bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of the effectiveness of expandable cages for reconstruction of the anterior column of the spine
Authors: Cappelletto Barbara , Giorgiutti Fabrizia , Balsano Massimo 
Published: January 2020

Purpose: For anterior spine column reconstruction after corpectomy, expandable cages offer solid anterior support and allow correction of deformity, providing excellent primary stability. To provide a larger body of clinical observations concerning the effectiveness of the approach, this retrospective study examines patients treated by corpectomy and reconstruction with an expandable cage for different pathologies. Methods: Across 5 years, 39 patients underwent vertebral reconstruction with expandable cages after single ( n = 34), double ( n = 4), or triple ( n = 1) corpectomy. Pathologies were tumors ( n = 21), fractures, or deformities in traumatic injuries ( n = 14), degenerative pathology ( n = 2), and infection ( n = 2). Levels were cervical ( n = 10), thoracic ( n = 14), and lumbar ( n = 15). All patients were evaluated clinically and radiographically. Results: There were no cases of neurologic deterioration. Nurick grade showed significant improvement at 3 months postoperative versus preoperative ( p < 0.01). Visual analog scale significantly improved preoperatively versus 3 and 12 months postoperatively (both p = 0). Regional angulation was significantly corrected, from preoperative to 3 and 12 months postoperative, at cervical, thoracic, and lumbar levels. We achieved reconstruction of the normal local anatomy with full recovery of the height of the vertebral body. Six patients (15.4%) had complications and two (5.1%) underwent revision surgery. Conclusions: In our experience, expandable cages confer stable anterior support, providing significant improvement of the segmental kyphosis angle and restoration of the original somatic height. Our clinical results are favorable, and the low rate of complications and revision accentuates the expandable cage as a valuable tool to replace the vertebral body in diverse pathologies and different spine levels.
Treatment of Acute Proximal Anterior Cruciate Ligament Tears—Part 1: Gap Formation and Stabilization Potential of Repair Techniques
Authors: Bachmaier Samuel , DiFelice Gregory S. , Sonnery-Cottet Bertrand , Douoguih Wiemi A. , Smith Patrick A. , Pace Lee J. , Ritter Daniel , Wijdicks Coen A. 
Published: January 2020

Background: Recently, there has been a resurgence of interest in primary repair of the anterior cruciate ligament (ACL), with fixation techniques evolving. However, to date, there have been no biomechanical studies comparing fixed to adjustable fixation repair techniques. Hypothesis: Adjustable ACL repair provides for improved stabilization compared with fixed techniques with respect to both gap formation and residual load-bearing capability. Study Design: Controlled laboratory study. Methods: A total of 4 different ACL repair techniques (n = 5 per group), including single– and double–cinch loop (CL) cortical button fixation as well as knotless single–suture anchor fixation, were tested using a porcine model. For adjustable single-CL loop fixation, additional preconditioning (10 cycles at 0.5 Hz) was performed. The force after fixation and the actuator displacement to achieve a time-zero preload of 10 N were measured for fixed techniques. Incrementally increasing cycling (1 mm/500 cycles) from 1 to 8 mm was performed for 4000 cycles at 0.75 Hz before pull to failure (50 mm/min). The final residual peak load and gap formation for each test block were analyzed as well as ultimate strength. Results: Knot tying of a single-CL over a button (mean ± SD, 0.66 ± 0.23 mm) and knotless anchor fixation (0.20 ± 0.12 mm) resulted in significant time-zero gaps ( P < .001) and significantly higher overall gap formation at reduced residual loading (analysis of covariance, P < .001) compared with both the double-CL loop and adjustable fixation techniques. The adjustable group showed the highest failure load and stiffness, at 305.7 N and 117.1 N/mm, respectively. The failure load of the knotted single-CL group was significantly reduced compared with all other groups ( P < .001). Conclusion: Adjustable single-CL cortical button fixation with intraoperative preconditioning optimized time-zero ACL tension and led to significantly improved stabilization and reduced gap formation, with the highest ultimate strength. Single-CL loop knot tying over the button and knotless anchor fixation resulted in time-zero gaps to achieve slight tension on the ACL and significantly higher gap formation at reduced load-bearing capability. Clinical Relevance: Although the clinical relevance of gap formation is uncertain, a biomechanical understanding of the stabilization potential of current ACL repair techniques is pertinent to the continued evolution of surgical approaches to enable better clinical outcomes.
Facile Synthesis of Eggshell Membrane-Templated Au/CeO2 3D Nanocomposite Networks for Nonenzymatic Electrochemical Dopamine Sensor
Authors: Liu Qingquan , Chen Xiaoyu , Kang Ze-Wen , Zheng Chaohui , Yang Da-Peng 
Published: January 2020

