bluuebunny/crossref_metadata_2025_split huggingface dataset:
Values in evolutionary biology: a comparison between the contemporary debate on organic progress and Canguilhem’s biological philosophy
Authors: De Cesare Silvia 
Published: May 2022

AbstractThe aim of this paper is to make a comparison and build up a dialogue between two different philosophical approaches to values in evolutionary biology. First, I present the approach proposed by Alexander Rosenberg and Daniel McShea in their contribution to the contemporary debate on organic progress. i.e. the idea that there has been some kind of improvement concerning organisms over the history of life. Discussing organic progress raises the question of what “better” exactly means. This requires an explicit clarification on what legitimately means to speak about “good” in evolutionary biology, thus to speak about values. Second, I move on to present an approach to values that has been proposed by Georges Canguilhem in the context of a different philosophical tradition (i.e. the “continental” tradition). Canguilhem’s original theses are conceived in a Darwinian framework and clearly relate to the question of values in evolutionary biology. I shall then propose a comparison between these two heterogeneous perspectives on values by critically evaluating their common points and main differences. I will argue that both perspectives agree that the question of values in evolutionary biology takes on its full meaning with respect to the relationship between the organism and the environment. However, the framework for conceptualizing values in evolutionary biology provided by Rosenberg and McShea neglects a significant point highlighted by Canguilhem, i.e. the active role that the organism can play in evaluating the environment. In line with recent developments of biology (e.g. niche construction), this point can be easily integrated into Rosenberg and McShea’s framework. Finally, I will point out some main differences between the two perspectives relative to the specificity of Canguilhem’s biological philosophy.
ezQTL: A Web Platform for Interactive Visualization and Colocalization of QTLs and GWAS Loci
Authors: Zhang Tongwu , Klein Alyssa , Sang Jian , Choi Jiyeon , Brown Kevin M. 
Published: May 2022

Abstract
Genome-wide association studies (GWAS) have identified thousands of genomic loci associated with complex diseases and traits, including cancer. The vast majority of common trait-associated variants identified via GWAS fall in non-coding regions of the genome, posing a challenge in elucidating the causal variants, genes, and mechanisms involved. Expression quantitative trait locus (eQTL) and other molecular QTL studies have been valuable resources in identifying candidate causal genes from GWAS loci through statistical colocalization methods. While QTL colocalization is becoming a standard analysis in post-GWAS investigation, an easy web tool for users to perform formal colocalization analyses with either user-provided or public GWAS and eQTL datasets has been lacking. Here, we present ezQTL, a web-based bioinformatic application to interactively visualize and analyze genetic association data such as GWAS loci and molecular QTLs under different linkage disequilibrium (LD) patterns (1000 Genomes Project, UK Biobank, or user-provided data). This application allows users to perform data quality control for variants matched between different datasets, LD visualization, and two-trait colocalization analyses using two state-of-the-art methodologies (eCAVIAR and HyPrColoc), including batch processing. ezQTL is a free and publicly available cross-platform web tool, which can be accessed online at https://analysistools.cancer.gov/ezqtl.
Open Science and Epistemic Diversity: Friends or Foes?
Authors: Leonelli Sabina 
Published: May 2022

AbstractI argue that Open Science as currently conceptualized and implemented does not take sufficient account of epistemic diversity within research. I use three case studies to exemplify how Open Science threatens to privilege some forms of inquiry over others, thus exasperating divides within and across systems of practice, and overlooking important sources and forms of epistemic diversity. Building on insights from pluralist philosophy, I then identify four aspects of diverse research practices that should serve as reference points for debates around Open Science: (1) specificity to local conditions, (2) entrenchment within repertoires, (3) permeability to newcomers, and (4) demarcation strategies.
Unlimited Associative Learning as a Null Hypothesis
Authors: Halina Marta 
Published: May 2022

AbstractA common strategy in comparative cognition is to require that one reject associative learning as an explanation for behavior before concluding that an organism is capable of causal reasoning. In this paper, I argue that standard causal-reasoning tasks can be explained by a powerful form of associative learning: unlimited associative learning (UAL). The lesson, however, is not that researchers should conduct more studies to reject UAL, but that they should instead focus on 1) enriching the cognitive hypothesis space and 2) testing a broader range of information processing patterns—errors, biases and limits, rather than successful problem solving alone.
Cleft palate and ventilation tubes: a prophylactic dilemma
Authors: Machado A , Santos M , Leitao B , Silva A , Coutinho M 
Published: May 2022

