bluuebunny/crossref_metadata_2025 huggingface dataset:
Line-of-sight stabilization of roll-pitch seeker using differentiator-based disturbance compensation control
Authors: Liu Xiao , Mo Bo , Liu Fuxiang
Published: January 2020

A new control problem of roll-pitch seeker about the disturbance coupling is investigated in this work. Previous control strategies of roll-pitch seeker rarely considered the effects of the dynamic coupling disturbances from the missile angular motion, and because of the polar coordinate structure, the disturbance rejection strategies of yaw-pitch seeker cannot be utilized directly on roll-pitch seeker. Thus this article presents a new control strategy to improve the disturbance rejection ability of roll-pitch seeker. To analyze the disturbance coupling problem, the roll-pitch seeker model is derived with consideration of the missile body angular motion and torque disturbances. The motion equation of roll-pitch seeker shows that part of the dynamic coupling disturbance can be eliminated by certain choices of inertial parameters. The rest of disturbance is reduced by the stabilization loops using a differentiator-based disturbance compensation controller. Particularly, a missile body angular acceleration estimation method is designed for the compensator based on an adaptive differentiator. In addition, comparisons with other control strategies are carried out via numerical simulations, and the results confirm the effectiveness of the proposed method.
Transplant outcomes in kidney recipients with lupus nephritis, and systematic review
Authors: Kim J E , Kim Y C , Min S-l , Lee H , Ha J , Chin H J , Kim Y S , Han S S
Published: January 2020

Background

Despite improved survival of patients with lupus nephritis (LN), some require kidney transplantation because of progression to end-stage renal disease (ESRD). However, the transplant outcomes of these patients and other recipients have not been thoroughly compared.

Methods

In total, 1848 Korean kidney recipients who underwent transplantation from 1998 to 2017 at two tertiary referral centers were evaluated retrospectively. Among them, 28 recipients with LN, and 50 control recipients matched by age, sex, and donor type, were compared with respect to graft and patient survival. We pooled our data with 17 previous cohort studies in which the graft survival of recipients with LN was described in detail.

Results

During the median follow-up period of 9.5 years (maximum 21 years), graft failure (GF) occurred in 10.7% and 16.0% of LN and control recipients, respectively. No differences were found in the rates of GF and death-censored graft failure or patient survival between the two groups. The risks of acute T cell-mediated and antibody-mediated rejection were also similar between the two groups. The pooled analysis showed similar 1- and 5-year graft survival rates between LN and control recipients.

Conclusions

Kidney transplantation is an acceptable option in patients with concurrent LN and ESRD.
Rightward Leanings and Nonstandard Party-Position Perceptions
Authors: Urbatsch R.
Published: January 2020

Some individuals defy the consensus as to parties’ relative ideological positions, asserting that a party is more left-leaning than its rivals even when most observers have the opposite view. Such discrepancies undercut spatial models of politics. Rightward leaners’ tendency to use different, more self-anchored, bases for assessing ideology may make them especially likely to dissent in this way, as might their attention to distinct issues. Results from the Comparative Study of Electoral Systems confirm that those on the political right are likelier to reverse typical left-right orderings, even on right-leaning or major parties. Evidence from the Dutch Parliamentary Election Study further shows that right-leaners’ nonstandard ordering extends to parties’ specific issue-positions—particularly, notably, on issues of higher salience to the left. Standard models of politics may accordingly apply less well to those who identify as being on the political right.
Axial Rotational Alignment in Mobile-Bearing Total Ankle Arthroplasty
Authors: Hintermann Beat , Susdorf Roman , Krähenbühl Nicola , Ruiz Roxa
Published: January 2020

Background:

The presence of an interface between the tibial component and the polyethylene insert (PI) in mobile-bearing total ankle arthroplasty (TAA) may allow the talus to adapt its axial position according to the patient’s anatomy. However, little is known about differences of the axial talar rotation between patients following mobile-bearing TAA. Therefore, the aim of this study was to assess the relative axial rotation between the talar and tibial component intraoperatively and after a minimum follow-up of 3 years following mobile-bearing TAA.

Methods:

The relative axial rotation between the talar and the tibial component was measured intraoperatively in a cohort of 58 patients who underwent mobile-bearing TAA. In addition, it was measured on weightbearing computed tomography (CT) scans in 48 patients after a mean of 6.3 (3.0-16.3) years following mobile-bearing TAA. The pre- and postoperative alignment of the ankle joint/tibial component and hindfoot assessed on conventional radiographs was correlated with the intra- and postoperatively determined relative axial rotation of the talar and tibial component.

Results:

The mean intra- and postoperative axial talar component position was 1.7 (range, 14 internal to 14 external) and 1.4 (range, 12 internal to 20 external) degrees toward internal when compared to the tibial component ( P = .960). The preoperative sagittal alignment of the distal tibia correlated with the intraoperatively determined relative axial rotation between the talar and the tibial component ( P = .019).