Abstract
Dopamine acts as a neurotransmitter to regulate a variety of physiological functions of the central nervous system. Thus, the fabrication of electrochemical active nanomaterials for sensitive dopamine detection is extremely important for human health. Herein, we constructed a highly efficient dopamine nonenzymatic biosensor using eggshell membrane (ESM) as a 3D network-like carrier-loaded Au and CeO2 nanocomposites. This approach has led to the uniform distribution of CeO2 and Au nanoparticles on the surface of ESM. The structure and properties of the as-prepared ESM templated Au/CeO2 (ESM-AC) nanocomposites were characterized. The electrochemical properties of non-enzymatic oxidation of dopamine by ESM-AC electrode were studied by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The detection limit of the ESM-AC modified electrode for dopamine is 0.26 μM with a linear range from 0.1 to 10 mM. The ESM-AC-modified electrode performs a higher catalytic activity for dopamine electrocatalytic oxidation than that ESM-templated CeO2 (ESM-C) electrode, which is mainly due to the unique structure of ESM and more active sites provided from Au. Collectively, this biological waste-ESM provides a cheap and unique template for the preparation of 3D network-like nanostructures and expands the application in electrochemical dopamine detection.

Graphical abstract
ESM-AC nanocomposites prepared from biological waste was successfully modified on the surface of glassy carbon electrode and a dopamine-based electrochemical biosensor was constructed.
pSpatiocyte: a high-performance simulator for intracellular reaction-diffusion systems
Authors: Arjunan Satya N.V. , Miyauchi Atsushi , Iwamoto Kazunari , Takahashi Koichi 
Published: January 2020

Abstract
Background
Studies using quantitative experimental methods have shown that intracellular spatial distribution of molecules plays a central role in many cellular systems. Spatially resolved computer simulations can integrate quantitative data from these experiments to construct physically accurate models of the systems. Although computationally expensive, microscopic resolution reaction-diffusion simulators, such as Spatiocyte can directly capture intracellular effects comprising diffusion-limited reactions and volume exclusion from crowded molecules by explicitly representing individual diffusing molecules in space. To alleviate the steep computational cost typically associated with the simulation of large or crowded intracellular compartments, we present a parallelized Spatiocyte method called pSpatiocyte.

Results
The new high-performance method employs unique parallelization schemes on hexagonal close-packed (HCP) lattice to efficiently exploit the resources of common workstations and large distributed memory parallel computers. We introduce a coordinate system for fast accesses to HCP lattice voxels, a parallelized event scheduler, a parallelized Gillespie’s direct-method for unimolecular reactions, and a parallelized event for diffusion and bimolecular reaction processes. We verified the correctness of pSpatiocyte reaction and diffusion processes by comparison to theory. To evaluate the performance of pSpatiocyte, we performed a series of parallelized diffusion runs on the RIKEN K computer. In the case of fine lattice discretization with low voxel occupancy, pSpatiocyte exhibited 74% parallel efficiency and achieved a speedup of 7686 times with 663552 cores compared to the runtime with 64 cores. In the weak scaling performance, pSpatiocyte obtained efficiencies of at least 60% with up to 663552 cores. When executing the Michaelis-Menten benchmark model on an eight-core workstation, pSpatiocyte required 45- and 55-fold shorter runtimes than Smoldyn and the parallel version of ReaDDy, respectively. As a high-performance application example, we study the dual phosphorylation-dephosphorylation cycle of the MAPK system, a typical reaction network motif in cell signaling pathways.

