bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatial regulation of thermomorphogenesis by HY5 and PIF4 in Arabidopsis
Authors: Lee Sanghwa , Wang Wenli , Huq Enamul 
Published: June 2021

AbstractPlants respond to high ambient temperature by implementing a suite of morphological changes collectively termed thermomorphogenesis. Here we show that the above and below ground tissue-response to high ambient temperature are mediated by distinct transcription factors. While the central hub transcription factor, PHYTOCHROME INTERCTING FACTOR 4 (PIF4) regulates the above ground tissue response, the below ground root elongation is primarily regulated by ELONGATED HYPOCOTYL 5 (HY5). Plants respond to high temperature by largely expressing distinct sets of genes in a tissue-specific manner. HY5 promotes root thermomorphogenesis via directly controlling the expression of many genes including the auxin and BR pathway genes. Strikingly, the above and below ground thermomorphogenesis is impaired in spaQ. Because SPA1 directly phosphorylates PIF4 and HY5, SPAs might control the stability of PIF4 and HY5 to regulate thermomorphogenesis in both tissues. These data collectively suggest that plants employ distinct combination of SPA-PIF4-HY5 module to regulate tissue-specific thermomorphogenesis.
Total nitrogen estimation in agricultural soils via aerial multispectral imaging and LIBS
Authors: Hossen Md Abir , Diwakar Prasoon K , Ragi Shankarachary 
Published: June 2021

AbstractMeasuring soil health indicators (SHIs), particularly soil total nitrogen (TN), is an important and challenging task that affects farmers’ decisions on timing, placement, and quantity of fertilizers applied in the farms. Most existing methods to measure SHIs are in-lab wet chemistry or spectroscopy-based methods, which require significant human input and effort, time-consuming, costly, and are low-throughput in nature. To address this challenge, we develop an artificial intelligence (AI)-driven near real-time unmanned aerial vehicle (UAV)-based multispectral sensing solution (UMS) to estimate soil TN in an agricultural farm. TN is an important macro-nutrient or SHI that directly affects the crop health. Accurate prediction of soil TN can significantly increase crop yield through informed decision making on the timing of seed planting, and fertilizer quantity and timing. The ground-truth data required to train the AI approaches is generated via laser-induced breakdown spectroscopy (LIBS), which can be readily used to characterize soil samples, providing rapid chemical analysis of the samples and their constituents (e.g., nitrogen, potassium, phosphorus, calcium). Although LIBS was previously applied for soil nutrient detection, there is no existing study on the integration of LIBS with UAV multispectral imaging and AI. We train two machine learning (ML) models including multi-layer perceptron regression and support vector regression to predict the soil nitrogen using a suite of data classes including multispectral characteristics of the soil and crops in red (R), near-infrared, and green (G) spectral bands, computed vegetation indices (NDVI), and environmental variables including air temperature and relative humidity (RH). To generate the ground-truth data or the training data for the machine learning models, we determine the N spectrum of the soil samples (collected from a farm) using LIBS and develop a calibration model using the correlation between actual TN of the soil samples and the maximum intensity of N spectrum. In addition, we extract the features from the multispectral images captured while the UAV follows an autonomous flight plan, at different growth stages of the crops. The ML model’s performance is tested on a fixed configuration space for the hyper-parameters using various hyper-parameter optimization techniques at three different wavelengths of the N spectrum.
Primary production ultimately limits fisheries economic performance
Authors: Marshak Anthony R. , Link Jason S. 
Published: June 2021

AbstractLiving marine resources (LMRs) contribute considerably to marine economies. Oceans continue to respond to the effects of global change, with environmental factors anticipated to impact future seafood production and its associated economic performance. Here we document novel relationships between primary productivity and LMR-based economics for US regional marine ecosystems and 64 international large marine ecosystems (LMEs). Intermediate relationships between production, total biomass, fisheries landings, revenue, and LMR-based employment are also elucidated. We found that all these factors were dependent on the amount of basal production in a given system. In addition, factors including human population, exploitation history, and governance interventions significantly influenced these relationships. As system productivity plays a foundational role in determining fisheries-based economics throughout global LMEs, greater accounting for these relationships has significant implications for global seafood sustainability and food security. Quantifying the direct link between primary production and fisheries economic performance serves to better inform ecosystem overfishing thresholds and their economic consequences. Further recognition and understanding of these relationships is key to ensuring that these connections are accounted for more effectively in sustainable management practices.
Computation of distribution of relaxation times by Tikhonov regularization for Li ion batteries: usage of L-curve method
Authors: Paul T. , Chi P. W. , Wu Phillip M. , Wu M. K. 
Published: June 2021

