title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=585 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: Bacterial incidence and drug resistance from pathogens recovered from blood, cerebrospinal and pleural fluids in 2019–2020. Results of the Invifar network link: https://peerj.com/articles/14411 last-modified: 2023-01-17 description: BackgroundAntimicrobial resistance is a global concern. Analysis of sterile fluids is essential because microorganisms are defined as significant in most cases. Blood, cerebrospinal, and pleural fluids are frequently received in the microbiology lab because they are associated with considerable rates of morbi-mortality. Knowledge of epidemiology in these samples is needed to choose proper empirical treatments due to the importance of reducing selection pressure.MethodsWe used retrospective laboratory data of blood, CSF, and pleural fluid collected from patients in Mexico between 2019 and 2020. Each laboratory identified the strains and tested susceptibility using its routine methods. For Streptococcus pneumoniae, a comparative analysis was performed with data from the broth microdilution method.ResultsForty-five centers participated in the study, with 30,746 clinical isolates from blood, 2,429 from pleural fluid, and 2,275 from CSF. For blood and CSF, Staphylococcus epidermidis was the most frequent. For blood, among gram negatives, the most frequent was Escherichia coli. Among Enterobacterales, 9.8% of K. pneumoniae were carbapenem-resistant. For S. pneumoniae, similar resistance percentages were observed for levofloxacin, cefotaxime, and vancomycin. For CSF, the most frequent gram-negative was E. coli. In Acinetobacter baumannii, carbapenem resistance was 71.4%. The most frequent species detected for pleural fluid was E. coli; in A. baumannii, carbapenem resistance was 96.3%.ConclusionGram-negative bacteria, with E. coli most prevalent, are frequently recovered from CSF, blood, and pleural fluid. In S. pneumoniae, the routine, conventional methods showed good agreement in detecting resistance percentages for erythromycin, levofloxacin, and vancomycin. creator: Elvira Garza-González creator: Adrian Camacho-Ortiz creator: Alfredo Ponce-de-Leon creator: Edgar Ortiz-Brizuela creator: Luis Esaú López-Jácome creator: Claudia Colin creator: Fabian Rojas-Larios creator: Oscar A. Newton-Sánchez creator: Gabriela Echaniz-Aviles creator: Maria Noemi Carnalla-Barajas creator: Araceli Soto creator: Paola Bocanegra-Ibarias creator: Ana María del Rocío Hernández-Dueñas creator: María del Consuelo Velázquez-Acosta creator: Laura Karina Avilés-Benítez creator: Juan Pablo Mena-Ramirez creator: Daniel Romero creator: Isela Mora-Jiménez creator: Margarita Alcaraz-Espejel creator: José Manuel Feliciano-Guzmán creator: Maribel López-García creator: Patricia Rodriguez-Zulueta creator: María Angelina Quevedo-Ramos creator: Cecilia Padilla-Ibarra creator: Carlos Antonio Couoh-May creator: Maria Carolina Rivera-Ferreira creator: Cecilia Teresita Morales-de-la-Peña creator: Hector Zubiate creator: Raúl Peralta-Catalán creator: Carlos Miguel Cetina-Umaña creator: Joaquin Rincón-Zuno creator: Maria Lucia Perez-Ricardez creator: Iris Yazmin Hernández-Cordova creator: Eduardo López-Gutiérrez creator: Mariana Gil creator: Efren Aguirre-Burciaga creator: Guadalupe Soledad Huirache-Villalobos creator: Scarlett Munoz creator: Nicolás Rogelio Eric Barlandas-Rendón creator: Enrique Bolado-Martinez creator: Luis Javier Quintanilla-Cazares creator: Abraham C. Gómez-Choel creator: Laura Lopez creator: Juan Carlos Tinoco creator: Rosa Areli Martínez-Gamboa creator: Alejandro Molina creator: Samuel Pavel Escalante-Armenta creator: Lizbeth Duarte creator: Luis Alberto Ruiz-Gamboa creator: Dulce Isabel Cobos-Canul creator: Dulce López creator: Irma Elena Barroso-Herrera-y-Cairo creator: Eduardo Rodriguez-Noriega creator: Rayo Morfin-Otero uri: https://doi.org/10.7717/peerj.14411 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Garza-González et al. title: Upper Norian conodonts from the Baoshan block, western Yunnan, southwestern China, and implications for conodont turnover link: https://peerj.com/articles/14517 last-modified: 2023-01-17 description: The Sevatian of the late Norian is one of the key intervals in biotic turnover and in changes of