bluuebunny/crossref_metadata_2025_split huggingface dataset:
A matter of time: regulatory events behind the synchronization of C4 and crassulacean acid metabolism in Portulaca oleracea
Authors: Ferrari Renata Callegari , Kawabata Aline Bastos , Ferreira Sávio Siqueira , Hartwell James , Freschi Luciano 
Published: April 2022

Abstract
Portulaca species can switch between C4 and crassulacean acid metabolism (CAM) depending on environmental conditions. However, the regulatory mechanisms behind this rare photosynthetic adaptation remain elusive. Using Portulaca oleracea as a model system, here we investigated the involvement of the circadian clock, plant hormones, and transcription factors in coordinating C4 and CAM gene expression. Free-running experiments in constant conditions suggested that C4 and CAM gene expression are intrinsically connected to the circadian clock. Detailed time-course, drought, and rewatering experiments revealed distinct time frames for CAM induction and reversion (days versus hours, respectively), which were accompanied by changes in abscisic acid (ABA) and cytokinin metabolism and signaling. Exogenous ABA and cytokinins were shown to promote and repress CAM expression in P. oleracea, respectively. Moreover, the drought-induced decline in C4 transcript levels was completely recovered upon cytokinin treatment. The ABA-regulated transcription factor genes HB7, NFYA7, NFYC9, TT8, and ARR12 were identified as likely candidate regulators of CAM induction following this approach, whereas NFYC4 and ARR9 were connected to C4 expression patterns. Therefore, we provide insights into the signaling events controlling C4–CAM transitions in response to water availability and over the day/night cycle, highlighting candidate genes for future functional studies in the context of facultative C4–CAM photosynthesis.
Molecular mechanisms and evolutionary history of phytomelatonin in flowering
Authors: Mou Zongmin , Wang Houping , Chen Suiyun , Reiter Russel J , Zhao Dake 
Published: April 2022

Abstract
Flowering is a critical stage in plant life history, which is coordinated by environmental signals and endogenous cues. Phytomelatonin is a widely distributed indoleamine present in all living organisms and plays pleiotropic roles in plant growth and development. Recent evidence has established that phytomelatonin could modulate flowering in many species, probably in a concentration-dependent manner. Phytomelatonin seems to associate with floral meristem identification and floral organ formation, and the fluctuation of phytomelatonin might be important for flowering. Regarding the underlying mechanisms, phytomelatonin interacts with the central components of floral gene regulatory networks directly or indirectly, including the MADS-box gene family, phytohormones, and reactive oxygen species (ROS). From an evolutionary point of view, the actions of phytomelatonin in flowering probably evolved during the period of the diversification of flowering plants and could be regarded as a functional extension of its primary activities. The presumed evolutionary history of phytomelatonin-modulated flowering is proposed, presented in the chronological order of the appearance of phytomelatonin and core flowering regulators, namely DELLA proteins, ROS, and phytohormones. Further efforts are needed to address some intriguing aspects, such as the exploration of the association between phytomelatonin and photoperiodic flowering, phytomelatonin-related floral MADS-box genes, the crosstalk between phytomelatonin and phytohormones, as well as its potential applications in agriculture.
IgG-RBD Response Due to Inactivated SARS-CoV-2 Vaccine: Alteration in D-Dimer and Fibrinogen Concentrations, Association with Comorbidities and Adverse Effects
Authors: Kaytaz Murat , Akkaya Emre , Gumus Sefika Nur , Genc Sema , Issever Halim , Omer Beyhan 
Published: April 2022

Abstract

Objective
To examine the immunoglobulin G-receptor-binding domain (IgG-RBD) response and changes in fibrinogen and D-dimer concentrations in individuals with a past coronavirus infection and followed by CoronaVac.

Methods
The study consisted of a total of 116 participants. Blood samples were drawn from subjects 21–25 days after they received first and second doses of CoronaVac as well as from individuals with a past infection. Fibrinogen, D-dimer, and IgG-RBD concentrations were measured.