AbstractIn this paper, the distribution of relaxation times (DRTs) functions are calculated numerically in Matlab for synthetic impedance data from single parallel $$RC$$

RC

circuit and two parallel $$RC$$

RC

circuits connected in series, experimental impedance data from supercapacitors and α-LiFeO2 anode based Li ion batteries. The quality of the impedance data is checked with the Kramers–Krönig (KK) relations. The DRTs are calculated within the KK compatible regime for all the systems using Tikhonov regularization (TR) method. Here we use a fast and simple L-curve method to estimate the TR parameter (λ) for regularization of the Fredholm integral equations of first kind in impedance. Estimation of the regularization parameters are performed effectively from the offset of the global corner of the L-curve rather than simply using the global corner. The physical significances of DRT peaks are also discussed by calculating the effective resistances and capacitances coupled with peak fitting program. For instance, two peaks in the DRTs justify the electrical double layer capacitance and ion diffusion phenomena for supercapacitors in low to intermediate frequencies respectively. Moreover, the surface film effect, Li/electrolyte and electrode/electrolyte charge transfer related processes are identified for α-LiFeO2 anode based Li-ion batteries. This estimation of the offset of the global corner extends the L-curve approach coupled with the Tikhonov regularization in the field of electrochemistry and can also be applied in similar process detection methods.
Supplementary solvent irrigation efficacy on filling remnants removal comparing XP-endo Finisher R vs IrriSafe
Authors: Ferreira Inês , Babo Pedro S. , Braga Ana Cristina , Lopes Maria Ascensão , Gomes Manuela E. , Pina-Vaz Irene 
Published: June 2021

AbstractThis study aimed to compare the efficacy of XP-endo Finisher R and IrriSafe, with a solvent mixture of Methyl ethyl ketone/Tetrachloroethylene (MEK/TCE), in the removal of root filling residues. Twenty-four human mandibular incisors were pair-matched by micro-computed tomography according to volume and aspect ratio. After retreatment, specimens were allocated to two experimental groups (n = 12), according to the supplementary instrument used. The volume of residual filling material after each irrigating step and the time for retreatment was calculated. Statistical analyses were carried out using Mann–Whitney test, with a significance level of 5%. The volume of initial root canal filling material between the groups was similar (p > 0.05). With the final irrigation protocol (NaOCl and EDTA) the volume of the filling remnants decreased significantly (p < 0.05) with no differences between IrriSafe or XP-endo Finisher R (p > 0.05). The additional solvent mixture MEK/TCE increased the efficiency of filling materials reduction, regardless of the agitating instruments employed, IrriSafe or XP-endo Finisher R (p < 0.05). There was no difference between the two groups regarding the time (p = 0.149). Both supplementary instruments were effective in the reduction of filling remnants. The additional step with a solvent mixture of MEK/TCE enabled a total recovery of patency and the achievement of cleaner canals, independently of the agitation instrument.
3-Substituted 2-isocyanopyridines as versatile convertible isocyanides for peptidomimetic design
Authors: Hollanders Charlie , Elsocht Mathias , Van der Poorten Olivier , Jida Mouhamad , Renders Evelien , Maes Bert U. W. , Ballet Steven 
Published: June 2021

We report the use of 3-substituted 2-isocyanopyridines as convertible isocyanides in Ugi four-component reactions. The N-(3-substituted pyridin-2-yl)amide Ugi products can be cleaved by amines, alcohols, and water with Zn(OAc)2 as catalyst.
Hypoxia-induced PTTG3P contributes to colorectal cancer glycolysis and M2 phenotype of macrophage
Authors: Wang Yue , Yu Guilin , Liu Yiyang , Xie Longfei , Ge Jinnian , Zhao Guohua , Lin Jie 
Published: June 2021

