bluuebunny/crossref_metadata_2025_split huggingface dataset:
Prevalence of Gastrointestinal Pathogens Detected by Multiplex Polymerase Chain Reaction in a Prospective Cohort of Men Who Have Sex With Men Taking Human Immunodeficiency Virus Preexposure Prophylaxis—New York City, 2019–2020
Authors: Purpura Lawrence , Zucker Jason , LaSota Elijah , Lopez Mabel , Spicehandler Rebecca , Carnevale Caroline , Perez Edward , Richards Paul , Chang Jennifer , Cohall Al , Uhlemann Anne-Catrin , Whittier Susan , Sobieszczyk Magdalena E , Green Daniel A 
Published: August 2021

Abstract
Multiplex polymerase chain reaction testing for gastrointestinal pathogens was performed on a longitudinal cohort of 110 men who have sex with men taking human immunodeficiency virus preexposure prophylaxis. At least 1 pathogen was detected among 50 (45%) participants, with some participants testing positive for the same pathogen on multiple consecutive visits over a period of months.
Identification of the Genes Coding for Carthamin Synthase, Peroxidase Homologs that Catalyze the Final Enzymatic Step of Red Pigmentation in Safflower (Carthamus tinctorius L.)
Authors: Waki Toshiyuki , Terashita Miho , Fujita Naoki , Fukuda Keishi , Kato Mikiya , Negishi Takashi , Uchida Hiromi , Aoki Yuichi , Takahashi Seiji , Nakayama Toru 
Published: August 2021

ABSTRACT
Carthamin, a dimeric quinochalcone that is sparingly soluble in water, is obtained from the yellow-orange corolla of fully blooming safflower (Carthamus tinctorius L.) florets. Carthamin is a natural red colorant, which has been used worldwide for more than 4500 years and is the major component of Japanese ‘beni’ used for dyeing textiles, in cosmetics and as a food colorant. The biosynthetic pathway of carthamin has long remained uncertain. Previously, carthamin was proposed to be derived from precarthamin (PC), a water-soluble quinochalcone, via a single enzymatic process. In this study, we identified the genes coding for the enzyme responsible for the formation of carthamin from PC, termed ‘carthamin synthase’ (CarS), using enzyme purification and transcriptome analysis. The CarS proteins were purified from the cream-colored corolla of safflower and identified as peroxidase homologs (CtPOD1, CtPOD2 and CtPOD3). The purified enzyme catalyzed the oxidative decarboxylation of PC to produce carthamin using O2, instead of H2O2, as an electron acceptor. In addition, CarS catalyzed the decomposition of carthamin. However, this enzymatic decomposition of carthamin could be circumvented by adsorption of the pigment to cellulose. These CtPOD isozymes were not only expressed in the corolla of the carthamin-producing orange safflower cultivars but were also abundantly expressed in tissues and organs that did not produce carthamin and PC. One CtPOD isozyme, CtPOD2, was localized in the extracellular space. Based on the results obtained, a model for the stable red pigmentation of safflower florets during flower senescence and the traditional ‘beni’ manufacturing process is proposed.
The 5-formyl-tetrahydrofolate proteome links folates with C/N metabolism and reveals feedback regulation of folate biosynthesis
Authors: Li Weichao , Liang Qiuju , Mishra Ratnesh Chandra , Sanchez-Mu�oz Raul , Wang Huan , Chen Xin , Van Der Straeten Dominique , Zhang Chunyi , Xiao Youli 
Published: August 2021