Conclusions
pSpatiocyte demonstrates good accuracies, fast runtimes and a significant performance advantage over well-known microscopic particle methods in large-scale simulations of intracellular reaction-diffusion systems. The source code of pSpatiocyte is available at https://spatiocyte.org.
Unsupervised inference of implicit biomedical events using context triggers
Authors: Chung Jin-Woo , Yang Wonsuk , Park Jong C. 
Published: January 2020

AbstractBackgroundEvent extraction from the biomedical literature is one of the most actively researched areas in biomedical text mining and natural language processing. However, most approaches have focused on events within single sentence boundaries, and have thus paid much less attention to events spanning multiple sentences. The Bacteria-Biotope event (BB-event) subtask presented in BioNLP Shared Task 2016 is one such example; a significant amount of relations between bacteria and biotope span more than one sentence, but existing systems have treated them as false negatives because labeled data is not sufficiently large enough to model a complex reasoning process using supervised learning frameworks.ResultsWe present an unsupervised method for inferring cross-sentence events by propagating intra-sentence information to adjacent sentences using context trigger expressions that strongly signal the implicit presence of entities of interest. Such expressions can be collected from a large amount of unlabeled plain text based on simple syntactic constraints, helping to overcome the limitation of relying only on a small number of training examples available. The experimental results demonstrate that our unsupervised system extracts cross-sentence events quite well and outperforms all the state-of-the-art supervised systems when combined with existing methods for intra-sentence event extraction. Moreover, our system is also found effective at detecting long-distance intra-sentence events, compared favorably with existing high-dimensional models such as deep neural networks, without any supervised learning techniques.ConclusionsOur linguistically motivated inference model is shown to be effective at detecting implicit events that have not been covered by previous work, without relying on training data or curated knowledge bases. Moreover, it also helps to boost the performance of existing systems by allowing them to detect additional cross-sentence events. We believe that the proposed model offers an effective way to infer implicit information beyond sentence boundaries, especially when human-annotated data is not sufficient enough to train a robust supervised system.
TopoFilter: a MATLAB package for mechanistic model identification in systems biology
Authors: Rybiński Mikołaj , Möller Simon , Sunnåker Mikael , Lormeau Claude , Stelling Jörg 
Published: January 2020

Abstract
Background
To develop mechanistic dynamic models in systems biology, one often needs to identify all (or minimal) representations of the biological processes that are consistent with experimental data, out of a potentially large set of hypothetical mechanisms. However, a simple enumeration of all alternatives becomes quickly intractable when the number of model parameters grows. Selecting appropriate dynamic models out of a large ensemble of models, taking the uncertainty in our biological knowledge and in the experimental data into account, is therefore a key current problem in systems biology.

Results
The TopoFilter package addresses this problem in a heuristic and automated fashion by implementing the previously described topological filtering method for Bayesian model selection. It includes a core heuristic for searching the space of submodels of a parametrized model, coupled with a sampling-based exploration of the parameter space. Recent developments of the method allow to balance exhaustiveness and speed of the model space search, to efficiently re-sample parameters, to parallelize the search, and to use custom scoring functions. We use a theoretical example to motivate these features and then demonstrate TopoFilter’s applicability for a yeast signaling network with more than 250’000 possible model structures.