paleoclimate and paleoenvironments. Conodont faunas recovered from two sections of upper Norian strata of the Dashuitang and Nanshuba formations near Baoshan City in western Yunnan province provide new insights into the diversity and biostratigraphy of the Sevatian conodonts within China as well as globally. A lower Mockina (M.) bidentata Zone and an upper Parvigondolella (P.) andrusovi Zone are identified in this area according to the first occurrences of M. bidentata and of P. andrusovi. Rich conodont fauna of M. zapfei is detailed and presents various intraspecific forms. A total of 19 forms of P1 elements are presented, which, when combined with the reported conodonts in the M. bidentata Zone, suggest that there was a peak in conodont diversity within the M. bidentata Zone. A biotic crisis in the uppermost M. bidentata Zone is recognized from the contrast between the diverse conodont fauna in the M. bidentata Zone and the rare conodonts in the P. andrusovi Zone. The conodont turnover during the middle Sevatian highlights the fact that the prolonged phases of the end-Triassic mass extinction probably began in the transition interval from M. bidentata Zone to P. andrusovi Zone. creator: Weiping Zeng creator: Haishui Jiang creator: Yan Chen creator: James Ogg creator: Muhui Zhang creator: Hanxinshuo Dong uri: https://doi.org/10.7717/peerj.14517 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Zeng et al. title: Low temperature upregulating HSP70 expression to mitigate the paclitaxel-induced damages in NHEK cell link: https://peerj.com/articles/14630 last-modified: 2023-01-17 description: Scalp cooling is the most approved treatment for preventing chemotherapy-induced alopecia (CIA). However, the protective mechanism of scalp cooling has rarely been reported. The goal of the present study was to study the relationship between paclitaxel concentration and temperature and the inhibitory effect of low temperature on paclitaxel-induced alopecia. The results showed that the dose of paclitaxel should not exceed 60–70 mg/mL during scalp cooling treatment, and the optimal cooling temperature under different paclitaxel concentrations was determined. Normal human epidermal keratinocytes (NHEK) cells were analyzed by global transcriptome analysis, functional annotation and pathway analysis of differentially expressed genes (DEGs) and ELISA kit to analyze the mechanism of low temperature therapy. The expression of HSPA8, HSPA1A and HSPA1B, which belongs to HSP70, was up-regulated by low temperature. These genes are important target genes of low temperature treatment, which were confirmed by ELISA. The up-regulation of PLK2 and the down-regulation of TXNIP expression are the upstream of mitochondrial dysfunction and ROS, inhibiting the accumulation of ROS and up-regulating the mitochondrial membrane potential. Our research partially elucidates the therapeutic mechanism of scalp cooling, which provides a new idea on the drug research and development in CIA. creator: Liang Chen creator: Yi Xu uri: https://doi.org/10.7717/peerj.14630 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Chen and Xu title: Detect feature edges for diagnosis of bacterial vaginosis link: https://peerj.com/articles/14667 last-modified: 2023-01-17 description: One of the most common diseases among women of reproductive age is bacterial vaginosis (BV). However, the etiology of BV remains unknown. In this study, we modeled the temporal sample of the vaginal microbiome as a network and investigated the relationship between the network edges and BV. Furthermore, we used feature selection algorithms including decision tree (DT) and ReliefF (RF) to select the network feature edges associated with BV and subsequently validated these feature edges through logistic regression (LR) and support vector machine (SVM). The results show that: machine learning can distinguish vaginal community states (BV, ABV, SBV, and HEA) based on a few feature edges; selecting the top five feature edges of importance can achieve the best accuracy for the feature selection and classification model; the feature edges selected by DT outperform those selected by RF in terms of classification algorithm LR and SVM, and LR with DT feature edges is more suitable for diagnosing BV; two feature selection algorithms exhibit