AbstractObjectiveThis study aimed to understand, in a long-term follow-up study, whether the placement of grommets had been necessary after cleft palate surgical correction.MethodA case–control, retrospective study was carried out on consecutive paediatric patients who underwent surgical repair of a cleft palate.ResultsThe study population included 138 patients, divided into 2 groups: group 1 – patients in whom grommets were placed at the time of cleft palate surgery, and group 2 – patients in whom grommets were not placed at the time of cleft palate surgery. During the follow up, in groups 1 and 2, 65.2 per cent and 67.8 per cent, respectively, did not need subsequent grommet placement after cleft palate surgery.ConclusionOf patients, 56.5 per cent did not need ventilation tubes at any point during follow up. The placement of grommets is not innocuous; therefore, its use at the time of cleft palate surgical repair should be reconsidered.
The Hypomnemata of Hegesippus
Authors: Eurell John-Christian 
Published: May 2022

AbstractThis article deals with the lost work of the early Christian writer Hegesippus, whose Hypomnemata is only known through quotations in Eusebius. Faulty preconceptions regarding the dating and provenance of Hegesippus’ work are criticised, and it is argued that the Hypomnemata is a loose collection of bishop traditions from the late 170s or 180s. The purpose of the work is to connect orthodoxy with correct episcopal succession.
On the probability and direction of morphosyntactic lifespan change
Authors: Fonteyn Lauren , Petré Peter 
Published: May 2022

AbstractThe aim of this study is to further contribute to the ongoing debate regarding the nature of “morphosyntactic lifespan change,” defined here as observable shifts in the grammatical choices individuals make between competing morphosyntactic structures. Through a quantitative case study of competition between two types of ing-nominals in seventeenth-century English, in which we factor in the grammatical contexts in which the variant structures can be used, we show that individuals vary in the extent to which they participate in the contextual diffusion of a new structure. We furthermore show that there is interindividual variability with respect to whether and what kind of lifespan change—frequency, constraint, and inventory change—is attested and highlight different patterns of intraindividual change: progressive, retrograde, and “mixed.”
Altitude Distribution of Large and Small‐Scale Equatorial Ionospheric Irregularities Sampled From an Elliptical Low‐Earth Orbit
Authors: Mohandesi Ali , Knudsen David J. , Skone Susan , Langley Richard B. , Yau Andrew W. 
Published: May 2022

AbstractWe provide insight into the vertical distribution of multi‐scale scintillation‐inducing irregularities in the low‐latitude ionosphere. In four sets of novel experiments, we sampled altitudes from 330 to 1,280 km in the 18–24 magnetic local time (MLT) sector using the Swarm Echo GPS Attitude, Positioning, and Profiling Experiment occultation receiver (GAP‐O) GPS receiver with its antenna oriented toward zenith. In order to identify multi‐scale irregularities both above and at the satellite's position, we utilize high‐sample‐rate GAP‐O amplitude and phase measurements along with a measurement of net current on the surface of the imaging and rapid‐scanning ion mass spectrometer sensor on board, which serves as a proxy for density variations. By calculating the rate of change of total electron content index using two sets of GPS parameter choices, we are able to sample irregularities as small as 160 m, which is comparable to or smaller than the Fresnel scale responsible for scintillation‐inducing irregularities. During one campaign, we find that amplitude scintillations on the GPS signal coincide with strong in‐situ small‐scale density irregularities in 32% of cases, indicative of a broad irregularity region extending from the satellite's position to hundreds of kilometers above. Also, we show that large‐scale ionospheric disturbances (larger than 80 km) occur predominantly below 500 km, and down to the 330 km perigee of Swarm Echo in the 18–21 MLT sector. In contrast, small‐scale variations of total electron content are detected at all MLTs between 18 MLT and magnetic midnight and at all altitudes sampled in this experiment. However, they are more frequent in the 22–24 MLT range.
Empirical Evidence of Frequency‐Dependent Directivity Effects From Small‐To‐Moderate Normal Fault Earthquakes in Central Italy
Authors: Colavitti Leonardo , Lanzano Giovanni , Sgobba Sara , Pacor Francesca , Gallovič František 
Published: May 2022

