bluuebunny/crossref_metadata_2025_split huggingface dataset:
Complex cerebral aneurysms: intra-luminal reconstruction using Pipeline flow-diverting stent and the obliteration mechanism
Authors: Lv Xianli , Jiang Chuhan , Wu Zhongxue , Jiang Weijian , Wang Guihuai 
Published: December 2019

Objectives Patients with complex cerebral aneurysms can now be treated intravascularly with the help of flow-diverting stents. The primary purpose of this article is to document the clinical and angiographic outcomes in 80 patients who were treated with the Pipeline flow-diverting stent (PFS; Medtronic, Dublin, Ireland) and the obliteration mechanism was discussed. Patients and methods Between October 2015 and October 2019, 80 patients with 90 complex (undefined neck, large/giant, blood blister–like, and recurrent side-wall) cerebral aneurysms treated with the PFS were retrospectively reviewed. Forty-five patients were women and 35 were men, with a mean age of 52 years. Large or giant aneurysms were defined as 10 mm or larger and small aneurysms were defined as less than 10 mm at the largest diameter measured on angiogram. Results Forty-one aneurysms (45.6%) were large or giant, 41 (45.6%) were small, four (4.4%) were recurrent side-wall aneurysms and four (4.4%) were blood blister–like aneurysms. In total, 87 PFSs were placed in 80 patients with 90 aneurysms. In six patients, coexisting proximal stenosis of parent artery was also covered with PFS without balloon angioplasty. Adjunct coils were placed in 31 aneurysms (34%). One patient died of intracerebral hematoma after thrombolysis. There was one intrastent occlusion at six-month follow-up without any symptoms. The morbidity and the mortality rate is 0% and 1.3% (95% confidence interval (CI), 0%–3.7%). Control angiography was available in 74 (92.5%) patients with 83 aneurysms, and the aneurysm occlusion rate was 98.8% (95% CI, 96.5%–100%) in 6 to 12 months. Conclusion For wide-necked saccular, large/giant, blood blister–like aneurysms and recurrent side-wall aneurysms, PFS is a valid and safe treatment option.
Anteromedial Portal Double-Bundle Anterior Cruciate Ligament Reconstruction Yields Similar Outcomes to Non-AMP Femoral Drilling Double-Bundle Techniques: A Systematic Review of Comparative Studies
Authors: Tejpal Tushar , Gupta Arnav , Shanmugaraj Ajaykumar , Horner Nolan S. , Simunovic Nicole , Peterson Devin C. , Ayeni Olufemi R. 
Published: December 2019

Background: Biomechanical studies have shown double-bundle (DB) anterior cruciate ligament reconstruction (ACLR) to have increased anterior and rotational stability as compared with single-bundle ACLR. Various techniques exist to drill the femoral tunnel, such as anteromedial portal (AMP), outside-in (OI), and transtibial (TT) drilling. However, it is unclear whether one drilling technique is superior to others when a DB graft is used. Purpose: To systematically assess the outcomes and complications in patients undergoing DB ACLR through an AMP technique as compared with other femoral drilling techniques. Study Design: Systematic review; Level of evidence, 3. Methods: PubMed, Medline, and EMBASE databases were searched in April 2018. Nonrandomized studies were assessed with the MINORS (Methodological Index for Nonrandomized Studies), whereas randomized studies were assessed with the GRADE (Grading of Recommendations Assessment, Development and Evaluation) system. Results: Ten studies comprising 722 patients satisfied the inclusion criteria. A total of 351 patients underwent DB ACLR with AMP drilling (mean ± SD age, 32.7 ± 4.7 years); 318 patients had DB ACLR with OI drilling (age, 31.9 ± 4.1 years); and 53 received a DB ACLR with TT drilling (age, 26.5 ± 2.0 years). Graft types used included hamstring autograft (74.1%; n = 247), tibialis anterior autograft (6.0%; n = 20) and unspecified grafts (19.8%; n = 66). No significant difference in postoperative Tegner and Lysholm scores was found between the AMP and OI groups postoperatively. The AMP group had a lower anterior and posterior graft bending angle as compared with the OI group. Four patients (1.1%) in the AMP group had graft reruptures, as compared with 9 reruptures (2.8%) in the OI group. There were no reports of rerupture in the TT group. Conclusion: DB AMP ACLR results in significantly improved functional outcome scores postoperatively. AMP techniques yield similar functional outcomes to OI ACLR. No direct comparison in functional outcomes scores were available between the AMP and TT techniques. Low overall complication and revision rates were observed for patients undergoing DB AMP ACLR and were found to be similar to those of other femoral drilling techniques. Owing to a steeper graft bending angle in patients undergoing OI or TT ACLR relative to AMP ACLR, patients treated with OI or TT femoral drilling may have increased strain placed on the graft. Based on the various limitations in the available literature, it is not currently possible to make a definite conclusion of whether AMP is superior to non-AMP techniques in the setting of DB ACLR.
Results of a Survey of the National Psoriasis Foundation Medical Board on the Management of Ear Psoriasis
Authors: Blake Amy , Enos Clinton , Armstrong April W. , Garg Amit , Gottlieb Alice , Koo John , Mehta Nehal , Prussick Ronald , Ryan Caitriona , Schwartzman Sergio , Siegel Michael , Wu Jashin J. , Strasnick Barry , Van Voorhees Abby S. 
Published: December 2019

