bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Arabidopsis transcription factor AINTEGUMENTA orchestrates patterning genes and auxin signaling in the establishment of floral growth and form
Authors: Krizek Beth A. , Blakley Ivory C. , Ho Yen‐Yi , Freese Nowlan , Loraine Ann E. 
Published: April 2020

SUMMARYUnderstanding how flowers form is an important problem in plant biology, as human food supply depends on flower and seed production. Flower development also provides an excellent model for understanding how cell division, expansion and differentiation are coordinated during organogenesis. In the model plant Arabidopsis thaliana, floral organogenesis requires AINTEGUMENTA (ANT) and AINTEGUMENTA‐LIKE 6 (AIL6)/PLETHORA 3 (PLT3), two members of the Arabidopsis AINTEGUMENTA‐LIKE/PLETHORA (AIL/PLT) transcription factor family. Together, ANT and AIL6/PLT3 regulate aspects of floral organogenesis, including floral organ initiation, growth, identity specification and patterning. Previously, we used RNA‐Seq to identify thousands of genes with disrupted expression in ant ail6 mutant flowers, indicating that ANT and AIL6/PLT3 influence a vast transcriptional network. The immediate downstream targets of ANT and AIL6/PLT3 in flowers are unknown, however. To identify direct targets of ANT regulation, we performed an RNA‐Seq time‐course experiment in which we induced ANT activity in transgenic plants bearing an ANT‐glucocorticoid receptor fusion construct. In addition, we performed a ChIP‐Seq experiment that identified ANT binding sites in developing flowers. These experiments identified 200 potential ANT target genes based on their proximity to ANT binding sites and differential expression in response to ANT. These 200 candidate target genes were involved in functions such as polarity specification, floral organ development, meristem development and auxin signaling. In addition, we identified several genes associated with lateral organ growth that may mediate the role of ANT in organ size control. These results reveal new features of the ANT transcriptional network by linking ANT to previously unknown regulatory targets.
Optimization of Fin Parameters to Reduce Entropy Generation and Melting Time of a Latent Heat Storage Unit
Authors: Kalapala Lokesh , Devanuri Jaya Krishna 
Published: April 2020

Abstract
One of the challenges in the design and development of a latent heat storage unit (LHSU) is to increase the charging and discharging rates which are inherently low because of low thermal conductivity of phase change materials (PCM). Out of various heat transfer enhancement techniques, employing annular fins is very simple, efficient and no fabrication complexity is involved. Fin parameters (fin size and number of fins) significantly influence the enhancement in heat transfer rate. Hence, optimization of fin parameters is necessary for the efficient design of an LHSU. While designing an LHSU along with heat transfer rate, entropy generation should also be considered in order to make it exergetically efficient. Therefore, the present study is aimed at multi-objective optimization of annular fin parameters to minimize the melting time and entropy generation. Fin diameter and the number of fins are taken as the variables. The influence of these two variables on the melting time, average Nusselt number, energy stored, and distribution of entropy is presented. The melting rate is increased, and global entropy generation decreased by increasing the number of fins up to 15. An increase in the fin diameter reduced the melting time while entropy generation got increased. For the multi-objective optimization, the multi-objective optimization based on ratio analysis (MOORA) technique is chosen and the optimized values of fin diameter and number of fins are observed to be 80 mm and 15 respectively. Finally, optimized parameters are represented in non-dimensional form to make them applicable for any size of the LHSU.
Low Intensity Ultrasound Induces Epithelial Cell Adhesion Responses
Authors: Lim Jormay , Chu Yeh-Shiu , Chu Ya-Cherng , Lo Chun-Min , Wang Jaw-Lin 
Published: April 2020

