bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of Home-Based Exercise Rehabilitation on Functional Capacity in Patients With Acute Ischemic Stroke: A Randomized Controlled Trial
Authors: Saadatnia Mohammad , Shahnazi Hossein , Khorvash Fariborz , Esteki-Ghashghaei Fatemeh
Published: December 2019

One of the major consequences of stroke impairments is hemiparesis, which affects activities of daily living and contributes sedentary lifestyle. The purpose of this study was evaluation of the effectiveness of home-based exercise rehabilitation incentive on daily living activities and functional capacity among acute ischemic patients. This randomized controlled trial was done from August 2017 to September 2018. Iranian subjects with unilateral ischemic stroke were recruited from inpatient wards at educational hospital. Patients were randomly assigned to the home-based rehabilitation program (intervention group) or usual care (control group). National Institute of Health Stroke Scale (NIHSS), Barthel Index Score (BI), Modified Rankin Scale (MRS), and Fugl-Meyer Upper and Lower Extremity Sensorimotor Score were evaluated in both groups at baseline and 3 months later. Intervention group received home-based rehabilitation exercise program for 3 months. Control group did not receive home-based rehabilitation program and incentive telephone call. All data were collected and analyzed by SPSS software (Version 20.0; SPSS Inc., Chicago, Illinois) using chi-square test to compare demographic variables, and independent and paired t-tests to between- and within-group assessment, respectively. Forty ischemic stroke patients (20 intervention group and 20 control group) were examined. Results showed BI, Fugl-Meyer Upper and Lower Extremity Score, and MRS score in the interventional group were significantly higher than the control group after 3-month home-based exercise rehabilitation ( p < .001). Providing a home rehabilitation program in this study resulted in a motor recovery on ischemic stroke survivors in the acute phase of recovery. This was assumed to be cost-effective intervention in low-income countries
Customer Engagement and its Outcomes: The Cross-Level Effect of Service Environment and Brand Equity
Authors: Ou Juanjuan , Wong IpKin Anthony , Prentice Catherine , Liu Matthew Tingchi
Published: December 2019

This research seeks to address a void in the literature by exploring both individual and organizational attributes that associate with customer engagement. At the individual level, it builds a chain of relationship leading from customer engagement to attitudinal and behavioral loyalties through impulsive behaviors; and at the organizational level, it purports a cross-level influence from the service environment and brand equity on this relationship chain. Drawing on two independent surveys, results reveal that the service environment emanates direct and moderating effects on customer engagement, while brand equity exerts moderating effects only on certain loyalty attributes. The proposed model thus offers new insights into how research could synthesize both individual and organizational factors, thus enabling better understanding of the role of customer engagement.
Relationship of arteriovenous fistula stenosis and thrombosis with the platelet–lymphocyte ratio in hemodialysis patients
Authors: Sarioglu Orkun , Capar Ahmet Ergin , Belet Umit
Published: December 2019

Background:

The platelet–lymphocyte ratio, which was reported to have a strong relationship with chronic inflammation and thrombosis, is a useful biomarker. The purpose of this study was to evaluate the relationship between the platelet–lymphocyte ratio, arteriovenous stenosis, and thrombosis in patients with chronic renal failure.

Methods:

Patients who were referred to our interventional radiology department due to arteriovenous fistula dysfunction from dialysis units between August 2015 and December 2018 were retrospectively reviewed. In the study, 95 patients with arteriovenous fistula access problems were included. Patients were divided into two groups: stenosis ( n = 52) and thrombosis ( n = 43). Thirty-six subjects with a patent left radiocephalic arteriovenous fistula proven by both color Doppler ultrasonography and clinically were added to the control group. Blood samples were obtained on the same day before the fistulography.

Results:

Platelet counts, lymphocyte counts, and platelet–lymphocyte ratio were found to be significantly different between the three groups. After the Bonferroni post hoc analysis, there was a significant difference between the stenosis and control group ( p = 0.017), and the thrombosis and control group ( p < 0.001) in terms of the platelet–lymphocyte ratio. No significant difference for any parameter was found between stenosis and thrombosis group.

Conclusion:

High levels of the platelet–lymphocyte ratio may be a supportive finding of arteriovenous fistula stenosis and thrombosis and can be taken into consideration during hemodialysis-dependent patients’ follow-up.
Unusual Cause of Dysphagia in a Patient With Cervical Spondylosis
Authors: Chu Eric Chun Pu , Shum John Sing Fai , Lin Andy Fu Chieh
Published: December 2019

A variety of age-related problems, including salivary secretory disorders, poor oral motor coordination, neuromuscular weakness, neurodegenerative diseases, stroke, and structural changes, can result in swallowing disorders. Given that causes of dysphagia differ from patient to patient, individualized treatment plans tailored toward patients’ specific conditions are needed. Here we present a case of an elderly woman with upper neck stiffness and dysphagia sought chiropractic treatment. Radiographic findings suggested cervical spondylosis with a vertical atlantoaxial subluxation. Following 20 sessions of chiropractic treatment, the patient experienced complete relief from neck problems and difficulty in swallowing. Rhythmic swallowing movements are controlled by a central pattern-generating circuit of the brain stem. In this case, the brain stem could have been compressed by the odontoid process of the axis due to C1/2 instability. Cervicogenic dysphagia is a cervical cause of difficulty in swallowing. Cervical complaints in the context of dysphagia are mostly under-estimated. A high degree of clinical suspicion is pivotal in timely intervention.
A literature review of current technologies on health data integration for patient-centered health management
Authors: Peng Cong , Goswami Prashant , Bai Guohua
Published: December 2019