Conclusion:

The wide range of the relative axial rotation between the tibial and talar component suggests that it is crucial to allow the talus to intraoperatively find a position that corresponds to the patient’s individual anatomy. The fact that the range of axial rotation was similar after a minimum of 3 years measured under weightbearing conditions suggests that structural changes of the osteoarthritic ankle may be the main determining factors for the axial rotational position of the talus. Our findings improve current understanding of proper implant position during TAA. In addition, the current study provides a reliable method to assess the postoperative axial position of the prosthesis components. The high interindividual variability of the relative rotation between the tibial and talar component in the axial plane suggests that axial malpositioning following TAA may be a more common issue than currently expected. Our findings may help to improve the assessment of patients with persistent pain following TAA.

Level of Evidence:

Level III, comparative series.
Three-dimensional static and free vibration analysis of graphene platelet–reinforced porous composite cylindrical shell
Authors: Rahimi Alireza , Alibeigloo Akbar , Safarpour Mehran
Published: January 2020

Because of promoted thermomechanical performance of functionally graded graphene platelet–reinforced composite ultralight porous structural components, this article investigates bending and free vibration behavior of functionally graded graphene platelet–reinforced composite porous cylindrical shell based on the theory of elasticity. Effective elasticity modulus of the composite is estimated with the aid of modified version of Halpin–Tsai micromechanics. Rule of mixtures is used to obtain mass density and Poisson’s ratio of the graphene platelet–reinforced composite shell. An analytical solution is introduced to obtain the natural frequencies and static behavior of simply supported cylindrical shell by applying the state-space technique along the radial coordinate and Fourier series expansion along the circumferential and axial direction. In addition, differential quadrature method is used to explore the response of the cylindrical shell in the other cases of boundary conditions. Validity of the applied approach is examined by comparing the numerical results with those published in the available literature. A comprehensive parametric study is conducted on the effects of different combinations of graphene platelets distribution patterns and porosity distribution patterns, boundary conditions, graphene platelets weight fraction, porosity coefficient, and geometry of the shell (such as mid-radius to thickness ratio and length to mid-radius ratio) on the bending and free vibration behavior of the functionally graded graphene platelet–reinforced composite porous cylindrical shell. The results of this study provide useful practical tips for engineers designing composite structures.
Nonlinear free vibration analysis of delaminated composite circular cylindrical shells
Authors: Kamaloo Abbas , Jabbari Mohsen , Yarmohammad Tooski Mehdi , Javadi Mehrdad
Published: January 2020

This study aims to present an analysis of nonlinear free vibrations of simply supported laminated composite circular cylindrical shells with throughout circumference delamination. Governing equations of motion are derived by applying energy methods; using Galerkin’s method reduced the nonlinear partial differential equations to a system of coupled nonlinear ordinary differential equations, which are subsequently solved using a numerical method. This research examines the effects of delamination on the oscillatory motion of delaminated composite circular cylindrical shells and then the effects of increase in delamination length, shell middle surface radius, number of layers, and orthotropy as changes in material properties on the nonlinearity of these types of shells. The results show that delamination leads to a decrease in frequency of oscillations and displacement. An increase in delamination length, shell middle surface radius, and orthotropy of layers decreases nonlinearity and displacement, whereas an increase in the number of layers increases nonlinearity and displacement. It is also observed that an increase in the circumferential wave number can decrease the effect of delamination.
State Nurse Practitioner Practice Regulations and U.S. Health Care Delivery Outcomes: A Systematic Review
Authors: Yang Bo Kyum , Johantgen Mary E. , Trinkoff Alison M. , Idzik Shannon R. , Wince Jessica , Tomlinson Carissa
Published: January 2020

There is a great variation across states in nurse practitioner (NP) scope of practice moderated by state regulations. The purpose of this study was to synthesize the evidence from studies of the impact of state NP practice regulations on U.S. health care delivery outcomes (e.g., health care workforce, access to care, utilization, care quality, or cost of care), guided by Donabedian’s structure, process, and outcomes framework. This systematic review was performed using Medline, CINAHL, PsycINFO, and PubMed according to Preferred Reporting Items for Systematic and Meta-Analysis on the literature from January 2000 to August 2019. The results indicate that expanded state NP practice regulations were associated with greater NP supply and improved access to care among rural and underserved populations without decreasing care quality. This evidence could provide guidance for policy makers in states with more restrictive NP practice regulations when they consider granting greater practice independence to NPs.
Police Response to Active Shooter Events: How Officers See Their Role
Authors: Phillips Scott W.
Published: January 2020