Abstract
Long noncoding RNAs (lncRNAs) play critical factors in tumor progression and are ectopically expressed in malignant tumors. Until now, lncRNA pituitary tumor-transforming 3, pseudogene (PTTG3P) biological function in colorectal cancer (CRC) further needs to be clarified. qRT-PCR was used to measure the PTTG3P level and CCK-8, glucose uptake, lactate assay, adenosine triphosphate (ATP) assay, extracellular acidification rate (ECAR) assay, and xenograft mice model were adopted to evaluate the glycolysis and proliferation, and macrophage polarization were determined in CRC cells. Xenograft experiments were utilized to analyze tumor growth. Ectopic expression of PTTG3P was involved in CRC and related to dismal prognosis. Through gain- and loss-of-function approaches, PTTG3P enhanced cell proliferation and glycolysis through YAP1. Further, LDHA knockdown or glycolysis inhibitor (2-deoxyglucose (2-DG), 3-BG) recovered from PTTG3P-induced proliferation. And PTTG3P overexpression could facilitate M2 polarization of macrophages. Silenced PTTG3P decreased the level of inflammatory cytokines TNF-α, IL-1β and IL-6, and low PTTG3P expression related with CD8+ T, NK, and TFH cell infiltration. Besides, hypoxia-inducible factor-1α (HIF1A) could increase PTTG3P expression by binding to the PTTG3P promoter region. Hypoxia-induced PTTG3P contributes to glycolysis and M2 phenotype of macrophage, which proposes a novel approach for clinical treatment.
Microbial cell factories for the production of polyhydroxyalkanoates
Authors: Nagarajan Dillirani , Aristya Ganies Riza , Lin Yu-Ju , Chang Jui-Jen , Yen Hong-Wei , Chang Jo-Shu 
Published: June 2021

Abstract
Pollution caused by persistent petro-plastics is the most pressing problem currently, with 8 million tons of plastic waste dumped annually in the oceans. Plastic waste management is not systematized in many countries, because it is laborious and expensive with secondary pollution hazards. Bioplastics, synthesized by microorganisms, are viable alternatives to petrochemical-based thermoplastics due to their biodegradable nature. Polyhydroxyalkanoates (PHAs) are a structurally and functionally diverse group of storage polymers synthesized by many microorganisms, including bacteria and Archaea. Some of the most important PHA accumulating bacteria include Cupriavidus necator, Burkholderia sacchari, Pseudomonas sp., Bacillus sp., recombinant Escherichia coli, and certain halophilic extremophiles. PHAs are synthesized by specialized PHA polymerases with assorted monomers derived from the cellular metabolite pool. In the natural cycle of cellular growth, PHAs are depolymerized by the native host for carbon and energy. The presence of these microbial PHA depolymerases in natural niches is responsible for the degradation of bioplastics. Polyhydroxybutyrate (PHB) is the most common PHA with desirable thermoplastic-like properties. PHAs have widespread applications in various industries including biomedicine, fine chemicals production, drug delivery, packaging, and agriculture. This review provides the updated knowledge on the metabolic pathways for PHAs synthesis in bacteria, and the major microbial hosts for PHAs production. Yeasts are presented as a potential candidate for industrial PHAs production, with their high amenability to genetic engineering and the availability of industrial-scale technology. The major bottlenecks in the commercialization of PHAs as an alternative for plastics and future perspectives are also critically discussed.
Stress sensing within the breast tumor microenvironment: how glucocorticoid receptors live in the moment
Authors: Kerkvliet Carlos Perez , Truong Thu H. , Ostrander Julie Hanson , Lange Carol A. 
Published: June 2021

Abstract
The classification and treatment of breast cancer is largely defined by the expression of steroid hormone receptors (HRs), namely estrogen receptor (ER) and progesterone receptor (PR), and gene amplification/overexpression of human epidermal growth factor receptor 2 (HER2). More recently, studies of androgen receptor (AR), glucocorticoid receptor (GR), and mineralocorticoid receptor (MR) have revealed that targeting these related HRs may be a promising strategy for a more personalized approach to the treatment of specific subtypes of HR+ breast cancer. For example, GR expression is associated with a good prognosis in ER+ breast cancer, but predicts poor prognosis in triple-negative breast cancer (TNBC). GR, like ER, PRs, and AR, is a ligand-activated transcription factor, but also has significant ligand-independent signaling activities. GR transcriptional activity is classically regulated by circulating glucocorticoids (GCs; ligand-dependent). Recent studies demonstrate that GR transcriptional activity is also regulated by a variety of cellular stress stimuli that input to GR Ser134 phosphorylation via rapid activation of the p38 mitogen activated protein kinase (MAPK) signaling pathway (ligand-independent). Furthermore, ligand-independent GR activation promotes feedforward signaling loops that mediate sustained activation of stress signaling pathways to drive advanced cancer biology (i.e. migration, invasion, chemoresistance, survival, and cellular growth). In this review, we will focus on the role of GR as a key sensor and mediator of physiologic and tumor microenvironment (TME)-derived cellular stress signaling in TNBC and discuss how targeting GR and/or associated signaling pathways may provide a strategy to inhibit deadly TNBC progression.
Solar wind rotation rate and shear at coronal hole boundaries
Authors: Pinto R. F. , Poirier N. , Rouillard A. P. , Kouloumvakos A. , Griton L. , Fargette N. , Kieokaew R. , Lavraud B. , Brun A. S. 
Published: June 2021