Health data integration enables a collaborative utilization of data across different systems. It not only provides a comprehensive view of a patient’s health but can also potentially cope with challenges faced by the current healthcare system. In this literature review, we investigated the existing work on heterogeneous health data integration as well as the methods of utilizing the integrated health data. Our search was narrowed down to 32 articles for analysis. The integration approaches in the reviewed articles were classified into three classifications, and the utilization approaches were classified into five classifications. The topic of health data integration is still under debate and problems are far from being resolved. This review suggests the need for a more efficient way to invoke the various services for aggregating health data, as well as a more effective way to integrate the aggregated health data for supporting collaborative utilization. We have found that the combination of Web Application Programming Interface and Semantic Web technologies has the potential to cope with the challenges based on our analysis of the review result.
Stretchable strain sensor based on conductive polymer for structural health monitoring of high-speed train head
Authors: Cheng Xiao , Bao Chongzhi , Wang Xiaoming , Dong Wentao
Published: December 2019

Stretchable strain sensor has been widely applied to structural health monitor in the aerospace, high-speed train, wear electronics, and civil engineering areas. Stretchable strain sensor based on PDMS-CB (polydimethylsiloxane carbon-black) conductive polymer with large deformability is designed to collect the structural health data of the curved surface of high-speed train head (HSTH). The stretchability (>30%) of the strain sensor is validated by the FEM simulation and experimental results. Temperature effect and fatigue analysis of PDMS-CB strain sensors are considered to compensate the accuracy of strain data. The stretchable strain sensor has been applied to detect the cracks of the curved surface via the variable strain data corresponding to the crack length. A structural health monitor (SHM) based on the PDMS-CB strain sensor array is built to collect the continuous long-term strain data of the curved surface of HSTH. Wind pressure is applied to the strain sensor onto the curved surface of HSTH as external signal to simulate the strain distribution. It has been demonstrated that the PDMS-CB strain sensor is applied to structural health monitor of HSTH effectively during the driving process.
Marriage in the ruins of war: Intergenerational hauntings in the Afghan diaspora
Authors: Rytter Mikkel , Nielsen Andreas G
Published: December 2019

Marriage is a central life event and vital conjuncture in which the life trajectories and histories of two individuals and their respective families intersect. When the upcoming generation of Afghan refugees residing in Denmark marry, they often realise that the conflict, war and atrocities of the past seem to reappear and are expressed in different ways within and between the families. In this respect, Afghan families are haunted by the past. In this article, partner choice and marriage are used as prisms through which to explore how turbulent pasts and possible futures are articulated, negotiated and contested in the context of migration. Furthermore, the concept of ‘everyday diplomacy’ is suggested as a way to grasp how families negotiate who they are and where they come from. An ability and willingness to articulate new identities and place/perspectives might become a way to deal with the ghosts of memory and hauntings from the past.
Action research as sustainable healthcare quality improvement: Advances in neonatal care emphasising collaboration, communication and empowerment
Authors: Van Heerden Carlien , Janse van Rensburg Elsie S , Maree Carin
Published: December 2019

Neonatal resuscitation can save newborn lives when performed by competent staff in a setting that is adequately equipped and organised. To develop strategies to sustain quality improvement in neonatal resuscitation, an initiative was launched in a maternity section of a district hospital in Gauteng, South Africa, using Piggot-Irvine’s Problem Resolving Action Research model. The application of the Problem Resolving Action Research model, using multiple data collection and analysis techniques in three cycles, facilitated improvement and transformation towards sustainable changes related to neonatal resuscitation in the specific context. The changes included development of policies, improved infrastructure, enhanced teamwork and collaboration, empowerment and professional development of staff, and integrating theory in neonatal practice. The outcomes resulted in improved staff competency and reduced neonatal mortality and morbidity in the particular setting.
Facile development of electrically conductive comfortable fabrics using metal ions
Authors: Abou Taleb Marwa , Mowafi Salwa , El-Sayed Hosam , El-Newashy Rania
Published: December 2019

