bluuebunny/crossref_metadata_2025 huggingface dataset:
NfiR, a New Regulatory Noncoding RNA (ncRNA), Is Required in Concert with the NfiS ncRNA for Optimal Expression of Nitrogenase Genes in Pseudomonas stutzeri A1501
Authors: Zhan Yuhua , Deng Zhiping , Yan Yongliang , Zhang Hongyang , Lu Chao , Yang Zhimin , Shang Liguo , Huang Yi , Lv Fanyang , Liu Yaqun , Liu Yichao , Wang Shanshan , Chen Sanfeng , Zhang Xue-Xian , Cheng Qi , Lin Min
Published: May 2019

Biological nitrogen fixation is an energy-expensive process requiring the hydrolysis of 16 ATPs. Consequently, the expression of
nif
genes is highly regulated at both transcriptional and posttranscriptional levels through complex regulatory networks. Global regulation involves a number of regulatory proteins, such as the
nif
-specific activator NifA and the global nitrogen regulator NtrC, as well as various regulatory ncRNAs. We show that the two
P. stutzeri
ncRNAs, namely NfiS and NfiR (for
n
itrogen
f
ixation condition-
i
nducible nc
R
NA), optimize nitrogen fixation and environmental stress responses. NfiS and NfiR respond differently to various environmental signals and differ in their secondary structures. In addition, the two ncRNAs target the mRNAs of
nifK
and
nifD
, respectively. Such ncRNA-based posttranscriptional regulation of nitrogenase expression might be an evolved survival strategy, particularly in nitrogen-limiting environments. This study not only highlights the significant roles of regulatory ncRNAs in the coordination and ﬁne tuning of various physiological processes but also provides a new paradigm for posttranscriptional regulation in nitrogen-fixing bacteria.
Dietary Polyunsaturated Fatty Acids Promote Neutrophil Accumulation in the Spleen by Altering Chemotaxis and Delaying Cell Death
Authors: Svahn Sara L. , Gutiérrez Saray , Ulleryd Marcus A. , Nookaew Intawat , Osla Veronica , Beckman Fredrik , Nilsson Staffan , Karlsson Anna , Jansson John-Olov , Johansson Maria E.
Published: May 2019

Neutrophils are the most abundant circulating leukocytes in humans and are essential for the defense against invading pathogens. Like many other cells of an organism, neutrophils can be highly influenced by the diet. We have previously described that mice fed a high-fat diet rich in polyunsaturated fatty acids (HFD-P) present a higher frequency of neutrophils in bone marrow than mice fed a high-fat diet rich in saturated fatty acids (HFD-S).
A Mutagenic Screen Identifies a TonB-Dependent Receptor Required for the Lanthanide Metal Switch in the Type I Methanotroph “Methylotuvimicrobium buryatense” 5GB1C
Authors: Groom Joseph D. , Ford Stephanie M. , Pesesky Mitchell W. , Lidstrom Mary E.
Published: May 2019

Lanthanide metals, or rare earth elements, are abundant in nature and used heavily in technological devices. Biological interactions with lanthanides are just beginning to be unraveled. Until very recently, microbial mechanisms of lanthanide metal interaction and uptake were unknown. The TonB-dependent receptor LanA is the first lanthanum receptor identified in a methanotroph. Sequence homology searches with known metal transporters and regulators could not be used to identify LanA or other lanthanide metal switch components, and this method for mutagenesis and selection was required to identify the receptor. This work advances the knowledge of microbe-metal interactions in environmental niches that impact atmospheric methane levels and are thus relevant to climate change.
Large-scale mass wasting on the Miocene continental margin of western India
Authors: Dailey Sarah K. , Clift Peter D. , Kulhanek Denise K. , Blusztajn Jerzy , Routledge Claire M. , Calvès Gérôme , O’Sullivan Paul , Jonell Tara N. , Pandey Dhananjai K. , Andò Sergio , Coletti Giovanni , Zhou Peng , Li Yuting , Neubeck Nikki E. , Bendle James A.P. , Aharonovich Sophia , Griffith Elizabeth M. , Gurumurthy Gundiga P. , Hahn Annette , Iwai Masao , Khim Boo-Keun , Kumar Anil , Kumar A. Ganesh , Liddy Hannah M. , Lu Huayu , Lyle Mitchell W. , Mishra Ravi , Radhakrishna Tallavajhala , Saraswat Rajeev , Saxena Rakesh , Scardia Giancarlo , Sharma Girish K. , Singh Arun D. , Steinke Stephan , Suzuki Kenta , Tauxe Lisa , Tiwari Manish , Xu Zhaokai , Yu Zhaojie
Published: May 2019

