bluuebunny/crossref_metadata_2025_split huggingface dataset:
Topological bands and localized vibration modes in quasiperiodic beams
Authors: Pal Raj Kumar , Rosa Matheus I N , Ruzzene Massimo 
Published: August 2019

Abstract
We investigate a family of quasiperiodic continuous elastic beams, the topological properties of their vibrational spectra, and their relation to the existence of localized modes. We specifically consider beams featuring arrays of ground springs at locations determined by projecting from a circle onto an underlying periodic system. A family of periodic and quasiperiodic structures is obtained by smoothly varying a parameter defining such projection. Numerical simulations show the existence of vibration modes that first localize at a boundary, and then migrate into the bulk as the projection parameter is varied. Explicit expressions predicting the change in the density of states of the bulk define topological invariants that quantify the number of modes spanning a gap of a finite structure. We further demonstrate how modulating the phase of the ground springs distribution causes the topological states to undergo an edge-to-edge transition. The considered configurations and topological studies provide a framework for inducing localized modes in continuous elastic structural components through globally spanning, deterministic perturbations of periodic patterns defined by the considered projection operations.
Novel theoretical constraints for color-octet scalar models *
Authors: Cheng Li , Eberhardt Otto , Murphy Christopher W. 
Published: August 2019

Abstract
We study the theoretical constraints on a model whose scalar sector contains one color octet and one or two color singlet SU(2)
L
doublets. To ensure unitarity of the theory, we constrain the parameters of the scalar potential for the first time at the next-to-leading order in perturbation theory. Moreover, we derive new conditions guaranteeing the stability of the potential. We employ the HEPfit package to extract viable parameter regions at the electroweak scale and test the stability of the renormalization group evolution up to the multi-TeV region. Furthermore, we set upper limits on the scalar mass splittings. All results are given for both cases with and without a second scalar color singlet.
Anisotropic evolution of 4-brane in a 6D generalized Randall-Sundrum model *
Authors: Kang Guang-Zhen , Zhang De-Sheng , Du Long , Xu Jun , Zong Hong-Shi 
Published: August 2019

Abstract
We investigate a 6D generalized Randall-Sundrum brane world scenario with a bulk cosmological constant. Each stress-energy tensor

on the brane is shown to be similar to a constant vacuum energy. This is consistent with the Randall-Sundrum model, in which each 3-brane Lagrangian yielded a constant vacuum energy. By adopting an anisotropic metric ansatz, we obtain the 5D Friedmann-Robertson-Walker field equations. In a slightly later period, the expansion of the universe is proportional to the square root of time,

, which is similar to the period of the radiation-dominated regime. Moreover, we investigate the case with two

and two

. In a large range of

, we obtain the 3D effective cosmological constant

, which is independent of the integral constant. Here, the scale factor is an exponential expansion, which is consistent with our present observation of the universe. Our results demonstrate that it is possible to construct a model that solves the dark energy problem, while guaranteeing a positive brane tension.
pCRM1exportome: database of predicted CRM1-dependent Nuclear Export Signal (NES) motifs in cancer-related genes
Authors: Lee Yoonji , Baumhardt Jordan M , Pei Jimin , Chook Yuh Min , Grishin Nick V 
Published: August 2019

AbstractMotivationThe consensus pattern of Nuclear Export Signal (NES) is a short sequence motif that is commonly identified in protein sequences, whether the motif acts as an NES (true positive) or not (false positive). Finding more plausible NES functioning regions among the vast array of consensus-matching segments would provide an interesting resource for further experimental validation. Better defined NES should also allow meaningful mapping of cancer-related mutation positions, leading to plausible explanations for the relationship between nuclear export and disease.ResultsPossible NES candidate regions are extracted from the cancer-related human reference proteome. Extracted NES are scored for reliability by combining sequence-based and structure-based approaches. The confidently identified NES candidate motifs were checked for overlap with cancer-related mutation positions annotated in the COSMIC database. Among the ∼700 cancer-related sequences in the COSMIC Cancer Gene Census, 178 sequences are predicted to have possible NES motifs containing cancer-related mutations at their key positions. These lists are organized into our database (pCRM1exportome), and other protein sequences in the human reference proteome can also be retrieved by their UniProt IDs.Availability and implementationThe database is freely available at http://prodata.swmed.edu/pCRM1exportome.Supplementary informationSupplementary data are available at Bioinformatics online.
Improved representation of sequence bloom trees
Authors: Harris Robert S , Medvedev Paul 
Published: August 2019