“Active shooter” incidents and the police response to them receive considerable attention. There is a public expectation that officers should immediately enter active shooter events and engage the suspects. To explore how POLICE view their role in active shooter events, a vignette research design was used to gather opinion data from a convenience sample of police officers in two states. Respondents who evaluated vignettes describing a police officer’s response to an active shooter scenario clearly preferred options other than immediately entering the building. Policy implications and directions for future research are discussed.
Quantum-behaved particle swarm optimization-based active noise control system with timing varying path
Authors: Yu Ning , Li Zhaoxia , Wu Yinfeng , Feng Renjian
Published: January 2020

Active noise control systems can effectively suppress the impact of low-frequency noise and they have been applied in many fields. Recently, the evolutionary computation algorithm-based active noise control system has attracted considerable attention. To improve the noise reduction performance of the evolutionary computation algorithm-based active noise control system and solve the problem that the system cannot converge again when the path abruptly changes in steady state, we propose the path abruptly change-quantum-behaved particle swarm optimization algorithm. We apply quantum-behaved particle swarm optimization, a global optimization algorithm, to the active noise control system to improve noise reduction performance. In addition, the scheme of detecting the abrupt path change in steady state and performing re-convergence processing is designed to effectively address the problem that the system cannot regain convergence after a path change in steady state. The simulation study demonstrates that the proposed algorithm can efficiently improve noise reduction performance, accurately detect the path change, and re-converge to new global optimization.
Peripheral news workers expelled to the periphery: The case of camera reporters
Authors: Císařová Lenka Waschková , Metykova Monika
Published: January 2020

The professionals behind television cameras are peripheral contributors to journalism who are often overlooked in journalistic research in contrast with co-workers who occupy clearly demarcated journalistic roles. In this article, we use the term camera reporters rather than the more frequently used terms such as cameramen or camera operators as we argue that these professionals are part of the journalistic field and their job titles in themselves question their belonging to this field. The aim of our article is to focus on the role of camera reporters as peripheral actors in the news production process – in this respect we address their journalistic culture, identity, autonomy and practice – and to understand their role not only in the context of boundary work within journalism but perhaps even more importantly in relation to changes brought about by the move of a television studio from the city centre to a residential suburb. The relocation provides a rare opportunity to study camera reporters in their work places and spaces at a time of disruption and adjustment. Our case study is based in a Czech television studio where we have conducted interviews with camera reporters and news reporters. Our findings are in line with other research on peripheral news workers and illustrate complex issues in the professional standing of camera reporters.
Visualization in the preprocessing phase: Getting insights from enterprise professionals
Authors: Milani Alessandra Maciel Paz , Paulovich Fernando V. , Manssour Isabel Harb
Published: January 2020

The current information age has increasingly required organizations to become data-driven. However, analyzing and managing raw data is still a challenging part of the data mining process. Even though we can find interview studies proposing design implications or recommendations for future visualization solutions in the data mining scope, they cover the entire workflow and do not fully focus on the challenges during the preprocessing phase and on how visualization can support it. Moreover, they do not organize a final list of insights consolidating the findings of other related studies. Hence, to better understand the current practice of enterprise professionals in data mining workflows, in particular, during the preprocessing phase, and how visualization supports this process, we conducted semi-structured interviews with 13 data analysts. The discussion about the challenges and opportunities based on the responses of the interviewees resulted in a list of 10 insights. This list was compared with the closest related works, improving the reliability of our findings and providing background, as a consolidated set of requirements, for future visualization research articles applied to visual data exploration in data mining. Furthermore, we provide greater details on the profile of the data analysts, the main challenges they face, and the opportunities that arise while they are engaged in data mining projects in diverse organizational areas.
The crosstalk between hypoxia-inducible factor-1α and microRNAs in acute kidney injury
Authors: Wang Zhiyu , Zhang Wen
Published: January 2020

Acute kidney injury (AKI) is a common critical clinical disease that is characterized by a rapid decline in renal function and reduced urine output. Ischemia and hypoxia are dominant pathophysiological changes in AKI that are induced by many factors, and the role of the “master” regulator hypoxia-inducible factor-1α (HIF-1α) is well recognized in AKI-related studies. MicroRNAs have been found to act as critical regulators of AKI pathophysiological process. More studies now have reported mutual interactions between HIF-1α and microRNAs in AKI. Therefore, in this brief review, we look into the mutual regulatory mechanisms between HIF-1α and microRNAs and discuss their function in the process of AKI. Recent studies demonstrated that HIF-1α is involved in the regulation of multiple functional microRNAs in AKI, and in turn, the level of HIF-1α is regulated by specific microRNAs. However, the role of the interactions between HIF-1α and microRNAs in AKI are controversial, and whether interventions targeting relevant mechanisms could achieve clinical benefits is not clear. Much work remains to further explore the value of targeting the HIF-1α-microRNA pathway in AKI treatment.