A giant mass-transport complex was recently discovered in the eastern Arabian Sea, exceeding in volume all but one other known complex on passive margins worldwide. The complex, named the Nataraja Slide, was drilled by International Ocean Discovery Program (IODP) Expedition 355 in two locations where it is ∼300 m (Site U1456) and ∼200 m thick (Site U1457). The top of this mass-transport complex is defined by the presence of both reworked microfossil assemblages and deformation structures, such as folding and faulting. The deposit consists of two main phases of mass wasting, each consisting of smaller pulses, with generally fining-upward cycles, all emplaced just prior to 10.8 Ma based on biostratigraphy. The base of the deposit at each site is composed largely of matrix-supported carbonate breccia that is interpreted as the product of debris-flows. In the first phase, these breccias alternate with well-sorted calcarenites deposited from a high-energy current, coherent limestone blocks that are derived directly from the Indian continental margin, and a few clastic mudstone beds. In the second phase, at the top of the deposit, muddy turbidites dominate and become increasingly more siliciclastic. At Site U1456, where both phases are seen, a 20-m section of hemipelagic mudstone is present, overlain by a ∼40-m-thick section of calcarenite and slumped interbedded mud and siltstone. Bulk sediment geochemistry, heavy-mineral analysis, clay mineralogy, isotope geochemistry, and detrital zircon U-Pb ages constrain the provenance of the clastic, muddy material to being reworked, Indus-derived sediment, with input from western Indian rivers (e.g., Narmada and Tapti rivers), and some material from the Deccan Traps. The carbonate blocks found within the breccias are shallow-water limestones from the outer western Indian continental shelf, which was oversteepened from enhanced clastic sediment delivery during the mid-Miocene. The final emplacement of the material was likely related to seismicity as there are modern intraplate earthquakes close to the source of the slide. Although we hypothesize that this area is at low risk for future mass wasting events, it should be noted that other oversteepened continental margins around the world could be at risk for mass failure as large as the Nataraja Slide.
Triparesis: an unusual presentation of factitious disorder
Authors: Padhy Susanta Kumar , Sapkota Prabhat , Somani Aditya
Published: May 2019

Factitious disorder (FD) has diverse presentations but neurological presentation is unusual. In this report, we discuss a case of FD who presented with triparesis, that is, weakness of both lower limbs and right upper limb. Diagnosis of FD was made after detailed clinical evaluation, review of past medical records that revealed extensive evaluation to rule out physical illness, and inability to find any associated stressful event or material gain associated with illness. Management was largely supportive and was based on psychotherapy. Identification of FD depends on a high index of suspicion by the physician and the presence of atypical and medically unexplainable signs/symptoms.
Measles in pregnancy
Authors: Bansal Jassimran , Hameed Aisha
Published: May 2019

Measles is becoming more prevalent; it can be difficult to diagnose, with severe complications in pregnancy. We report a case of measles in a 27-year-old, parainfluenza virus type 2-infected woman who was 32 weeks pregnant. She presented with fever, tachycardia, sore throat and a pruritic rash. She never had the measles, mumps, rubella vaccine. Serology showed raised inflammatory markers with lymphopoenia. Throat swab showed parainfluenza virus. Chest radiography was normal. Despite appropriate antimicrobial therapy, she developed worsening respiratory failure requiring premature delivery via caesarean section.

Postoperatively, she was transferred to a tertiary centre for extracorporeal membrane oxygenation. She was decannulated and made a full recovery. Meanwhile, her husband was diagnosed with measles. She was then tested and measles was confirmed. The baby did not develop congenital measles.

This case emphasises the importance of vaccine histories at booking of pregnancy and early multidisciplinary team input to facilitate delivery in rapidly deteriorating pregnant women.
Perceptions of drones, digital adherence monitoring technologies and educational videos for tuberculosis control in remote Madagascar: a mixed-method study protocol
Authors: Nouvet Elysée , Knoblauch Astrid M , Passe Ian , Andriamiadanarivo Andry , Ravelona Manualdo , Ainanomena Ramtariharisoa Faniry , Razafimdriana Kimmerling , Wright Patricia C , McKinney Jesse , Small Peter M , Rakotosamimanana Niaina , Grandjean Lapierre Simon
Published: May 2019

Introduction

Poor road and communication infrastructure pose major challenges to tuberculosis (TB) control in many regions of the world. TB surveillance and patient support often fall to community health workers (CHWs) who may lack the time or knowledge needed for this work. To meet the End TB Strategy goal of reducing TB incidence by 90% by 2035, the WHO calls for intensified research and innovation including the rapid uptake of new tools, interventions and strategies. Technologies that ‘leapfrog’ infrastructure challenges and support CHWs in TB control responsibilities have the potential to dramatically change TB outcomes in remote regions. Such technologies may strengthen TB control activities within challenged national tuberculosis treatment and control programmes (NTPs), and be adapted to address other public health challenges. The deployment of innovative technologies needs to be differentially adapted to context-specific factors. The Drone Observed Therapy System (DrOTS) project was launched in Madagascar in 2017 and integrates a bundle of innovative technologies including drones, digital adherence monitoring technology and mobile device-based educational videos to support TB control.

Methods and analysis

This mixed-methods study gathers and analyses cultural perceptions of the DrOTS project among key stakeholders: patients, community members, CHWs, village chiefs and NTP–DrOTS mobile health teams. Data from questionnaires, semistructured interviews, focus group discussions (FGD) and ethnographic observation gathered from June 2018 to June 2019 are thematically analysed and compared to identify patterns and singularities in how DrOTS stakeholders perceive and interact with DrOTS technologies, its enrolment processes, objectives and team.

Ethics and dissemination

Ethics approval was obtained from the National Bioethics Research Committee of Madagascar and Stony Brook University institutional review board. Study results will be submitted for peer-reviewed publication. In Madagascar, results will be presented in person to Ministry and other Malagasy decision-makers through the Institut Pasteur de Madagascar.