AbstractFolates are indispensable for plant development, but their molecular mode of action remains elusive. We synthesized a probe, “5-F-THF-Dayne,” comprising 5-formyl-tetrahydrofolate (THF) coupled to a photoaffinity tag. Exploiting this probe in an affinity proteomics study in Arabidopsis thaliana, we retrieved 51 hits. Thirty interactions were independently validated with in vitro expressed proteins to bind 5-F-THF with high or low affinity. Interestingly, the interactors reveal associations beyond one-carbon metabolism, covering also connections to nitrogen (N) metabolism, carbohydrate metabolism/photosynthesis, and proteostasis. Two of the interactions, one with the folate biosynthetic enzyme DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE 1 (AtDHFR-TS1) and another with N metabolism-associated glutamine synthetase 1;4 (AtGLN1;4), were further characterized. In silico and experimental analyses revealed G35/K36 and E330 as key residues for the binding of 5-F-THF in AtDHFR-TS1 and AtGLN1;4, respectively. Site-directed mutagenesis of AtGLN1;4 E330, which co-localizes with the ATP-binding pocket, abolished 5-F-THF binding as well as AtGLN1;4 activity. Furthermore, 5-F-THF was noted to competitively inhibit the activities of AtDHFR-TS1 and AtGLN1;4. In summary, we demonstrated a regulatory role for 5-F-THF in N metabolism, revealed 5-F-THF-mediated feedback regulation of folate biosynthesis, and identified a total of 14 previously unknown high-affinity binding cellular targets of 5-F-THF. Together, this sets a landmark toward understanding the role of folates in plant development.
Light-dependent phosphorylation of THRUMIN1 regulates its association with actin filaments and 14-3-3 proteins
Authors: Dwyer Matthew E , Hangarter Roger P 
Published: August 2021

Abstract
Light-dependent chloroplast movements in leaf cells contribute to the optimization of photosynthesis. Low-light conditions induce chloroplast accumulation along periclinal cell surfaces, providing greater access to available light, whereas high light induces movement of chloroplasts to anticlinal cell surfaces, providing photodamage protection and allowing more light to reach underlying cell layers. The THRUMIN1 protein is required for normal chloroplast movements in Arabidopsis (Arabidopsis thaliana) and has been shown to localize at the plasma membrane and to undergo rapid light-dependent interactions with actin filaments through the N-terminal intrinsically disordered region (IDR). A predicted WASP-Homology 2 domain was found in the IDR but mutations in this domain did not disrupt localization of THRUMIN1:YFP to actin filaments. A series of other protein truncations and site-directed mutations of known and putative phosphorylation sites indicated that a phosphomimetic mutation (serine to aspartic acid) at position 170 disrupted localization of THRUMIN1 to actin filaments. However, the phosphomimetic mutant rescued the thrumin1-2 mutant phenotype for chloroplast movement and raises questions about the role of THRUMIN1’s interaction with actin. Mutation of serine 146 to aspartic acid also resulted in cytoplasmic localization of THRUMIN1:YFP in Nicotiana benthamiana. Mutations to a group of putative zinc-binding cysteine clusters implicate the C-terminus of THRUMIN1 in chloroplast movement. Phosphorylation-dependent association of THRUMIN1 with 14-3-3 KAPPA and OMEGA were also identified. Together, these studies provide insights into the mechanistic role of THRUMIN1 in light-dependent chloroplast movements.
COMPARISON OF RADIATION DOSE AND IMAGE QUALITY IN HEAD CT SCANS AMONG MULTIDETECTOR CT SCANNERS
Authors: Abuzaid Mohamed M , Elshami Wiam , Tekin H O , Sulieman Abdelmoneim , Bradley D A 
Published: August 2021

Abstract
The present study compares three different multidetector CT (MDCT) scanners for routine brain imaging in terms of image quality and radiation doses. The volume CT dose index (CTDIvol), dose-length product (DLP), and effective dose (E) were calculated. Subjective image assessment was obtained based on a scale ranging from 1 (unacceptable) to 5 (optimum). All images scored 3.5 or over, with the 160-slice MDCT images being favoured. For the 4-, 16- and 160-slice MDCT scanners, the respective median values for CTDIvol were 57 mGy, 41 mGy, and 28 mGy; DLP values were 901 mGy.cm, 680 mGy.cm, and 551 mGy.cm; and effective doses were 2 mSv, 1.5 mSv, and 1 mSv, respectively. Compared to the 160-slice MDCT, the dose values for the 4- and 16-slice units were significantly greater. In practice, the CT modality used must be carefully selected to avoid elevated radiation doses and maintain image quality.
Researchers’ institutional mobility: bibliometric evidence on academic inbreeding and internationalization
Authors: Macháček Vít , Srholec Martin , Ferreira Márcia R , Robinson-Garcia Nicolas , Costas Rodrigo 
Published: August 2021

