title: PeerJ
description:  Articles published in PeerJ
link: https://peerj.com/articles/index.rss3?journal=peerj&page=629
creator: info@peerj.com PeerJ
errorsTo: info@peerj.com PeerJ
language: en

title: Xenobennettella coralliensis a new monoraphid diatom genus characterized by the alveolate sternum valve with cavum, observed from coral reef habitats
link: https://peerj.com/articles/13977
last-modified: 2022-10-19
description: During a survey of benthic diatoms from the coral reefs of the Indian Ocean (Scattered Islands) and Pacific Ocean (Tuamotu Archipelago), an interesting monoraphid diatom was observed and examined by light microscopy and various electron microscopy methods including Focus Ion Beam milling. Our thorough analysis revealed the similarity of this diatom to Bennettella R.W.Holmes, which we reference in the name: Xenobennettella Witkowski & Riaux-Gobin gen. nov., with Xenobennettella coralliensis Witkowski & Riaux-Gobin sp. nov. as the generitype. The type habitat for this new species is the sublittoral coral reef of Juan de Nova in the Mozambique Channel. The sternum valve of the new genus is characterized by an alveolate ultrastructure with the rim of the alveola opening along the valve margin, resembling the sternum valve of Bennettella. Internally, Xenobennettella differs from the latter by possessing a cavum (horseshoe-shaped chamber) on one side of the valve, in a central axial position. The raphe valve of Xenobennettella has small, marginal, apically elongate chambers, which are internally delineated by transapical ribs that are very similar to Bennettella. However, the raphe in the new genus is different from the latter, resembling some Cocconeis and Planothidium with internal raphe endings bent in the opposite direction, while resembling some Planothidium taxa externally by ending on the apical part of the mantle. This contrasts to Bennettella, which has a unique raphe system, with external raphe endings below the apices, a prominent axial structure and a transapically expanded central area. Likewise, the external surface of Bennettella is different from that of the new genus with a complex mantle structure and biseriate striae. In Xenobennettella, the valve mantle of the raphe valve is simple and perforated by areola. The transapical striae occur in the valve margin and the axial area is ornamented along its course with a single row of densely packed areola on both sides. The characteristics of the raphe valve and alveolate sternum valve place the new genus among the Achnanthidiaceae.
creator: Andrzej Witkowski
creator: Catherine Riaux-Gobin
creator: Adrian Kryk
creator: Tomasz Płociński
creator: Izabela Zgłobicka
creator: Krzysztof Kurzydłowski
uri: https://doi.org/10.7717/peerj.13977
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Witkowski et al.

title: Learning about the meanings of ambiguous words: evidence from a word-meaning priming paradigm with short narratives
link: https://peerj.com/articles/14070
last-modified: 2022-10-19
description: Fluent language comprehension requires people to rapidly activate and integrate context-appropriate word meanings. This process is challenging for meanings of ambiguous words that are comparatively lower in frequency (e.g., the “bird” meaning of “crane”). Priming experiments have shown that recent experience makes such subordinate (less frequent) word meanings more readily available at the next encounter. These experiments used lists of unconnected sentences in which each ambiguity was disambiguated locally by neighbouring words. In natural language, however, disambiguation may occur via more distant contextual cues, embedded in longer, connected communicative contexts. In the present experiment, participants (N = 51) listened to 3-sentence narratives that ended in an ambiguous prime. Cues to disambiguation were relatively distant from the prime; the first sentence of each narrative established a situational context congruent with the subordinate meaning of the prime, but the remainder of the narrative did not provide disambiguating information. Following a short delay, primed subordinate meanings were more readily available (compared with an unprimed control), as assessed by responses in a word association task related to the primed meaning. This work confirms that listeners reliably disambiguate spoken ambiguous words on the basis of cues from wider narrative contexts, and that they retain information about the outcome of these disambiguation processes to inform subsequent encounters of the same word form.
creator: Lena M. Blott
creator: Oliver Hartopp
creator: Kate Nation
creator: Jennifer M. Rodd
uri: https://doi.org/10.7717/peerj.14070
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Blott et al.