Abstract

Motivation
Algorithmic solutions to index and search biological databases are a fundamental part of bioinformatics, providing underlying components to many end-user tools. Inexpensive next generation sequencing has filled publicly available databases such as the Sequence Read Archive beyond the capacity of traditional indexing methods. Recently, the Sequence Bloom Tree (SBT) and its derivatives were proposed as a way to efficiently index such data for queries about transcript presence.

Results
We build on the SBT framework to construct the HowDe-SBT data structure, which uses a novel partitioning of information to reduce the construction and query time as well as the size of the index. Compared to previous SBT methods, on real RNA-seq data, HowDe-SBT can construct the index in less than 36% of the time and with 39% less space and can answer small-batch queries at least five times faster. We also develop a theoretical framework in which we can analyze and bound the space and query performance of HowDe-SBT compared to other SBT methods.

Availability and implementation
HowDe-SBT is available as a free open source program on https://github.com/medvedevgroup/HowDeSBT.

Supplementary information
Supplementary data are available at Bioinformatics online.
miComplete: weighted quality evaluation of assembled microbial genomes
Authors: Hugoson Eric , Lam Wai Tin , Guy Lionel 
Published: August 2019

AbstractSummaryMetagenomics and single-cell genomics have revolutionized the study of microorganisms, increasing our knowledge of microbial genomic diversity by orders of magnitude. A major issue pertaining to metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) is to estimate their completeness and redundancy. Most approaches rely on counting conserved gene markers. In miComplete, we introduce a weighting strategy, where we normalize the presence/absence of markers by their median distance to the next marker in a set of complete reference genomes. This approach alleviates biases introduced by the presence/absence of shorter DNA pieces containing many markers, e.g. ribosomal protein operons.Availability and implementationmiComplete is written in Python 3 and released under GPLv3. Source code and documentation are available at https://bitbucket.org/evolegiolab/micomplete.Supplementary informationSupplementary data are available at Bioinformatics online.
Gut Microbiome Signatures Are Predictive of Infectious Risk Following Induction Therapy for Acute Myeloid Leukemia
Authors: Galloway-Peña Jessica R , Shi Yushu , Peterson Christine B , Sahasrabhojane Pranoti , Gopalakrishnan Vancheswaran , Brumlow Chelcy E , Daver Naval G , Alfayez Mansour , Boddu Prajwal C , Khan Md Abdul Wadud , Wargo Jennifer A , Do Kim-Anh , Jenq Robert R , Kontoyiannis Dimitrios P , Shelburne Samuel A 
Published: August 2019