Impact statement

At first, we have discussed the role of hypoxia-inducible factor-1α (HIF-1α) and microRNAs in the acute kidney injury (AKI) pathophysiology. Then we have summarized the interactions between HIF-1α and microRNAs reported by AKI-related studies and concluded their regulatory effects in AKI process. Finally, we have made a vision of HIF-1α/microRNAs pathway’s potential as the intervention target in AKI. The mini review provides a systematic understanding of the crosstalk between HIF-1α and microRNAs in AKI and their effects on AKI pathophysiology and treatment.
Structural Characterization and Hepatoprotective Activity of Naphthoquinone From Cucumis bisexualis
Authors: Ma Qinge , Wei Rongrui , Sang Zhipei
Published: January 2020

Three new naphthoquinones, namely 5,8-dihydroxy-7′-isopropyl-furan ring-1″-prenyl-naphthoquinone (1), 5,8-dihydroxy-7′-propenyl-furan ring-1″-isopropanol-naphthoquinone (2), and 5,8-dihydroxy-7′-isopropanol-furan ring-1″-(5″-hydroxyphenyl)-naphthoquinone (3), along with 10 known naphthoquinone derivatives (4-13) were isolated from Cucumis bisexualis for the first time. All the compounds were elucidated on the basis of spectroscopic data analysis and chemical evidence. Compounds (1-13) were evaluated for their hepatoprotective activites on human L-O2 cells. Among them, compounds 1, 4, and 8 exhibited significant promotion effects on the proliferation of L-O2 cells.
Exploring African American community perspectives about genomic medicine research: A literature review
Authors: Hendricks-Sturrup Rachele M , Edgar Lauren M , Johnson-Glover Tracey , Lu Christine Y
Published: January 2020

Genomic medicine research is an important topic in the African American health care community. African American nurses and advance practice nursing professionals are poised to encourage and educate themselves and their communities about the importance of diversity in genomic medicine research. The Southern Nevada Black Nurses Association, a chapter within the larger National Black Nurses Association’s, recently engaged in the National Institutes of Health All of Us research program to educate their members about formularies and other treatment modalities that could clinically benefit African-Americans and other populations of color. During this event, the Southern Nevada Black Nurses Association discovered that National Black Nurses Association members held ethical, legal, and social concerns about engaging in genomic medicine research that align with respective concerns reported in the literature. In this review, we discuss National Black Nurses Association concerns and how they relate to qualitative themes emerging from the literature and a recent National Academies of Science, Engineering, and Medicine event on disparities in access to genomic medicine. We conclude that researchers should engage with African American health community leaders to effectively engage the African American community in genomic medicine research and help ensure that genomic medicine does not exacerbate existing health disparities.
Validation of prognostic accuracy of MESH, HKLC, and BCLC classifications in a large German cohort of hepatocellular carcinoma patients
Authors: Heinrich Sophia , Sprinzl Martin , Schmidtmann Irene , Heil Elena , Koch Sandra , Czauderna Carolin , Heinrich Bernd , Philippe P Diggs Laurence , Wörns Marcus‐Alexander , Kloeckner Roman , Galle Peter R , Marquardt Jens U , Weinmann Arndt
Published: January 2020

Background and aim

The Barcelona Clinic Liver Cancer (BCLC) staging system is commonly used to classify hepatocellular carcinoma (HCC) patients. However, other staging classification schemes have been proposed. We aimed to compare the prognostic accuracy of the Hong Kong Liver Cancer Staging (HKLC), the Model to Estimate Survival for HCC (MESH), and the BCLC staging systems using a Western cohort of HCC patients.

Methods

We retrospectively analyzed 918 patients diagnosed with HCC treated at the University Medical Center of Mainz between 2005 and 2014. We compared the predictive power of survival time of the BCLC, HKLC, and MESH. Predictive ability was tested using the integrated Brier score (IBS) and Harrell’s C index.

Results

Kaplan–Meier analyses showed significant differences in survival between stages defined by the BCLC, HKLC, and MESH. The HKLC classification demonstrated a more robust classification concordance and lower prediction error compared to the BCLC and MESH. In addition, we found that the BCLC offers superior predictive ability to the MESH in the first four years, whereas the MESH is superior for long‐term predictions.

Conclusion

Our analyses confirm the prognostic value of three different HCC scoring systems. When compared, the HKLC provides superior prognostication ability.
Shameful Secrets and Self-Presentation: Negotiating Privacy Practices Among Youth and Rural Women in China
Authors: Wang Yini , Balnaves Mark , Sandner Judith
Published: January 2020

