bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of pressure loss in a circular pipe under ultrasonic waves released along main stream flow
Authors: Treegosol Pongsapak , Priyadumkol Jetsadaporn , Katchasuwanmanee Kanet , Chaiworapuek Weerachai 
Published: May 2021

Abstract
Recently, ultrasound was discovered to have great potential in enhancing heat transfer from thermal systems., However, there is little information of the flow resistance, induced by its waves. Therefore, this research investigates the pressure loss of turbulent water flow in a circular pipe disturbed by 25 kHz ultrasound at the Reynolds number of 10,000, 12,500, 15,000, 17,500, 20,000, 22,500, and 25,000. The size of test section was modeled in accordance with the power plant’s condenser and the flow had been verified by the comparison of friction factor with theory. The maximum and minimum differences were 9.79 and 0.33%, respectively, confirming the reliability of the test setup. In this study, ultrasound was released along the mainstream flow from 3 and 15 transducers, installed upstream of the pipe. The results confirmed that the ultrasound was slightly affected on the friction loss of turbulent pipe flow. The average increase of pressure loss was 0.077% and 0.833% by the waves when they were emitted from 3 and 15 transducers, respectively. With very low inducement of flow resistance, ultrasound can be accounted as one of the most promising techniques for heat transfer enhancement, applicable to many thermal systems such as condensers, in the future.
Effect of low-frequency ultrasonic waves on heat transfer of laminar water flow over a heating flat plate
Authors: Phetchoo Satanon , Mingbunjerdsuk Jirachai , Katchasuwanmanee Kanet , Chaiworapuek Weerachai 
Published: May 2021

Abstract
This research investigates the effect of 40, 80, and 120 kHz ultrasound on heat transfer of laminar water flow over a heating flat plate using thin leaf thermocouples in a low turbulence water tunnel. The mainstream velocity was set at 0.127 m/s, corresponding to the local Reynolds number during 65,181 – 148,390 in the test section. The ultrasonic waves were released perpendicular to the mainstream and vertically from the upper wall at the distance of 0.15 m to the heating plate having constant heat flux of 1,040 W/m2. The results show that the ultrasound, having frequencies of 40 and 120 kHz provides the maximum Nusselt number up to 15% and 31%, respectively at the most downstream position of the test region. In the meantime, the 80 kHz waves slightly affect the heat transfer over a flat plate. Hence, in an attempt to employ the ultrasound for heat transfer enhancement over a flat plate, the distance and ultrasonic frequency must be well considered.
Analyze open channel for continuously low speed used carbon dioxide bubbles
Authors: Kirasamutranon L. , Kirasamutranon K. , Saimek S. 
Published: May 2021

Abstract
Designing a recirculating open-channel for continuously low speed in place of a towing tank required checking on its flow characteristics. There are many methods for checking the flow characteristics such as food coloring techniques, using buoys and hydrogen gas bubbles, etc. For this research, we use carbon dioxide bubbles which are caused by the reaction between sodium bicarbonate (NaHCO3) and hydrochloric acid (HCl) that is diluted in water until the acidity is equal to pH 3. Our experiments were carried at the area near the wall and the center of the test range at depths 6, 8 and 10 centimeters from the free surface level respectively. From the experimental results, the trend of water flow patterns in the center of the channel using food coloring needles technique tends to form the fluid flow close to the computational fluid dynamics (CFD) while the results from the carbon dioxide bubble technique are different compared with the two previous techniques by less than 20 percent, and the trends of the water flow pattern results of the numerical method, the food coloring needle, and the carbon dioxide bubble techniques. The tendency of the flow pattern in the same direction.
On the origin and correction for inner filter effects in fluorescence. Part II: secondary inner filter effect -the proper use of front-face configuration for highly absorbing and scattering samples
Authors: Ceresa Luca , Kimball Joseph , Chavez Jose , Kitchner Emma , Nurekeyev Zhangatay , Doan Hung , Borejdo Julian , Gryczynski Ignacy , Gryczynski Zygmunt 
Published: May 2021