AbstractRupture directivity and its potential frequency dependence is an open issue within the seismological community, especially for small‐to‐moderate events. Here, we provide a statistical overview based on empirical evidence of seismological observations, thanks to the large amount of high‐quality seismic recordings (more than 30,000 waveforms) from Central Italy, which represents an excellent and almost unique natural laboratory of normal faulting earthquakes in the magnitude range between 3.4 and 6.5 within the time frame 2008–2018. In order to detect an anisotropic distribution of ground motion amplitudes due to the rupture directivity, we fit the smoothed Fourier Amplitude Spectra (FAS) cleared of source‐, site‐ and path‐effects. According to our criteria, about 36% of the analyzed events (162 out of 456) are directive and the distribution of rupture direction is aligned with the strikes of the major faults of the Central Apennines. We find that the directivity is a band‐limited phenomenon whose width may extend up to five times the corner frequency. The results of this research provide useful insights to parameterize directivity, to be explicitly implemented in future ground motion modeling and scenario predictions.
Physical and Chemical Properties of Cloud Droplet Residuals and Aerosol Particles During the Arctic Ocean 2018 Expedition
Authors: Karlsson Linn , Baccarini Andrea , Duplessis Patrick , Baumgardner Darrel , Brooks Ian M. , Chang Rachel Y.‐W. , Dada Lubna , Dällenbach Kaspar R. , Heikkinen Liine , Krejci Radovan , Leaitch W. Richard , Leck Caroline , Partridge Daniel G. , Salter Matthew E. , Wernli Heini , Wheeler Michael J. , Schmale Julia , Zieger Paul 
Published: May 2022

AbstractDetailed knowledge of the physical and chemical properties and sources of particles that form clouds is especially important in pristine areas like the Arctic, where particle concentrations are often low and observations are sparse. Here, we present in situ cloud and aerosol measurements from the central Arctic Ocean in August–September 2018 combined with air parcel source analysis. We provide direct experimental evidence that Aitken mode particles (particles with diameters ≲70 nm) significantly contribute to cloud condensation nuclei (CCN) or cloud droplet residuals, especially after the freeze‐up of the sea ice in the transition toward fall. These Aitken mode particles were associated with air that spent more time over the pack ice, while size distributions dominated by accumulation mode particles (particles with diameters ≳70 nm) showed a stronger contribution of oceanic air and slightly different source regions. This was accompanied by changes in the average chemical composition of the accumulation mode aerosol with an increased relative contribution of organic material toward fall. Addition of aerosol mass due to aqueous‐phase chemistry during in‐cloud processing was probably small over the pack ice given the fact that we observed very similar particle size distributions in both the whole‐air and cloud droplet residual data. These aerosol–cloud interaction observations provide valuable insight into the origin and physical and chemical properties of CCN over the pristine central Arctic Ocean.
Effects of Ionospheric Inhomogeneities on Remote Sensing of the Earth by Space‐Borne P‐Band SAR
Authors: Kryukovsky A. S. , Bova Y. I. , Kutuza B. G. , Rastyagaev D. V. 
Published: May 2022

AbstractNumerical modeling of the effect of the polarization vector rotation in the ionospheric plasma on the radio waves of the high frequency range is performed. The relevance of the work is associated with the creation of space‐based P‐band synthetic aperture radars (SARs) for the Biomass mission and the MKS‐RSA (P) experiment on board ISS station. These instruments are intended for surface and subsurface sounding of the Earth and their readings are strongly influenced by the ionosphere. Another problem of EM propagation is the reconstruction of the profile e‐ionospheric plasma density by radio tomography methods. The source of radiation is located on the moving spacecraft at a distance of 400 km from the Earth's surface. The angle of rays inclination varies from 150 to 30° relative to the horizontal axis. The receiver is located on the surface of the Earth. Three spherical two‐layer models of the ionosphere are compared. To determine the ray paths, a bi‐characteristic system of equations is used. The dependence of the aiming angle deviation on group time is investigated. The phase variation due to the influence of the ionosphere and the angle of the Faraday rotation are studied. It is shown that the changes in the Faraday rotation angle for the selected parameters lie in the range from 6° to 54°, which will have a strong impact on the operation of the P‐band SAR and requires a sufficiently accurate quantitative account of the variability of the angle when probing vegetation and soil covers.
Extremely Stable, Highly Conductive Boron‐Hydrogen Complexes in Forsterite and Olivine
Authors: Muir Joshua M. R. , Chen Yuying , Liu Xi , Zhang Feiwu 
Published: May 2022