Background: There is limited literature on the occurrence and management of psoriasis involving the ear. Objective: To better understand psoriasis of the ear and current approaches for management. Methods: The Medical Board of the National Psoriasis Foundation was surveyed on the frequency and presentation of psoriasis of the ear, the types of examinations performed, and the rationale for choice of treatment. Results: In this survey, the observed frequency of ear psoriasis was wide (10%-70%). The scalp was the most common concurrent site of extra-auricular psoriasis. Inspection of the ear was commonly reported; however, 75% of respondents report not inspecting the canal. Topical corticosteroids were the most commonly used treatment. Systemic and biologic therapies are infrequently used. Limitations: This study is limited by the sample size of respondents. Not every question of the survey was answered by all those surveyed. Conclusions: Results from our survey suggest that the evaluation of psoriasis of the ear is often not complete. Inspection of the ear, including the canal, is recommended, especially if the scalp is involved. Routine inspection of the ear is recommended both to evaluate treatment response and for potential adverse side effects. In the setting of persistent ear disease, collaboration between dermatologists and otolaryngologists is encouraged.
Lack of the multidrug transporter MRP4/ABCC4 defines the PEL-negative blood group and impairs platelet aggregation
Authors: Azouzi Slim , Mikdar Mahmoud , Hermand Patricia , Gautier Emilie-Fleur , Salnot Virginie , Willemetz Alexandra , Nicolas Gaël , Vrignaud Cédric , Raneri Alexandre , Mayeux Patrick , Bole-Feysot Christine , Nitschké Patrick , Cartron Jean-Pierre , Colin Yves , Hermine Olivier , Jedlitschky Gabriele , Cloutier Marc , Constanzo-Yanez Jessica , Ethier Carole , Robitaille Nancy , St-Louis Maryse , Le Van Kim Caroline , Peyrard Thierry 
Published: December 2019

Abstract
The rare PEL-negative phenotype is one of the last blood groups with an unknown genetic basis. By combining whole-exome sequencing and comparative global proteomic investigations, we found a large deletion in the ABCC4/MRP4 gene encoding an ATP-binding cassette (ABC) transporter in PEL-negative individuals. The loss of PEL expression on ABCC4-CRISPR-Cas9 K562 cells and its overexpression in ABCC4-transfected cells provided evidence that ABCC4 is the gene underlying the PEL blood group antigen. Although ABCC4 is an important cyclic nucleotide exporter, red blood cells from ABCC4null/PEL-negative individuals exhibited a normal guanosine 3′,5′-cyclic monophosphate level, suggesting a compensatory mechanism by other erythroid ABC transporters. Interestingly, PEL-negative individuals showed an impaired platelet aggregation, confirming a role for ABCC4 in platelet function. Finally, we showed that loss-of-function mutations in the ABCC4 gene, associated with leukemia outcome, altered the expression of the PEL antigen. In addition to ABCC4 genotyping, PEL phenotyping could open a new way toward drug dose adjustment for leukemia treatment.
Estimation of antioxidant, antimicrobial activity and brine shrimp toxicity of plants collected from Oymyakon region of the Republic of Sakha (Yakutia), Russia
Authors: Paudel Babita , Bhattarai Hari Datta , Kim Il Chan , Lee Hyoungseok , Sofronov Roman , Ivanova Lena , Poryadina Lena , Yim Joung Han 
Published: December 2019

