bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparisons of the antibody repertoires of a humanized rodent and humans by high throughput sequencing
Authors: Joyce Collin , Burton Dennis R. , Briney Bryan 
Published: September 2019

ABSTRACTThe humanization of animal model immune systems by genetic engineering has shown great promise for antibody discovery, tolerance studies and for the evaluation of vaccines. Assessment of the baseline antibody repertoire of unimmunized model animals will be useful as a benchmark for future immunization experiments. We characterized the heavy chain and kappa chain antibody repertoires of a model animal, the OmniRat, by high throughput antibody sequencing and made use of two novel datasets for comparison to human repertoires. Intra-animal and inter-animal repertoire comparisons reveal a high level of conservation in antibody diversity between the lymph node and spleen and between members of the species. Multiple differences were found in both the heavy and kappa chain repertoires between OmniRats and humans including gene segment usage, CDR3 length distributions, class switch recombination, somatic hypermutation levels and in features of V(D)J recombination. The Inference and Generation of Repertoires (IGoR) software tool was used to model recombination in VH regions which allowed for the quantification of some of these differences. Diversity estimates of the OmniRat heavy chain repertoires almost reached that of humans, around two orders of magnitude less. Despite variation between the species repertoires, a high frequency of OmniRat clonotypes were also found in the human repertoire. These data give insights into the development and selection of humanized animal antibodies and provide actionable information for use in vaccine studies.
Neutrophil-mediated dynamic capillary stalls in ischemic penumbra: persistent traffic jams after reperfusion contribute to injury
Authors: Erdener Şefik Evren , Tang Jianbo , Kılıç Kıvılcım , Postnov Dmitry , Giblin John Thomas , Kura Sreekanth , Chen I-chun Anderson , Vayisoğlu Tuğberk , Sakadžić Sava , Schaffer Chris B. , Boas David A. 
Published: September 2019

AbstractEver since the introduction of thrombolysis and the subsequent expansion of endovascular treatments for acute ischemic stroke, it remains to be identified why the actual outcomes are less favorable despite recanalization. Here, by high spatio-temporal resolution imaging of capillary circulation in mice, we introduce the pathological phenomenon of dynamic flow stalls in cerebral capillaries, occurring persistently in the salvageable penumbra after recanalization. These stalls, which are distinct from permanent cellular plugs that can lead to no-flow, were temporarily and repetitively occurring in the capillary network, impairing the overall circulation like small focal traffic jams. In vivo microscopy in the ischemic penumbra revealed leukocytes traveling through capillary lumen or getting stuck, while red blood cell flow was being disturbed in the neighboring segments, within 3 hours after stroke onset. Stall dynamics could be modulated, by injection of an anti-Ly6G antibody specifically targeting neutrophils. By decreasing the number and duration of stalls, we were able to improve the blood flow in the penumbra within 2-24 hours after reperfusion, increase capillary oxygenation, decrease cellular damage and improve functional outcome. Thereby the dynamic microcirculatory stall phenomenon contributes to the ongoing penumbral injury and is a potential hyperacute stage mechanism adding on previous observations of detrimental effects of activated neutrophils in ischemic stroke.SignificanceThis work provides in vivo evidence that, even in perfused capillaries, abnormal capillary flow patterns in the form of dynamic stalls can contribute to ongoing tissue injury in the salvageable penumbra in very early hours of cerebral ischemia. These events resembling micro traffic jams in a complex road network, are mediated by passage of neutrophils through the microcirculation and persist despite recanalization of the occluded artery.
Adiponectin and related C1q/TNF-related proteins bind selectively to anionic phospholipids and sphingolipids
Authors: Ye Jessica , Bian Xin , Lim Jaechul , Medzhitov Ruslan 
Published: September 2019