AbstractBoron is an important tracer in the mantle but its fate during deep subduction is poorly constrained. In this work we use density functional theory and a thermodynamic model to study the stability of boron‐hydrogen defects in forsterite and olivine and predict their effect on olivine properties. In the absence of water/hydrogen we predict that in all conditions B3+ replaces Si4+ charge balanced by an oxygen vacancy and thus pure boron increases oxygen diffusion rates. In the presence of hydrogen two boron‐hydrogen defects are found to be stable, an “associated” boron‐silicon hydrate (B‐Si‐H) with planar BO3 at low temperatures and an attached hydrogen and a “dissociated” B‐Si‐H with tetrahedral BO4 and interstitial free hydrogen at high temperatures. These B‐Si‐H complexes are extremely stable compared to non‐hydrous boron and form to the exclusion of all other water defects regardless of pressure, temperature, SiO2 activity and Fe# thus forsterite and olivine should behave identically. The stability of B‐Si‐H defects against pressure and temperature suggests that dissolved boron will remain dissolved deep into the mantle and that boron should induce a near linear increase in the solubility of water in olivine. We predict that at high temperatures water associated with boron in olivine will not have FTIR signals in the standard measurement range 3,000–3,600 cm−1 and that instead a large rise in conductivity will be seen. The change in the coordination of boron in B‐Si‐H with temperature will impact upon its fractionation.
Standardization of molecular monitoring of CML: results and recommendations from the European treatment and outcome study
Authors: White Helen E. , Salmon Matthew , Albano Francesco , Andersen Christina Søs Auður , Balabanov Stefan , Balatzenko Gueorgui , Barbany Gisela , Cayuela Jean-Michel , Cerveira Nuno , Cochaux Pascale , Colomer Dolors , Coriu Daniel , Diamond Joana , Dietz Christian , Dulucq Stéphanie , Engvall Marie , Franke Georg N. , Gineikiene-Valentine Egle , Gniot Michal , Gómez-Casares María Teresa , Gottardi Enrico , Hayden Chloe , Hayette Sandrine , Hedblom Andreas , Ilea Anca , Izzo Barbara , Jiménez-Velasco Antonio , Jurcek Tomas , Kairisto Veli , Langabeer Stephen E. , Lion Thomas , Meggyesi Nora , Mešanović Semir , Mihok Luboslav , Mitterbauer-Hohendanner Gerlinde , Moeckel Sylvia , Naumann Nicole , Nibourel Olivier , Oppliger Leibundgut Elisabeth , Panayiotidis Panayiotis , Podgornik Helena , Pott Christiane , Rapado Inmaculada , Rose Susan J. , Schäfer Vivien , Touloumenidou Tasoula , Veigaard Christopher , Venniker-Punt Bianca , Venturi Claudia , Vigneri Paolo , Vorkinn Ingvild , Wilkinson Elizabeth , Zadro Renata , Zawada Magdalena , Zizkova Hana , Müller Martin C. , Saussele Susanne , Ernst Thomas , Machova Polakova Katerina , Hochhaus Andreas , Cross Nicholas C. P. 
Published: May 2022

