and RNA-seq libraries were generated from cultured and compared to in vivo-grown oocytes. In the in vitro cultured oocytes, global and CpG-island (CGI) methylation increased gradually along with oocyte growth, and methylation of the imprinted genes was similar to in vivo-grown oocytes. Transcriptomes of the oocytes grown in normoxia revealed chromatin reorganisation and enriched expression of female reproductive genes, whereas in the 5% O2 condition, transcripts were biased towards cellular stress responses. To further confirm the results, we developed a functional assay based on our model for characterising oocyte methylation using drugs that reduce methylation and transcription. When histone methylation and transcription processes were reduced, DNA methylation at CGIs from gene bodies of grown oocytes presented a lower methylation profile.

Conclusions
Our observations reveal changes in DNA methylation and transcripts between oocytes cultured in vitro with different oxygen concentrations and in vivo-grown murine oocytes. Oocytes grown under 20% O2 had a higher correlation with in vivo oocytes for DNA methylation and transcription demonstrating that higher oxygen concentration is beneficial for the oocyte maturation in ex vivo culture condition. Our results shed light on epigenetic mechanisms for the development of oocytes from an immature to GV oocyte in an in vitro culture model.
Investigating errors in medical imaging: medical malpractice cases in Finland
Authors: Tarkiainen Tarja , Turpeinen Miia , Haapea Marianne , Liukkonen Esa , Niinimäki Jaakko 
Published: June 2021

Abstract
Objective
The objectives of the study were to survey patient injury claims concerning medical imaging in Finland in 1991–2017, and to investigate the nature of the incidents, the number of claims, the reasons for the claims, and the decisions made concerning the claims.

Materials and methods
The research material consisted of patient claims concerning imaging, sent to the Finnish Patient Insurance Centre (PVK). The data contained information on injury dates, the examination code, the decision code, the description of the injury, and the medical grounds for decisions.

Results
The number of claims included in the study was 1054, and the average number per year was 87. The most common cause was delayed diagnosis (404 claims, 38.3%). Most of the claims concerned mammography (314, 29.8%), radiography (170, 16.1%), and MRI (162, 15.4%). According to the decisions made by the PVK, there were no delays in 54.6% of the examinations for which claims were made. About 30% of all patient claims received compensation, the most typical reason being medical malpractice (27.7%), followed by excessive injuries and injuries caused by infections, accidents and equipment (2.7%).

Conclusion
Patient injury in imaging examinations and interventions cannot be completely prevented. However, injury data are an important source of information for health care. By analysing claims, we can prevent harm, increase the quality of care, and improve patient safety in medical imaging.
Cost effective reproduction number based strategies for reducing deaths from COVID-19
Authors: Thron Christopher , Mbazumutima Vianney , Tamayo Luis V. , Todjihounde Léonard 
Published: June 2021

AbstractIn epidemiology, the effective reproduction number $R_{e}$

R
e

is used to characterize the growth rate of an epidemic outbreak. If $R_{e} >1$

R
e

>
1
, the epidemic worsens, and if $R_{e}< 1$

R
e

<
1
, then it subsides and eventually dies out. In this paper, we investigate properties of $R_{e}$

R
e

for a modified SEIR model of COVID-19 in the city of Houston, TX USA, in which the population is divided into low-risk and high-risk subpopulations. The response of $R_{e}$

R
e

to two types of control measures (testing and distancing) applied to the two different subpopulations is characterized. A nonlinear cost model is used for control measures, to include the effects of diminishing returns. Lowest-cost control combinations for reducing instantaneous $R_{e}$

R
e

to a given value are computed. We propose three types of heuristic strategies for mitigating COVID-19 that are targeted at reducing $R_{e}$

R
e

, and we exhibit the tradeoffs between strategy implementation costs and number of deaths. We also consider two variants of each type of strategy: basic strategies, which consider only the effects of controls on $R_{e}$

R
e

, without regard to subpopulation; and high-risk prioritizing strategies, which maximize control of the high-risk subpopulation. Results showed that of the three heuristic strategy types, the most cost-effective involved setting a target value for $R_{e}$

R
e

and applying sufficient controls to attain that target value. This heuristic led to strategies that begin with strict distancing of the entire population, later followed by increased testing. Strategies that maximize control on high-risk individuals were less cost-effective than basic strategies that emphasize reduction of the rate of spreading of the disease. The model shows that delaying the start of control measures past a certain point greatly worsens strategy outcomes. We conclude that the effective reproduction can be a valuable real-time indicator in determining cost-effective control strategies.
Meta-analysis of AKI to CKD transition in perioperative patients
Authors: Abdala Pedro M. , Swanson Elizabeth A. , Hutchens Michael P. 
Published: June 2021

Abstract
Background
Recent research shows AKI increases the risk of incident CKD. We hypothesized that perioperative AKI may confer increased risk of subsequent CKD compared to nonperioperative AKI.