Abstract

Background
Several plants are reported to be produced various biological active compounds. Lichens from the extreme environments such as high altitude, high UV, drought and cold are believed to be synthesized unique types of secondary metabolites than the other one. Several human pathogenic bacteria and fungi have been muted into drug resistant strains. Various synthetic antioxidant compounds have posed carcinogenic effects. This phenomenon needs further research for new effective drugs of natural origin. This manuscript aimed to screen new source of biological active compounds from plants of subarctic origin.

Results
A total of 114 plant species, including 80 species of higher plants, 19 species of lichens and 15 species of mosses, were collected from Oymyakon region of the Republic of Sakha (Yakutia), Russia (63˚20′N, 141˚42′E–63˚15′N, 142˚27′E). Antimicrobial, DPPH free radical scavenging and brine shrimp (Artemia salina) toxicity of all crude extract were evaluated. The obtained result was analyzed and compared with commercial standards. A total of 28 species of higher plants showed very strong antioxidant activity (DPPH IC50, 0.45-5.0 μg/mL), 13 species showed strong activity (DPPH IC50, 5-10 μg/mL), 22 species showed moderate antioxidant activity (DPPH IC50,10-20 μg/mL) and 17 species showed weak antioxidant activity (DPPH IC50 more than 20 μg/mL). Similarly, 3 species of lichen showed strong antioxidant activity, one species showed moderate and 15 species showed weak DPPH reducing activity. In addition, 4 species of mosses showed moderate antioxidant activity and 11 species showed weak antioxidant activity. Similarly, extracts of 51 species of higher plants showed antimicrobial (AM) activity against Staphylococcus aureus and 2 species showed AM activity against Candida albicans. Similarly, 11 species of lichen showed AM activity against S. aureus and 3 species showed AM activity against Escherichia coli. One species of moss showed AM activity against S. aureus. And finally, one species of higher plant Rheum compactum and one species of lichen Flavocetraria cucullata showed the toxicity against Brine shrimp larvae in 100 μg/mL of concentration.

Conclusion
The experimental results showed that subarctic plant species could be potential sources of various biologically active natural compounds.
Latitudinal diversity patterns of Chilean coastal fishes: searching for causal processes
Authors: Navarrete Arturo H , Lagos Nelson A , Ojeda F Patricio 
Published: December 2019

Abstract

Background
Several particular aspects of diversity patterns of Chilean littoral fishes are still poorly understood, and existing studies within this scope are fundamentally based on bibliographic compilations. In this study, we use empirical data to assess whether the diversity patterns of fish fauna along 4000 km of the Chilean coast (20°–55° S)can be explained in relation to the environmental latitudinal gradient. Fish were collected from intertidal pools and subtidal habitats (<35 m). Analyses focused on the spatial scales of diversity patterns and latitudinal breaks in species diversity, comparing the observed patterns among intertidal and subtidal habitats. Correlations between variance in environmental factors and species richness were calculated.

Results
Richness was positively autocorrelated at spatial scales <1000 km. Overall, richness was observed to progressively decrease toward higher latitudes, but values for intertidal fish in particular decreased towards the north and south from the point of maximum richness. This is a pattern that has already been recorded for other intertidal organisms. Similarity was seen to decrease with distance, and turnover point for intertidal fishes was high around 30°–32° S, while northern species disappeared between 36°–39° S. Subtidally, there is an invasion of subantarctic species between 53°–55° S.

Conclusions
Environmental variables are significant to the diversity patterns recorded. However, richness variations could result from many types of variables acting together and not from one single factor.
Sensitivity analysis of dynamic biological systems with time-delays
Authors: Wu Wu Hsiung , Wang Feng Sheng , Chang Maw Shang 
Published: December 2019

Abstract

Background
Mathematical modeling has been applied to the study and analysis of complex biological systems for a long time. Some processes in biological systems, such as the gene expression and feedback control in signal transduction networks, involve a time delay. These systems are represented as delay differential equation (DDE) models. Numerical sensitivity analysis of a DDE model by the direct method requires the solutions of model and sensitivity equations with time-delays. The major effort is the computation of Jacobian matrix when computing the solution of sensitivity equations. The computation of partial derivatives of complex equations either by the analytic method or by symbolic manipulation is time consuming, inconvenient, and prone to introduce human errors. To address this problem, an automatic approach to obtain the derivatives of complex functions efficiently and accurately is necessary.