Abstract
Fluorescence is an established technology for studying molecular processes and molecular interactions. More recently fluorescence became a leading method for detection, sensing, medical diagnostics, biotechnology, imaging, DNA analysis, and gene expression. Consequently, precise and accurate measurements in various conditions have become more critical for proper result interpretations. Previously, in Part 1, we discussed inner filter effect type I, which is a consequence of the instrumental geometrical sensitivity factor and absorption of the excitation. In this part, we analyze inner filter effect type II and discuss the practical consequences for fluorescence measurements in samples of high optical density (absorbance/scattering). We consider both the standard square and front-face experimental configurations, discuss experimental approaches to limit/mitigate the effect and discuss methods for correcting and interpreting experimental results.
Surfactant-free commercial electroless bath with low concentration of SiC nanoparticles to prepare the NiP-SiC nanocomposite coatings
Authors: Khodaei M , Gholizadeh A Mohammad 
Published: May 2021

AbstractFabrication of NiP-SiC nanocomposite coatings through the electroless deposition in a commercial electrolyte containing the low concentrations of SiC nanoparticles on carbon steel substrate was studied in this work. The confirmation of co-deposition of Ni matrix and SiC nanoparticles was investigated by evaluating the effect on morphology, crystal structure, and corrosion behavior of the heat-treated coatings which were investigated by scanning electron microscope, x-ray diffraction (XRD), and electrochemical measurements, respectively. The XRD results revealed that the heat-treated NiP and NiP-SiC coatings consisted of Ni and Ni3P phases, which the calculated faction of Ni3P phase for NiP and NiP-SiC samples is 58.2 and 62.2%, respectively. The corrosion resistance of nanocomposite samples is higher than that of pure NiP sample (9 to 76% corrosion inhibition efficiency. The tribological behavior of the coatings was characterized by microhardness measurement and ‘pin on disk’ wear test. By co-deposition of SiC nanoparticles, the hardness of heat-treated NiP is significantly increased (near 25%) and the wear loss is reduced (near 48%), especially at high sliding distance during wear test. The sample prepared through the surfactant-free electroless bath containing the 1 g l−1SiC nanoparticle showed the best corrosion as well as wear resistance.
Structural transition from a ring to a folded structure of a seamless nanobelt
Authors: Inui Norio , Makimoto Taichi , Moritani Kousuke 
Published: May 2021

Abstract
Stable structures of a rolled seamless belt of atoms arranged in a two-dimensional honeycomb lattice such as a carbon nano-belt, transit from a ring-shaped structure with a rotational invariance to folded structures as the circumference of the belt increases. Using molecular mechanics, we consider the size dependence of the structures obtained by simulated annealing. In addition, the relationship between the variety of metastable structures and the rate of temperature decrease during annealing is also examined. Furthermore, we investigate the effects of the van der Waals interaction between the surfaces on the structural transitions.
Differential expression of phosphorylated MEK and ERK correlates with aggressive BCC subtypes
Authors: Rahman Muhammad M , Herath Dimalee , Bladen John C , Atkar Ravinder , Pirzado Muhammad S , Harwood Catherine , Philpott Michael P , Neill Graham W 
Published: May 2021