ABSTRACTAdiponectin (also known as Acrp30) is a well-known adipokine associated with protection from cardiovascular disease, insulin resistance, and inflammation. Though multiple studies have investigated the mechanism of action of adiponectin and its relationship with tissue ceramide levels, several aspects of adiponectin biology remain unexplained, including its high circulating levels, tendency to oligomerize, and marked structural similarity to the opsonin C1q. Given the connection between adiponectin and ceramide metabolism, and the lipid-binding properties of C1q, we hypothesized that adiponectin may function as a lipid binding protein. Indeed, we found that recombinant adiponectin bound to various anionic phospholipids and sphingolipids, including phosphatidylserine, ceramide-1-phosphate, and sulfatide. The globular head-domain of adiponectin was necessary and sufficient for lipid binding. Adiponectin oligomerization was also observed to be critical for efficient lipid binding. In addition to lipids in liposomes, adiponectin bound LDL in an oligomerization-dependent manner. Other C1qTNF-related protein (CTRP) family members Cbln1, CTRP1, CTRP5, and CTRP13 also bound similar target lipids in liposomes. These findings suggest that adiponectin and other CTRP family members may not only function as classical hormones, but also as lipid binding opsonins or carrier proteins.
A Structurally-Validated Multiple Sequence Alignment of 497 Human Protein Kinase Domains
Authors: Modi Vivek , Dunbrack Roland L. 
Published: September 2019

AbstractStudies on the structures and functions of individual kinases have been used to understand the biological properties of other kinases that do not yet have experimental structures. The key factor in accurate inference by homology is an accurate sequence alignment. We present a parsimonious, structure-based multiple sequence alignment (MSA) of 497 human protein kinase domains excluding atypical kinases, even those with related but somewhat different folds. The alignment is arranged in 17 blocks of conserved regions and unaligned blocks in between that contain insertions of varying lengths present in only a subset of kinases. The aligned blocks contain well-conserved elements of secondary structure and well-known functional motifs, such as the DFG and HRD motifs. From pairwise, all-against-all alignment of 272 human kinase structures, we estimate the accuracy of our MSA to be 97%. The remaining inaccuracy comes from a few structures with shifted elements of secondary structure, and from the boundaries of aligned and unaligned regions, where compromises need to be made to encompass the majority of kinases. A new phylogeny of the protein kinase domains in the human genome based on our alignment indicates that ten kinases previously labeled as “OTHER” can be confidently placed into the CAMK group. These kinases comprise the Aurora kinases, Polo kinases, and calcium/calmodulin-dependent kinase kinases.
A novel nuclear speckle factor, USP42, promotes homologous recombination repair by resolving DNA double-strand break induced R-loop
Authors: Matsui Misaki , Sakasai Ryo , Abe Masako , Kimura Yusuke , Kajita Shoki , Torii Wakana , Katsuki Yoko , Ishiai Masamichi , Iwabuchi Kuniyoshi , Takata Minoru , Nishi Ryotaro 
Published: September 2019

AbstractThe nucleus of mammalian cells is highly compartmentalized by nuclear bodies, including nuclear speckles. While nuclear bodies are known to function in regulating gene expression, their involvement in DNA repair has not been actively investigated. Here, our focused screen for nuclear speckle factors involved in homologous recombination (HR), which is a faithful DNA double-strand break (DSB) repair mechanism, revealed that nuclear speckle factors regulating transcription are potentially involved in the regulation of HR. Among the top hits, we provide evidence showing that USP42, which is a deubiquitylating enzyme and a hitherto unidentified nuclear speckles factor, promotes HR by facilitating BRCA1 recruitment to DSB sites and DNA-end resection. We further showed that USP42 localizes to nuclear speckles via an intrinsically disordered region, which is required for efficient HR. Furthermore, we established that USP42 interacts with DHX9, which possesses DNA-RNA helicase activity, and is required for efficient resolution of DSB-induced R-loop. Mechanistically, USP42 antagonizes mono-ubiquitylation of DHX9 that is evoked after DSB induction. In conclusion, our data propose a model in which a novel nuclear speckle factor, USP42, facilitates DSB-induced R-loop resolution, BRCA1 loading to DSB sites and preferential DSB repair by HR, indicating the importance of spatial regulation of DSB repair choice mediated by nuclear bodies.Significant statementDefects in the repair of DNA double-strand break (DSB), which is one of the most harmful DNA insults, cause human diseases including cancers. It has been suggested that DSBs generated in the coding region tend to be repaired by homologous recombination (HR) that is error-free DSB repair pathway. To reveal the spatial regulation of HR, in this study, we investigated the potential contribution of nuclear bodies, especially nuclear speckles, to HR, identifying a deubiquitylating enzyme USP42 as a HR promoting factor. We found that USP42 deubiquitylates DHX9, facilitates resolution of DNA-RNA hybrid structure and enhances HR through BRCA1 loading to DSB sites.ClassificationBiological Sciences, Cell Biology
Short paired-end reads trump long single-end reads for expression analysis
Authors: Freedman Adam H. , Gaspar John M. , Sackton Timothy B. 
Published: September 2019