Results
We have proposed an efficient algorithm with an adaptive step size control to compute the solution and dynamic sensitivities of biological systems described by ordinal differential equations (ODEs). The adaptive direct-decoupled algorithm is extended to solve the solution and dynamic sensitivities of time-delay systems describing by DDEs. To save the human effort and avoid the human errors in the computation of partial derivatives, an automatic differentiation technique is embedded in the extended algorithm to evaluate the Jacobian matrix. The extended algorithm is implemented and applied to two realistic models with time-delays: the cardiovascular control system and the TNF-α signal transduction network. The results show that the extended algorithm is a good tool for dynamic sensitivity analysis on DDE models with less user intervention.

Conclusions
By comparing with direct-coupled methods in theory, the extended algorithm is efficient, accurate, and easy to use for end users without programming background to do dynamic sensitivity analysis on complex biological systems with time-delays.
A quantitatively-modeled homozygosity mapping algorithm, qHomozygosityMapping, utilizing whole genome single nucleotide polymorphism genotyping data
Authors: Huqun*  , Fukuyama Shun-ichiro , Morino Hiroyuki , Miyazawa Hiroshi , Tanaka Tomoaki , Suzuki Tomoko , Kohda Masakazu , Kawakami Hideshi , Okazaki Yasushi , Seyama Kuniaki , Hagiwara Koichi 
Published: December 2019

Abstract
Homozygosity mapping is a powerful procedure that is capable of detecting recessive disease-causing genes in a few patients from families with a history of inbreeding. We report here a homozygosity mapping algorithm for high-density single nucleotide polymorphism arrays that is able to (i) correct genotyping errors, (ii) search for autozygous segments genome-wide through regions with runs of homozygous SNPs, (iii) check the validity of the inbreeding history, and (iv) calculate the probability of the disease-causing gene being located in the regions identified. The genotyping error correction restored an average of 94.2% of the total length of all regions with run of homozygous SNPs, and 99.9% of the total length of them that were longer than 2 cM. At the end of the analysis, we would know the probability that regions identified contain a disease-causing gene, and we would be able to determine how much effort should be devoted to scrutinizing the regions. We confirmed the power of this algorithm using 6 patients with Siiyama-type α1-antitrypsin deficiency, a rare autosomal recessive disease in Japan. Our procedure will accelerate the identification of disease-causing genes using high-density SNP array data.
Phylogenetic search through partial tree mixing
Authors: Sundberg Kenneth , Clement Mark , Snell Quinn , Ventura Dan , Whiting Michael , Crandall Keith 
Published: December 2019

Abstract

Background
Recent advances in sequencing technology have created large data sets upon which phylogenetic inference can be performed. Current research is limited by the prohibitive time necessary to perform tree search on a reasonable number of individuals. This research develops new phylogenetic algorithms that can operate on tens of thousands of species in a reasonable amount of time through several innovative search techniques.

Results
When compared to popular phylogenetic search algorithms, better trees are found much more quickly for large data sets. These algorithms are incorporated in the PSODA application available at http://dna.cs.byu.edu/psoda

Conclusions
The use of Partial Tree Mixing in a partition based tree space allows the algorithm to quickly converge on near optimal tree regions. These regions can then be searched in a methodical way to determine the overall optimal phylogenetic solution.
Mapping small molecule binding data to structural domains
Authors: Kruger Felix A , Rostom Raghd , Overington John P 
Published: December 2019