Abstract
In this study, we investigated the cellular mechanosensitive responses to a low intensity ultrasound (LIUS) stimulation (ISATA = 1 mW/cm2, pressure = 10 kPa). The dose and temporal effects at cell–substrate adhesion (CSA) at the basal level and cell–cell adhesion (CCA) at the apical level are reported in detail. A model of mouse mammary gland epithelial cells (EpH4) and the phosphorylation of mechanosensitive 130 kDa Crk-associated substrate (p130CAS) as an indicator for cellular responses were used. The intensity of phospho-p130CAS was found to be dependent on LIUS stress level, and the p130CAS was phosphorylated after 1 min stimulation at CSA. The phospho-p130CAS was also found to increase significantly at CCA upon LIUS stimulation. We confirmed that the cellular responses to ultrasound are immediate and dose dependent. Ultrasound affects not only CSA but also CCA. An E-cadherin knockout (EpH4ECad−/−) model also confirmed that phosphorylation of p130CAS at CCA is related to E-cadherins.
Estimation of Minimum Design Metal Temperature by MDMT Curve and Correlations of Charpy Impact and Fracture Toughness
Authors: Zhou Zhongqiang , Huang Song , Hui Hu , Zhang Yalin 
Published: April 2020

Abstract
Charpy impact specimens are preferred to characterize the deterioration of steel in irradiation surveillance program in nuclear industry. But the fracture toughness cannot be acquired by the Charpy impact experiment directly. In this paper, the reference temperature T0MC of Q345R and A508-3 are determined by experiment and empirical formulas between Charpy impact energy (CVN) and fracture toughness. The measured values of T0MC are compared with predicted values. Empirical formulas combined with minimum design metal temperature (MDMT) curve is put forward to determine the minimum design metal temperature of ferritic steel conservatively.
Identification of a Cytopathogenic Toxin from Sneathia amnii
Authors: Gentile Gabriella L. , Rupert Amy Sanford , Carrasco Lizette I. , Garcia Erin M. , Kumar Naren Gajenthra , Walsh Scott W. , Jefferson Kimberly K. 
Published: April 2020

ABSTRACT
Sneathia amnii is a poorly characterized emerging pathogen that has been implicated in amnionitis and urethritis. We found that S. amnii damages fetal membranes, and we identified and purified a cytotoxic exotoxin that lyses human red blood cells and damages cells from fetal membranes. The gene appears to be cotranscribed with a second gene that encodes a protein with identity to two-partner system transporters, suggesting that it is the “A,” or secreted component of a type Vb system. The toxin is 1,881 amino acids with a molecular weight of approximately 200 kDa. It binds to red blood cell membranes and forms pores with a diameter of 2.0 to 3.0 nm, resulting in osmolysis. Because it appears to be the “A” or passenger component of a two-partner system, we propose to name this novel cytotoxin/hemolysin CptA for cytopathogenic toxin component A.
IMPORTANCE Sneathia amnii is a very poorly characterized emerging pathogen that can affect pregnancy outcome and cause urethritis and other infections. To date, nothing is known about its virulence factors or pathogenesis. We have identified and isolated a cytotoxin, named CptA for cytopathogenic toxin, component A, that is produced by S. amnii. CptA is capable of permeabilizing chorionic trophoblasts and lysing human red blood cells and, thus, may play a role in virulence. Except for small domains conserved among two-partner secretion system passenger proteins, the cytotoxin exhibits little amino acid sequence homology to known toxins. In this study, we demonstrate the pore-forming activity of this novel toxin.
Francisella novicida CRISPR-Cas Systems Can Functionally Complement Each Other in DNA Defense while Providing Target Flexibility
Authors: Ratner Hannah K. , Weiss David S. 
Published: April 2020