Development of conductive fabrics causes usually deterioration of the some of the comfort attributes of the final textile product. In this work, we propose a simple non-deteriorative method for preparation of electrical conductive fabrics based on wool and polyester as well as the blended fabric thereof. The unmodified fabrics or saponified polyester or oxidized wool were treated in aqueous solution containing heavy metal ion salts, namely, silver nitrate, copper II sulfate using exhaustion technique at 70°C for 1 h followed by reduction step. Nano zinc oxide was also used directly for treatment on the said fabrics. The electrical conductivity of the metal ions-treated fabrics and the influence of sewing on their conductivity was measured. The effect of pretreatment of the fabrics, saponification of polyester or oxidation of wool on their ability to absorb metal ions was monitored. Scanning electron microscopy and energy dispersive X-ray spectroscopy were used to prove the incorporation of metal particles onto the treated fabrics. The change in chemical composition of the treated fabrics was studied using Fourier transform infrared spectroscopy. Atomic absorption was adopted to measure the amount of metal incorporated onto the treated fabrics. The formation of nanometal crystals was proved using X-ray diffraction pattern. Different parameters of comfort, namely, air/water permeability of the treated as well as untreated fabrics were assessed. The treated fabrics exhibit enhanced electrical conductivity as well as some improved comfort properties without any effect on their inherent mechanical properties.
Use CT Imaging to Predict the Short-Term Outcome of Concurrent Chemoradiotherapy in Patients With Locally Advanced Esophageal Squamous Cell Carcinoma
Authors: Cao Xiaolan , Li Xindi , Wang Xiaoyue , Duan Jinghao , Zhu Shouhui , Zeng Haiyan , Yin Yong , Yuan Shuanghu , Hu Xudong
Published: December 2019

Objective:

To extract the computed tomography (CT) imaging features of the primary lesions in patients with advanced esophageal squamous cell carcinoma (ESCC) and to study whether these imaging features can predict the short-term outcome after concurrent chemoradiotherapy (CCRT).

Methods:

From January 2014 to December 2015, a total of 49 patients with locally advanced ESCC who underwent CCRT were analyzed retrospectively. They were randomly categorized into the training and validation groups. Collection of CT imaging of patients before and intermediate stage undergoing radiotherapy. The correlations between imaging characteristics and short-term outcome were analyzed. The accuracy of cutoff value was verified by imaging characteristics of patients in validation group.

Result:

There were 38 patients in the training group and 11 patients in the validation group. 13 patients in the training group were classified as responders and 25 patients as nonresponders. According to the CT imaging before radiotherapy, there are no significant differences between responders and nonresponders. According to the CT imaging in the middle stage of radiotherapy, responders showed significantly higher Roundness than nonresponders ( P = .004, 95% confidence interval [CI] = 0.0419-0.212). The areas under the ROC curves for the ability to predict significantly tumor response were 0.768 for Roundness ( P = .001, 95% CI = 0.603-0.889). The cutoff value of Roundness is 0.3099. Roundness showed no significant associations with survival parameters.

Conclusions:

Computed tomography imaging in the middle stage of radiotherapy can predict the short-term outcome of concurrent chemoradiotherapy for patients with locally advanced ESCC but have no predictive effect on the total survival time.
Coupled simulation of elastohydrodynamics and multi-flexible body dynamics in piston-lubrication system
Authors: Kim Seongsu , Choi Juhwan , Kim Jin-Gyun , Hatakeyama Ryo , Kuribara Hiroshi , Choi Jin Hwan
Published: December 2019

In this work, we propose a robust modeling and analysis technique of the piston-lubrication system considering fluid–structure interaction. The proposed schemes are based on combining the elastohydrodynamic analysis and multi-flexible body dynamics. In particular, multi-flexible body dynamics analysis can offer highly precise numerical results regarding nonlinear deformation of the piston skirt and cylinder bore, which can lead to more accurate results of film thickness for gaps filled with lubricant and of relative velocity of facing surfaces between the piston skirt and the cylinder block. These dynamic analysis results are also used in the elastohydrodynamic analysis to compute the oil film pressure and asperity contact pressure that are used as external forces to evaluate the dynamic motions of the flexible bodies. A series of processes are repeated to accurately predict the lubrication characteristics such as the clearance and oil film pressure. In addition, the Craig–Bampton modal reduction, which is a standard type of component mode synthesis, is employed to accelerate the computational speed. The performance of the proposed modeling schemes implemented in the RecurDyn™ multi-flexible body dynamics environment is demonstrated using a well-established numerical example, and the proposed simulation methods are also verified with the experimental results in a motor cycle engine (gasoline) which has a four cycle, single cylinder, overhead camshaft (OHC), air cooled.
Passenger car equivalents for urban roads using average time headway of car following conditions
Authors: Li Hongwei , Zhou Yunyue , Li Sulan , Zhu Hongwei
Published: December 2019

Passenger car equivalents are used to calculate capacity and evaluate service level of urban roads. This article uses the average time headway of different car following conditions to replace the total average time headway of road vehicles, and the proportion of large vehicles to improve the headway method. This article analyzes the influence of several factors such as the proportion of large vehicles, road attributes, and traffic flow on passenger car equivalents, and obtains the following conclusions: (1) the behavior of vehicles crossing the opposite lanes has an important influence on the passenger car equivalents of the road; (2) passenger car equivalents of vertical sections at the center of central isolation belt are different from those at the start of the road; (3) the road attributes affect the passenger car equivalents; and (4) the passenger car equivalents of heavy vehicles on roads that allow two-way crossover are less than the specific value, however, the passenger car equivalents of heavy vehicles in the road segment without two-way crossing-line are greater than the specific value.
Modeling and analysis of engagement behavior of one-way clutch with a variable rectangular cross-section torsional spring
Authors: Cao Yuming , Yan Hongzhi , Wang Zhibiao , Cai Mengkai , Wu Shunxin
Published: December 2019