China, like the United States, has no defined concept of privacy in its Constitution and Chinese citizens have to work out how to negotiate their presence online, just as others elsewhere do. Online privacy in China has not received strong legislative protection compared with the U.S. and European countries as privacy has never written as an individual right in China’s Constitution, nor in the Civil Law. Chinese privacy perceptions and everyday privacy practices in social media have not been fully examined. This article presents an original, ethnographic study of how 26 Chinese youth, men and women, and 25 older rural women from Changsha, south-central China are negotiating what counts as privacy online in their everyday practices. It finds out that youth group in Changsha has a stronger understanding of the technical level of deployment of the social media technologies, enacting both positive and protective self-presentation instantiated by “human flesh search,” “public online privacy,” and “improved firewall.” However, the notion of shameful secrets touches on the protection of the reputation of those concerned, and social relationships play an important role in privacy boundary negotiation, common to both groups. This demonstrates that sociocultural contexts need to be taken into consideration and should be more nuancedly examined when studying online privacy and working out privacy protection methods.
Neuromuscular Exercises Improve Shoulder Function More Than Standard Care Exercises in Patients With a Traumatic Anterior Shoulder Dislocation: A Randomized Controlled Trial
Authors: Eshoj Henrik Rode , Rasmussen Sten , Frich Lars Henrik , Hvass Inge , Christensen Robin , Boyle Eleanor , Jensen Steen Lund , Søndergaard Jens , Søgaard Karen , Juul-Kristensen Birgit
Published: January 2020

Background:

There is an important gap in knowledge about the effectiveness of nonoperative treatment (exercise) for patients with traumatic primary and recurrent anterior shoulder dislocations (ASDs).

Purpose/Hypothesis:

The purpose of this study was to assess the efficacy and safety of physical therapist–supervised, shoulder instability neuromuscular exercise (SINEX) versus self-managed, home-based, standard care shoulder exercise (HOMEX) in patients with traumatic ASDs. The hypothesis was that SINEX would have a larger effect and fewer adverse events compared with HOMEX.

Study Design:

Randomized controlled trial; Level of evidence, 2.

Methods:

A total of 56 participants with radiographically verified, trauma-initiated primary or recurrent ASDs and self-reported decreased shoulder function were randomized to 12 weeks of either SINEX or HOMEX. The SINEX program consisted of 7 exercises, individually progressing from basic (2 × 20 repetitions each day) to elite (2 × 10 repetitions, 3 times weekly). The HOMEX program included 5 shoulder exercises performed 3 times weekly (2 × 10 repetitions). The primary outcome was the Western Ontario Shoulder Instability Index (WOSI) score, ranging from 0 (best possible) to 2100. The between-group minimal clinically important difference at 12 weeks was 250 points. Secondary outcomes included WOSI subdomain scores, patient-reported ratings of kinesiophobia and pain, objective shoulder function, patient satisfaction, and number of adverse events.

Results:

The between-group mean difference in the WOSI total score at 12 weeks significantly favored SINEX over HOMEX (–228.1 [95% CI, –430.5 to –25.6]). SINEX was furthermore superior to HOMEX in most of the secondary outcomes (3/4 subdomains of the WOSI and pain level during the past 7 days as well as clinical signs of anterior shoulder instability). Also, although not statistically significant, less than half the proportion of the SINEX patients compared with the HOMEX patients (3/27 [11%] vs 6/24 [25%], respectively; P = .204) underwent or were referred for shoulder stabilizing surgery. Satisfaction with both exercise programs was high, and no serious adverse events were reported.

Conclusion:

Neuromuscular shoulder exercise (SINEX) was superior to standard care exercise (HOMEX) in patients with traumatic ASDs. Further long-term follow-ups on treatment effects are needed.

Registration:

NCT02371928 ( ClinicalTrials.gov identifier).
Correlation of Provider Burnout With Patient Experience
Authors: McKee Kathleen E , Tull Andrea , Carmen Marcela G del , Edgman-Levitan Susan
Published: January 2020

Initiatives to mitigate physician burnout and improve patient experience occur largely in isolation. At the level of the department/division, we found lower physician burnout was associated with a more positive patient experience. Physician Maslach Burnout Inventory data and patient Consumer Assessment of Healthcare Providers and Systems Clinician and Group experience scores were significantly correlated with 5 of 12 patient experience questions: “Got Routine Care Appointment” (−0.632, P = .001), “Recommend Provider” (−0.561, P = .005), “Provider Knew Medical History” (−0.532, P = .009), “Got Urgent Care Appointment” (−0.518, P = .014), and “Overall Rating” (−0.419, P = .047). These correlations suggest burnout and experience might be better addressed in tandem. Principles to guide an integrated approach are suggested.
Income Segregation and the Incomplete Integration of Islam in the Paris Metropolitan Area
Authors: Drouhot Lucas G.
Published: January 2020

In France as in many other Western European countries, the purported concentration of large Muslim populations in disadvantaged areas at the outskirts of major cities has been associated with public and scholarly concerns for failed integration, but few spatial data exist for the purposes of empirical study. Relying on a unique geolocated data set built from online repositories of Muslim places comprising halal butcher shops, prayer spaces, religious schools, and bookstores, the author uses a geographic information system to map Islamic institutions in the Paris metropolitan area. Contrary to the religious segregation narrative, the presence of Islamic institutions is widespread within the city. Using census income data aggregated by neighborhoods, however, the author shows that the spatial distribution of Muslim institutions matches broader dynamics of income segregation within the entire metropolitan area. Despite urban mainstreaming suggested by a substantial presence within the city proper, the spatial integration of Islam thus remains incomplete.
A cryptic imatinib-sensitive G3BP1-PDGFRB rearrangement in a myeloid neoplasm with eosinophilia
Authors: Jan Max , Grinshpun Daniel E. , Villalba Julian A. , Dal Cin Paola , Sykes David B. , Iafrate A. John , Ebert Benjamin L. , Hobbs Gabriela S. , Nardi Valentina
Published: January 2020