ABSTRACT
CRISPR-Cas systems are prokaryotic adaptive immune systems that facilitate protection of bacteria and archaea against infection by external mobile genetic elements. The model pathogen Francisella novicida encodes a CRISPR-Cas12a (FnoCas12a) system and a CRISPR-Cas9 (FnoCas9) system, the latter of which has an additional and noncanonical function in bacterial virulence. Here, we investigated and compared the functional roles of the FnoCas12a and FnoCas9 systems in transformation inhibition and bacterial virulence. Unlike FnoCas9, FnoCas12a was not required for F. novicida virulence. However, both systems were highly effective at plasmid restriction and acted independently of each other. We further identified a critical protospacer-adjacent motif (PAM) necessary for transformation inhibition by FnoCas12a, demonstrating a greater flexibility for target identification by FnoCas12a than previously appreciated and a specificity that is distinct from that of FnoCas9. The effectors of the two systems exhibited different patterns of expression at the mRNA level, suggesting that they may confer distinct benefits to the bacterium in diverse environments. These data suggest that due to the differences between the two CRISPR-Cas systems, together they may provide F. novicida with a more comprehensive defense against foreign nucleic acids. Finally, we demonstrated that the FnoCas12a and FnoCas9 machineries could be simultaneously engineered to restrict the same nonnative target, thereby expanding the toolset for prokaryotic genome manipulation.
IMPORTANCE CRISPR-Cas9 and CRISPR-Cas12a systems have been widely commandeered for genome engineering. However, they originate in prokaryotes, where they function as adaptive immune systems. The details of this activity and relationship between these systems within native host organisms have been minimally explored. The human pathogen Francisella novicida contains both of these systems, with the Cas9 system also exhibiting a second activity, modulating virulence through transcriptional regulation. We compared and contrasted the ability of these two systems to control virulence and restrict DNA within their native host bacterium, highlighting differences and similarities in these two functions. Collectively, our results indicate that these two distinct and reprogrammable endogenous systems provide F. novicida with a more comprehensive defense against mobile genetic elements.
Global Regulatory Roles of the Histidine-Responsive Transcriptional Repressor HutC in Pseudomonas fluorescens SBW25
Authors: Naren Naran , Zhang Xue-Xian 
Published: April 2020

ABSTRACT
HutC is known as a transcriptional repressor specific for histidine utilization (hut) genes in Gram-negative bacteria, including Pseudomonas fluorescens SBW25. However, its precise mode of protein-DNA interactions hasn’t been examined with purified HutC proteins. Here, we performed electrophoretic mobility shift assay (EMSA) and DNase I footprinting using His6-tagged HutC and biotin-labeled probe of the hut promoter (PhutU). Results revealed a complex pattern of HutC oligomerization, and the specific protein-DNA interaction is disrupted by urocanate, a histidine derivative, in a concentration-dependent manner. Next, we searched for putative HutC-binding sites in the SBW25 genome. This led to the identification of 143 candidate targets with a P value less than 10−4. HutC interaction with eight selected candidate sites was subsequently confirmed by EMSA analysis, including the type IV pilus assembly protein PilZ, phospholipase C (PlcC) for phosphatidylcholine hydrolyzation, and key regulators of cellular nitrogen metabolism (NtrBC and GlnE). Finally, an isogenic hutC deletion mutant was subjected to transcriptome sequencing (RNA-seq) analysis and phenotypic characterization. When bacteria were grown on succinate and histidine, hutC deletion caused upregulation of 794 genes and downregulation of 525 genes at a P value of <0.05 with a fold change cutoff of 2.0. The hutC mutant displayed an enhanced spreading motility and pyoverdine production in laboratory media, in addition to the previously reported growth defect on the surfaces of plants. Together, our data indicate that HutC plays global regulatory roles beyond histidine catabolism through low-affinity binding with operator sites located outside the hut locus.
IMPORTANCE HutC in Pseudomonas is a representative member of the GntR/HutC family of transcriptional regulators, which possess a N-terminal winged helix-turn-helix (wHTH) DNA-binding domain and a C-terminal substrate-binding domain. HutC is generally known to repress expression of histidine utilization (hut) genes through binding to the PhutU promoter with urocanate (the first intermediate of the histidine degradation pathway) as the direct inducer. Here, we first describe the detailed molecular interactions between HutC and its PhutU target site in a plant growth-promoting bacterium, P. fluorescens SBW25, and further show that HutC possesses specific DNA-binding activities with many targets in the SBW25 genome. Subsequent RNA-seq analysis and phenotypic assays revealed an unexpected global regulatory role of HutC for successful bacterial colonization in planta.
The exhumation detachment factory
Authors: Peron-Pinvidic Gwenn , Naliboff John 
Published: April 2020