This article presents a study on the transient dynamic responses of engagement process of one-way clutch using variable rectangular cross-section torsional spring, which is usually installed on the end of engine for preventing torque being transmitted back. A 2-degree-of-freedom torsional dynamic model is proposed in this article to study the engagement process of clutch under two conditions. Due to the variation of parameters, the torque transfer of the wrap–spring clutch during engagement is described by a multi-parameter equation. The torque transmitted by clutch during engagement process has been described by two phases, spring expanding and spring locking. Physical parameters of spring determining the torque during expanding are discussed. To verify the model, a dynamic experiment on clutch engagement is conducted.
The Rise of the Second Dominant Party System in India: BJP’s New Social Coalition in 2019
Authors: Chhibber Pradeep , Verma Rahul
Published: December 2019

The social coalition that supported the Bharatiya Janata Party in 2019 mirrored the demographic profile of the Hindu society. The party made substantial gains among the lower castes, the poor, rural voters, and less educated. How did BJP manage to attract these new voters? We argue that the immediate context of 2019 elections along with a profound ideological shift in Indian politics lies at the heart of the BJP’s success. Underpinning the short-term factors of Modi’s popularity, BJP’s organizational advantage, heightened nationalistic sentiments, and expansive welfare politics, a new form of ethno-political majoritarianism delinked from religious Hindu nationalism was key to the party’s ability to attract new voters.
Book review: Devesh Kapur and Milan Vaishnav, eds. Costs of Democracy: Political Finance in India
Authors: Roy Anupama
Published: December 2019

Devesh Kapur and Milan Vaishnav, eds. Costs of Democracy: Political Finance in India. Delhi, India: Oxford University Press. 2018. 324 pages. ₹750. ISBN: 9780199487271.
Understanding User Involvement in Research in Aging and Health
Authors: Iwarsson Susanne , Edberg Anna-Karin , Ivanoff Synneve Dahlin , Hanson Elizabeth , Jönson Håkan , Schmidt Steven
Published: December 2019

User involvement in research is advocated as an avenue for efficient societal developments. In this article, we identify potentials, problems, and challenges related to research on aging and health, and identify and illustrate research priorities using an evolving research program as an example. Involving user representatives in the development phase, the UserAge program engages researchers at four universities in Sweden. The program builds upon previous and ongoing research with user involvement. The goals are to maximize the impact of user involvement, enhance the execution of high-quality research, increase the knowledge about what difference user involvement can make, and evaluate the impact of research about and with user involvement. Taken together and communicated in the international scientific community as well as in a wide range of public arenas, the empirical results, capacity-building, and modeling efforts of UserAge will have an impact not only on the present situation but also on the future.
The impact of a school-based tooth-brushing program on dental caries: a cross-sectional study
Authors: Tashiro Yuri , Nakamura Keiko , Seino Kaoruko , Ochi Shiro , Ishii Hiroshi , Hasegawa Masaru , Kawauchi Yoshimichi , Chiba Mitsuyuki
Published: December 2019

Background

Promotion of oral health in children is recognized as one of the components of health-promoting schools (HPSs). However, few studies have addressed supportive school environments for children’s oral health. This study aimed to evaluate the status of dental caries in school children at HPSs, with the objective of examining the impact of a supportive school environment for oral health, considering the lifestyles of individual children and the socioeconomic characteristics of their communities.

Methods

Data of 2043 5th-grade students in 21 elementary schools in Ichikawa city between 2008 and 2013 were analyzed. Children’s oral health status was evaluated using the decayed, missing, and filled permanent teeth (DMFT) index. A self-reported lifestyle questionnaire, a survey of the school environment promoting tooth-brushing, and community socioeconomic characteristics derived from the National Census data were included in the analyses. Bivariate analyses were conducted to evaluate the children’s DMFT status, and zero-inflated negative binominal (ZINB) regression was used to assess the relationships between DMFT and other variables.

Results

Prevalence of dental caries in the permanent teeth of 5th-grade children (aged 10–11 years) was 33.3%, with a mean DMFT score (± SD) of 0.83 ± 1.50. According to multilevel ZINB regression analysis, children from schools with after-lunch tooth-brushing time showed a higher odds ratio (OR) for excess zero DMFT (OR = 1.47, 95% CI = 1.00–2.15, P = 0.049) as compared to those from schools without it. Neither bivariate analysis nor ZINB model analysis revealed any significant influence of children’s gender or use of a toothpaste with fluoride.

Conclusions

The school-based environment supportive of oral health was significantly associated with a zero DMFT status in children. School-based efforts considering the socioeconomic characteristics of the area warrant attention even with declining prevalence of dental caries.
Benchmarking the PEPOP methods for mimicking discontinuous epitopes
Authors: Demolombe Vincent , de Brevern Alexandre G. , Molina Franck , Lavigne Géraldine , Granier Claude , Moreau Violaine
Published: December 2019

Background

Computational methods provide approaches to identify epitopes in protein Ags to help characterizing potential biomarkers identified by high-throughput genomic or proteomic experiments. PEPOP version 1.0 was developed as an antigenic or immunogenic peptide prediction tool. We have now improved this tool by implementing 32 new methods (PEPOP version 2.0) to guide the choice of peptides that mimic discontinuous epitopes and thus potentially able to replace the cognate protein Ag in its interaction with an Ab. In the present work, we describe these new methods and the benchmarking of their performances.