Key Points

Targeted RNA sequencing detected a cryptic G3BP1-PDGFRB rearrangement in a myeloid neoplasm with eosinophilia and normal FISH studies. Consistent with the patient’s response to imatinib, we demonstrate this rearrangement is oncogenic and sensitive to TKI in cell culture.
Expression of Concern to: Diet restriction inhibits apoptosis and HMGB1 oxidation and promotes inflammatory cell recruitment during acetaminophen hepatoxicity
Authors: Antoine Daniel James , Williams Dominic P. , Kipar Anja , Laverty Hugh , Park B. Kevin
Published: January 2020

The Editors-in-Chief would like to alert readers that this article [1] is part of an investigation being conducted by the journal following the conclusions of an institutional enquiry at the University of Liverpool with respect to the quantitative mass spectrometry-generated results regarding acetylated and redox-modified HMGB1.
Detection of suspicious interactions of spiking covariates in methylation data
Authors: Sieg Miriam , Richter Gesa , Schaefer Arne S. , Kruppa Jochen
Published: January 2020

Background

In methylation analyses like epigenome-wide association studies, a high amount of biomarkers is tested for an association between the measured continuous outcome and different covariates. In the case of a continuous covariate like smoking pack years (SPY), a measure of lifetime exposure to tobacco toxins, a spike at zero can occur. Hence, all non-smokers are generating a peak at zero, while the smoking patients are distributed over the other SPY values. Additionally, the spike might also occur on the right side of the covariate distribution, if a category “heavy smoker” is designed. Here, we will focus on methylation data with a spike at the left or the right of the distribution of a continuous covariate. After the methylation data is generated, analysis is usually performed by preprocessing, quality control, and determination of differentially methylated sites, often performed in pipeline fashion. Hence, the data is processed in a string of methods, which are available in one software package. The pipelines can distinguish between categorical covariates, i.e. for group comparisons or continuous covariates, i.e. for linear regression. The differential methylation analysis is often done internally by a linear regression without checking its inherent assumptions. A spike in the continuous covariate is ignored and can cause biased results.

Results

We have reanalysed five data sets, four freely available from ArrayExpress, including methylation data and smoking habits reported by smoking pack years. Therefore, we generated an algorithm to check for the occurrences of suspicious interactions between the values associated with the spike position and the non-spike positions of the covariate. Our algorithm helps to decide if a suspicious interaction can be found and further investigations should be carried out. This is mostly important, because the information on the differentially methylated sites will be used for post-hoc analyses like pathway analyses.

Conclusions

We help to check for the validation of the linear regression assumptions in a methylation analysis pipeline. These assumptions should also be considered for machine learning approaches. In addition, we are able to detect outliers in the continuous covariate. Therefore, more statistical robust results should be produced in methylation analysis using our algorithm as a preprocessing step.
Knowledge-enhanced biomedical named entity recognition and normalization: application to proteins and genes
Authors: Zhou Huiwei , Ning Shixian , Liu Zhe , Lang Chengkun , Liu Zhuang , Lei Bizun
Published: January 2020

Background

Automated biomedical named entity recognition and normalization serves as the basis for many downstream applications in information management. However, this task is challenging due to name variations and entity ambiguity. A biomedical entity may have multiple variants and a variant could denote several different entity identifiers.

Results

To remedy the above issues, we present a novel knowledge-enhanced system for protein/gene named entity recognition (PNER) and normalization (PNEN). On one hand, a large amount of entity name knowledge extracted from biomedical knowledge bases is used to recognize more entity variants. On the other hand, structural knowledge of entities is extracted and encoded as identifier (ID) embeddings, which are then used for better entity normalization. Moreover, deep contextualized word representations generated by pre-trained language models are also incorporated into our knowledge-enhanced system for modeling multi-sense information of entities. Experimental results on the BioCreative VI Bio-ID corpus show that our proposed knowledge-enhanced system achieves 0.871 F1-score for PNER and 0.445 F1-score for PNEN, respectively, leading to a new state-of-the-art performance.