Abstract
Rifted margins include series of tectonic structures and basement geometries that record the thinning of continental crust and the birth of oceanic spreading centers. A consensus has been reached on the fact that the evolution is composite, including a phase of basement exhumation during which detachment faults play a major role. Rolling-hinge–type models are often advocated as the driving mechanism for basement exhumation, although the structural complexity of the exhumed regions frequently prohibits detailed analysis of the ways in which the faults form and evolve through time. Here, we place constraints on this process through an analysis of continental rifting numerical simulations, which we used to map fault network activity. The high-resolution models and mapping reveal a specific weak surface where detachments initiate at depth and terminate while migrating upward to the seafloor. This “detachment factory” model provides constraints on where, when, and how detachment faults originate in an exhumation system. Our model also predicts how abandoned detachments migrate off-axis with time, within the footwall and hanging wall, generating specific signals in geophysical data sets.
The origin of neotectonics on the lunar nearside
Authors: Valantinas A. , Schultz P.H. 
Published: April 2020

Abstract
New observations of wrinkle ridges on the nearside maria of the Moon display signs of ongoing ridge modification. In association with the wrinkle ridges, we observed an absence of superposed craters, narrow (&lt;30 m) lobate scarps and graben, and thermal anomalies related to exposures of meter-size blocks. Many of these active wrinkle ridge systems are well beyond the influence of mascon basins and unrelated to any global tectonic pattern. Nevertheless, they spatially correlate with ancient deep-seated dike intrusions on the lunar nearside revealed by gravity data analysis. We propose that this active nearside tectonic system (ANTS) reflects ongoing reactivation of an ancient system related to offset antipodal effects from the South Pole–Aitken basin.
Hepatitis C elimination in the Netherlands (CELINE): study protocol for nationwide retrieval of lost to follow-up patients with chronic hepatitis C
Authors: Isfordink Cas J , Brakenhoff Sylvia M , van Dijk Marleen , van der Valk Marc , de Knegt Rob J , Arends Joop E , Drenth Joost PH 
Published: April 2020

BackgroundThe Netherlands has a low hepatitis C virus (HCV) prevalence, estimated at 0.16%. Previous studies have shown that up to 30% of the diagnosed HCV population in the Netherlands has been lost to follow-up (LTFU). Retrieval of these patients could halt progression of liver disease in infected patients, reduce the number of infected individuals and limit HCV transmission. Several regional Dutch retrieval projects have already been executed, which demonstrated that retrieval is feasible. Therefore, we initiated a nationwide retrieval project, aiming to achieve microelimination in previously diagnosed but LTFU patients with chronic HCV through retrieval.MethodsLaboratory records will be used to identify possible patients with chronic hepatitis C, defined as either a positive most recent HCV RNA or positive HCV antibodies without known RNA result. Reviewing patient records and obtaining current contact information from municipality databases will identify LTFU patients who are eligible for retrieval. These patients will be invited for outpatient clinic care. The primary outcome of the study is the total number of LTFU patients who have been successfully linked to care.DiscussionHepatitis C ELimination In the NEtherlands (CELINE) is within the remit of WHO elimination targets and the Dutch National Hepatitis Plan. The methodology of CELINE is based on previously conducted regional retrieval projects and is designed to overcome some of their limitations. After ethical approval was obtained in 2018, the first centre initiated retrieval in 2018 and the project is expected to finish in 2021.Trial registration numberNCT04208035.
Impact of ‘HIV-related stigma-reduction workshops’ on knowledge and attitude of healthcare providers and students in Central India: a pre-test and post-test intervention study
Authors: Machowska Anna , Bamboria Babu Lal , Bercan Courtney , Sharma Megha 
Published: April 2020