Patient and public involvement

This study is designed to foreground the voices of patients and potential patients in the DrOTS programme. CHW participants in this study also supported the design of study information sessions and recruitment strategies. One member of the mobile health team provided detailed input on the wording and content of FGD and interview guides. Study findings will be presented via a report in French and Malagasy to CHW, mobile health team and other village-level participants who have email/internet access.
Understanding how to enhance efficacy and effectiveness of feedback via e-portfolio: a realist synthesis protocol
Authors: Babovič Mojca , Fu Ren-Huei , Monrouxe Lynn V
Published: May 2019

Introduction

The validity of feedback as one of the defining components for electronic portfolios (e-portfolios) to be effective and efficacious has yet to be demonstrated. While the literature has shown individual beneficial features of e-portfolios and feedback per se, evidence of feedback as mediated through technology directly resulting in improved educational practice is scarce. The explanation of how feedback via e-portfolio improves educational practice is particularly vague.

Methods and analysis

The aim of this research is to unpack how and why feedback via e-portfolio is likely to flourish or wither in its path. Given the complexity of intervention, we will apply a theory-driven approach for evidence synthesis called realist synthesis. Informed by realist philosophy of science, it seems the most appropriate method because it explores observed outcomes (O) in terms of causal relationship between relevant contexts (C) and generating mechanisms (M). Initial programme theory will be developed through literature scoping. Later on it will be tested against purposively gathered evidence (through database and journal search), which simultaneously will be evaluated for rigour and relevance (whether method used are trustworthy and whether data contributes to theory building). We strive to (1) uncover ‘context sensitive’ mechanisms that generate feedback via e–portfolio to be (in) effective and (2) define in what circumstances is this mostly likely to occur.

Ethics and dissemination

The synthesis report will be written according to the RAMESES guidelines and its findings will be published in peer reviewed articles and presented at relevant conferences. The aim is to inform: (1) policy and decision makers for future-course design; (2) medical educators/clinical supervisors and learners for improved educational use. No formal ethical approval is required.

PROSPERO registration number

120863.
Systematic review of mydriatics used for screening of retinopathy in premature infants
Authors: Kremer Lisa Jean , Reith David M , Medlicott Natalie , Broadbent Roland
Published: May 2019

Introduction

Routine retinopathy of prematurity eye examinations are an important part of neonatal care, and mydriatic medicines are essential in dilating the pupil for the eye examination. There are concerns about the level of evidence for efficacy and safety of these mydriatic medicines.

Objective

This review evaluates both efficacy and safety evidence of mydriatics used during the retinopathy of prematurity eye examination.

Method

Systematic literature review.

Results

There is limited evidence guiding clinical practice for safety and efficacy of mydriatics. The majority of publications are underpowered and with an unclear to high level of bias. There are a wide variety of mydriatic regimens evaluated for efficacy and safety, and multiple regimens are associated with case reports.

Conclusions

Current international guideline seems unnecessarily high, especially when the reviewed literature suggest that lower doses are effective, albiet from underpowered studies. The lowest effective combination regimen appears to be phenylephrine 1% and cyclopentolate 0.2% (1 drop). Microdrop administration of this regimen would further increase the safety profile, however, efficacy needs to be assessed.
No pain no gain: a survey of use of healthcare and reasons not to seek healthcare by Norwegian climbers with chronic injuries
Authors: Grønhaug Gudmund , Saeterbakken Atle
Published: May 2019

Objectives

To assess the use of healthcare, and reasons not to seek healthcare, by climbers with a chronic injury.

Method

Retrospective survey.

Setting

Web-based questionnaire.

Participants

667 active climbers (385 with chronic injuries).

Outcome measure

Use of healthcare (including reasons not to seek healthcare if the patient was not attended by health professionals), performance level in sport climbing, onset of a climbing-related injury, site of injury, preferred style of climbing and gender differences.

Result

Of the 667 respondents, 385 had experienced a chronic injury in the past 6 months. Climbers with a chronic injury are reluctant to seek healthcare, and male climbers are less likely to seek healthcare than female climbers. The two most frequent reasons not to seek healthcare were: (1) an assumption that the injury was not serious enough (70%) and (2) a belief that a health professional could not help (60%). Only one in five of the climbers with a finger injury sought healthcare. The more experienced climbers were less likely to seek healthcare than recreational climbers.

Conclusion

Use of healthcare among climbers with a chronic injury is limited and injured climbers self-assess the injury before seeking medical aid. Experience is a strong predictor for not seeking healthcare after an injury. These findings open up the possibility that some of those who do not seek healthcare after self-assessing the injury are underestimating the seriousness of the injury due to lack of confidence in the health professionals’ abilities to help treating chronic climbing related injuries.
Targeting monocyte-intrinsic enhancer reprogramming improves immunotherapy efficacy in hepatocellular carcinoma
Authors: Liu Man , Zhou Jingying , Liu Xiaoyu , Feng Yu , Yang Weiqin , Wu Feng , Cheung Otto Ka-Wing , Sun Hanyong , Zeng Xuezhen , Tang Wenshu , Mok Myth T S , Wong John , Yeung Philip Chun , Lai Paul Bo San , Chen Zhiwei , Jin Hongchuan , Chen Jie , Chan Stephen Lam , Chan Anthony W H , To Ka Fai , Sung Joseph J Y , Chen Minhu , Cheng Alfred Sze-Lok
Published: May 2019

Objective

Hepatocellular carcinoma (HCC), mostly developed in fibrotic/cirrhotic liver, exhibits relatively low responsiveness to immune checkpoint blockade (ICB) therapy. As myeloid-derived suppressor cell (MDSC) is pivotal for immunosuppression, we investigated its role and regulation in the fibrotic microenvironment with an aim of developing mechanism-based combination immunotherapy.