Methods
A MEDLINE search was performed for “AKI, CKD, chronic renal insufficiency, surgery, and perioperative” and related terms yielded 5209 articles. One thousand sixty-five relevant studies were reviewed. One thousand six were excluded because they were review, animal, or pediatric studies. Fifty-nine studies underwent full manuscript review by two independent evaluators. Seventeen met all inclusion criteria and underwent analysis. Two-by-two tables were constructed from AKI +/− and CKD +/− data. The R package metafor was employed to determine odds ratio (OR), and a random-effects model was used to calculate weighted ORs. Leave-1-out, funnel analysis, and structured analysis were used to estimate effects of study heterogeneity and bias.

Results
Nonperioperative studies included studies of oncology, percutaneous coronary intervention, and myocardial infarction patients. Perioperative studies comprised patients from cardiac surgery, vascular surgery, and burns. There was significant heterogeneity, but risk of bias was overall assessed as low. The OR for AKI versus non-AKI patients developing CKD in all studies was 4.31 (95% CI 3.01–6.17; p < 0.01). Nonperioperative subjects demonstrated OR 3.32 for developing CKD compared to non-AKI patients (95% CI 2.06–5.34; p < 0.01) while perioperative patients demonstrated OR 5.20 (95% CI 3.12–8.66; p < 0.01) for the same event.

Conclusions
We conclude that studies conducted in perioperative and nonperioperative patient populations suggest similar risk of development of CKD after AKI.
The Boyen Fortress: structural analysis of selecting complementary forms of use for a proposed adaptive reuse project
Authors: Śladowski Grzegorz , Szewczyk Bartłomiej , Barnaś Krzysztof , Kania Olga , Barnaś Janusz 
Published: June 2021

Abstract
Extending the life cycle of heritage buildings through their adaptive reuse can ensure their survival and is concordant with the policy of sustainable development. Selecting a new form of use for heritage building adaptive reuse projects is a multidimensional process that can be significantly aided by multi-criteria decision-making approaches. In this paper, the authors have proposed a hybrid form of structural analysis, which is a formulation of a multi-criteria approach to the analysis of complementary forms of use for a complex of historical buildings, to be used during the early planning stages of adaptive reuse projects for heritage building complexes. The approach has been demonstrated on the example of the Boyen Fortress complex in Giżycko, Poland. The outcome of the analysis indicated that the highest share of floor space to be adapted should be dedicated to exhibition spaces, which is justified concerning cultural heritage benefits. This approach can be of significant aid to decision-makers during adaptive reuse project planning phases, thereby facilitating the continued survival of heritage sites.
Expression of TNF, IL1B, and iNOS2 in the neural cell after induced by Porphyromonas gingivalis with and without coating antibody anti-Porphyromonas gingivalis
Authors: Bachtiar Endang Winiati , Putri Citra F. , Soejoedono Retno D. , Bachtiar Boy M. 
Published: June 2021

Porphyromonas gingivalis has virulence factors such as gingipain and lipopolysaccharide, causing bacteremia to reach the brain and activate neuroinflammatory release cytokines. This study analyzed the effect of the co-culture of neuron cells with P. gingivalis coated with anti-P. gingivalis antibodies against cytokines produced by neuron cells. The gene expressions of the TNF, IL1B, iNOS2 in neurons was evaluated using RT-qPCR. The results showed that P. gingivalis coated with anti-P. gingivalis antibody before co-culture with neuron cells could decrease the gene expression of TNF, IL1B, and iNOS2 of neuron cells.
Comparison of two multiplexed technologies for profiling >1,000 serum proteins that may associate with tumor burden
Authors: Ren Annie , Prassas Ioannis , Sugumar Vijithan , Soosaipillai Antoninus , Bernardini Marcus , Diamandis Eleftherios P , Kulasingam Vathany 
Published: June 2021

Background: In this pilot study, we perform a preliminary comparison of two targeted multiplex proteomics technologies for discerning serum protein concentration changes that may correlate to tumor burden in ovarian cancer (OC) patients. Methods: Using the proximity extension assay (PEA) and Quantibody® Kiloplex Array (QKA), we measured >1,000 proteins in the pre-surgical and post-surgical serum from nine OC patients (N=18 samples). We expect that proteins that have decreased significantly in the post-surgical serum concentration may correlate to tumor burden in each patient. Duplicate sera from two healthy individuals were used as controls (N=4 samples). We employed in-house ELISAs to measure five proteins with large serum concentration changes in pre- and post-surgical sera, from four of the original nine patients and the two original controls. Results: Both platforms showed a weak correlation with clinical cancer antigen 125 (CA125) data. The two multiplexed platforms showed a significant correlation with each other for >400 overlapping proteins. PEA uncovered 15 proteins, while QKA revealed 11 proteins, with more than a two-fold post-surgical decrease in at least six of the nine patients. Validation using single enzyme-linked immunosorbent assays (ELISAs) showed at least a two-fold post-surgical decrease in serum concentration of the same patients, as indicated by the two multiplex assays. Conclusion: Both methods identified proteins that had significantly decreased in post-surgical serum concentration, as well as recognizing proteins that had been implicated in OC patients. Our findings from a limited sample size suggest that novel targeted proteomics platforms are promising tools for identifying candidate serological tumor-related proteins. However further studies are essential for the improvement of accuracy and avoidance of false results.