title: Radiomics combined with clinical features in distinguishing non-calcifying tuberculosis granuloma and lung adenocarcinoma in small pulmonary nodules
link: https://peerj.com/articles/14127
last-modified: 2022-10-19
description: AimTo evaluate the performance of radiomics models with the combination of clinical features in distinguishing non-calcified tuberculosis granuloma (TBG) and lung adenocarcinoma (LAC) in small pulmonary nodules.MethodologyWe conducted a retrospective analysis of 280 patients with pulmonary nodules confirmed by surgical biopsy from January 2017 to December 2020. Samples were divided into LAC group (n = 143) and TBG group (n = 137). We assigned them to a training dataset (n = 196) and a testing dataset (n = 84). Clinical features including gender, age, smoking, CT appearance (size, location, spiculated sign, lobulated shape, vessel convergence, and pleural indentation) were extracted and included in the radiomics models. 3D slicer and FAE software were used to delineate the Region of Interest (ROI) and extract clinical features. The performance of the model was evaluated by the Area Under the Receiver Operating Characteristic (ROC) Curve (AUC).ResultsBased on the model selection, clinical features gender, and age in the LAC group and TBG group showed a significant difference in both datasets (P < 0.05). CT appearance lobulated shape was also significantly different in the LAC group and TBG group (Training dataset, P = 0.034; Testing dataset, P = 0.030). AUC were 0.8344 (95% CI [0.7712–0.8872]) and 0.751 (95% CI [0.6382–0.8531]) in training and testing dataset, respectively.ConclusionWith the capacity to detect differences between TBG and LAC based on their clinical features, radiomics models with a combined of clinical features may function as the potential non-invasive tool for distinguishing TBG and LAC in small pulmonary nodules.
creator: Qing Dong
creator: Qingqing Wen
creator: Nan Li
creator: Jinlong Tong
creator: Zhaofu Li
creator: Xin Bao
creator: Jinzhi Xu
creator: Dandan Li
uri: https://doi.org/10.7717/peerj.14127
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Dong et al.

title: Evaluation of pulpal anesthesia and injection pain using IANB with pre-heated, buffered and conventional 2% lignocaine in teeth with symptomatic irreversible pulpitis—a randomized clinical study
link: https://peerj.com/articles/14187
last-modified: 2022-10-19
description: BackgroundThe efficacy of 2% lignocaine is reduced in a hot tooth. Local aesthetic agents can be preheated and buffered to increase their effectiveness. The present investigation was carried out due to limited information concerning adult patients with symptomatic irreversible pulpitis in mandibular teeth.MethodsA total of 252 individuals were included in the clinical trial in accordance with the selection criteria only after clinical study was registered with the Clinical Trial Registry of India (CTRI/2020/09/027796). Scores on the visual analog scale (VAS) and electric pulp test (EPT) on a 1–10 scale were recorded prior to the commencement of therapy. In this double-blinded study, patients were randomly divided by a co-investigator using computer randomisation (www.randomizer.org) into three groups, group A: inferior alveolar nerve blocks (IANB) with 2% lignocaine preheated at 42 °C (injected at 37 °C) (N = 84), group B: IANB of 2% lignocaine buffered with 0.18 ml of 8.4% sodium bicarbonate (N = 80) and group C: 2% lignocaine (N = 88). Excluding the dropouts of individuals (n = 11), wherein the anaesthesia failed, a total of 241 people were finally assessed 15 minutes after profound anaesthesia, endodontic access, and intraoperative pain were quantified using VAS. Pain on injection for all three groups was recorded immediately after IANB with VAS. The analysis was performed using one way ANOVA with Tukey’s post hoc test and Paired T-Test using SPSS version 21.ResultsPreheated, Buffered, and conventional 2% lignocaine showed statistically significant reduction in intraoperative pain (P < 0.001) compared to pre-operative but on inter-group comparison preheated and buffered showed highly significant pain reduction compared with conventional 2% lignocaine (P < 0.001).ConclusionsWarm and buffered local anaesthetic (LA) were effective in reducing intraoperative discomfort than conventional LA. Preheated local anesthetics caused the least pain, followed by buffered local anesthetics, while conventional local anesthetics caused the most pain.
creator: Namita Gandhi
creator: Nimisha Shah
creator: Dian Agustin Wahjuningrum
creator: Sweetly Purnomo
creator: Riana Nooshian
creator: Suraj Arora
creator: Ajinkya M. Pawar
uri: https://doi.org/10.7717/peerj.14187
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Gandhi et al.