Design

Functional significance of MDSCs was evaluated by flow cytometry using two orthotopic HCC models in fibrotic liver setting via carbon tetrachloride or high-fat high-carbohydrate diet and verified by clinical specimens. Mechanistic studies were conducted in human hepatic stellate cell (HSC)-peripheral blood mononuclear cell culture systems and fibrotic-HCC patient-derived MDSCs. The efficacy of single or combined therapy with anti-programmed death-1-ligand-1 (anti-PD-L1) and a clinically trialled BET bromodomain inhibitor i-BET762 was determined.

Results

Accumulation of monocytic MDSCs (M-MDSCs), but not polymorphonuclear MDSCs, in fibrotic livers significantly correlated with reduced tumour-infiltrating lymphocytes (TILs) and increased tumorigenicity in both mouse models. In human HCCs, the tumour-surrounding fibrotic livers were markedly enriched with M-MDSC, with its surrogate marker CD33 significantly associated with aggressive tumour phenotypes and poor survival rates. Mechanistically, activated HSCs induced monocyte-intrinsic p38 MAPK signalling to trigger enhancer reprogramming for M-MDSC development and immunosuppression. Treatment with p38 MAPK inhibitor abrogated HSC-M-MDSC crosstalk to prevent HCC growth. Concomitant with patient-derived M-MDSC suppression by i-BET762, combined treatment with anti-PD-L1 synergistically enhanced TILs, resulting in tumour eradication and prolonged survival in the fibrotic-HCC mouse model.

Conclusion

Our results signify how non-tumour-intrinsic properties in the desmoplastic microenvironment can be exploited to reinstate immunosurveillance, providing readily translatable combination strategies to empower HCC immunotherapy.
Leaky gut: mechanisms, measurement and clinical implications in humans
Authors: Camilleri Michael
Published: May 2019

The objectives of this review on ‘leaky gut’ for clinicians are to discuss the components of the intestinal barrier, the diverse measurements of intestinal permeability, their perturbation in non-inflammatory ‘stressed states’ and the impact of treatment with dietary factors. Information on ‘healthy’ or ‘leaky’ gut in the public domain requires confirmation before endorsing dietary exclusions, replacement with non-irritating foods (such as fermented foods) or use of supplements to repair the damage. The intestinal barrier includes surface mucus, epithelial layer and immune defences. Epithelial permeability results from increased paracellular transport, apoptosis or transcellular permeability. Barrier function can be tested in vivo using orally administered probe molecules or in vitro using mucosal biopsies from humans, exposing the colonic mucosa from rats or mice or cell layers to extracts of colonic mucosa or stool from human patients. Assessment of intestinal barrier requires measurements beyond the epithelial layer. ‘Stress’ disorders such as endurance exercise, non-steroidal anti-inflammatory drugs administration, pregnancy and surfactants (such as bile acids and dietary factors such as emulsifiers) increase permeability. Dietary factors can reverse intestinal leakiness and mucosal damage in the ‘stress’ disorders. Whereas inflammatory or ulcerating intestinal diseases result in leaky gut, no such disease can be cured by simply normalising intestinal barrier function. It is still unproven that restoring barrier function can ameliorate clinical manifestations in GI or systemic diseases. Clinicians should be aware of the potential of barrier dysfunction in GI diseases and of the barrier as a target for future therapy.
Daily supplementation with 5 mg of folic acid in Brazilian patients with hereditary spherocytosis
Authors: Paniz Clóvis , Lucena Maylla Rodrigues , Bertinato Juliano Felix , Lourenço Felipe Rebello , Barros Bruna Cipriano A , Gomes Guilherme Wataru , Figueiredo Maria Stella , Cançado Rodolfo Delfini , Blaia-D Avila Vera Lúcia Nascimento , Pfeiffer Christine M , Fazili Zia , Green Ralph , Carvalho Valdemir Melechco , Guerra-Shinohara Elvira Maria
Published: May 2019

Patients with hereditary spherocytosis (HS) have increased rates of erythropoiesis and higher folate requirements. In a case-control study of patients with HS, we evaluated the associations between the use of 5 mg folic acid (FA) daily and serum concentrations of folate, unmetabolized folic acid (UMFA), interleukin (IL)-6, IL-8, IL-10, interferon-γ (IFN-γ) and tumor necrosis factor-α (TNF-α); and mRNA expression of dihydrofolate reductase ( DHFR), methylene tetrahydrofolate reductase ( MTHFR), IL8, IFNG and TNFA genes. Total serum folate and folate forms were measured in 27 patients with HS (21 users [HS-U] and 6 non-users [HS-NU] of supplemental FA) and 54 healthy controls not consuming 5 mg/day supplemental FA. Each patient was matched to two controls based on age, sex and body mass index. The mononuclear leucocyte mRNA expression of relevant genes and their products were determined. Serum folate, UMFA, 5-methyl-tetrahydrofolate (5-methyl-THF) and tetrahydrofolate (THF) concentrations were significantly higher in HS-U compared with matched healthy controls (p<0.001, n=42). HS-NU had lower serum folate concentrations than matched healthy controls (p=0.044, n=12). HS-U and HS-NU presented similar hematological and biochemical markers profiles. No differences were found between HS-U and HS-NU for cytokine serum concentrations and mRNA expression genes. DHFR mRNA expression was higher in HS-U than in HS-NU. The use of high daily doses of FA for treatment of patients with HS may be excessive and is associated with elevated serum UMFA and elevated DHFR mRNA expression. It is not known whether long-term high-dose FA use by patients with HS might have adverse health effects.
Evaluating the impact of a national clinical leadership fellow scheme
Authors: McKimm Judy , Hickford Donna , Lees Peter , Armit Kirsten
Published: May 2019

Background

The drive towards engaging UK doctors in clinical leadership and management has involved a number of initiatives at various levels, including specific fellowships for doctors in training which enable them to take a year out of programme to work with senior leaders on service improvement or policy development projects.