Results

Benchmarking was carried out by comparing the peptides predicted by the different methods and the corresponding epitopes determined by X-ray crystallography in a dataset of 75 Ag-Ab complexes. The Sensitivity (Se) and Positive Predictive Value (PPV) parameters were used to assess the performance of these methods. The results were compared to that of peptides obtained either by chance or by using the SUPERFICIAL tool, the only available comparable method.

Conclusion

The PEPOP methods were more efficient than, or as much as chance, and 33 of the 34 PEPOP methods performed better than SUPERFICIAL. Overall, “optimized” methods (tools that use the traveling salesman problem approach to design peptides) can predict peptides that best match true epitopes in most cases.
Alignment-free genomic sequence comparison using FCGR and signal processing
Authors: Lichtblau Daniel
Published: December 2019

Background

Alignment-free methods of genomic comparison offer the possibility of scaling to large data sets of nucleotide sequences comprised of several thousand or more base pairs. Such methods can be used for purposes of deducing “nearby” species in a reference data set, or for constructing phylogenetic trees.

Results

We describe one such method that gives quite strong results. We use the Frequency Chaos Game Representation (FCGR) to create images from such sequences, We then reduce dimension, first using a Fourier trig transform, followed by a Singular Values Decomposition (SVD). This gives vectors of modest length. These in turn are used for fast sequence lookup, construction of phylogenetic trees, and classification of virus genomic data. We illustrate the accuracy and scalability of this approach on several benchmark test sets.

Conclusions

The tandem of FCGR and dimension reductions using Fourier-type transforms and SVD provides a powerful approach for alignment-free genomic comparison. Results compare favorably and often surpass best results reported in prior literature. Good scalability is also observed.
Expression analysis of Rab11 during zebrafish embryonic development
Authors: Zhang Haijun , Gao Yu , Qian Peipei , Dong Zhangji , Hao Wenjin , Liu Dong , Duan Xuchu
Published: December 2019

Background

Rab proteins are GTPases responsible for intracellular vesicular trafficking regulation. Rab11 proteins, members of the Rab GTPase family, are known to regulate vesicular recycling during embryonic development. In zebrafish, there are 3 rab11 paralogues, known as rab11a, rab11ba and rab11bb, sharing high identity with each other. However, the expression analysis of rab11 is so far lacking.

Results

Here, by phylogeny analysis, we found the three rab11 genes are highly conserved especially for their GTPase domains. We examined the expression patterns of rab11a, rab11ba and rab11bb using RT-PCR and in situ hybridization. We found that all the three genes were highly enriched in the central nervous system, but in different areas of the brain. Apart from brain, rab11a was also expressed in caudal vein, pronephric duct, proctodeum, pharyngeal arches and digestive duct, rab11ba was detected to express in muscle, and rab11bb was expressed in kidney, fin and spinal cord. Different from rab11a and rab11ba, which both have maternal expressions in embryos, rab11bb only expresses during 24hpf to 96hpf.

Conclusions

Our results suggest that rab11 genes play important but distinct roles in the development of the nervous system in zebrafish. The findings could provide new evidences for better understanding the functions of rab11 in the development of zebrafish embryos.
The geography of evolutionary divergence in the highly endemic avifauna from the Sierra Madre del Sur, Mexico
Authors: Rocha-Méndez Alberto , Sánchez-González Luis A. , González Clementina , Navarro-Sigüenza Adolfo G.
Published: December 2019

Background

Mesoamerica is a remarkable region with a high geological and ecological complexity. Within northern Mesoamerica, the biotic province of the Sierra Madre del Sur (SMS) in southwestern Mexico harbors exceptionally high avian endemism and diversity. Herein, we searched for spatially and temporally concordant phylogeographic patterns, in four bird genera from three distinct avian orders co-distributed across Mesoamerica and investigated their causes through hypothesis testing regarding historical processes. Selected species include endemic and differentiated populations across the montane forests of Mesoamerica, and particularly within the SMS.

Results

We gathered mitochondrial DNA sequences for at least one locus from 177 individuals across all species. We assessed genetic structure, demographic history, and defined a framework for the coalescent simulations used in biogeographic hypothesis testing temporal and spatial co-variance. Our analyses suggested shared phylogeographic breaks in areas corresponding to the SMS populations, and between the main montane systems in Mesoamerica, with the Central Valley of Oaxaca and the Nicaragua Depression being the most frequently shared breaks among analyzed taxa. Nevertheless, dating analyses and divergence patterns observed were consistent with the hypothesis of broad vicariance across Mesoamerica derived from mechanisms operating at distinct times across taxa in the SMS.