title: Morphometric and meristic diversity of the species Androctonus crassicauda (Olivier, 1807) (Scorpiones: Buthidae) in Saudi Arabia
link: https://peerj.com/articles/14198
last-modified: 2022-10-19
description: Intraspecific molecular and morphological variations among geographically isolated populations are useful for understanding the evolutionary processes, which is considered early stage of allopatric speciation. Also, the knowledge of the regional variation of scorpion venom composition is needed to improve antivenom therapeutic management. Androctonus crassicauda (Olivier, 1807) is the most common and medically important species in Arabia and the Middle East. Therefore, this study aimed to investigate the geographic morphological variation among A.crassicaudapopulations, regarding its geographical distribution in unexplored arid regions in Saudi Arabia. Samples were collected and examined morphologically under a dissecting microscope from different four eco-geographical regions. The results of ANOVA and multivariate statistical analyses provide strong evidence of geographical variation. The two populations from OTU3 and OUT4 showed the greatest degree of morphological difference from populations of OUT1 and OUT2. Each OTU3 and OTU4 populations showed significant speciation without overlapping in the two groups, while the remaining overlapped groups comprised two other populations. Several body variables influenced male separation, including carapace posterior width, metasoma 3rd length, and metasoma 2nd length. For females, telson length, metasoma 1st width, and sternite 7th width were highly influential variables. Such variation may suggest the existence of cryptic taxa within A. crassicauda populations in Saudi Arabia. Moreover, metasoma ratios can be used as good indicators in intraspecific variation studies of Scorpions.
creator: Abdulaziz R. Alqahtani
creator: Ahmed Badry
creator: Fahd Mohammed Abd Al Galil
creator: Zuhair S. Amr
uri: https://doi.org/10.7717/peerj.14198
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Alqahtani et al.

title: Genomics and cellulolytic, hemicellulolytic, and amylolytic potential of Iocasia fonsfrigidae strain SP3-1 for polysaccharide degradation
link: https://peerj.com/articles/14211
last-modified: 2022-10-19
description: BackgroundCellulolytic, hemicellulolytic, and amylolytic (CHA) enzyme-producing halophiles are understudied. The recently defined taxon Iocasia fonsfrigidae consists of one well-described anaerobic bacterial strain: NS-1T. Prior to characterization of strain NS-1T, an isolate designated Halocella sp. SP3-1 was isolated and its genome was published. Based on physiological and genetic comparisons, it was suggested that Halocella sp. SP3-1 may be another isolate of I. fronsfrigidae. Despite being geographic variants of the same species, data indicate that strain SP3-1 exhibits genetic, genomic, and physiological characteristics that distinguish it from strain NS-1T. In this study, we examine the halophilic and alkaliphilic nature of strain SP3-1 and the genetic substrates underlying phenotypic differences between strains SP3-1 and NS-1T with focus on sugar metabolism and CHA enzyme expression.MethodsStandard methods in anaerobic cell culture were used to grow strains SP3-1 as well as other comparator species. Morphological characterization was done via electron microscopy and Schaeffer-Fulton staining. Data for sequence comparisons (e.g., 16S rRNA) were retrieved via BLAST and EzBioCloud. Alignments and phylogenetic trees were generated via CLUTAL_X and neighbor joining functions in MEGA (version 11). Genomes were assembled/annotated via the Prokka annotation pipeline. Clusters of Orthologous Groups (COGs) were defined by eegNOG 4.5. DNA-DNA hybridization calculations were performed by the ANI Calculator web service.ResultsCells of strain SP3-1 are rods. SP3-1 cells grow at NaCl concentrations of 5-30% (w/v). Optimal growth occurs at 37 °C, pH 8.0, and 20% NaCl (w/v). Although phylogenetic analysis based on 16S rRNA gene indicates that strain SP3-1 belongs to the genus Iocasia with 99.58% average nucleotide sequence identity to Iocasia fonsfrigida NS-1T, strain SP3-1 is uniquely an extreme haloalkaliphile. Moreover, strain SP3-1 ferments D-glucose to acetate, butyrate, carbon dioxide, hydrogen, ethanol, and butanol and will grow on L-arabinose, D-fructose, D-galactose, D-glucose, D-mannose, D-raffinose, D-xylose, cellobiose, lactose, maltose, sucrose, starch, xylan and phosphoric acid swollen cellulose (PASC). D-rhamnose, alginate, and lignin do not serve as suitable culture substrates for strain SP3-1. Thus, the carbon utilization profile of strain SP3-1 differs from that of I. fronsfrigidae strain NS-1T. Differences between these two strains are also noted in their lipid composition. Genomic data reveal key differences between the genetic profiles of strain SP3-1 and NS-1T that likely account for differences in morphology, sugar metabolism, and CHA-enzyme potential. Important to this study, I. fonsfrigidae SP3-1 produces and extracellularly secretes CHA enzymes at different levels and composition than type strain NS-1T. The high salt tolerance and pH range of SP3-1 makes it an ideal candidate for salt and pH tolerant enzyme discovery.
creator: Sobroney Heng
creator: Sawannee Sutheeworapong
creator: Verawat Champreda
creator: Ayaka Uke
creator: Akihiko Kosugi
creator: Patthra Pason
creator: Rattiya Waeonukul
creator: Ruben Michael Ceballos
creator: Khanok Ratanakhanokchai
creator: Chakrit Tachaapaikoon
uri: https://doi.org/10.7717/peerj.14211
license: https://creativecommons.org/licenses/by/4.0/
rights: ©2022 Heng et al.