Conclusions
TopoFilter is a flexible software framework that makes Bayesian model selection and reduction efficient and scalable to network models of a complexity that represents contemporary problems in, for example, cell signaling. TopoFilter is open-source, available under the GPL-3.0 license at https://gitlab.com/csb.ethz/TopoFilter. It includes installation instructions, a quickstart guide, a description of all package options, and multiple examples.
Correction to: Identifying miRNA synergism using multiple-intervention causal inference
Authors: Zhang Junpeng , Pham Vu Viet Hoang , Liu Lin , Xu Taosheng , Truong Buu , Li Jiuyong , Rao Nini , Le Thuc Duy 
Published: January 2020

After publication of this supplement article [1], it was brought to our attention that the Fig. 3 was incorrect. The correct Fig. 3 is as below:
Absence of reproduction-immunity trade-off in male Drosophila melanogaster evolving under differential sexual selection
Authors: Syed Zeeshan Ali , Gupta Vanika , Arun Manas Geeta , Dhiman Aatashi , Nandy Bodhisatta , Prasad Nagaraj Guru 
Published: January 2020

Abstract
Background
The theory of trade-off suggests that limited resources should lead to trade-off in resource intensive traits such as, immunity related and sexually selected traits in males. Alternatively, sexual exaggerations can also act as an honest indicator of underlying immunocompetence, leading to positive correlations between these traits. Evidences in support of either hypothesis in invertebrates are equivocal. Whereas several studies have addressed this question, few have used naturally occurring pathogens and realized post infection realized immunity (e.g., survivorship) to assay the fitness correlations between these two sets of traits.

Results
Adopting an experimental evolution approach, we evolved replicate populations of Drosophila melanogaster under high and low sexual selection regimes for over a hundred generations and found the following in virgin and mated males in three separate assays:
Post infection survivorship against two natural pathogens - Pseudomonas entomophila (Pe) and Staphylococcus succinus (Ss): Mated males survived better against Pe, but were no different than virgins against Ss.Bacterial clearance ability against a third natural pathogen Providencia rettgeri (Pr): Mated males had significantly lower CFUs than virgins.
However, sexual selection history had no effect on realized immunity of either virgin or mated males.

Conclusion
We show that while mating can affect realized immunity in a pathogen specific way, sexual selection did not affect the same. The results highlight that complex polygenic traits such as immunity and reproductive traits not necessarily evolve following a binary trade-off model. We also stress the importance natural pathogens while studying sexual selection-immunity correlations.
New insights on intercontinental origins of paternal lineages in Northeast Brazil
Authors: Schaan Ana Paula , Gusmão Leonor , Jannuzzi Juliana , Modesto Antonio , Amador Marcos , Marques Diego , Rabenhorst Silvia Helena , Montenegro Raquel , Lopes Thayson , Yoshioka France Keiko , Pinto Giovanny , Santos Sidney , Costa Lorenna , Silbiger Vivian , Ribeiro-dos-Santos Ândrea 
Published: January 2020

Abstract
Background
The current Brazilian population is the product of centuries of admixture between intercontinental founding groups. Although previous results have revealed a heterogeneous distribution of mitochondrial lineages in the Northeast region, the most targeted by foreign settlers during the sixteenth century, little is known about the paternal ancestry of this particular population. Considering historical records have documented a series of territorial invasions in the Northeast by various European populations, we aimed to characterize the male lineages found in Brazilian individuals in order to discover to what extent these migrations have influenced the present-day gene pool. Our approach consisted of employing four hierarchical multiplex assays for the investigation of 45 unique event polymorphisms in the non-recombining portion of the Y-chromosome of 280 unrelated men from several Northeast Brazilian states.

Results
Primary multiplex results allowed the identification of six major haplogroups, four of which were screened for downstream SNPs and enabled the observation of 19 additional lineages. Results reveal a majority of Western European haplogroups, among which R1b-S116* was the most common (63.9%), corroborating historical records of colonizations by Iberian populations. Nonetheless, FST genetic distances show similarities between Northeast Brazil and several other European populations, indicating multiple origins of settlers. Regarding Native American ancestry, our findings confirm a strong sexual bias against such haplogroups, which represented only 2.5% of individuals, highly contrasting previous results for maternal lineages. Furthermore, we document the presence of several Middle Eastern and African haplogroups, supporting a complex historical formation of this population and highlighting its uniqueness among other Brazilian regions.