Results
The IgG concentrations of the vaccinated subjects were significantly higher (P &lt; .001), fibrinogen levels were lower (P &lt; .001), and D-dimer levels increased following the second vaccination compared with the first vaccination (P = .083). No difference was obtained in IgG-RBD between vaccinated and previously infected individuals (P = .063). The differences in fibrinogen and D-dimer were statistically nonsignificant between both groups.

Conclusion
The CoronaVac vaccine appears to be safe and effective. It is essential for individuals to take personal protective measures, such as using masks and distancing.
T Cell Senescence by Extensive Phenotyping: An Emerging Feature of COVID-19 Severity
Authors: Zuin Jenny , Fogar Paola , Musso Giulia , Padoan Andrea , Piva Elisa , Pelloso Michela , Tosato Francesca , Cattelan Annamaria , Basso Daniela , Plebani Mario 
Published: April 2022

Abstract

Objective
To identify the potential prognostic value of lymphocyte subsets in COVID-19 patients, where lymphopenia is a common finding.

Methods
In 353 COVID-19 inpatients and 40 controls T cell subsets with markers of senescence and exhaustion were studied by flow cytometry.

Results
In severe illness, total lymphocytes B, NK, and all T subsets were dampened. Senescent CD4+, but mainly CD8+ T cells, increased in patients with respect to controls. The most significant index predicting fatal outcome was neutrophils/CD3+ T ratio.

Conclusion
In conclusion, an altered T cell pattern underlies COVID-19 severity and is involved in predicting the outcome.
Validating the HPA-1 to -5 and -15 Detection by Homemade PCR-SSP, Real-Time PCR, and PCR-RFLP Methods
Authors: Ghader Azizi Seyed , Samiee Shahram , Zadsar Maryam , Shaiegan Mojgan 
Published: April 2022

AbstractObjectiveHuman platelet antigens (HPAs) are antigenic determinants on platelet membrane glycoproteins that stimulate the host’s immune system and cause platelet destruction. In this study, we share our experience with implementing sequence-specific primer-polymerase chain reaction (PCR-SSP), real-time PCR, and PCR-RFLP (restriction fragment length polymorphism) and the validation process used to evaluate the results.MethodsAt the Ardabil Blood Transfusion Center, 10 samples were obtained from blood donors. Validation using PCR-SSP, real-time PCR, and PCR-RFLP methods for genotyping HPAs was done by sequencing. A commercial DNA sample and a commercial kit were also used for validation.ResultsThe results of PCR-SSP, TaqMan Real-Time PCR, melting curve analysis (HPA-15), and PCR-RFLP (HPA-3) were 100% consistent with sequencing (gold standard) and commercial kit results.ConclusionsThere was a 100% correlation between repeating the methods and the expected results for repeatability, and no false positives and negatives were observed.
Use of Self-Collected Saliva Samples for the Detection of SARS-CoV-2
Authors: Sogbesan Kehinde , Sogbesan Taiwo , Hata D Jane , White Edward L , Daniel Wyeth , Gasson Samuel L , Jones Dylan S , Vicari Brittany R , Van Siclen Carleen P , Palmucci Carla , Marquez Christopher P , Parkulo Mark A , Thielen Kent R , Nassar Aziza 
Published: April 2022

Abstract

Objective
Using a US Food and Drug Administration (FDA) emergency use authorization (EUA) reverse transcription polymerase chain reaction (RT-PCR) method, we examined the analytic performance accuracy of saliva specimens as compared to nasopharyngeal (NP) specimens in symptomatic patients. Correlation between test results and symptoms was also evaluated.

Methods
Over a 5-week period in 2020, 89 matched saliva and nasopharyngeal swabs were collected from individuals exhibiting symptoms consistent with SARS-CoV-2. Specimens were tested with an FDA EUA-approved RT-PCR method, and performance characteristics were compared.