AbstractBackgroundThe majority of studies that provide insights into the influence of the microbiome on the health of hematologic malignancy patients have concentrated on the transplant setting. Here, we sought to assess the predictive capacity of the gastrointestinal microbiome and its relationship to infectious outcomes in patients with acute myeloid leukemia (AML).Methods16s rRNA-based analysis was performed on oral swabs and stool samples obtained biweekly from baseline until neutrophil recovery following induction chemotherapy (IC) in 97 AML patients. Microbiome characteristics were correlated with clinical outcomes both during and after IC completion.ResultsAt the start of IC, higher stool Shannon diversity (hazard ratio [HR], 0.36; 95% confidence interval [CI], .18–.74) and higher relative abundance of Porphyromonadaceae (HR, 0.36; 95% CI, .18–.73) were associated with increased probability of remaining infection-free during neutropenia. A baseline stool Shannon diversity cutoff of &lt;2 had optimal operating characteristics for predicting infectious complications during neutropenia. Although 56 patients received therapy &gt;72 hours with a carbapenem, none of the patients had an infection with an extended spectrum β-lactamase–producing organism. Patients who received carbapenems for &gt;72 hours had significantly lower α-diversity at neutrophil recovery (P = .001) and were approximately 4 times more likely to have infection in the 90 days following neutrophil recovery (HR, 4.55; 95% CI, 1.73–11.93).ConclusionsOur results suggest that gut microbiome evaluation could assist with infectious risk stratification and that improved targeting of antibiotic administration during IC could decrease subsequent infectious complications in AML patients.Baseline microbiome diversity is a strong independent predictor of infection during acute myeloid leukemia induction chemotherapy (IC) among clinical and microbiome covariates. Higher baseline levels of Porphyromonadaceae appear protective against infection, while carbapenem use is associated with consequences to the microbiome and infection susceptibility post-IC.
Impact of a Multidisciplinary eBoard on the Management of Patients With Complex Inflammatory Bowel Disease
Authors: Quinn Kevin P , Prothero Breanne L , Russell Jennifer M , Hegge Ryan J , von Bormann Alexander G , Larson Putchalee A , Christofferson Sara N , Smyrk Thomas C , Mathis Kellie L , Goenka Ajit H , Sheedy Shannon P , Bruining David H , Fletcher Joel G , Loftus Edward V , Raffals Laura E 
Published: August 2019

Abstract

Background
We aim to assess the impact of a multidisciplinary inflammatory bowel disease (IBD) conference on the management of patients with complex IBD.

Methods
Data were collected during each conference from February 2017 through October 2018 with chart review performed at 6 months to determine if conference recommendations were successfully implemented.

Results
Eighty-five patients were discussed. The presenting diagnosis was changed by 11.8%. Recommendations for further testing, medical therapy, and surgery were successfully implemented in 77.1%, 98.1%, and 88.4%, respectively.

Conclusions
This study supports the role of IBD multidisciplinary conferences in the management of patients with complex IBD.
Diagnosis and management of left atrial appendage thrombus in patients with atrial fibrillation undergoing cardioversion or percutaneous left atrial procedures: results of the European Heart Rhythm Association survey
Authors: Farkowski Michal M , Jubele Kristine , Marín Francisco , Gandjbakhch Estelle , Ptaszynski Pawel , Merino Jose L , Lenarczyk Radoslaw , Potpara Tatjana S 
Published: August 2019

Abstract
Practices regarding indications and timing for transoesophageal echocardiography (TOE) before cardioversion (CV) of atrial fibrillation (AF) or left atrial (LA) interventional procedures, and preferred imaging techniques and pharmacotherapy, in cases of thrombus resistant to chronic oral anticoagulation (OAC) treatment, are largely unknown. The European Heart Rhythm Association (EHRA) conducted a survey to capture contemporary clinical practice in those areas of AF care. A 22-item online questionnaire was developed and distributed among the EHRA electrophysiology research network centres. The survey contained questions regarding indications, type and timing of imaging before CV or LA procedures and management of LA appendage (LAA) thrombus with special emphasis on thrombus resistant to OAC. Of 54 responding centres 63% were university hospitals. Most commonly, TOE would be performed in cases of inadequate or unclear pre-procedural anticoagulation, even in AF lasting &lt;48 h (52% and 50%, respectively), and 15% of centres would perform TOE before AF ablation in all patients. If thrombus was diagnosed despite chronic OAC, the prevalent strategy was to change current OAC to another with different mechanism of action; 51% of centres would wait 3–4 weeks after changing the OAC before using another imaging test, and 60% of centres reported two attempts to dissolve the thrombus. Our survey showed a significant utilization of TOE before CV or AF ablation in European centres, extending beyond AF guidelines-suggested indications. When thrombus was diagnosed despite chronic pre-procedural OAC, most centres would use another anticoagulant drug with different mode of action.
Vision-Based Assessment of Gait Features Associated With Falls in People With Dementia
Authors: Mehdizadeh Sina , Dolatabadi Elham , Ng Kimberley-Dale , Mansfield Avril , Flint Alastair , Taati Babak , Iaboni Andrea 
Published: August 2019

Abstract

Background
Gait impairments contribute to falls in people with dementia. In this study, we used a vision-based system to record episodes of walking over a 2-week period as participants moved naturally around their environment, and from these calculated spatiotemporal, stability, symmetry, and acceleration gait features. The aim of this study was to determine whether features of gait extracted from a vision-based system are associated with falls, and which of these features are most strongly associated with falling.