ABSTRACTBackgroundTypical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the additional benefits obtained from paired-end sequencing are not worth the additional cost. However, in many cases (e.g., with Illumina NextSeq and NovaSeq instruments), shorter paired-end reads and longer single-end reads can be generated for the same cost, and it is not obvious which strategy should be preferred. Using publicly available data, we test whether short-paired end reads can achieve more robust expression estimates and differential expression results than single-end reads of approximately the same total number of sequenced bases.ResultsAt both the transcript and gene levels, 2×40 paired-end reads unequivocally provide expression estimates that are more highly correlated with 2×125 than 1×75 reads; in nearly all cases, those correlations are also greater than for 1×125, despite the greater total number of sequenced bases for the latter. Across an array of metrics, differential expression tests based upon 2×40 consistently outperform those using 1×75.ConclusionResearchers seeking a cost-effective approach for gene-level expression analysis should prefer short paired-end reads over a longer single-end strategy. Short paired-end reads will also give reasonably robust expression estimates and differential expression results at the isoform level.
Evaluation of a compact triangular crinkle-shaped multiband antenna with circular polarized for ITU band based on MADM method
Authors: Beigi Payam , Zehforoosh Yashar , Rezvani Mirhamed , Nourinia Javad 
Published: September 2019

Purpose
This paper aims to present a new triangular crinkle-shaped multiband antenna for multiband operation.

Design/methodology/approach
This paper refers to increasing the number of resonance frequency by appending triangular crinkle. Experimental frequency results of the presented antenna are 1.60/2.80/4.00/5.80/7.12/8.32/10.06 GHz.

Findings
The triangular shaped antenna is manufactured on a low-priced FR-4 substrate with small size and tested. The reported antenna with full size 14 × 14 mm2 with a half elliptical ground sheet on the bottom plane of the substrate and a triangular crinkle strip patch in the front of the substrate. The reported antenna has dual polarized, by rectangular slits on the ground sheet can produce the CP radiation on ITU band. The radiation characteristics indicate the mentioned antenna plays good task for multiband structures. Simulation and measured consequences are in desirable agreement and refer to agreeable operation for the introduced antenna.

Originality/value
Also, an evaluation is done based on multiple attribute decision-making method for comparison the proposed monopole antenna with some previously presented multiband monopole antennas.
Employees’ proactive behavior and innovation performance
Authors: Segarra-Ciprés Mercedes , Escrig-Tena Ana , García-Juan Beatriz 
Published: September 2019