title: Ectopic expression of HIV-1 Tat modifies gene expression in cultured B cells: implications for the development of B-cell lymphomas in HIV-1-infected patients
link: https://peerj.com/articles/13986
last-modified: 2022-10-18
description: An increased frequency of B-cell lymphomas is observed in human immunodeficiency virus-1 (HIV-1)-infected patients, although HIV-1 does not infect B cells. Development of B-cell lymphomas may be potentially due to the action of the HIV-1 Tat protein, which is actively released from HIV-1-infected cells, on uninfected B cells. The exact mechanism of Tat-induced B-cell lymphomagenesis has not yet been precisely identified. Here, we ectopically expressed either Tat or its TatC22G mutant devoid of transactivation activity in the RPMI 8866 lymphoblastoid B cell line and performed a genome-wide analysis of host gene expression. Stable expression of both Tat and TatC22G led to substantial modifications of the host transcriptome, including pronounced changes in antiviral response and cell cycle pathways. We did not find any strong action of Tat on cell proliferation, but during prolonged culturing, Tat-expressing cells were displaced by non-expressing cells, indicating that Tat expression slightly inhibited cell growth. We also found an increased frequency of chromosome aberrations in cells expressing Tat. Thus, Tat can modify gene expression in cultured B cells, leading to subtle modifications in cellular growth and chromosome instability, which could promote lymphomagenesis over time.
creator: Anna A. Valyaeva
creator: Maria A. Tikhomirova
creator: Daria M. Potashnikova
creator: Alexandra N. Bogomazova
creator: Galina P. Snigiryova
creator: Aleksey A. Penin
creator: Maria D. Logacheva
creator: Eugene A. Arifulin
creator: Anna A. Shmakova
creator: Diego Germini
creator: Anastasia I. Kachalova
creator: Aleena A. Saidova
creator: Anastasia A. Zharikova
creator: Yana R. Musinova
creator: Andrey A. Mironov
creator: Yegor S. Vassetzky
creator: Eugene V. Sheval
uri: https://doi.org/10.7717/peerj.13986
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Valyaeva et al.

title: Fossil Sirenia from the Pleistocene of Qatar: new questions about the antiquity of sea cows in the Gulf Region
link: https://peerj.com/articles/14075
last-modified: 2022-10-18
description: One of the largest and least documented populations of dugongs (Dugong dugon) resides in the coastal waters of the United Arab Emirates, and waters surrounding Saudi Arabia, Bahrain, and Qatar. The archaeological record of dugongs in the Gulf Region is abundant, but little is known about their fossil record in the region. Here we report an isolated sirenian rib fragment from the Futaisi Member of the Fuwayrit Formation near the town of Al Ruwais, in northern Qatar. The Fuwayrit Formation is a marine Pleistocene deposit exposed onshore in Qatar and the United Arab Emirates. Based on the correlative dating of the basal Futaisi Member with other onshore platforms, the rib fragment is approximately 125 ka. We propose that this isolated rib (likely the first rib from the right side) belongs to Dugongidae, with strong similarities to extant Dugong. We cannot, however, eliminate the possibility that it belongs to an extinct taxon, especially given its similarities with other fossil dugongid material from both Qatar and elsewhere in the world. Aside from reflecting the presence of Gulf seagrass communities in the Pleistocene, this occurrence also suggests that different (and potentially multiple) lineages of sirenians inhabited the Gulf Region in the geologic past.
creator: Nicholas D. Pyenson
creator: Mehsin Al-Ansi
creator: Clare M. Fieseler
creator: Khalid Hassan Al Jaber
creator: Katherine D. Klim
creator: Jacques LeBlanc
creator: Ahmad Mujthaba Dheen Mohamed
creator: Ismail Al-Shaikh
creator: Christopher D. Marshall
uri: https://doi.org/10.7717/peerj.14075
license: https://creativecommons.org/publicdomain/zero/1.0/
rights: 