Results
The concordance rate between saliva and nasopharyngeal testing was 93.26%. The mean cycle threshold value of saliva when compared to the NP specimen was 3.56 cycles higher. As compared to NP swab, saliva testing demonstrates acceptable agreement but lower sensitivity.

Conclusion
When compared to a reference method using NP swabs, the use of saliva testing proved to be a reliable method. Self-collected saliva testing for SARS-CoV-2 allows for a viable option when trained staff or collection materials are in short supply.
Effects of boosting on extragalactic components: methods and statistical studies
Authors: Coulton William , Feldman Sydney , Maamari Karime , Pierpaoli Elena , Yasini Siavash , Dolag Klaus 
Published: April 2022

ABSTRACT
In this work, we examine the impact of our motion with respect to the Cosmic Microwave Background (CMB) rest frame on statistics of CMB maps by examining the one-, two-, three-, and four- point statistics of simulated maps of the CMB and Sunyaev–Zeldovich (SZ) effects. We validate boosting codes by comparing their outcomes for temperature and polarization power spectra up to ℓ ≃ 6000. We derive and validate a new analytical formula for the computation of the boosted power spectrum of a signal with a generic frequency dependence. As an example we show how this increases the boosting correction to the power spectrum of CMB intensity measurements by ${\sim}30{{\ \rm per\ cent}}$ at 150 GHz. We examine the effect of boosting on thermal and kinetic SZ power spectra from semianalytical and hydrodynamical simulations; the boosting correction is generally small for both simulations, except when considering frequencies near the tSZ null. For the non-Gaussian statistics, in general we find that boosting has no impact with two exceptions. We find that, whilst the statistics of the CMB convergence field are unaffected, quadratic estimators that are used to measure this field can become biased at the $O(1){{\ \rm per\ cent}}$ level by boosting effects. We present a simple modification to the standard estimators that removes this bias. Second, bispectrum estimators can receive a systematic bias from the Doppler induced quadrupole when there is anisotropy in the sky – in practice this anisotropy comes from masking and inhomogeneous noise. This effect is unobservable and already removed by existing analysis methods.
Decoding the star forming properties of gas-rich galaxy pairs
Authors: Bok J , Cluver M E , Jarrett T H , Skelton R E , Jones M G , Verdes-Montenegro L 
Published: April 2022

ABSTRACT
We extend the analysis of Bok et al. (2020) in which the H i content of isolated galaxies from the AMIGA (Analysis of the interstellar Medium in Isolated GAlaxies) sample and selected paired galaxies from ALFALFA (Arecibo Legacy Fast ALFA) were examined as a potential driver of galaxy location on the WISE (Wide-field Infrared Survey Explorer) mid-infrared SFR–M⋆ sequence. By further characterizing the isolated and pair galaxy samples, i.e. in terms of optical galaxy morphology, a more detailed and quantitative description of local galaxy environment by way of the local number density (η) and tidal strength (Q) parameters, star formation efficiency (SFE$_{\rm {H{\small {\rm ~I}}}}$), and H i integrated profile asymmetries, we present plausible pathways for the broadening of the pair sample H i deficiency distribution towards both high and low deficiencies compared to the narrower isolated galaxy sample distribution (i.e. σPAIRS = 0.34 versus σAMIGA = 0.28). We associate the gas-rich tail of the pair deficiency distribution with the highest Q values, large profile asymmetries, and low SFEs. From this, we infer that merger activity is enhancing gas supplies, as well as disrupting the efficiency of star formation, via strong gravitational torques. The gas-poor wing of the deficiency distribution appears to be populated with galaxies in denser environments (with larger η values on average), more akin to groups. Despite our gas-rich selection criterion, there is a small population of early-type galaxies in the pair sample, which primarily fall in the positive deficiency wing of the distribution. These results suggest that a combination of a denser galaxy environment, early-type morphology, and higher stellar mass is contributing to the broadening of the deficiency distribution towards larger deficiencies.
The average dust attenuation curve at z ∼ 1.3 based on HST grism surveys
Authors: Battisti A J , Bagley M B , Baronchelli I , Dai Y S , Henry A L , Malkan M A , Alavi A , Calzetti D , Colbert J , McCarthy P J , Mehta V , Rafelski M , Scarlata C , Shivaei I , Wisnioski E 
Published: April 2022