Abstract
Basal cell carcinoma (BCC) is associated with aberrant Hedgehog (HH) signalling through mutational inactivation of PTCH1; however, there is conflicting data regarding MEK/ERK signalling in BCC and the signalling pathway interactions in these carcinomas. To address this, expression of active phospho (p) MEK and ERK was examined in a panel of 15 non-aggressive and 14 aggressive BCCs. Although not uniformly expressed, both phospho-proteins were detected in the nuclei and/or cytoplasm of normal and tumour-associated epidermal cells however, whereas phospho-MEK (pMEK) was present in all non-aggressive BCCs (14/14), phospho-ERK (pERK) was rarely expressed (2/14). In contrast pERK expression was more prevalent in aggressive tumours (11/14). Interestingly, pMEK was only localized to the tumour mass whereas pERK was expressed in tumours and stroma of aggressive BCCs. Similarly, pERK (but not pMEK) was absent in mouse BCC-like tumours derived from X-ray irradiated Ptch1+/− mice with stromal pERK observed in myofibroblasts of the aggressive variant as well as in the tumour mass. RNA sequencing analysis of tumour epithelium and stroma of aggressive and non-aggressive BCC revealed the upregulation of epidermal growth factor receptor- and ERK-related pathways. Angiogenesis and immune response pathways were also upregulated in the stroma compared with the tumour. PTCH1 suppressed NEB1 immortalized keratinocytes (shPTCH1) display upregulated pERK that can be independent of MEK expression. Furthermore, epidermal growth factor pathway inhibitors affect the HH pathway by suppressing GLI1. These studies reveal differential expression of pERK between human BCC subtypes that maybe active by a pathway independent of MEK.
Antibiotic Utilization in Deceased Organ Donors
Authors: Anesi Judith A , Lautenbach Ebbing , Han Jennifer , Lee Dong Heun , Clauss Heather , Climaco Antonette , Hasz Richard , Bilker Warren B , Molnar Esther , Alimenti Darcy , West Sharon , Tolomeo Pam , Blumberg Emily A 
Published: May 2021

Abstract
Antibiotic use in deceased organ donors has not been previously described. In a retrospective cohort of 440 donors, we found 427 (97%) received at least one antibiotic course, 312 (71%) received broad-spectrum antibiotics, and 61 (14%) received potentially redundant antibiotics during their terminal hospitalization, suggesting a need for stewardship.
Cardionephrology from the point of view of the cardiologist: no more agree to disagree—getting to ‘yes’ for every patient
Authors: Burlacu Alexandru , McCullough Peter A , Covic Adrian 
Published: May 2021

Abstract
Whether one wants to or not, interactions between the heart and the kidneys exist and manifest nevertheless. Both from theoretical and clinical perspectives, it seems the need for a subspecialty of cardionephrology seems justified. Our editorial is a cardiologist perspective on the article by Diez and Ortiz published in Clinical Kidney Journal related to the ‘need for a cardionephrology subspecialty’. We analysed the historical similarities of the emergence of already ingrained clinical fields with the current needs in the cardionephrology sector. We motivated our approach based on novel cardiovascular diagnostic and therapeutic developments and significant pathophysiological differences from a cardiological perspective, accounting for the foundation of a novel sustainable medical field. One of the sensitive issues we also addressed was the operationality and applicability of the principles. We answered with some examples from high-risk debatable contexts the question of where a cardionephrologist should be integrated. Clarifying the operationality aspects would be a positive shift towards improving guidelines adherence in managing complex patients. In conclusion, we underline that the necessity of a cardionephrologist must be addressed from an operational and scientific perspective, with the ultimate goal of reducing mortality and complications in cardiorenal patients.
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses
Authors: Choteau Sebastien A , Wagner Audrey , Pierre Philippe , Spinelli Lionel , Brun Christine 
Published: May 2021

Abstract
The development of high-throughput technologies revealed the existence of non-canonical short open reading frames (sORFs) on most eukaryotic ribonucleic acids. They are ubiquitous genetic elements conserved across species and suspected to be involved in numerous cellular processes. MetamORF (https://metamorf.hb.univ-amu.fr/) aims to provide a repository of unique sORFs identified in the human and mouse genomes with both experimental and computational approaches. By gathering publicly available sORF data, normalizing them and summarizing redundant information, we were able to identify a total of 1 162 675 unique sORFs. Despite the usual characterization of ORFs as short, upstream or downstream, there is currently no clear consensus regarding the definition of these categories. Thus, the data have been reprocessed using a normalized nomenclature. MetamORF enables new analyses at locus, gene, transcript and ORF levels, which should offer the possibility to address new questions regarding sORF functions in the future. The repository is available through an user-friendly web interface, allowing easy browsing, visualization, filtering over multiple criteria and export possibilities. sORFs can be searched starting from a gene, a transcript and an ORF ID, looking in a genome area or browsing the whole repository for a species. The database content has also been made available through track hubs at UCSC Genome Browser. Finally, we demonstrated an enrichment of genes harboring upstream ORFs among genes expressed in response to reticular stress.
Database URL https://metamorf.hb.univ-amu.fr/
Case report of recurrent haemoptysis in an older patient with repaired tetralogy of Fallot
Authors: Vanderschueren Emma , Budts Werner , Van De Bruaene Alexander 
Published: May 2021