Conclusions

We propose a knowledge-enhanced system that combines both entity knowledge and deep contextualized word representations. Comparison results show that entity knowledge is beneficial to the PNER and PNEN task and can be well combined with contextualized information in our system for further improvement.
Transcriptomic analysis of dead end knockout testis reveals germ cell and gonadal somatic factors in Atlantic salmon
Authors: Kleppe Lene , Edvardsen Rolf Brudvik , Furmanek Tomasz , Andersson Eva , Skaftnesmo Kai Ove , Thyri Segafredo Frida , Wargelius Anna
Published: January 2020

Background

Sustainability challenges are currently hampering an increase in salmon production. Using sterile salmon can solve problems with precocious puberty and genetic introgression from farmed escapees to wild populations. Recently sterile salmon was produced by knocking out the germ cell-specific dead end (dnd). Several approaches may be applied to inhibit Dnd function, including gene knockout, knockdown or immunization. Since it is challenging to develop a successful treatment against a gene product already existing in the body, alternative targets are being explored. Germ cells are surrounded by, and dependent on, gonadal somatic cells. Targeting genes essential for the survival of gonadal somatic cells may be good alternative targets for sterility treatments. Our aim was to identify and characterize novel germ cell and gonadal somatic factors in Atlantic salmon.

Results

We have for the first time analysed RNA-sequencing data from germ cell-free (GCF)/dnd knockout and wild type (WT) salmon testis and searched for genes preferentially expressed in either germ cells or gonadal somatic cells. To exclude genes with extra-gonadal expression, our dataset was merged with available multi-tissue transcriptome data. We identified 389 gonad specific genes, of which 194 were preferentially expressed within germ cells, and 11 were confined to gonadal somatic cells. Interestingly, 5 of the 11 gonadal somatic transcripts represented genes encoding secreted TGF-β factors; gsdf, inha, nodal and two bmp6-like genes, all representative vaccine targets. Of these, gsdf and inha had the highest transcript levels. Expression of gsdf and inha was further confirmed to be gonad specific, and their spatial expression was restricted to granulosa and Sertoli cells of the ovary and testis, respectively. Finally, we show that inha expression increases with puberty in both ovary and testis tissue, while gsdf expression does not change or decreases during puberty in ovary and testis tissue, respectively.

Conclusions

This study contributes with transcriptome data on salmon testis tissue with and without germ cells. We provide a list of novel and known germ cell- and gonad somatic specific transcripts, and show that the expression of two highly active gonadal somatic secreted TGF-β factors, gsdf and inha, are located within granulosa and Sertoli cells.
Transcriptomics supports local sensory regulation in the antenna of the kissing-bug Rhodnius prolixus
Authors: Latorre-Estivalis Jose Manuel , Sterkel Marcos , Ons Sheila , Lorenzo Marcelo Gustavo
Published: January 2020

Background

Rhodnius prolixushas become a model for revealing the molecular bases of insect sensory biology due to the publication of its genome and its well-characterized behavioural repertoire. Gene expression modulation underlies behaviour-triggering processes at peripheral and central levels. Still, the regulation of sensory-related gene transcription in sensory organs is poorly understood. Here we study the genetic bases of plasticity in antennal sensory function, usingR. prolixusas an insect model.

Results

Antennal expression of neuromodulatory genes such as those coding for neuropeptides, neurohormones and their receptors was characterized in fifth instar larvae and female and male adults by means of RNA-Sequencing (RNA-Seq). New nuclear receptor andtakeoutgene sequences were identified for this species, as well as those of enzymes involved in the biosynthesis and processing of neuropeptides and biogenic amines.

Conclusions

We report a broad repertoire of neuromodulatory and neuroendocrine-related genes expressed in the antennae ofR. prolixusand suggest that they may serve as the local basis for modulation of sensory neuron physiology. Diverse neuropeptide precursor genes showed consistent expression in the antennae of all stages studied. Future studies should characterize the role of these modulatory components acting over antennal sensory processes to assess the relative contribution of peripheral and central regulatory systems on the plastic expression of insect behaviour.
The effects of common structural variants on 3D chromatin structure
Authors:   Human Genome Structural Variation Consortium (HGSVC), Shanta Omar , Noor Amina , Sebat Jonathan
Published: January 2020

Background

Three-dimensional spatial organization of chromosomes is defined by highly self-interacting regions 0.1–1 Mb in size termed Topological Associating Domains (TADs). Genetic factors that explain dynamic variation in TAD structure are not understood. We hypothesize that common structural variation (SV) in the human population can disrupt regulatory sequences and thereby influence TAD formation. To determine the effects of SVs on 3D chromatin organization, we performed chromosome conformation capture sequencing (Hi-C) of lymphoblastoid cell lines from 19 subjects for which SVs had been previously characterized in the 1000 genomes project. We tested the effects of common deletion polymorphisms on TAD structure by linear regression analysis of nearby quantitative chromatin interactions (contacts) within 240 kb of the deletion, and we specifically tested the hypothesis that deletions at TAD boundaries (TBs) could result in large-scale alterations in chromatin conformation.