Conclusions
We performed a comprehensive analysis of the major Y-chromosome lineages that form the most dynamic migratory region from the Brazilian colonial period. This evidence suggests that the ongoing entry of European, Middle Eastern, and African males in the Brazilian Northeast, since at least 500 years, was significantly responsible for the present-day genetic architecture of this population.
The evolutionary arms race between transposable elements and piRNAs in Drosophila melanogaster
Authors: Luo Shiqi , Zhang Hong , Duan Yuange , Yao Xinmin , Clark Andrew G. , Lu Jian 
Published: January 2020

AbstractBackgroundThepiwi-interacting RNAs (piRNAs) are small non-coding RNAs that specifically repress transposable elements (TEs) in the germline ofDrosophila. Despite our expanding understanding of TE:piRNA interaction, whether there is an evolutionary arms race between TEs and piRNAs was unclear.ResultsHere, we studied the population genomics of TEs and piRNAs in the worldwide strains ofD. melanogaster. By conducting a correlation analysis between TE contents and the abundance of piRNAs from ovaries of representative strains ofD. melanogaster, we find positive correlations between TEs and piRNAs in six TE families. Our simulations further highlight that TE activities and the strength of purifying selection against TEs are important factors shaping the interactions between TEs and piRNAs. Our studies also suggest that the de novo generation of piRNAs is an important mechanism to repress the newly invaded TEs.ConclusionsOur results revealed the existence of an evolutionary arms race between the copy numbers of TEs and the abundance of antisense piRNAs at the population level. Although the interactions between TEs and piRNAs are complex and many factors should be considered to impact their interaction dynamics, our results suggest the emergence, repression specificity and strength of piRNAs on TEs should be considered in studying the landscapes of TE insertions inDrosophila. These results deepen our understanding of the interactions between piRNAs and TEs, and also provide novel insights into the nature of genomic conflicts of other forms.
Evaluation of genetic diversity, agronomic traits, and anthracnose resistance in the NPGS Sudan Sorghum Core collection
Authors: Cuevas Hugo E. , Prom Louis K. 
Published: January 2020

AbstractBackgroundThe United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS) sorghum core collection contains 3011 accessions randomly selected from 77 countries. Genomic and phenotypic characterization of this core collection is necessary to encourage and facilitate its utilization in breeding programs and to improve conservation efforts. In this study, we examined the genome sequences of 318 accessions belonging to the NPGS Sudan sorghum core set, and characterized their agronomic traits and anthracnose resistance response.ResultsWe identified 183,144 single nucleotide polymorphisms (SNPs) located within or in proximity of 25,124 annotated genes using the genotyping-by-sequencing (GBS) approach. The core collection was genetically highly diverse, with an average pairwise genetic distance of 0.76 among accessions. Population structure and cluster analysis revealed five ancestral populations within the Sudan core set, with moderate to high level of genetic differentiation. In total, 171 accessions (54%) were assigned to one of these populations, which covered 96% of the total genomic variation. Genome scan based on Tajima’s D values revealed two populations under balancing selection. Phenotypic analysis showed differences in agronomic traits among the populations, suggesting that these populations belong to different ecogeographical regions. A total of 55 accessions were resistant to anthracnose; these accessions could represent multiple resistance sources. Genome-wide association study based on fixed and random model Circulating Probability (farmCPU) identified genomic regions associated with plant height, flowering time, panicle length and diameter, and anthracnose resistance response. Integrated analysis of the Sudan core set and sorghum association panel indicated that a large portion of the genetic variation in the Sudan core set might be present in breeding programs but remains unexploited within some clusters of accessions.ConclusionsThe NPGS Sudan core collection comprises genetically and phenotypically diverse germplasm with multiple anthracnose resistance sources. Population genomic analysis could be used to improve screening efforts and identify the most valuable germplasm for breeding programs. The new GBS data set generated in this study represents a novel genomic resource for plant breeders interested in mining the genetic diversity of the NPGS sorghum collection.