AbstractStandardized monitoring of BCR::ABL1 mRNA levels is essential for the management of chronic myeloid leukemia (CML) patients. From 2016 to 2021 the European Treatment and Outcome Study for CML (EUTOS) explored the use of secondary, lyophilized cell-based BCR::ABL1 reference panels traceable to the World Health Organization primary reference material to standardize and validate local laboratory tests. Panels were used to assign and validate conversion factors (CFs) to the International Scale and assess the ability of laboratories to assess deep molecular response (DMR). The study also explored aspects of internal quality control. The percentage of EUTOS reference laboratories (n = 50) with CFs validated as optimal or satisfactory increased from 67.5% to 97.6% and 36.4% to 91.7% for ABL1 and GUSB, respectively, during the study period and 98% of laboratories were able to detect MR4.5 in most samples. Laboratories with unvalidated CFs had a higher coefficient of variation for BCR::ABL1IS and some laboratories had a limit of blank greater than zero which could affect the accurate reporting of DMR. Our study indicates that secondary reference panels can be used effectively to obtain and validate CFs in a manner equivalent to sample exchange and can also be used to monitor additional aspects of quality assurance.
The mitochondrial chaperone TRAP1 regulates F-ATP synthase channel formation
Authors: Cannino Giuseppe , Urbani Andrea , Gaspari Marco , Varano Mariaconcetta , Negro Alessandro , Filippi Antonio , Ciscato Francesco , Masgras Ionica , Gerle Christoph , Tibaldi Elena , Brunati Anna Maria , Colombo Giorgio , Lippe Giovanna , Bernardi Paolo , Rasola Andrea 
Published: May 2022

AbstractBinding of the mitochondrial chaperone TRAP1 to client proteins shapes bioenergetic and proteostatic adaptations of cells, but the panel of TRAP1 clients is only partially defined. Here we show that TRAP1 interacts with F-ATP synthase, the protein complex that provides most cellular ATP. TRAP1 competes with the peptidyl-prolyl cis-trans isomerase cyclophilin D (CyPD) for binding to the oligomycin sensitivity-conferring protein (OSCP) subunit of F-ATP synthase, increasing its catalytic activity and counteracting the inhibitory effect of CyPD. Electrophysiological measurements indicate that TRAP1 directly inhibits a channel activity of purified F-ATP synthase endowed with the features of the permeability transition pore (PTP) and that it reverses PTP induction by CyPD, antagonizing PTP-dependent mitochondrial depolarization and cell death. Conversely, CyPD outcompetes the TRAP1 inhibitory effect on the channel. Our data identify TRAP1 as an F-ATP synthase regulator that can influence cell bioenergetics and survival and can be targeted in pathological conditions where these processes are dysregulated, such as cancer.
FAT10 promotes chemotherapeutic resistance in pancreatic cancer by inducing epithelial-mesenchymal transition via stabilization of FOXM1 expression
Authors: Zhu Jinfeng , Zhao Jiefeng , Luo Chen , Zhu Zhengming , Peng Xingyu , Zhu Xiaojian , Lin Kang , Bu Fanqin , Zhang Wenjun , Li Qing , Wang Kai , Hu Zhigang , Yu Xin , Chen Leifeng , Yuan Rongfa 
Published: May 2022

AbstractPancreatic cancer (PC) is one of the deadliest malignant tumors, and its resistance to gemcitabine chemotherapy is the primary reason for poor prognosis in patients. Ubiquitin-like protein FAT10 has recently been reported to promote tumor chemotherapy resistance. In this study, the expression of FAT10 in PC was significantly higher than that in adjacent noncancerous tissues. Increased expression of FAT10 in PC was related to a late TNM stage and decreased overall survival. Functional experiments revealed that downregulating the expression of FAT10 inhibits the proliferation and epithelial-mesenchymal transition (EMT) of PC cells, promotes the apoptosis of PC cells, and enhances sensitivity to gemcitabine chemotherapy. In addition, upregulation of FAT10 increased the expression of FOXM1 protein. The effect of downregulating FAT10 was reversed by FOXM1 overexpression, and FOXM1 knockdown inhibited EMT driven by FAT10 overexpression. Mechanistically, FAT10 stabilized the expression of FOXM1 by competing with ubiquitin to bind FOXM1 and inhibiting the ubiquitination-mediated degradation of FOXM1. In conclusion, the FAT10-FOXM1 axis is a pivotal driver of PC proliferation and gemcitabine resistance, and the results provide novel insights into chemotherapy resistance in PC.