Abstract

Background
Tetralogy of Fallot (TOF) is the most common cyanotic congenital heart defect. Although most infants nowadays undergo surgical repair approximately at the age of 6 months with excellent outcomes, older patients typically underwent a staged approach with an initial systemic-to-pulmonary Blalock–Taussig–Thomas (BTT) shunt reducing hypoxaemia, followed by surgical TOF repair at an older age (with takedown of the BTT shunt). Late complications related to the BTT shunt are rare.

Case summary
We report a case of recurrent haemoptysis late after classic BTT shunt and subsequent surgical TOF repair. Axial imaging indicated a stellate nodule with isotope accumulation in the right upper lung lobe, whereas bronchoscopy showed a rope-like structure in the bronchus to the right upper lung lobe. The patient underwent a lobectomy of the superior right lobe, with identification of what appeared to be the old suture around the BTT shunt. Anatomopathology confirmed diffuse necrotizing inflammation with erosion into the bronchus which eventually caused haemoptysis.

Discussion
Management of older patients with congenital heart disease requires a thorough knowledge of the anatomy and surgical history of the patient. Although late complications related to a BTT shunt are rare, a residual shunt, endocarditis, pseudoaneurysm, or chronic inflammation with haemoptysis may occur.
Differences in Vaginal Microbiota, Host Transcriptome, and Proteins in Women With Bacterial Vaginosis Are Associated With Metronidazole Treatment Response
Authors: Serebrenik Joyce , Wang Tao , Hunte Richard , Srinivasan Sujatha , McWalters Jessica , Tharp Gregory K , Bosinger Steven E , Fiedler Tina L , Atrio Jessica M , Murphy Kerry , Barnett Rebecca , Ray Laurie R , Krows Meighan L , Fredricks David N , Irungu Elizabeth , Ngure Kenneth , Mugo Nelly , Marrazzo Jeanne , Keller Marla J , Herold Betsy C 
Published: May 2021

Abstract

Background
Bacterial vaginosis (BV) treatment failures and recurrences are common. To identify features associated with treatment response, we compared vaginal microbiota and host ectocervical transcriptome before and after oral metronidazole therapy.

Methods
Women with BV (Bronx, New York and Thika, Kenya) received 7 days of oral metronidazole at enrollment (day 0) and underwent genital tract sampling of microbiome (16S ribosomal RNA gene sequencing), transcriptome (RNAseq), and immune mediator concentrations on day 0, 15, and 35.

Results
Bronx participants were more likely than Thika participants to clinically respond to metronidazole (19/20 vs 10/18, respectively, P = .0067) and by changes in microbiota composition and diversity. After dichotomizing the cohort into responders and nonresponders by change in α-diversity between day 35 and day 0, we identified that transcription differences associated with chemokine signaling (q = 0.002) and immune system process (q = 2.5 × 10–8) that differentiated responders from nonresponders were present at enrollment. Responders had significantly lower levels of CXCL9 in cervicovaginal lavage on day 0 (P &lt; .007), and concentrations of CXCL9, CXCL10, and monocyte chemoattractant protein 1 increased significantly between day 0 and day 35 in responders vs nonresponders.

Conclusions
Response to metronidazole is characterized by significant changes in chemokines and related transcripts, suggesting that treatments that promote these pathways may prove beneficial.
Suitability of open digital species records for assessing biodiversity patterns in cities: a case study using avian records
Authors: Sultana Marufa , Storch Ilse 
Published: May 2021