title: The complete organellar genomes of the entheogenic plant Psychotria viridis (Rubiaceae), a main component of the ayahuasca brew
link: https://peerj.com/articles/14114
last-modified: 2022-10-18
description: Psychotria viridis (Rubioideae: Rubiaceae), popularly known as chacrona, is commonly found as a shrub in the Amazon region and is well-known to produce psychoactive compounds, such as the N,N-dimethyltryptamine (DMT). Together with the liana Banisteropsis caapi, P. viridis is one of the main components of the Amerindian traditional, entheogenic beverage known as ayahuasca. In this work, we assembled and annotated the organellar genomes (ptDNA and mtDNA), presenting the first genomics resources for this species. The P. viridis ptDNA exhibits 154,106 bp, encoding all known ptDNA gene repertoire found in angiosperms. The Psychotria genus is a complex paraphyletic group, and according to phylogenomic analyses, P. viridis is nested in the Psychotrieae clade. Comparative ptDNA analyses indicate that most Rubiaceae plastomes present conserved ptDNA structures, often showing slight differences at the junction sites of the major four regions (LSC-IR-SSC). For the mitochondrion, assembly graph-based analysis supports a complex mtDNA organization, presenting at least two alternative and circular mitogenomes structures exhibiting two main repeats spanning 24 kb and 749 bp that may symmetrically isomerize the mitogenome into variable arrangements and isoforms. The circular mtDNA sequences (615,370 and 570,344 bp) encode almost all plant mitochondrial genes (except for the ccmC, rps7, rps10, rps14, rps19, rpl2 and rpl16 that appears as pseudogenes, and the absent genes sdh3, rps2, rsp4, rsp8, rps11, rpl6, and rpl10), showing slight variations related to exclusive regions, ptDNA integration, and relics of previous events of LTR-RT integration. The detection of two mitogenomes haplotypes is evidence of heteroplasmy as observed by the complex organization of the mitochondrial genome using graph-based analysis. Taken together, these results elicit the primary insights into the genome biology and evolutionary history of Psychotria viridis and may be used to aid strategies for conservation of this sacred, entheogenic species.
creator: Alessandro M. Varani
creator: Saura R. Silva
creator: Simone Lopes
creator: Jose Beethoven Figueiredo Barbosa
creator: Danilo Oliveira
creator: Maria Alice Corrêa
creator: Ana Paula Moraes
creator: Vitor F.O. Miranda
creator: Francisco Prosdocimi
uri: https://doi.org/10.7717/peerj.14114
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Varani et al.

title: Clinical associations and genetic interactions of oncogenic BRAF alleles
link: https://peerj.com/articles/14126
last-modified: 2022-10-18
description: BRAF is a serine/threonine-specific protein kinase that regulates the MAPK/ERK signaling pathway, and mutations in the BRAF gene are considered oncogenic drivers in diverse types of cancer. Based on the signaling mechanism, oncogenic BRAF mutations can be assigned to three different classes: class 1 mutations constitutively activate the kinase domain and lead to RAS-independent signaling, class 2 mutations induce artificial dimerization of BRAF and RAS-independent signaling and class 3 mutations display reduced or abolished kinase function and require upstream signals.Despite the importance of BRAF mutations in cancer, the clinical associations, genetic interactions and therapeutic implications of non-V600 BRAF mutations have not been explored comprehensively yet. In this study, the author analyzed publically available data from the AACR Project GENIE to further understand clinical associations and genetic interactions of oncogenic BRAF mutations. The analyses identified 93 recurrent BRAF mutations, out of which 50 could be assigned to a functional class based on literature review. The author could show that the frequency of BRAF mutations varies across cancer types and subtypes, and that the BRAF mutation classes are unequally distributed across cancer types and subtypes. Using permutation testing-based co-occurrence analyses, the author defined the genetic interactions of BRAF mutations in multiple cancer types and revealed unexplored genetic interactions that might define clinically relevant subgroups. With non-small cell lung cancer as example, the author further showed that the genetic interactions are BRAF mutation class-specific. The presented analyses explore the properties of oncogenic BRAF mutations and will help to further delineate the complex role of BRAF in cancer.
creator: Sebastian A. Wagner
uri: https://doi.org/10.7717/peerj.14126
license: https://creativecommons.org/licenses/by/4.0/
rights: © 2022 Wagner