AbstractBackgroundLarge-scale bioactivity/SAR Open Data has recently become available, and this has allowed new analyses and approaches to be developed to help address the productivity and translational gaps of current drug discovery. One of the current limitations of these data is the relative sparsity of reported interactions per protein target, and complexities in establishing clear relationships between bioactivity and targets using bioinformatics tools. We detail in this paper the indexing of targets by the structural domains that bind (or are likely to bind) the ligand within a full-length protein. Specifically, we present a simple heuristic to map small molecule binding to Pfam domains. This profiling can be applied to all proteins within a genome to give some indications of the potential pharmacological modulation and regulation of all proteins.ResultsIn this implementation of our heuristic, ligand binding to protein targets from the ChEMBL database was mapped to structural domains as defined by profiles contained within the Pfam-A database. Our mapping suggests that the majority of assay targets within the current version of the ChEMBL database bind ligands through a small number of highly prevalent domains, and conversely the majority of Pfam domains sampled by our data play no currently established role in ligand binding. Validation studies, carried out firstly against Uniprot entries with expert binding-site annotation and secondly against entries in the wwPDB repository of crystallographic protein structures, demonstrate that our simple heuristic maps ligand binding to the correct domain in about 90 percent of all assessed cases. Using the mappings obtained with our heuristic, we have assembled ligand sets associated with each Pfam domain.ConclusionsSmall molecule binding has been mapped to Pfam-A domains of protein targets in the ChEMBL bioactivity database. The result of this mapping is an enriched annotation of small molecule bioactivity data and a grouping of activity classes following the Pfam-A specifications of protein domains. This is valuable for data-focused approaches in drug discovery, for example when extrapolating potential targets of a small molecule with known activity against one or few targets, or in the assessment of a potential target for drug discovery or screening studies.
B-cell epitope prediction through a graph model
Authors: Zhao Liang , Wong Limsoon , Lu Lanyuan , Hoi Steven CH , Li Jinyan 
Published: December 2019

Abstract

Background
Prediction of B-cell epitopes from antigens is useful to understand the immune basis of antibody-antigen recognition, and is helpful in vaccine design and drug development. Tremendous efforts have been devoted to this long-studied problem, however, existing methods have at least two common limitations. One is that they only favor prediction of those epitopes with protrusive conformations, but show poor performance in dealing with planar epitopes. The other limit is that they predict all of the antigenic residues of an antigen as belonging to one single epitope even when multiple non-overlapping epitopes of an antigen exist.

Results
In this paper, we propose to divide an antigen surface graph into subgraphs by using a Markov Clustering algorithm, and then we construct a classifier to distinguish these subgraphs as epitope or non-epitope subgraphs. This classifier is then taken to predict epitopes for a test antigen. On a big data set comprising 92 antigen-antibody PDB complexes, our method significantly outperforms the state-of-the-art epitope prediction methods, achieving 24.7% higher averaged f-score than the best existing models. In particular, our method can successfully identify those epitopes with a non-planarity which is too small to be addressed by the other models. Our method can also detect multiple epitopes whenever they exist.

Conclusions
Various protrusive and planar patches at the surface of antigens can be distinguishable by using graphical models combined with unsupervised clustering and supervised learning ideas. The difficult problem of identifying multiple epitopes from an antigen can be made easied by using our subgraph approach. The outstanding residue combinations found in the supervised learning will be useful for us to form new hypothesis in future studies.
Discovery of a new class of inhibitors for the protein arginine deiminase type 4 (PAD4) by structure-based virtual screening
Authors: Teo Chian Ying , Shave Steven , Thean Chor Adam Leow , Salleh Abu Bakar , Abdul Rahman Mohd Basyaruddin Bin , Walkinshaw Malcolm D , Tejo Bimo A 
Published: December 2019

Abstract

Background
Rheumatoid arthritis (RA) is an autoimmune disease with unknown etiology. Anticitrullinated protein autoantibody has been documented as a highly specific autoantibody associated with RA. Protein arginine deiminase type 4 (PAD4) is the enzyme responsible for catalyzing the conversion of peptidylarginine into peptidylcitrulline. PAD4 is a new therapeutic target for RA treatment. In order to search for inhibitors of PAD4, structure-based virtual screening was performed using LIDAEUS (Ligand discovery at Edinburgh university). Potential inhibitors were screened experimentally by inhibition assays.

Results
Twenty two of the top-ranked water-soluble compounds were selected for inhibitory screening against PAD4. Three compounds showed significant inhibition of PAD4 and their IC50 values were investigated. The structures of the three compounds show no resemblance with previously discovered PAD4 inhibitors, nor with existing drugs for RA treatment.

Conclusion
Three compounds were discovered as potential inhibitors of PAD4 by virtual screening. The compounds are commercially available and can be used as scaffolds to design more potent inhibitors against PAD4.