Conclusions

Our study provides a framework for understanding the evolutionary origins and historical factors enhancing speciation in well-defined regions within Mesoamerica, indicating that the evolutionary history of extant biota inhabiting montane forests is complex and often idiosyncratic.
Morphology and evolutionary significance of phosphatic otoliths within the inner ears of cartilaginous fishes (Chondrichthyes)
Authors: Schnetz Lisa , Pfaff Cathrin , Libowitzky Eugen , Johanson Zerina , Stepanek Rica , Kriwet Jürgen
Published: December 2019

Background

Chondrichthyans represent a monophyletic group of crown group gnathostomes and are central to our understanding of vertebrate evolution. Like all vertebrates, cartilaginous fishes evolved concretions of material within their inner ears to aid with equilibrium and balance detection. Up to now, these materials have been identified as calcium carbonate-bearing otoconia, which are small bio-crystals consisting of an inorganic mineral and a protein, or otoconial masses (aggregations of otoconia bound by an organic matrix), being significantly different in morphology compared to the singular, polycrystalline otolith structures of bony fishes, which are solidified bio-crystals forming stony masses. Reinvestigation of the morphological and chemical properties of these chondrichthyan otoconia revises our understanding of otolith composition and has implications on the evolution of these characters in both the gnathostome crown group, and cartilaginous fishes in particular.

Results

Dissections ofAmblyraja radiata,Potamotrygon leopoldi, andScyliorhinus canicularevealed three pairs of singular polycrystalline otolith structures with a well-defined morphology within their inner ears, as observed in bony fishes. IR spectroscopy identified the material to be composed of carbonate/collagen-bearing apatite in all taxa. These findings contradict previous hypotheses suggesting these otoconial structures were composed of calcium carbonate in chondrichthyans. A phylogenetic mapping using 37 chondrichthyan taxa further showed that the acquisition of phosphatic otolith structures might be widespread within cartilaginous fishes.

Conclusions

Differences in the size and shape of otoliths between taxa indicate a taxonomic signal within elasmobranchs. Otoliths made of carbonate/collagen-bearing apatite are reported for the first time in chondrichthyans. The intrinsic pathways to form singular, polycrystalline otoliths may represent the plesiomorphic condition for vertebrates but needs further testing. Likewise, the phosphatic composition of otoliths in early vertebrates such as cyclostomes and elasmobranchs is probably closely related to the lack of bony tissue in these groups, supporting a close relationship between skeletal tissue mineralization patterns and chemical otolith composition, underlined by physiological constraints.
Functional mutation allele mining of plant architecture and yield-related agronomic traits and characterization of their effects in wheat
Authors: Guo Huijun , Xiong Hongchun , Xie Yongdun , Zhao Linshu , Gu Jiayu , Zhao Shirong , Ding Yuping , Liu Luxiang
Published: December 2019

Background

Wheat mutant resources with phenotypic variation have been developed in recent years. These mutants might carry favorable mutation alleles, which have the potential to be utilized in the breeding process. Plant architecture and yield-related features are important agronomic traits for wheat breeders and mining favorable alleles of these traits will improve wheat characteristics.

Results

Here we used 190 wheat phenotypic mutants as material and by analyzing their SNP variation and phenotypic data, mutation alleles for plant architecture and yield-related traits were identified, and the genetic effects of these alleles were evaluated. In total, 32 mutation alleles, including three pleiotropic alleles, significantly associated with agronomic traits were identified from the 190 wheat mutant lines. The SNPs were distributed on 12 chromosomes and were associated with plant height (PH), tiller number, flag leaf angle (FLA), thousand grain weight (TGW), and other yield-related traits. Further phenotypic analysis of multiple lines carrying the same mutant allele was performed to determine the effect of the allele on the traits of interest. PH-associated SNPs on chromosomes 2BL, 3BS, 3DL, and 5DL might show additive effects, reducing PH by 10.0 cm to 31.3 cm compared with wild type, which means that these alleles may be favorable for wheat improvement. Only unfavorable mutation alleles that reduced TGW and tiller number were identified. A region on chromosome 5DL with mutation alleles for PH and TGW contained several long ncRNAs, and their sequences shared more than 90% identity with cytokinin oxidase/dehydrogenase genes. Some of the mutation alleles we mined were colocalized with previously reported QTLs or genes while others were novel; these novel alleles could also result in phenotypic variation.

Conclusion

Our results demonstrate that favorable mutation alleles are present in mutant resources, and the region between 409.5 to 419.8 Mb on chromosome 5DL affects wheat plant height and thousand grain weight.
Deep analysis and optimization of CARD antibiotic resistance gene discovery models
Authors: Yao Haobin , Yiu Siu-Ming
Published: December 2019

Background

Identification of antibiotic resistance genes from environmental samples has been a critical sub-domain of gene discovery which is directly connected to human health. However, it is drawing extraordinary attention in recent years and regarded as a severe threat to human health by many institutions around the world. To satisfy the needs for efficient ARG discovery, a series of online antibiotic resistance gene databases have been published. This article will conduct an in-depth analysis of CARD, one of the most widely used ARG databases.

Results

The decision model of CARD is based the alignment score with a single ARG type. We discover the occasions where the model is likely to make false prediction, and then propose an optimization method on top of the current CARD model. The optimization is expected to raise the coherence with BLAST homology relationships and improve the confidence for identification of ARGs using the database.