Objectives

This paper reports on the findings of an impact evaluation of a national Fellowship Scheme for doctors in training. The evaluation aimed to determine: What were the key success factors and areas for improvement of the Scheme? How did the Fellows experience the Scheme and how has this influenced their subsequent engagement, behaviours and thinking about healthcare leadership and management? What was the perceived impact of the Scheme?

Participants

Six cohorts of Fellows and key stakeholders were involved in the evaluation .

Results

The evaluation has clearly demonstrated the impact of this long-standing national Fellowship Scheme and the huge benefits for the individuals and organisations involved. For the Fellows, a national scheme such as this provides a unique experience, allowing them to learn first-hand from a range of senior decision-makers and engage in policy and strategic developments and processes.

Conclusions

This evaluation has demonstrated the wide impact of the Scheme but has also highlighted that more evaluations are needed of the wide range of fellowship schemes on offer to evidence broader impact, and raised issues around some of the difficulties these Fellows encounter on their return to practice in using their new skills to engage in service and healthcare improvement initiatives.
Interplay between alcohol, smoking and HLA genes in RA aetiology
Authors: Hedström Anna Karin , Hössjer Ola , Klareskog Lars , Alfredsson Lars
Published: May 2019

Objectives

The relationship between alcohol consumption and risk for rheumatoid arthritis (RA) is incompletely understood. We aimed to determine the influence of alcohol on anticitrullinated protein antibody (ACPA) positive and ACPA-negative RA and investigate potential interactions between alcohol consumption, smoking and the presence of human leucocyte antigen (HLA)-DRB1-shared epitope (SE).

Methods

A Swedish population-based case–control study with incident cases of RA was used (3353 cases, 2836 matched controls). Subjects with different HLA-DRB1-SE status, smoking and alcohol consumption were compared regarding risk of ACPA-positive and ACPA-negative RA, by calculating OR with 95% CI employing logistic regression. Interaction on the additive scale between alcohol, HLA-DRB1-SE and smoking was estimated by calculating the attributable proportion (AP) due to interaction.

Results

Compared with non-drinking, low and moderate alcohol consumption was dose dependently associated with a reduced risk of ACPA-positive and ACPA-negative RA. Independent of smoking habits, non-drinking and the presence of HLA-DRB1-SE interacted to increase the risk of ACPA-positive RA. Among HLA-DRB1-SE positive subjects, there was also a significant interaction between non-drinking and smoking with regard to risk for ACPA-positive RA. A three-way interaction was observed between alcohol, smoking and HLA-DRB1-SE with regard to risk for ACPA-positive RA (AP 0.7, 95% CI 0.6 to 0.8) that remained significant when the influence from the two-way interactions was removed (AP 0.4, 95% CI 0.2 to 0.6).

Conclusions

Our findings emphasize the need to investigate complex interactions between several environmental and genetic factors in order to better understand the etiology of RA. Whereas of great interest in an aetiological perspective, the finding of a protective role of alcohol on risk for RA must, however, be interpreted with caution in a clinical and public health perspective.
Understanding exercise-dependent plasticity of motoneurons using intracellular and intramuscular approaches
Authors: Button Duane C. , Kalmar Jayne M.
Published: May 2019

Spinal motoneurons (MN) exhibit exercise-dependent adaptations to increased activity, such as exercise and locomotion, as well as decreased activity associated with disuse, spinal cord injury, and aging. The development of several experimental approaches, in both human and animal models, has contributed significantly to our understanding of this plasticity. The purpose of this review is to summarize how intracellular recordings in an animal model and motor unit recordings in a human model have, together, contributed to our current understanding of exercise-dependent MN plasticity. These approaches and techniques will allow neuroscientists to continue to advance our understanding of MN physiology and the plasticity of the “final common path” of the motor system, and to design experiments to answer the critical questions that are emerging in this field.
A phase-field-based lattice Boltzmann method for moving contact line problems on curved stationary boundaries in two dimensions
Authors: Zhao Weifeng
Published: May 2019

In this work, we propose a phase-field-based lattice Boltzmann method to simulate moving contact line (MCL) problems on curved boundaries. The key point of this method is to implement the boundary conditions on curved solid boundaries. Specifically, we use our recently proposed single-node scheme for the no-slip boundary condition and a new scheme is constructed to deal with the wetting boundary conditions (WBCs). In particular, three kinds of WBCs are implemented: two wetting conditions derived from the wall free energy and a characteristic MCL model based on geometry considerations. The method is validated with several MCL problems and numerical results show that the proposed method has utility for all the three WBCs on both straight and curved boundaries.
Implementing ♢P with Bounded Messages on a Network of ADD Channels
Authors: Kumar Saptaparni , Welch Jennifer L.
Published: May 2019