Methods
Fifty-two people with dementia admitted to a specialized dementia unit participated in this study. Thirty different features describing baseline gait were extracted from Kinect recordings of natural gait over a 2-week period. Baseline clinical and demographic measures were collected, and falls were tracked throughout the participants’ admission.

Results
A total of 1,744 gait episodes were recorded (mean 33.5 ± 23.0 per participant) over a 2-week baseline period. There were a total of 78 falls during the study period (range 0–10). In single variable analyses, the estimated lateral margin of stability, step width, and step time variability were significantly associated with the number of falls during admission. In a multivariate model controlling for clinical and demographic variables, the estimated lateral margin of stability (p = .01) was remained associated with number of falls.

Conclusions
Information about gait can be extracted from vision-based recordings of natural walking. In particular, the lateral margin of stability, a measure of lateral gait stability, is an important marker of short-term falls risk.
Prevalence of American Heart Association defined ideal cardiovascular health metrics in Nepal: findings from a nationally representative cross-sectional study
Authors: Ghimire Umesh , Shrestha Nipun , Gyawali Bishal , Pradhan Pranil Man Singh , Mishra Shiva Raj 
Published: August 2019

Abstract

Background
The ever-increasing burden of non-communicable diseases (NCDs) is posing a serious health challenge for Nepal. This study examines the status of ideal cardiovascular health (ICH) and its associated determinants in Nepal using the American Heart Association (AHA) definition of ICH metrics.

Methods
The AHA has defined ICH as having five to seven of the ideal health metrics. A representative sample from the NCD risk factors STEPS survey 2013 were drawn to analyse the prevalence and sociodemographic determinants of ideal, intermediate and poor cardiovascular health in Nepal. Multivariable logistic regression was used to measure the determinants of ICH.

Results
More than half of the participants had ICH metrics (51.6%), with the 45–69 y age group having the lowest prevalence of ICH (28%) and females having better cardiovascular health compared with their male counterparts (60.6% vs 41.7%). The prevalence of low intake of fruit and vegetables, tobacco smoking and elevated blood pressure were quite high (99%, 18.8% and 31.4%, respectively). The status of ICH declined with age: individuals 15–29 y of age had 6 times (95% confidence interval [CI] 4.80–8.60) higher odds of having ICH compared with those who were 45–69 y, and it was low among urban residents (referent: rural; adjusted odds ratio 0.77 [95% CI 0.58–1.01]).

Conclusions
Nearly half of the participants had ICH, which declined with ageing. Further, urban residents had poor cardiovascular health. This highlights the need for a comprehensive population-based intervention targeting elderly and urban residents to improve overall cardiovascular health.
Variability of the HIV-1 3′ polypurine tract (3′PPT) region and implication in integrase inhibitor resistance
Authors: Malet Isabelle , Delelis Olivier , Nguyen Thuy , Leducq Valentin , Abdi Besma , Morand-Joubert Laurence , Calvez Vincent , Marcelin Anne-Geneviève 
Published: August 2019

Abstract

Background
Integrase strand-transfer inhibitors (INSTIs) are efficient at impairing retroviral integration, which is a critical step in HIV-1 replication. To date, resistance to these compounds has been explained by mutations in the viral protein integrase, which catalyses the integration step. Recently, it has been shown that selected mutations in the 3′ polypurine tract (3′PPT), a sequence involved in the reverse transcription mechanism, result in high-level resistance to these compounds. This observation was reinforced by the description of a patient who failed INSTI treatment by selecting mutations in the 3′PPT sequence.