Results

Large (> 10 kb) deletions had significant effects on long-range chromatin interactions. Deletions were associated with increased contacts that span the deleted region and this effect was driven by large deletions that were not located within a TAD boundary (nonTB). Some deletions at TBs, including a 80 kb deletion of the genes CFHR1 and CFHR3, had detectable effects on chromatin contacts. However for TB deletions overall, we did not detect a pattern of effects that was consistent in magnitude or direction. Large inversions in the population had a distinguishable signature characterized by a rearrangement of contacts that span its breakpoints.

Conclusions

Our study demonstrates that common SVs in the population impact long-range chromatin structure, and deletions and inversions have distinct signatures. However, the effects that we observe are subtle and variable between loci. Genome-wide analysis of chromatin conformation in large cohorts will be needed to quantify the influence of common SVs on chromatin structure.
Repetitive DNA content in the maize genome is uncoupled from population stratification at SNP loci
Authors: Renny-Byfield Simon , Baumgarten Andy
Published: January 2020

Background

Repetitive DNA is a major component of plant genomes and is thought to be a driver of evolutionary novelty. Describing variation in repeat content among individuals and between populations is key to elucidating the evolutionary significance of repetitive DNA. However, the cost of producing references genomes has limited large-scale intraspecific comparisons to a handful of model organisms where multiple reference genomes are available.

Results

We examine repeat content variation in the genomes of 94 elite inbred maize lines using graph-based repeat clustering, a reference-free and rapid assay of repeat content. We examine population structure using genome-wide repeat profiles, and demonstrate the stiff-stalk and non-stiff-stalk heterotic populations are homogenous with regard to global repeat content. In contrast, and similar to previously reported results, the same individuals show clear differentiation, and aggregate into two populations when examining population structure using genome-wide SNPs. Additionally, we develop a novel kmer based technique to examine the chromosomal distribution of repeat clusters in silico and show a cluster dependent association with gene density.

Conclusion

Our results indicate global repeat content variation in the heterotic populations of maize has not diverged, and is uncoupled from population stratification at SNP loci. We show that repeat families exhibit divergent patterns with regard to chromosomal distribution, some repeat clusters accumulate in regions of high gene density, whereas others aggregate in regions of low gene density.
The C3HC type zinc-finger protein (ZFC3) interacting with Lon/MAP1 is important for mitochondrial gene regulation, infection hypha development and longevity of Magnaporthe oryzae
Authors: Liu Shaoshuai , Wei Yi , Zhang Shi-Hong
Published: January 2020

Background

The rice blast is a typical fungal disease caused by Magnaporthe oryzae, and the mitochondrial ATP-dependent Lon protease (MAP1) has been proven to be involved in blast development. We previously screened a C3HC type Zinc-finger domain protein (ZFC3), which is interacted with MAP1. The purpose of this research was to study the biological function of ZFC3 protein in M. oryzae.

Results

We first confirmed that the ZFC3-RFP fusion protein is localized within the mitochondria. The deleted mutant strains of ZFC3 (∆ZFC3) showed the enhanced expression level of mtATP6, particularly mtATP8, and almost unchanged nATP9. ΔZFC3 produces more conidia and more tolerance to multiple stressors. The knock-out strain shows more melanin accumulation suggests the susceptibility to aging. ΔZFC3 displays faster early-stage hypha infiltration involved in MAP1-mediated pathogenicity in host rice.

Conclusion

These results support the view that ZFC3 is a key regulator involved in gene regulation, stress response, cell wall integrity, longevity, conidiation, infection hypha development and MAP1-mediated pathogenicity in M. oryzae.
Comparative proteomic and transcriptomic analyses provide new insight into the formation of seed size in castor bean
Authors: Yu Anmin , Li Fei , Liu Aizhong
Published: January 2020

Background

Little is known about the molecular basis of seed size formation in endospermic seed of dicotyledons. The seed of castor bean (Ricinus communis L.) is considered as a model system in seed biology studies because of its persistent endosperms throughout seed development.

Results

We compared the size of endosperm and endospermic cells between ZB107 and ZB306 and found that the larger seed size of ZB107 resulted from a higher cell count in the endosperm, which occupy a significant amount of the total seed volume. In addition, fresh weight, dry weight, and protein content of seeds were remarkably higher in ZB107 than in ZB306. Comparative proteomic and transcriptomic analyses were performed between large-seed ZB107 and small-seed ZB306, using isobaric tags for relative and absolute quantification (iTRAQ) and RNA-seq technologies, respectively. A total of 1416 protein species were identified, of which 173 were determined as differentially abundant protein species (DAPs). Additionally, there were 9545 differentially expressed genes (DEGs) between ZB306 and ZB107. Functional analyses revealed that these DAPs and DEGs were mainly involved in cell division and the metabolism of carbohydrates and proteins.

Conclusions

These findings suggest that both cell number and storage-component accumulation are critical for the formation of seed size, providing new insight into the potential mechanisms behind seed size formation in endospermic seeds.