Abstract
Openly available species observation records on various online platforms achieve good coverage in urban areas. Thus, such digital data could provide a basis for biodiversity assessments in cities. Here, we investigated suitability of open digital species occurrence data, compared with systematically field surveyed data, in Freiburg, Germany (a Western city) and Dhaka, Bangladesh (a global-South city). We focused on resident bird species richness as an indicator of local biodiversity. We collected avian records for urban areas from ‘ornitho.de’ in Freiburg and ‘gbif.org’ in Dhaka. Additionally, we conducted point count surveys at several urban locations in both cities. Using these records, we prepared three grid (cell size 250 m × 250 m) based datasets—open digital dataset (i.e. records compiled from well-surveyed grid cells), field surveyed dataset (i.e. records of systematic bird surveys) and combined dataset (i.e. digital data and field data combined). We compared the relationship of resident bird richness with different habitat factors by applying linear regression models, separately using each of the three datasets. We assessed suitability of data from online platforms by comparing the variables retained after model selection based on digital data versus field surveyed data. We found that field surveyed data and combined data did not alter general understanding of the key driving factors of bird richness patterns we obtained from open digital data. This held for both case examples, Freiburg vs. Dhaka, respectively. This suggests that open digital data from well-surveyed urban locations can provide a suitable basis to assess drivers of biodiversity patterns within cities.
Reweighting of molecular simulations with explicit-solvent SAXS restraints elucidates ion-dependent RNA ensembles
Authors: Bernetti Mattia , Hall Kathleen B , Bussi Giovanni 
Published: May 2021

Abstract
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of forward models that relate measured SAXS intensities and structural features, and that are suitable to model either explicit-solvent effects or solute dynamics, have been proposed in the past years. Here, we introduce an approach that integrates atomistic molecular dynamics simulations and SAXS experiments to reconstruct RNA structural ensembles while simultaneously accounting for both RNA conformational dynamics and explicit-solvent effects. Our protocol exploits SAXS pure-solute forward models and enhanced sampling methods to sample an heterogenous ensemble of structures, with no information towards the experiments provided on-the-fly. The generated structural ensemble is then reweighted through the maximum entropy principle so as to match reference SAXS experimental data at multiple ionic conditions. Importantly, accurate explicit-solvent forward models are used at this reweighting stage. We apply this framework to the GTPase-associated center, a relevant RNA molecule involved in protein translation, in order to elucidate its ion-dependent conformational ensembles. We show that (a) both solvent and dynamics are crucial to reproduce experimental SAXS data and (b) the resulting dynamical ensembles contain an ion-dependent fraction of extended structures.
The aging slow wave: a shifting amalgam of distinct slow wave and spindle coupling subtypes define slow wave sleep across the human lifespan
Authors: McConnell Brice V , Kronberg Eugene , Teale Peter D , Sillau Stefan H , Fishback Grace M , Kaplan Rini I , Fought Angela J , Dhanasekaran A Ranjitha , Berman Brian D , Ramos Alberto R , McClure Rachel L , Bettcher Brianne M 
Published: May 2021

AbstractStudy ObjectivesSlow wave and spindle coupling supports memory consolidation, and loss of coupling is linked with cognitive decline and neurodegeneration. Coupling is proposed to be a possible biomarker of neurological disease, yet little is known about the different subtypes of coupling that normally occur throughout human development and aging. Here we identify distinct subtypes of spindles within slow wave upstates and describe their relationships with sleep stage across the human lifespan.MethodsCoupling within a cross-sectional cohort of 582 subjects was quantified from stages N2 and N3 sleep across ages 6–88 years old. Results were analyzed across the study population via mixed model regression. Within a subset of subjects, we further utilized coupling to identify discrete subtypes of slow waves by their coupled spindles.ResultsTwo different subtypes of spindles were identified during the upstates of (distinct) slow waves: an “early-fast” spindle, more common in stage N2 sleep, and a “late-fast” spindle, more common in stage N3. We further found stages N2 and N3 sleep contain a mixture of discrete subtypes of slow waves, each identified by their unique coupled-spindle timing and frequency. The relative contribution of coupling subtypes shifts across the human lifespan, and a deeper sleep phenotype prevails with increasing age.ConclusionsDistinct subtypes of slow waves and coupled spindles form the composite of slow wave sleep. Our findings support a model of sleep-dependent synaptic regulation via discrete slow wave/spindle coupling subtypes and advance a conceptual framework for the development of coupling-based biomarkers in age-associated neurological disease.