We present an implementation of the eventually perfect failure detector [Formula: see text] from the original hierarchy of the Chandra-Toueg [3] oracles on an arbitrary partitionable network composed of unreliable channels that can lose and reorder messages. Prior implementations of [Formula: see text] have assumed different partially synchronous models ranging from bounded point-to-point message delay and reliable communication to unbounded message size and known network topologies. We implement [Formula: see text] under very weak assumptions on an arbitrary, partitionable network composed of Average Delayed/Dropped (ADD) channels [11] to model unreliable communication. Unlike older implementations, our failure detection algorithm uses bounded-sized messages to eventually detect all nodes that are unreachable (crashed or disconnected) from it.
Bounds on dipole moments of tau-neutrino from single photon searches in SU(4)L × U(1)X model at CLIC and ILC energies
Authors: Binh D. T. , On Vo Van , Long H. N.
Published: May 2019

We investigate the dipole moments of the tau-neutrino at high-energy and high luminosity at linear electron–positron colliders, such as CLIC or ILC through the analysis of the reaction [Formula: see text] in the framework of the [Formula: see text] model. The limits on dipole moment were obtained for integrated luminosity of [Formula: see text] and mass ranging from 0.25 to 1.0 TeV. The estimated limits for the tau-neutrino magnetic and electric dipole moments at 95% of confidence level are [Formula: see text] and [Formula: see text] improved by 2–3 orders of magnitude compared to L3 and complement previous studies on the dipole moments.
Theoretical study of the effects of Mn: N ratios on electronic structure and magnetic properties of (Mn, N)-codoped ZnO
Authors: Wang Chun-An , Fu Si-Lie
Published: May 2019

(Mn, N)-codope is an effective method to achieve both magnetism and p-type stability of ZnO system. In this paper, the magnetism and the p-type stability of (Mn, N)-codoped ZnO with the ratios of 1:1, 1:2 and 2:1 were analyzed through establishing a (2 × 2 × 2) ZnO supercell, in which Zn site was replaced by Mn atom and O site was replaced by N atom. The results of electronic structure analysis show that (Mn, N)-codope is easier to form stable p-type ZnO in comparison to N-mono dope. The p-d coupling between Mn 3d and N 2p states weakens the repulsive force between ions under (Mn, N)-codope condition and results in stable p-type. Especially, the (Mn, N)-codoped ZnO with 2:1 ratio has lower formation energy and higher p-type stability. Furthermore, the results of magnetic analysis also show that the (Mn, N)-codoped ZnO system with 2:1 ratio has higher total magnetic moment than 1:1 and 1:2. A significant ferromagnetic coupling raised by strong p-d interaction between Mn 3d and N 2p in the Mn-N-Mn complex is responsible for these results. However, high N doping ratio is not beneficial to the enhancement of ferromagnetism and p-type stability.
Particle-like behavior of defects near a defect line in 2D Ising model: Defect–antidefect pair production and interaction
Authors: Mostovoy S. D. , Pavlovsky O. V.
Published: May 2019

The aim of this work is to investigate Casimir effect in a system comprising of a defect line along with isolated defects (vacancies) in 2D Ising model. We have found out that the interaction energy has a decaying exponent with distance between defects. We are interested in an analogy between Casimir behavior of this defect structure and quantum field theory. The simplest deformation of a defect line (a defect’s position change) can be treated as defect–“antidefect” pair creation. Single defect is attracted to a defect line. By means of Monte Carlo simulation, the energy of pair creation and Casimir interaction potential are calculated. The interaction turned out that a Yukawa potential turns to the Coulomb’s one at phase transition point.
New Technique for Binary Morphological Shape-Based Interpolation
Authors: Oliveira Walter Alexandre A. de , Guliato Denise , Oliveira Douglas Coelho Braga de , Silva Rodrigo Luis de Souza da , Giraldi Gilson Antonio
Published: May 2019

In this paper we consider shape-based methods to generate additional slices in 3D binary volumes. The focused interpolation approaches, named SIMOL and BORS, are based on morphological and logical operators. Given two adjacent slices [Formula: see text] and [Formula: see text] of the binary image set, the methods iteratively generate a sequence of new slices showing a gradual transition between the corresponding shapes. First, we analyze the SIMOL and BORS techniques and highlight their problems. Then we present the main contribution of this paper: a new interpolation scheme, called SIMOL-NEW, that combines the iterative scheme of BORS and an interpolation kernel generated through SIMOL framework. Next, we compare SIMOL-NEW and BORS approaches using theoretical elements and computational experiments. The latter are executed using: (a) benchmark shapes; (b) simple volumes defined by sphere and paraboloid; (c) combination of ellipsoids; (d) a fork-like volume; (e) Cylinder Minus Sphere. The conclusion is that SIMOL-NEW performs closer to BORS for the cases (a) and (c) but it is more accurate than BORS in the tests (b) and (d). Besides, we offer comparisons of state-of-the-art approaches in shape-based interpolation and SIMOL-NEW using ground truth volumes (d) and (e). The computational experiment report that SIMOL-NEW gets outstanding results regarding the ability to recover the target volume.
Line and Polygon Clipping Techniques on Natural Images — A Mathematical Solution and Performance Evaluation
Authors: Raja S. P.
Published: May 2019