Context.In situ measurements by several spacecraft have revealed that the solar wind is frequently perturbed by transient structures that have been interpreted as magnetic folds, jets, waves, and flux ropes that propagate rapidly away from the Sun over a large range of heliocentric distances. Parker Solar Probe (PSP), in particular, has detected very frequent rotations of the magnetic field vector at small heliocentric radial distances, accompanied by surprisingly large solar wind rotation rates. The physical origin of such magnetic field bends and switchbacks, the conditions for their survival across the interplanetary space, and their relation to solar wind rotation are yet to be clearly understood.Aims.We aim to characterise the global properties of the solar wind flows crossed by PSP, to relate those flows to the rotational state of the low solar corona, and to identify regions of the solar surface and corona that are likely to be sources of switchbacks and bends.Methods.We traced measured solar wind flows from the spacecraft position down to the surface of the Sun to identify their potential source regions, and used a global magneto-hydrodynamic model of the corona and solar wind to analyse the dynamical properties of those regions. We identify regions of the solar corona for which solar wind speed and rotational shear are important and long-lived that can be favourable to the development of magnetic deflections and to their propagation across extended heights in the solar wind.Results.We show that coronal rotation is highly structured, and that enhanced flow shear and magnetic field gradients develop near the boundaries between coronal holes and streamers, and around and above pseudo-streamers, even when such boundaries are aligned with the direction of solar rotation. The exact properties and amplitudes of the shears are a combined effect of the forces exerted by the rotation of the corona and of its magnetic topology. A large fraction of the switchbacks identified by PSP map back to these regions, both in terms of instantaneous magnetic field connectivity and of the trajectories of wind streams that reach the spacecraft.Conclusions.We conclude that these regions of strong shears are likely to leave an imprint on the solar wind over large distances and to increase the transverse speed variability in the slow solar wind. The simulations and connectivity analysis suggest they could be a source of the switchbacks and spikes observed by PSP.
Online-Befragung von Ernährungsfachkräften mit klinischem Arbeitsfeld in Deutschland zum Thema Variablen des Ernährungsassessments
Authors: Girsemihl Caroline , Blumenschein Birgit , Rubin Diana 
Published: June 2021

Zusammenfassung
Hintergrund Für die Behandlung von Patienten mit ernährungsbedingten Erkrankungen wird in Deutschland die Ernährungstherapie als Teil der klinischen Ernährung empfohlen. Grundvoraussetzung für optimales ernährungstherapeutisches Handeln ist dabei ein von qualifizierten Ernährungsfachkräften erhobenes systematisches Ernährungsassessment.
Methoden In einem standardisierten, halboffenen Fragebogen gaben Ernährungsfachkräfte eine Selbstauskunft zur regelhaften Nutzung verschiedener Variablen im Ernährungsassessment (Erhebungszeitraum Mai 2019). Die Daten wurden mittels einer 3-stufigen Likert-Skala („ja“, „nein“, „nur wenn nötig“) erfasst und über die relative Häufigkeit, die in „häufig“, „weniger häufig“ und „selten“ prozentual eingeteilt wurde, ausgewertet.
Ergebnisse Ernährungsfachkräfte gaben mit einer relativen Häufigkeit von mindestens 70 % an, folgende Variablen regelhaft bei Patienten zu erheben: Name, Vorname, Geburtsdatum, Alter, Geschlecht, Gewicht, Größe, BMI, NRS, aktuelle Medikation, Diagnosen, gastrointestinale Symptome, Schluckstörungen, 24-h-Recall, Abneigungen gegenüber Lebensmitteln, Art der Sonde (PEG, PEJ, FKJ, nasogastral usw.), Gewichtsverlust, Nahrungsmittelallergien, Unverträglichkeiten/Intoleranzen, Berechnung enteraler Ernährung, Energiebedarf, Eiweißbedarf, Zielkalorien.
Schlussfolgerung Die wesentlichen Variablen für die Ernährungstherapie im Assessment werden regelhaft erhoben. Aufgrund fehlender einheitlicher Richtlinien und ernährungsmedizinischer Strukturen in deutschen Krankenhäusern, zur Erhebung eines Ernährungsassessments, erfolgt das Assessment deutschlandweit heterogen. Um eine qualitativ hochwertige konsekutive Ernährungstherapie flächendeckend zu garantieren, wird die strukturelle Schaffung von Ernährungsexpertise in Krankenhäusern deutschlandweit empfohlen, um standardisierte Prozesse auch bezüglich des Ernährungsassessments zu implementieren.
MedTech: Wie Innovationen durch die Kosten des Scheiterns asymmetrisch aus Europa abgedrängt werden
Authors: Leonhard Martin , Djamshidi Karim 
Published: June 2021