PurposeThe purpose of this paper is to analyze the degree to which employees’ proactive behavior contributes to innovation performance in firms operating in high-technology sectors. Despite the benefits of these behaviors for individuals and organizations, few studies have analyzed the contextual conditions that enable firms to capture their value in order to improve innovation performance. Drawing on the interactionist perspective, the authors also examine the extent to which informal and formal controls, such as perceived support for innovation and innovation process formalization, can facilitate the contribution of proactive behaviors to improve innovation performance (product and process innovation).Design/methodology/approachBased on an empirical study with a sample of 173 firms operating in chemical and information technology service sectors, hierarchical regression analysis was used to test the relationship between employees’ proactive behavior and innovation performance, and the moderating effects of informal and formal controls.FindingsThe results reveal a positive and significant association between proactive behaviors and product and process innovation performance. Both control mechanisms positively moderate the association between proactive behavior and product innovation, but no moderating role was found for process innovation. Moreover, rather than inhibiting innovation performance, innovation process formalization is positively associated with innovation. More specifically, a curvilinear relationship was found, which implies that when the level of formalization is high, it is able to improve product and process innovation.Practical implicationsThe findings suggest that managers should consider proactive behavior in selection processes and performance management, and should cultivate a climate to support innovation and establish formal controls for innovation as a way to channel employees’ initiatives into product innovation.Originality/valueThis study contributes to the theoretical and managerial understanding of the extent to which proactive employees and organizational controls are able to enhance innovation in a technologically dynamic context.
Numerical simulation of dissolution of solid particles in fluid flow using the SPH method
Authors: Rahmat Amin , Barigou Mostafa , Alexiadis Alessio 
Published: September 2019

Purpose
The purpose of this paper is to numerically study the dissolution of solid particles using the smoothed particle hydrodynamics (SPH) method.

Design/methodology/approach
To implement dissolution, an advection–diffusion mass transport equation is solved over computational particles. Subsequently, these particles disintegrate from the solute when their concentration falls below a certain threshold.

Findings
It is shown that the implementation of dissolution is in good agreement with available data in the literature. The dissolution of solid particles is studied for a wide range of Reynolds and Schmidt numbers. Two-dimensional (2D) results are compared with three-dimensional (3D) cases to identify where 2D results are accurate for modelling 3D dissolution phenomena.

Originality/value
The present numerical model is capable of addressing related problems in pharmaceutical, biochemical, food processing and detergent industries.
Bungee jumping and rocket launching
Authors: Christie Michael , Simon Susan , Graham Wayne , Call Kairen , Farragher Yvonne 
Published: September 2019

Purpose
A plethora of principal development programs based on myriad leadership theories currently abounds in many educational jurisdictions globally. Today’s principals, consequently and fortuitously, often feel less isolated and better supported that has been indicated in school leadership research over the past two decades. The purpose of this paper is to discover, however, how principals, through well-designed postgraduate study, can effectively become the transformational leaders, schools regularly require of them.

Design/methodology/approach
Action research involving postgraduate leadership students at an Australian university over a two year period, involved three cycles: identification of leadership learning needs, introduction of innovations to their learning and identification of the transformative learning which contributed to their leadership development.

Findings
Transformative learning impacts significantly on transformational leadership development. This happens when disorienting dilemmas challenge and open minds to possibilities, and paradigmatic assumptions are questioned. The ensuing awareness enables leaders to demonstrate characteristics of transformational leadership especially the dimension of individualised consideration.

Originality/value
Few studies have aligned transformative learning with transformational leadership theory, but this paper found that school leaders benefit from transformative learning in their quest to become such a leader. The scariness of a metaphoric principal bungee-jump could ultimately lead to rocket launching of the most transformative kind.
Application of digital technologies in health insurance for social good of bottom of pyramid customers in India
Authors: Nayak Bishwajit , Bhattacharyya Som Sekhar , Krishnamoorthy Bala 
Published: September 2019

Purpose
Social health insurance framework of any country is the national identifier of the country’s policy for taking care of its population which cannot access or afford quality healthcare. The purpose of this paper is to highlight the strategic imperatives of digital technology for the inclusive social health models for the BoP customers.