The objective of this paper is to apply clipping techniques on natural images and to analyze the performance of various clipping algorithms in computer graphics. The clipping techniques used in this paper is Cohen–Sutherland line clipping, Liang–Barsky line clipping, Nicholl–Lee–Nicholl line clipping and Sutherland–Hodgman polygon clipping. The clipping algorithms are evaluated by using the three parameters: time complexity, space complexity and image accuracy. Previously, there is no performance evaluation on clipping algorithms done. Motivating by this factor, in this paper an evaluation of clipping algorithms is made. The novelty of this paper is to apply the clipping algorithms on natural images. It is justified that the above mentioned clipping algorithms outperform well on clipping the natural images.
Distinguishing Stock Indices and Detecting Economic Crises Based on Weighted Symbolic Permutation Entropy
Authors: Zhang Ningning , Sun Yupeng , Zhang Yongbo , Yang Pengbo , Lin Aijing , Shang Pengjian
Published: May 2019

Permutation entropy (PE) is evolved as an important way to reveal the intrinsic characteristics of complex systems. While PE does not consider that the amplitudes of identical order sequences might be different, weighted permutation entropy (WPE), the extended technique, weighs each vector to alleviate this problem. Furthermore, experimental investigation shows that symbolizing the time series contributes to detecting sudden dynamical changes. As an exemplary measure, we study weighted symbolic permutation entropy (WSPE) which is a combination of WPE and threshold-dependent symbolic entropy to mount the intrinsic information of four stock indices from China and America stock markets, and six sector indices of banking, aviation industry and pharmacy from China stock markets. One thing needs to be especially pointed out is that symbolic method we use in this work is not the most common method which divides time series into some small bins, but a two-step process, including symbolic process and coding process. The statistical analysis in stock indices shows that WSPE method is capable of distinguishing stock indices and detecting economic crises.
Inferring disease and pathway associations of long non-coding RNAs using heterogeneous information network model
Authors: Sunil Kumar P. V. , Gopakumar G.
Published: May 2019

Recent findings from biological experiments demonstrate that long non-coding RNAs (lncRNAs) are actively involved in critical cellular processes and are associated with innumerable diseases. Computational prediction of lncRNA–disease association draws tremendous research attention nowadays. This paper proposes a machine learning model that predicts lncRNA–disease associations using Heterogeneous Information Network (HIN) of lncRNAs and diseases. A Support Vector Machine classifier is developed using the feature set extracted from a meta-path-based parameter, Association Index derived from the HIN. Performance of the model is validated using standard statistical metrics and it generated an AUC value of 0.87, which is better than the existing methods in the literature. Results are further validated using the recent literature and many of the predicted lncRNA–disease associations are identified as actually existing. This paper also proposes an HIN-based methodology to associate lncRNAs with pathways in which they may have biological influence. A case study on the pathway associations of four well-known lncRNAs (HOTAIR, TUG1, NEAT1, and MALAT1) has been conducted. It has been observed that many times the same lncRNA is associated with more than one biologically related pathways. Further exploration is needed to substantiate whether such lncRNAs have any role in determining the pathway interplay. The script and sample data for the model construction is freely available at http://bdbl.nitc.ac.in/LncDisPath/index.html .
A new algorithm for DNA motif discovery using multiple sample sequence sets
Authors: Yu Qiang , Zhao Xiang , Huo Hongwei
Published: May 2019

DNA motif discovery plays an important role in understanding the mechanisms of gene regulation. Most existing motif discovery algorithms can identify motifs in an efficient and effective manner when dealing with small datasets. However, large datasets generated by high-throughput sequencing technologies pose a huge challenge: it is too time-consuming to process the entire dataset, but if only a small sample sequence set is processed, it is difficult to identify infrequent motifs. In this paper, we propose a new DNA motif discovery algorithm: first divide the input dataset into multiple sample sequence sets, then refine initial motifs of each sample sequence set with the expectation maximization method, and finally combine all the results from each sample sequence set. Besides, we design a new initial motif generation method with the utilization of the entire dataset, which helps to identify infrequent motifs. The experimental results on the simulated data show that the proposed algorithm has better time performance for large datasets and better accuracy of identifying infrequent motifs than the compared algorithms. Also, we have verified the validity of the proposed algorithm on the real data.
A sparse and decomposed particle swarm optimization for inferring gene regulatory networks based on fuzzy cognitive maps
Authors: Liu Luowen , Liu Jing
Published: May 2019

Inferring gene regulatory networks (GRNs) is vital to understand the complex cellular processes and reveal the regulatory mechanisms among genes. Although various methods have been developed, more accurate algorithms which can control the sparseness of GRNs still need to be developed. In this work, we model GRNs by fuzzy cognitive maps (FCMs), and a node in an FCM means a gene. Then, a new sparse and decomposed particle swarm optimization, termed as SDPSOFCM-GRN, is proposed to train FCMs, which employs the least absolute shrinkage and selection operator (Lasso) to control the network sparseness with a decomposed strategy. In the experiments, the performance of SDPSOFCM-GRN is validated on synthetic data and the well-known benchmark DREAM3 and DREAM4. The results show that SDPSOFCM-GRN can well control the sparseness of GRNs, and infer directed GRNs with high accuracy and efficiency.
GEREDB: Gene expression regulation database curated by mining abstracts from literature
Authors: Huang Tinghua , Huang Xiali , Shi Bomei , Yao Min
Published: May 2019