ABSTRACT
We present the first characterization of the average dust attenuation curve at z ∼ 1.3 by combining rest-frame ultraviolet through near-IR photometry with Balmer decrement (H α/H β) constraints for ∼900 galaxies with 8 ≲ log (M⋆/M⊙) &lt; 10.2 at 0.75 &lt; z &lt; 1.5 in the HST WFC3 IR Spectroscopic Parallel and 3D-HST grism surveys. Using galaxies in SDSS, we establish that the (H α + [N ii])/[O iii] line ratio and stellar mass are good proxies for the Balmer decrement in low-spectral resolution grism data when only upper limits on H β are available and/or H α is blended with [N ii]. The slope of the z ∼ 1.3 attenuation curve ($A(0.15\, \rm{\mu m})/A(V)=3.15$) and its normalization (RV = 3.26) lie in-between the values found for z = 0 and z ∼ 2 dust attenuation curves derived with similar methods. These provide supporting evidence that the average dust attenuation curve of star-forming galaxies evolves continuously with redshift. The z ∼ 1.3 curve has a mild 2175 Å feature (bump amplitude, Eb = 0.83; ∼25 per cent that of the MW extinction curve), which is comparable to several other studies at 0 &lt; z ≲ 3, and suggests that the average strength of this feature may not evolve significantly with redshift. The methods we develop to constrain dust attenuation from HST grism data can be applied to future grism surveys with JWST, Euclid, and RST. These new facilities will detect millions of emission line galaxies and offer the opportunity to significantly improve our understanding of how and why dust attenuation curves evolve.
Remnant masses of core collapse supernovae in the jittering jets explosion mechanism
Authors: Shishkin Dmitry , Soker Noam 
Published: April 2022

ABSTRACT
We conduct one-dimensional (1D) stellar evolution simulations of non-rotating stars with initial masses in the range of $11\!-\!48 \, \mathrm{M}_{\odot }$ to the time of core collapse and, using a criterion on the specific angular momentum fluctuations in the inner convective zones, estimate the masses of the neutron star (NS) remnants according to the jittering jets explosion mechanism. From the 1D simulations, we find that several convective zones with specific angular momentum fluctuations of $j_{\rm {conv}} \gtrsim 2.5 \times 10^{15} {\, \rm cm}^2 {\, \rm s}^{-1}$ develop near the edge of the iron core in all models. For this condition for explosion, we find the NS remnant masses to be in the range of $1.3\!-\!1.8 \, \mathrm{M}_\odot$, while if we require twice as large values, i.e. $j_{\rm {conv}} \gtrsim 5 \times 10^{15} {\, \rm cm}^2 {\, \rm s}^{-1}$, we find the NS remnant masses to be in the range of $1.4\!-\!2.8 \, \mathrm{M}_\odot$ (the upper values here might form black holes). Note that in general, the formation of black holes in the jittering jets explosion mechanism requires a rapidly rotating pre-collapse core, while we simulate non-rotating stars.
Exotic image formation in strong gravitational lensing by clusters of galaxies – III. Statistics with HUDF
Authors: Meena Ashish Kumar , Bagla Jasjeet Singh 
Published: April 2022