IntroductionPeople living with HIV and AIDS (PLWHA) experience stigma and discrimination throughout their life. The consequences of stigma and discrimination are severe when enacted by healthcare providers (HCPs), and result in a delay in or poor adherence to treatment. Studies have demonstrated the presence of stigmatising behaviours among HCPs, yet only a few have presented the impact of interventions on the knowledge and attitude of practising (clinicians and nurses) and future (students) HCPs.ObjectivesTo evaluate knowledge, attitudes and infection risk perceptions related to HIV/AIDS among practising and future HCPs in central India. In addition, the impact of the ‘HIV-related stigma-reduction workshop’ using a pre-intervention and post-intervention study design was evaluated.Settings and participantsThe study was conducted in 2016 at two tertiary-care hospitals and three healthcare colleges in central India. Overall, 650 HCPs (75 clinicians and 211 nurses) and students (205 medical, 123 nursing and 36 Diploma in Medical and Laboratory Technology (DMLT)) voluntarily participated in the study.InterventionThe educational intervention comprised of training in epidemiology, the transmission and treatment of the HIV infection, the rights of PLWHA, the duties of HCPs and the use of standard precautions.ResultsAt pre-intervention, DMLT students had the lowest and clinicians the highest knowledge scores (24% and 45%, respectively). The stigmatised attitude was reflected in all groups, the lowest among clinicians (21%) and the highest among DMLT students (34%). Improvement in the post-intervention knowledge scores was the highest in medical students (36%) and the lowest among clinicians (16%). The participants’ attitudes improved between 3% and 17% across all groups.ConclusionsSignificant post-intervention improvements were seen in both knowledge and attitudes in all groups. Students had a higher tendency to improve than HCPs. Further long-term studies are needed to evaluate the sustainability of the improvements in knowledge and attitudes of the participants.
Definitions of blinding in randomised controlled trials of interventions published in high-impact anaesthesiology journals: a methodological study and survey of authors
Authors: Penić Antonija , Begić Dinka , Balajić Karolina , Kowalski Martin , Marušić Ana , Puljak Livia 
Published: April 2020

ObjectivesTo analyse the completeness of reporting of blinding in randomised controlled trials (RCTs) of interventions in anaesthesiology, the actual blinding status of various persons associated with an RCT and trial authors’ interpretation of blinding terminology related to RCTs.MethodsThis was a methodological study and a cross-sectional survey. We analysed reporting related to blinding in published RCTs of interventions published in seven highly cited anaesthesiology journals from 2014 to 2016 and registered protocols in ClinicalTrials.gov. We surveyed corresponding authors of included RCTs about their definitions of blinding. The primary outcome was the number of RCTs that explicitly described who was blinded in a trial. Secondary outcomes were definitions of blinding terminology in the trials; trial authors’ interpretation of blinding terminology; discrepancies in the blinding description within registered protocols and between registered protocols and publications.ResultsOut of 622 analysed RCTs, 38% were not explicitly described as either open label or blinded studies and 10% did not report any information about blinding or lack of blinding. Only one manuscript fully reported the status of blinding for various individuals that may be involved with a trial. The most common descriptor was that a trial was double-blind. We found discrepant information regarding blinding in the majority of registered protocols. Even when there were no discrepancies in the registration, we found discrepancies in the reporting of blinding between the majority of registered protocols and published manuscripts. The survey of authors (40 responses from 231 eligible authors; 17% response rate) of analysed RCTs showed that they differed in how they defined different levels of blinding in trials.ConclusionsReporting of the blinding status of key individuals involved in analysed anaesthesiology RCTs was insufficient. For reporting guidelines, peer reviewers and editors should insist on clear information on who was blinded in a trial instead of using the term ‘double-blind’ for different blinding practices.