Understanding how genes are expressed and regulated in different biological processes are fundamental and challenging issues. Considerable progress has been made in studying the relationship between the expression and regulation of human genes. However, it is difficult to use these resources productively to analyze gene expression data. GEREDB ( www.thua45.cn/geredb ) has been developed to facilitate analyses that will provide insights into the regulation of genes that govern specific biological responses. GEREDB is a publicly available, manually curated biological database that stores the data regarding relationships between expression and regulation of human genes. To date, more than 39,000 Links have been contextually annotated by reviewing more than 53,000 abstracts. GEREDB can be searched using the official NCBI gene symbol as a query, and it can be downloaded along with the GEREA software package. GEREDB has the ability to analyze user-supplied gene expression data in a causal analysis oriented manner using the GEREA bioinformatics tool.
A simple criterion for the class number of a quadratic number field to be one
Authors: Viñas Víctor Julio Ramírez
Published: May 2019

Let [Formula: see text] be a square-free positive integer, [Formula: see text] if [Formula: see text] and [Formula: see text] otherwise. Let [Formula: see text] and [Formula: see text] be integers, where [Formula: see text] is a prime. Suppose that [Formula: see text] for some integer [Formula: see text]. Suppose that there exist integers [Formula: see text] and [Formula: see text] such that [Formula: see text]. We prove that if [Formula: see text] is [Formula: see text] or a prime for all integers [Formula: see text] with [Formula: see text], then the class number of the field [Formula: see text] is [Formula: see text].
On conjectural rank parities of quartic and sextic twists of elliptic curves
Authors: Weidner Matthew
Published: May 2019

We study the behavior under twisting of the Selmer rank parities of a self-dual prime-degree isogeny on a principally polarized abelian variety defined over a number field, subject to compatibility relations between the twists and the isogeny. In particular, we study isogenies on abelian varieties whose Selmer rank parities are related to the rank parities of elliptic curves with [Formula: see text]-invariant 0 or 1728, assuming the Shafarevich–Tate conjecture. Using these results, we show how to classify the conjectural rank parities of all quartic or sextic twists of an elliptic curve defined over a number field, after a finite calculation. This generalizes the previous results of Hadian and Weidner on the behavior of [Formula: see text]-Selmer ranks under [Formula: see text]-twists.
A q-congruence involving the Jacobi symbol
Authors: Guo Victor J. W. , Ni He-Xia
Published: May 2019

Let [Formula: see text] be a positive odd integer and [Formula: see text] a positive integer with [Formula: see text]. We prove that [Formula: see text] Here [Formula: see text], [Formula: see text] denotes the Jacobi symbol, and [Formula: see text] is the [Formula: see text]th cyclotomic polynomial in [Formula: see text]. This confirms a recent conjecture of the first author.
Multidither coherent optical adaptive technique for deep tissue two-photon microscopy
Authors: Zhang Biwei , Gong Wei , Wu Chenxue , Hu Lejia , Zhu Xinpei , Si Ke
Published: May 2019

Two-photon microscopy normally suffers from the scattering of the tissue in biological imaging. Multidither coherent optical adaptive technique (COAT) can correct the scattered wavefront in parallel. However, the determination of the corrective phases may not be completely accurate using conventional method, which undermines the performance of this technique. In this paper, we theoretically demonstrate a method that can obtain more accurate corrective phases by determining the phase values from the square root of the fluorescence signal. A numerical simulation model is established to study the performance of adaptive optics in two-photon microscopy by combining scalar diffraction theory with vector diffraction theory. The results show that the distortion of the wavefront can be corrected more thoroughly with our method in two-photon imaging. In our simulation, with the scattering from a 450-[Formula: see text]m-thick mouse brain tissue, excitation focal spots with higher peak-to-background ratio (PBR) and images with higher contrast can be obtained. Hence, further enhancement of the multidither COAT correction performance in two-photon imaging can be expected.
Plio-Quaternary transpressive tectonics: a key factor in the structural evolution of the outer Apennine–Adriatic system, Italy
Authors: Pierantoni P.P. , Chicco J. , Costa M. , Invernizzi C.
Published: May 2019

We used data from seismic reflection profiles and well logs from both onshore and offshore locations along the Adriatic coast to investigate the structural style and recent active deformation in the external area of the northern Apennines adjoining the Po Plain. We prepared four NE–SW sub-parallel transects based on a detailed interpretation of the available subsurface data, supported by surface geological data. Through analysis of the well logs, we identified two significant seismo-stratigraphic markers, together with some unconformities within the Middle Pliocene/Quaternary succession. We propose a detailed structural scheme for the area that identifies and interprets both the outcropping and buried Apennine structures. NW/NNW–SE/SSE high-angle transpressive or flower structures, referred to the recent and actual deformation history, may be responsible for surface features and features at shallow depths, with possible implications for active tectonics. We show the continuity of some of these structures towards the Conero area to the south, suggesting a wider and more regional meaning for the proposed tectonic style. These Apenninic structures close against the active NNE–SSW Cattolica fault system in the northern offshore part of the area to form an asymmetrical arch. This study contributes to the interpretation of the deformation style of the outer northern Apennines.

Supplementary material:
High resolution seismic lines not interpreted are available at
https://doi.org/10.6084/m9.figshare.c.4497542

Thematic collection:
This article is part of the ‘Apennines and Tyrrhenian system’ collection available at:
https://www.lyellcollection.org/cc/the-apennines-tyrrhenian-system