ABSTRACT
We study the image formation near point singularities (swallowtail and umbilics) in the simulated strongly lensed images of Hubble Ultra Deep Field (HUDF) by the Hubble Frontier Fields (HFF) clusters. In this work, we only consider nearly half of the brightest (a total of 5271) sources in the HUDF region. For every HFF cluster, we constructed 11 realizations of strongly lensed HUDF with an arbitrary translation of the cluster centre within the central region of HUDF and an arbitrary rotation. In each of these realizations, we visually identify the characteristic/exotic image formation corresponding to the different point singularities. We find that our current results are consistent with our earlier results based on different approaches. We also study time delay in these exotic image formations and compare it with typical five-image geometries. We find that the typical time delay in exotic image formations is an order of magnitude smaller than the typical time delay in a generic five-image geometry.
The mitoXplorer 2.0 update: integrating and interpreting mitochondrial expression dynamics within a cellular context
Authors: Marchiano Fabio , Haering Margaux , Habermann Bianca Hermine 
Published: April 2022

AbstractMitochondria are subcellular organelles present in almost all eukaryotic cells, which play a central role in cellular metabolism. Different tissues, health and age conditions are characterized by a difference in mitochondrial structure and composition. The visual data mining platform mitoXplorer 1.0 was developed to explore the expression dynamics of genes associated with mitochondrial functions that could help explain these differences. It, however, lacked functions aimed at integrating mitochondria in the cellular context and thus identifying regulators that help mitochondria adapt to cellular needs. To fill this gap, we upgraded the mitoXplorer platform to version 2.0 (mitoXplorer 2.0). In this upgrade, we implemented two novel integrative functions, network analysis and transcription factor enrichment, to specifically help identify signalling or transcriptional regulators of mitochondrial processes. In addition, we implemented several other novel functions to allow the platform to go beyond simple data visualization, such as an enrichment function for mitochondrial processes, a function to explore time-series data, the possibility to compare datasets across species and an IDconverter to help facilitate data upload. We demonstrate the usefulness of these functions in three specific use cases. mitoXplorer 2.0 is freely available without login at http://mitoxplorer2.ibdm.univ-mrs.fr.
Targeted delivery to macrophages and dendritic cells by chemically modified mannose ligand-conjugated siRNA
Authors: Uehara Keiji , Harumoto Toshimasa , Makino Asana , Koda Yasuo , Iwano Junko , Suzuki Yasuhiro , Tanigawa Mari , Iwai Hiroto , Asano Kana , Kurihara Kana , Hamaguchi Akinori , Kodaira Hiroshi , Atsumi Toshiyuki , Yamada Yoji , Tomizuka Kazuma 
Published: April 2022

Abstract
Extrahepatic delivery of small interfering RNAs (siRNAs) may have applications in the development of novel therapeutic approaches. However, reports on such approaches are limited, and the scarcity of reports concerning the systemically targeted delivery of siRNAs with effective gene silencing activity presents a challenge. We herein report for the first time the targeted delivery of CD206-targetable chemically modified mannose–siRNA (CMM–siRNA) conjugates to macrophages and dendritic cells (DCs). CMM–siRNA exhibited a strong binding ability to CD206 and selectively delivered contents to CD206-expressing macrophages and DCs. Furthermore, the conjugates demonstrated strong gene silencing ability with long-lasting effects and protein downregulation in CD206-expressing cells in vivo. These findings could broaden the use of siRNA technology, provide additional therapeutic opportunities, and establish a basis for further innovative approaches for the targeted delivery of siRNAs to not only macrophages and DCs but also other cell types.
Pleiotropic MLLT10 variation confers risk of meningioma and estrogen-mediated cancers
Authors: Walsh Kyle M , Zhang Chenan , Calvocoressi Lisa , Hansen Helen M , Berchuck Andrew , Schildkraut Joellen M , Bondy Melissa L , Wrensch Margaret , Wiemels Joseph L , Claus Elizabeth B 
Published: April 2022

Abstract

Background
Risk of tumors of the breast, ovary, and meninges has been associated with hormonal factors and with one another. Genome-wide association studies (GWAS) identified a meningioma risk locus on 10p12 near previous GWAS hits for breast and ovarian cancers, raising the possibility of genetic pleiotropy.