Conclusions

The absence of public recognized benchmark makes it challenging to evaluate the performance of ARG identification. However, possible wrong predictions and methods for resolving the problem can be inferred by computational analysis of the identification method and the underlying reference sequences. We hope our work can bring insight to the mission of precise ARG type classifications.
ManiNetCluster: a novel manifold learning approach to reveal the functional links between gene networks
Authors: Nguyen Nam D. , Blaby Ian K. , Wang Daifeng
Published: December 2019

Background

The coordination of genomic functions is a critical and complex process across biological systems such as phenotypes or states (e.g., time, disease, organism, environmental perturbation). Understanding how the complexity of genomic function relates to these states remains a challenge. To address this, we have developed a novel computational method, ManiNetCluster, which simultaneously aligns and clusters gene networks (e.g., co-expression) to systematically reveal the links of genomic function between different conditions. Specifically, ManiNetCluster employs manifold learning to uncover and match local and non-linear structures among networks, and identifies cross-network functional links.

Results

We demonstrated that ManiNetCluster better aligns the orthologous genes from their developmental expression profiles across model organisms than state-of-the-art methods (p-value <2.2×10−16). This indicates the potential non-linear interactions of evolutionarily conserved genes across species in development. Furthermore, we applied ManiNetCluster to time series transcriptome data measured in the green alga Chlamydomonas reinhardtii to discover the genomic functions linking various metabolic processes between the light and dark periods of a diurnally cycling culture. We identified a number of genes putatively regulating processes across each lighting regime.

Conclusions

ManiNetCluster provides a novel computational tool to uncover the genes linking various functions from different networks, providing new insight on how gene functions coordinate across different conditions. ManiNetCluster is publicly available as an R package at https://github.com/daifengwanglab/ManiNetCluster.
Cloud accelerated alignment and assembly of full-length single-cell RNA-seq data using Falco
Authors: Yang Andrian , Kishore Abhinav , Phipps Benjamin , Ho Joshua W. K.
Published: December 2019

Background

Read alignment and transcript assembly are the core of RNA-seq analysis for transcript isoform discovery. Nonetheless, current tools are not designed to be scalable for analysis of full-length bulk or single cell RNA-seq (scRNA-seq) data. The previous version of our cloud-based tool Falco only focuses on RNA-seq read counting, but does not allow for more flexible steps such as alignment and read assembly.

Results

The Falco framework can harness the parallel and distributed computing environment in modern cloud platforms to accelerate read alignment and transcript assembly of full-length bulk RNA-seq and scRNA-seq data. There are two new modes in Falco: alignment-only and transcript assembly. In the alignment-only mode, Falco can speed up the alignment process by 2.5–16.4x based on two public scRNA-seq datasets when compared to alignment on a highly optimised standalone computer. Furthermore, it also provides a 10x average speed-up compared to alignment using published cloud-enabled tool for read alignment, Rail-RNA. In the transcript assembly mode, Falco can speed up the transcript assembly process by 1.7–16.5x compared to performing transcript assembly on a highly optimised computer.

Conclusion

Falco is a significantly updated open source big data processing framework that enables scalable and accelerated alignment and assembly of full-length scRNA-seq data on the cloud. The source code can be found athttps://github.com/VCCRI/Falco.
High-level integration of murine intestinal transcriptomics data highlights the importance of the complement system in mucosal homeostasis
Authors: Benis Nirupama , Wells Jerry M. , Smits Mari A. , Kar Soumya Kanti , van der Hee Bart , dos Santos Vitor A. P. Martins , Suarez-Diez Maria , Schokker Dirkjan
Published: December 2019

Background

The mammalian intestine is a complex biological system that exhibits functional plasticity in its response to diverse stimuli to maintain homeostasis. To improve our understanding of this plasticity, we performed a high-level data integration of 14 whole-genome transcriptomics datasets from samples of intestinal mouse mucosa. We used the tool Centrality based Pathway Analysis (CePa), along with information from the Reactome database.

Results

The results show an integrated response of the mouse intestinal mucosa to challenges with agents introduced orally that were expected to perturb homeostasis. We observed that a common set of pathways respond to different stimuli, of which the most reactive was the Regulation of Complement Cascade pathway. Altered expression of the Regulation of Complement Cascade pathway was verified in mouse organoids challenged with different stimuli in vitro.

Conclusions

Results of the integrated transcriptomics analysis and data driven experiment suggest an important role of epithelial production of complement and host complement defence factors in the maintenance of homeostasis.
Amentoflavone ameliorates cold stress-induced inflammation in lung by suppression of C3/BCR/NF-κB pathways
Authors: Cai Jiayi , Zhao Chunyang , Du Yajie , Huang Yuan , Zhao Qingchun
Published: December 2019

Background

Cold stress, which may lead to local and systemic injury, is reported to be related to the immune system, especially the complement system. At present, the lack of effective treatment is a critical issue. Amentoflavone (AF), which can inhibit cold stress-induced inflammation in lung by multiple mechanisms, is the main therapeutic ingredient in plants of the genus Selaginella.