Design/methodology/approach
A qualitative exploratory study using in-depth personal interviews with 53 Indian health insurance CXOs was conducted with a semi-structured questionnaire. Using MaxQDA software, the interview transcripts were analyzed by means of thematic content analysis technique and patterns identified based on the expert opinions.

Findings
A framework for the strategic imperatives of digital technology in social health insurance emerged from the study highlighting three key themes for technology implementation in the social health insurance sector – analytics for risk management, cost optimization for operations and enhancement of customer experience. The study results provide key insights about how insurers can enhance the coverage of BoP population by leveraging technology.

Social implications
The framework would help health insurers and policymakers to select strategic choices related to technology that would enable creation of inclusive health insurance models for BoP customers.

Originality/value
The absence of specific studies highlighting the strategic digital imperatives in social health insurance creates a unique value proposition for this framework which can help health insurers in developing a convergence in their risk management and customer delight objectives and assist the government in the formulation of a sustainable social health insurance framework.
Understanding the role of social networking platforms in addressing the challenges of Islamic banks
Authors: Naeem Muhammad 
Published: September 2019

PurposeCustomers are increasingly interested in reading discussions, experiences, recommendations and reviews on social media platforms related to services and products in which they are highly interested. The purpose of this paper is to find the availability of user-generated content (UGC) in the context of Islamic banks and how it can enhance the level of brand engagement and purchase intention of customers.Design/methodology/approachThe methodology for this research is designed by following the features of qualitative research methods and a social constructivism approach. Furthermore, non-directive and semi-structured in-depth interviews are constructed to accumulate research data from marketing teams and customers of Islamic banks. The respondents have been carefully chosen on the basis of purposive sampling and their level of awareness related to Islamic banks.FindingsIslamic banks are more frequently using traditional marketing tools that are unable to enhance levels of information among the targeted population and prove an expensive way of marketing. The findings reveal that Islamic banks lag behind in adopting the latest information exchanging technologies compared to conventional banking systems. A lack of skilled people, reputation and trust, lack of e-marketing strategy and lower levels of investment in social media platforms are major barriers to generate UGC, brand engagement and purchase intention among the targeted market of Islamic banks.Practical implicationsThe effective and competent use of various social networking platforms can enhance UGC related to Islamic banking products and services. UGC can generate interactive communication, services reviews, feedbacks, intention to purchase, social influence, social trust and positive customer perception among the targeted population of Islamic banks. The study has summarized and offered practical recommendations to show how Islamic banks can address challenges and enjoy a high level of profitability compared to conventional banking systems.Originality/valueThe present study uncovered the steps that must be taken by the top management of Islamic banks to enhance levels of awareness, online product reviews and recommendations, e-word of mouth and purchase intentions of the targeted market. The study enhanced understanding regarding how a higher level of investment in social networking platforms, safe and secure banking systems and skilled IT professionals can address the challenges of Islamic banks. Furthermore, these factors can create positive UGC, social influence, social brand engagement and purchase intention of customers in Islamic banks. These primary factors must be considered by Islamic banks to compete with conventional banking products and services.
Structure and catalytic performance of Zn-doped TiO2 film
Authors: Yang Mei , Huang Tingyu , Tang Ning , Ou Ben , Zhang Wenhao 
Published: September 2019

Purpose
This paper aims to investigate the photocatalytic activity of zinc doped MAO-TiO2 films under the optimum MAO treatment condition.

Design/methodology/approach
The coating was prepared by micro arc oxidation, and the influence of doping on the properties of the coating was also investigated.

Findings
The results show that the BET surface area is 78.25±0.03m2/g, total pore area is 76.32 ± 0.04m2/g, and the total pore volume is 0.2135 ± 0.0004cm3/g. The degradation ratio of the film electrode with Zn-doped in methyl orange solution is up to 94%. When the react circles is 10 times, the degradation ratio is up to more than 85% and remains steady. With the different reaction conditions, these kinetics of the reactions show some different formulas.

Originality/value
A kinetic equation for photocatalytic activity is established.