Methods
Sequences of the 3′PPT region were analysed in 30706 treatment-naive patients from the public Los Alamos database belonging to six different subtypes and, in parallel, in 107 patients failing INSTI treatment.

Results
The analysis showed that the sequences of patients failing INSTI treatment, in the same way as those of treatment-naive patients, are very well conserved regardless of the presence or absence of resistance mutations in the integrase gene.

Conclusions
This study confirms that the selection of a mutation in the 3′PPT region conferring high-level resistance to INSTIs is a rare event. It would require a particular in vivo context and especially a long enough time to be selected, this exposure time being generally reduced by the rapid change of treatment in the case of virological failure. Larger-scale studies in patients with INSTI treatment failure are needed to determine whether the 3′PPT region can play an important role in vivo in INSTI resistance.
The corresponding relationship between the change of goaf pressure and the key stratum breaking
Authors: Xie Jianlin , Xu Jialin 
Published: August 2019

Abstract
Existing studies mostly focus on the stress change of coal in front of a goaf, but rarely conduct field monitoring on the internal pressure of a goaf, primarily due to the complex environment and other restrictive conditions of goafs. This paper first used physical simulation to monitor and analyze the internal pressure of goaf and found that goaf pressure presented a stepwise growth with the key stratum breaking. In addition, field measurements were conducted to monitor the goaf pressures of two different working faces. Goaf pressures both presented linear growth with the advance of the working face. According to comparative analysis, there were some differences between the two monitoring methods in terms of the corresponding relationship. This reflects that in the actual rock mass, after the breaking of a key stratum, the loads of the strata under its control are not transferred to the goaf instantaneously and load transfer characteristics are probably related to roof separation distribution characteristics of overlying strata, the bulking characteristics of caved rock mass, lateral stress limitation and other factors. The results of this study will offer some guidance for studies on the movement laws of overlying strata and the load transfer of overlying strata above goafs.
A parallel electric field penetration technique for identifying hazardous water sources beneath coal seam mining face floors
Authors: Hu Xiongwu , Meng Dangdang , Luo Bin , Zhang Pingsong , Wu Rongxin 
Published: August 2019

Abstract
In this work, a highly applicable multi-channel parallel electric field penetration technique is proposed to facilitate identification of hazardous water sources beneath coal seam mining face floors. The effects of various parameters on the characteristics of the apparent resistivity curves of a spherical model were analyzed through numerical simulation. It was determined that the proposed technique was sensitive to several model parameters (resistivity, size and spatial location). In addition, physical model experiments were also performed. Resistivity was determined from a three-dimensional inversion of the measurements. The results showed that the proposed technique was highly effective in determining the electrical characteristics and spatial distribution range of the anomalous bodies in the physical model. An engineering application of the proposed technique further demonstrated its effectiveness and reliability. The proposed technique can provide a basis for formulating water disaster prevention and control measures for mining faces.
The mechanical behaviour of rock specimens with specific edge crack distributions under triaxial loading conditions
Authors: Duan Guoyong , Li Jianlin , Zhang Jingyu , Luo Zuosen , Wan Liangpeng , Li Bing 
Published: August 2019

Abstract
Research on the mechanical behaviour of rock masses with multiple joints has become a popular topic and has practical applications in natural slope stability. This paper aims to clarify the influence of joint geometry, joint orientation and joint connectivity ratio on the mechanical behaviour of rock specimens containing two pre-existing joints. Triaxial compression tests were conducted under various confining pressures to simulate the variation in external conditions. An exponential criterion was used to describe the relationship between the axial stress and confining pressure. The experimental crack propagation was explored by varying the joint orientation, joint connectivity ratio and confining pressure. The structural plane with a greater angle of inclination controlled the failure of the rock sample. Two failure patterns were observed under the loading conditions: shear failure and mixed failure. The failure surface trajectory presented similar deviations with the increase in joint inclination angle, joint connectivity ratio and confining pressure, which also accelerates the transition from mixed failure to shear failure. The experimental results highlight the significance of elucidating the influence of structural planes in practical engineering to predict the stability of natural slopes.