Results

In the current study, we found that cold could induce lung inflammation related to the complement system and its downstream pathways. AF treatment significantly inhibited lung inflammation from cold exposure. We presented evidence that AF can bind to complement component 3 (C3) to regulate inflammation-related pathways involving Lck/Yes novel tyrosine kinase (Lyn), protein kinase B (Akt), nuclear factor-κB (NF-κB) and immune factors. Moreover, 30 mg/kg of AF caused significantly greater improvement than 15 mg/kg in reducing the level of C3 in lung tissue.

Conclusions

AF can protect lung tissue from cold exposure. The protective effect may be achieved by inhibition of C3 and negative regulation of the B cell receptor (BCR)/NF-κB signaling pathways and high mobility group box 1 (HMGB1), which ultimately ameliorates the inflammatory response.
An in vitro collagen perfusion wound biofilm model; with applications for antimicrobial studies and microbial metabolomics
Authors: Slade Elisabeth A. , Thorn Robin M. S. , Young Amber , Reynolds Darren M.
Published: December 2019

Background

The majority of in vitro studies of medically relevant biofilms involve the development of biofilm on an inanimate solid surface. However, infection in vivo consists of biofilm growth on, or suspended within, the semi-solid matrix of the tissue, whereby current models do not effectively simulate the nature of the in vivo environment. This paper describes development of an in vitro method for culturing wound associated microorganisms in a system that combines a semi-solid collagen gel matrix with continuous flow of simulated wound fluid. This enables culture of wound associated reproducible steady state biofilms under conditions that more closely simulate the dynamic wound environment. To demonstrate the use of this model the antimicrobial kinetics of ceftazidime, against both mature and developing Pseudomonas aeruginosa biofilms, was assessed. In addition, we have shown the potential application of this model system for investigating microbial metabolomics by employing selected ion flow tube mass spectrometry (SIFT-MS) to monitor ammonia and hydrogen cyanide production by Pseudomonas aeruginosa biofilms in real-time.

Results

The collagen wound biofilm model facilitates growth of steady-state reproducible Pseudomonas aeruginosa biofilms under wound like conditions. A maximum biofilm density of 1010 cfu slide− 1 was achieved by 30 h of continuous culture and maintained throughout the remainder of the experiment. Treatment with ceftazidime at a clinically relevant dose resulted in a 1.2–1.6 log reduction in biofilm density at 72 h compared to untreated controls. Treatment resulted in loss of complex biofilm architecture and morphological changes to bacterial cells, visualised using confocal microscopy. When monitoring the biofilms using SIFT-MS, ammonia and hydrogen cyanide levels peaked at 12 h at 2273 ppb (±826.4) and 138 ppb (±49.1) respectively and were detectable throughout experimentation.

Conclusions

The collagen wound biofilm model has been developed to facilitate growth of reproducible biofilms under wound-like conditions. We have successfully used this method to: (1) evaluate antimicrobial efficacy and kinetics, clearly demonstrating the development of antimicrobial tolerance in biofilm cultures; (2) characterise volatile metabolite production by P. aeruginosa biofilms, demonstrating the potential use of this method in metabolomics studies.
Primary progressive multiple sclerosis in a Russian cohort: relationship with gut bacterial diversity
Authors: Kozhieva Madina , Naumova Natalia , Alikina Tatiana , Boyko Alexey , Vlassov Valentin , Kabilov Marsel R.
Published: December 2019

Background

Gut microbiota has been increasingly acknowledged to shape significantly human health, contributing to various autoimmune diseases, both intestinal and non-intestinal, including multiple sclerosis (MS). Gut microbiota studies in patients with relapsing remitting MS strongly suggested its possible role in immunoregulation; however, the profile and potential of gut microbiota involvement in patients with primary progressive MS (PPMS) patients has received much less attention due to the rarity of this disease form. We compared the composition and structure of faecal bacterial assemblage using Illumina MiSeq sequencing of V3-V4 hypervariable region of 16S rRNA genes amplicons in patients with primary progressive MS and in the healthy controls.

Results

Over all samples 12 bacterial phyla were identified, containing 21 classes, 25 orders, 54 families, 174 genera and 1256 operational taxonomic units (OTUs). The Firmicutes phylum was found to be ultimately dominating both in OTUs richness (68% of the total bacterial OTU number) and in abundance (71% of the total number of sequence reads), followed by Bacteroidetes (12 and 16%, resp.) and Actinobacteria (7 and 6%, resp.). Summarily in all samples the number of dominant OTUs, i.e. OTUs with ≥1% relative abundance, was 13, representing much less taxonomic richness (three phyla, three classes, four orders, six families and twelve genera) as compared to the total list of identified OTUs and accounting for 30% of the sequence reads number in the healthy cohort and for 23% in the PPMS cohort. Human faecal bacterial diversity profiles were found to differ between PPMS and healthy cohorts at different taxonomic levels in minor or rare taxa. Marked PPMS-associated increase was found in the relative abundance of two dominant OTUs (Gemmiger sp. and an unclassified Ruminococcaceae). The MS-related differences were also found at the level of minor and rare OTUs (101 OTUs). These changes in OTUs’ abundance translated into increased bacterial assemblage diversity in patients.

Conclusion

The findings are important for constructing a more detailed global picture of the primary progressive MS-associated gut microbiota, contributing to better understanding of the disease pathogenesis.