ZusammenfassungScheitern kostet Geld, das ist normal. Das Risiko des Scheiterns einzugehen ist Grundlage jeder Innovation. Wir diskutieren hier die Frage, ob Europa am Beispiel der Medizintechnik das globale Gefüge zu seinen Ungunsten verändert. Mit vereinfachten Modellannahmen arbeiten wir heraus, dass bei sonst vergleichbaren Rahmenbedingungen die globalen Märkte profitieren, die die geringsten Kosten für die Phase des Scheiterns haben. Ziel sollte es sein, das Scheitern nicht durch weiter steigende Kosten zu verteuern, sonst werden Innovatoren bestraft.
Formation of a Ti–Cu(111) single atom alloy: Structure and CO binding
Authors: Shi Junjie , Owen Cameron J. , Ngan Hio Tong , Qin Siyu , Mehar Vikram , Sautet Philippe , Weaver Jason F. 
Published: June 2021

A single atom Ti–Cu(111) surface alloy can be generated by depositing small amounts of Ti onto Cu(111) at slightly elevated surface temperatures (∼500 to 600 K). Scanning tunneling microscopy shows that small Ti-rich islands covered by a Cu single layer form preferentially on ascending step edges of Cu(111) during Ti deposition below about 400 K but that a Ti–Cu(111) alloy replaces these small islands during deposition between 500 and 600 K, producing an alloy in the brims of the steps. Larger partially Cu-covered Ti-containing islands also form on the Cu(111) terraces at temperatures between 300 and 700 K. After surface exposure to CO at low temperatures, reflection absorption infrared spectroscopy (RAIRS) reveals distinct C–O stretch bands at 2102 and 2050 cm−1 attributed to CO adsorbed on Cu-covered Ti-containing domains vs sites in the Ti–Cu(111) surface alloy. Calculations using density functional theory (DFT) suggest that the lower frequency C–O stretch band originates specifically from CO adsorbed on isolated Ti atoms in the Ti–Cu(111) surface alloy and predicts a higher C–O stretch frequency for CO adsorbed on Cu above subsurface Ti ensembles. DFT further predicts that CO preferentially adsorbs in flat-lying configurations on contiguous Ti surface structures with more than one Ti atom and thus that CO adsorbed on such structures should not be observed with RAIRS. The ability to generate a single atom Ti–Cu(111) alloy will provide future opportunities to investigate the surface chemistry promoted by a representative early transition metal dopant on a Cu(111) host surface.
Proteomic analysis identifies the E3 ubiquitin ligase Pdzrn3 as a regulatory target of Wnt5a-Ror signaling
Authors: Konopelski Snavely Sara E. , Susman Michael W. , Kunz Ryan C. , Tan Jia , Srinivasan Srisathya , Cohen Michael D. , Okada Kyoko , Lamb Helen , Choi Shannon S. , Karuna Edith P. , Scales Michael K. , Gygi Steven P. , Greenberg Michael Eldon , Ho Hsin-Yi Henry 
Published: June 2021

SignificanceWnt5a-Ror signaling is a master regulator of tissue shape, and dysfunction of the pathway contributes to congenital birth defects and cancer metastasis. The molecular underpinnings of this pathway, however, remain unclear. To identify subcellular protein changes driven by Wnt5a-Ror signaling, we conducted a large-scale proteomic screen and identified the E3 ubiquitin ligase Pdzrn3 as a downstream target. Wnt5a-Ror signaling initially induces Pdzrn3 phosphorylation, which subsequently triggers the ubiquitin-proteasome–dependent degradation of Pdzrn3. Importantly, Wnt5a-Ror signaling uses this phospho-degradation process to regulate cell migration. From these findings, we further developed a flow cytometry-based reporter to monitor Pdzrn3 abundance and delineated the signaling cascade regulating Pdzrn3 stability. Collectively, our study establishes Pdzrn3 phosphorylation and degradation as a key component of Wnt5a-Ror signaling.