Abstract
We propose institutional mobility indicators based on researchers’ mobility flows in 22 major fields of science across 1,130 Leiden Ranking institutions from 64 countries. We base our indicators on data from the Dimensions database and Global Research Identifier Database. We use researchers’ first and last affiliations to estimate the extent authors have moved across institutions as well as countries. For each institution, we quantify the shares of researchers with the same affiliation (insiders), those who came from another institution within the country (domestic outsiders), and those coming from a different country (foreign outsiders). Institutions in Central, Eastern, and Southern Europe have the highest share of insiders, whereas institutions in Northern America and Western and Northern Europe have a higher share of foreign outsiders. Foreign outsiders are most common in small and wealthy countries. No disciplinary differences are observed, as captured by the field classification scheme of Dimensions.
High-yield ‘one-pot’ biosynthesis of raspberry ketone, a high-value fine chemical
Authors: Moore Simon J , Tosi Tommaso , Bell David , Hleba Yonek B , Polizzi Karen M , Freemont Paul S 
Published: August 2021

AbstractCell-free extract and purified enzyme-based systems provide an attractive solution to study biosynthetic strategies towards a range of chemicals. 4-(4-hydroxyphenyl)-butan-2-one, also known as raspberry ketone, is the major fragrance component of raspberry fruit and is used as a natural additive in the food and sports industry. Current industrial processing of the natural form of raspberry ketone involves chemical extraction from a yield of ∼1–4 mg kg−1 of fruit. Due to toxicity, microbial production provides only low yields of up to 5–100 mg L−1. Herein, we report an efficient cell-free strategy to probe into a synthetic enzyme pathway that converts either L-tyrosine or the precursor, 4-(4-hydroxyphenyl)-buten-2-one, into raspberry ketone at up to 100% conversion. As part of this strategy, it is essential to recycle inexpensive cofactors. Specifically, the final enzyme step in the pathway is catalyzed by raspberry ketone/zingerone synthase (RZS1), an NADPH-dependent double bond reductase. To relax cofactor specificity towards NADH, the preferred cofactor for cell-free biosynthesis, we identify a variant (G191D) with strong activity with NADH. We implement the RZS1 G191D variant within a ‘one-pot’ cell-free reaction to produce raspberry ketone at high-yield (61 mg L−1), which provides an alternative route to traditional microbial production. In conclusion, our cell-free strategy complements the growing interest in engineering synthetic enzyme cascades towards industrially relevant value-added chemicals.
High parental vaccine motivation at a neighborhood-based vaccine and testing site serving a predominantly Latinx community
Authors: Naso Jamie , Rojas Susy , Peng James , Marquez Carina , Contreras Maria , Castellanos Edgar , Rojas Susana , Rubio Luis , Jones Diane , Jacobo Jon , Black Douglas , Tulier-Laiwa Valerie , Martinez Jacqueline , Chamie Gabriel , Pilarowski Genay , DeRisi Joseph , Havlir Diane , Petersen Maya 
Published: August 2021

AbstractPurposeTo understand vaccine attitudes of Latinx parents highly impacted by COVID-19. Methods. In April 2021, we surveyed parents about their attitudes for COVID-19 vaccination of their children at a community-based outdoor testing/vaccination site serving predominantly low-income, Latinx persons in San Francisco.ResultsAmong 1,033 parents (75% Latinx), 92% would “definitely” or “probably” vaccinate their children. Vaccine hesitancy was higher for younger children; concerns included side effects and impacts on fertility. Doctors and community organizations were noted as trusted sources of information, including among vaccine-hesitant parents.ConclusionLatinx parents accessing neighborhood-based COVID-19 testing/vaccination services are highly motivated to vaccinate their children for COVID-19.
Analysis of Preplatelets and Their Barbell Platelet Derivatives by Imaging Flow Cytometry
Authors: Kemble Sam , Dalby Amanda , Lowe Gillian C , Nicolson Phillip LR , Watson Steve P , Senis Yotis , Thomas Steven G. , Harrison Paul 
Published: August 2021