Methods
We performed imputation-based fine-mapping in three case-control datasets of meningioma (927 cases, 790 controls), female breast cancer (28 108 cases, 22 209 controls), and ovarian cancer (25 509 cases, 40 941 controls). Analyses were stratified by sex (meningioma), estrogen receptor (ER) status (breast), and histotype (ovarian), then combined using subset-based meta-analysis in ASSET. Lead variants were assessed for association with additional traits in UK Biobank to identify potential effect-mediators.

Results
Two-sided subset-based meta-analysis identified rs7084454, an expression quantitative trait locus (eQTL) near the MLLT10 promoter, as lead variant (5.7 × 10–14). The minor allele was associated with increased risk of meningioma in females (odds ratio (OR) = 1.42, 95% Confidence Interval (95%CI):1.20–1.69), but not males (OR = 1.19, 95%CI: 0.91–1.57). It was positively associated with ovarian (OR = 1.09, 95%CI:1.06–1.12) and ER+ breast (OR = 1.05, 95%CI: 1.02–1.08) cancers, and negatively associated with ER– breast cancer (OR = 0.91, 95%CI: 0.86–0.96). It was also associated with several adiposity traits (P &lt; 5.0 × 10–8), but adjusting for body mass index did not attenuate its association with meningioma. MLLT10 and ESR1 expression were positively correlated in normal meninges (P = .058) and meningioma tumors (P = .0065).

Conclusions
We identify a MLLT10 eQTL positively associated with risk of female meningioma, ER+ breast cancer, ovarian cancer, and obesity, and implicate a potential estrogenic mechanism underlying this pleiotropy.
Variable Genomic Landscapes of Advanced Melanomas with Heavy Pigmentation
Authors: Huang Richard S P , Tse Julie Y , Harries Lukas , Graf Ryon P , Lin Douglas I , Murugesan Karthikeyan , Hiemenz Matthew C , Parimi Vamsi , Janovitz Tyler , Decker Brennan , Severson Eric , Levy Mia A , Ramkissoon Shakti H , Elvin Julia A , Ross Jeffrey S , Williams Erik A 
Published: April 2022

Abstract

Background
In the current study, we examined the real-world prevalence of highly pigmented advanced melanomas (HPMel) and the clinicopathologic, genomic, and ICPI biomarker signatures of this class of tumors.

Materials and Methods
Our case archive of clinical melanoma samples for which the ordering physician requested testing for both PD-L1 immunohistochemistry (IHC) and comprehensive genomic profiling (CGP) was screened for HPMel cases, as well as for non-pigmented or lightly pigmented advanced melanoma cases (LPMel).

Results
Of the 1268 consecutive melanoma biopsies in our archive that had been submitted for PD-L1 IHC, 13.0% (165/1268) were HPMel and 87.0% (1103/1268) were LPMel. In the HPMel cohort, we saw a significantly lower tumor mutational burden (TMB, median 8.8 mutations/Mb) than in the LPMel group (11.4 mut/Mb), although there was substantial overlap. In examining characteristic secondary genomic alterations (GA), we found that the frequencies of GA in TERTp, CDKN2A, TP53, and PTEN were significantly lower in the HPMel cases than in LPMel. A higher rate of GA in CTNNB1, APC, PRKAR1A, and KIT was identified in the HPMel cohort compared with LPMel.

Conclusions
In this study, we quantified the failure rates of melanoma samples for PD-L1 testing due to high melanin pigmentation and showed that CGP can be used in these patients to identify biomarkers that can guide treatment decisions for HPMel patients. Using this practical clinical definition for tumor pigmentation, our results indicate that HPMel are frequent at 13% of melanoma samples, and in general appear molecularly less developed, with a lower TMB and less frequent secondary GA of melanoma progression.