AbstractCirculating large “preplatelets” undergo fission via barbell platelet intermediates into two smaller, mature platelets. In this study, we determine whether preplatelets and/or barbells are equivalent to reticulated/immature platelets by using ImageStream flow cytometry (ISFC) and super-resolution microscopy. Immature platelets, preplatelets and barbells were quantified in healthy and thrombocytopenic mice, healthy human volunteers, and patients with immune thrombocytopenia (ITP) or undergoing chemotherapy. Preplatelets and barbells were 1.9%+0.18/1.7%+0.48 (n=6) and 3.3%+1.6/0.5%+0.27 (n=12) of total platelet counts in murine and human whole blood, respectively. Both preplatelets and barbells exhibited high expression of HLA-I with high thiazole orange and mitotracker fluorescence. Tracking dye experiments confirmed that preplatelets transform into barbells and undergo fissionex vivoto increase platelet counts, with dependence upon the cytoskeleton and normal mitochondrial respiration. Samples from antibody-induced thrombocytopenia in mice and patients with ITP had increased levels of both preplatelets and barbells correlating with immature platelet levels. Furthermore, barbells were absent post-chemotherapy in patients. In mice,in vivobiotinylation confirmed that barbells, but not all large platelets, were immature. This study demonstrates that a subpopulation of large platelets are immature preplatelets that can transform into barbells and undergo fission during maturation.
AlphaMap: An open-source Python package for the visual annotation of proteomics data with sequence specific knowledge
Authors: Voytik Eugenia , Bludau Isabell , Willems Sander , Hansen Fynn , Brunner Andreas-David , Strauss Maximilian T. , Mann Matthias 
Published: August 2021

AbstractSummaryIntegrating experimental information across proteomic datasets with the wealth of publicly available sequence annotations is a crucial part in many proteomic studies that currently lacks an automated analysis platform. Here we present AlphaMap, a Python package that facilitates the visual exploration of peptide-level proteomics data. Identified peptides and post-translational modifications in proteomic datasets are mapped to their corresponding protein sequence and visualized together with prior knowledge from UniProt and with expected proteolytic cleavage sites. The functionality of AlphaMap can be accessed via an intuitive graphical user interface or – more flexibly – as a Python package that allows its integration into common analysis workflows for data visualization. AlphaMap produces publication-quality illustrations and can easily be customized to address a given research question.Availability and implementationAlphaMap is implemented in Python and released under an Apache license. The source code and one-click installers are freely available at https://github.com/MannLabs/alphamap.Supplementary informationA detailed user guide for AlphaMap is provided as supplementary data.
OPT3 Transports Copper to the Phloem, Mediates Shoot-to-Root Copper Signaling and Crosstalk Between Copper and Iron Homeostasis inA. thaliana
Authors: Chia Ju-Chen , Yan Jiapei , Ishka Maryam Rahmati , Faulkner Marta Marie , Simons Eli , Huang Rong , Smieska Louisa , Woll Arthur , Tappero Ryan , Kiss Andrew , Jiao Chen , Fei Zhangjun , Kochian Leon V. , Walker Elsbeth , Piñeros Miguel , Vatamaniuk Olena K. 
Published: August 2021

AbstractCopper and iron are essential micronutrients but are toxic when accumulating in cells in excess. Thus, their uptake by roots is tightly regulated. While plants sense and respond to local copper availability, the systemic regulation of copper uptake has not been documented. By contrast, both local and systemic control for iron uptake has been reported. Iron abundance in the phloem has been suggested to act systemically, regulating the expression of iron uptake genes in the root. Consistently, shoot-to-root iron signaling is disrupted inA. thalianamutants lacking the phloem companion cell-localized iron transporter, AtOPT3:opt3mutants overaccumulate iron in leaves while constitutively upregulating iron deficiency-responsive genes in roots. We report that AtOPT3 transports copper and mediates its delivery from source leaves to sinks including young leaves and developing embryos. Consequently, theopt3mutant accumulates less copper in the phloem, is sensitive to copper deficiency, and mounts transcriptional copper deficiency response in roots. Copper rescues these defects. Notably, feeding theopt3mutant with copper or ironviathe phloem in leaves downregulates the expression of both copper and iron-deficiency marker genes in roots, suggesting that copper and iron can substitute each other’s function in the phloem in shoot-to-root communication.One-sentence summaryAtOPT3 loads copper and iron into the phloem companion cells, for subsequent distribution to sink tissues and systemic signaling of copper and iron deficiency.
Novel compound inhibitors of HIV-1NL4-3 Vpu
Authors: Robinson Carolyn A. , Lyddon Terri D. , Gil Hwi Min , Evans David T. , Kuzmichev Yury V. , Richard Jonathan , Finzi Andrés , Welbourn Sarah , Rasmussen Lynn , Miranda Nebane N. , Gupta Vandana V. , Ananthan Sam , Cai Zhaohui , Wonderlich Elizabeth R. , Augelli-Szafran Corinne E. , Bostwick Robert , Ptak Roger G. , Schader Susan M. , Johnson Marc C. 
Published: August 2021

ABSTRACTHIV-1 Vpu targets the host cell proteins CD4 and BST-2/Tetherin for degradation, ultimately resulting in enhanced virus spread and host immune evasion. The discovery and characterization of small molecules that antagonize Vpu would further elucidate the contribution of Vpu to pathogenesis and lay the foundation for the study of a new class of novel HIV-1 therapeutics. To identify novel compounds that block Vpu activity, we developed a cell-based ‘gain of function’ assay that produces a positive signal in response to Vpu inhibition. To develop this assay, we took advantage of the viral glycoprotein, GaLV Env. In the presence of Vpu, GaLV Env is not incorporated into viral particles, resulting in non-infectious virions. Vpu inhibition restores infectious particle production. Using this assay, a high throughput screen of >650,000 compounds was performed to identify inhibitors that block the biological activity of Vpu. From this screen, we identified several positive hits but focused on two compounds from one structural family, SRI-41897 and SRI-42371. It was conceivable that the compounds inhibited the formation of infectious virions by targeting host cell proteins instead of Vpu directly, so we developed independent counter-screens for off target interactions of the compounds and found no off target interactions. Additionally, these compounds block Vpu-mediated modulation of CD4, BST-2/Tetherin and antibody dependent cell-mediated toxicity (ADCC). Unfortunately, both SRI-41897 and SRI-42371 were shown to be specific to the N-terminal region of NL4-3 Vpu and did not function against other, more clinically relevant, strains of Vpu.
WGA-LP: a pipeline for Whole Genome Assembly of contaminated reads
Authors: Rossi N. , Colautti A. , Iacumin L. , Piazza C. 
Published: August 2021

AbstractSummaryWhole Genome Assembly (WGA) of bacterial genomes with short reads is a quite common task as DNA sequencing has become cheaper with the advances of its technology. The process of assembling a genome has no absolute golden standard (Del Angel et al. (2018)) and it requires to perform a sequence of steps each of which can involve combinations of many different tools. However, the quality of the final assembly is always strongly related to the quality of the input data. With this in mind we built WGA-LP, a package that connects state-of-art programs and novel scripts to check and improve the quality of both samples and resulting assemblies.WGA-LP, with its conservative decontamination approach, has shown to be capable of creating high quality assemblies even in the case of contaminated reads.Availability and ImplementationWGA-LP is available on GitHub (https://github.com/redsnic/WGA-LP) and Docker Hub (https://hub.docker.com/r/redsnic/wgalp). The web app for node visualization is hosted by shinyapps.io (https://redsnic.shinyapps.io/ContigCoverageVisualizer/).ContactNicolò Rossi, olocin.issor@gmail.comSupplementary informationSupplementary data are available at bioRxiv online.
Photorealistic reconstruction of visual texture from EEG signals
Authors: Wakita Suguru , Orima Taiki , Motoyoshi Isamu 
Published: August 2021

AbstractRecent advances in brain decoding have made it possible to classify image categories based on neural activity. Increasing numbers of studies have further attempted to reconstruct the image itself. However, because images of objects and scenes inherently involve spatial layout information, the reconstruction usually requires retinotopically organized neural data with high spatial resolution, such as fMRI signals. In contrast, spatial layout does not matter in the perception of ‘texture’, which is known to be represented as spatially global image statistics in the visual cortex. This property of ‘texture’ enables us to reconstruct the perceived image from EEG signals, which have a low spatial resolution. Here, we propose an MVAE-based approach for reconstructing texture images from visual evoked potentials measured from observers viewing natural textures such as the textures of various surfaces and object ensembles. This approach allowed us to reconstruct images that perceptually resemble the original textures with a photographic appearance. A subsequent analysis of the dynamic development of the internal texture representation in the VGG network showed that the reproductivity of texture rapidly improves at 200 ms latency in the lower layers but improves more gradually in the higher layers. The present approach can be used as a method for decoding the highly detailed ‘impression’ of sensory stimuli from brain activity.