differences in the importance of ranking of edges; the feature edges selected by DT and RF cannot construct sub-network associated with BV. In short, the feature edges selected by our method can serve as indicators for personalized diagnosis of BV and aid in the clarification of a more mechanistic interpretation of its etiology. creator: Jie Li creator: Yaotang Li uri: https://doi.org/10.7717/peerj.14667 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2023 Li and Li title: Prenatal diagnosis of fetuses conceived by assisted reproductive technology by karyotyping and chromosomal microarray analysis link: https://peerj.com/articles/14678 last-modified: 2023-01-17 description: BackgroundInvasive prenatal evaluation by chromosomal microarray analysis (CMA) and karyotyping might represent an important option in pregnant women, but limited reports have applied CMA and karyotyping of fetuses conceived by assisted reproductive technology (ART). This study aimed to examine the value of CMA and karyotyping in prenatal diagnosis after ART.MethodsThis retrospective study included all singleton fetuses conceived by ART from January 2015 to December 2021. Anomalies prenatally diagnosed based on karyotyping and CMA were analyzed. Prevalence rates for various CMA and karyotyping results were stratified based on specific testing indications including isolated—and non-isolated ART groups. The rates of CMA findings with clinical significance (pathogenic/likely pathogenic) and karyotype anomalies were assessed and compared to those of local control individuals with naturally conceived pregnancies and without medical indications.ResultsIn total, 224 subjects were assessed by karyotyping and CMA. In the examined patients, chromosomal and karyotype abnormality rates were 3.57% (8/224) and 8.93% (20/224), respectively. This finding indicated a 5.35% (12/224)-incremental rate of abnormal CMA was obtained over karyotype analysis (p = 0.019). The risk of CMA with pathogenic findings for all pregnancies conceived by ART (5.80%, 13/224) was markedly elevated in comparison with the background value obtained in control individuals (1.47%, 9/612; p = 0.001). In addition, risk of CMA with clinically pathogenic results in isolated ART groups was significant higher compared to the background risk reported in the control cohort (p = 0.037).ConclusionsPrenatal diagnosis including karyotyping and CMA is recommended for fetuses conceived by ART, with or without ultrasound findings. creator: Huan Guo creator: Rui Sheng creator: Xiu Zhang creator: Xuemei Jin creator: Wenjing Gu creator: Ting Liu creator: Haixin Dong creator: Ran Jia uri: https://doi.org/10.7717/peerj.14678 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Guo et al. title: Hard-bottom habitats support commercially important fish species: a systematic review for the North Atlantic Ocean and Baltic Sea link: https://peerj.com/articles/14681 last-modified: 2023-01-17 description: Hard-bottom habitats span a range of natural substrates (e.g., boulders, cobble) and artificial habitats (e.g., the base of wind turbines, oil platforms). These hard-bottom habitats can provide a variety of ecosystem services, ranging from the enhancement of fish biomass and production to providing erosion control. Management decisions regarding the construction or fate of hard-bottom habitats require information on the ecological functions of these habitats, particularly for species targeted in ecosystem-based fisheries management. This study provides a systematic review of the relationships of various hard-bottom habitats to individual commercially harvested species that are managed jointly across the Atlantic by the International Council for the Exploration of the Sea (ICES). We systemically reviewed peer-reviewed publications on hard-bottom habitats including both natural and artificial reefs, after applying various exclusion criteria. Most studies were conducted on near-shore hard-bottom habitats, and habitat importance varied according to fish species and region. We quantified the frequency with which studies demonstrate that natural and artificial hard-bottom habitats function as spawning grounds, settlement and nursery areas, and foraging grounds, as well as provide stepping-stones during migration, or new home ranges. Hard-bottom habitats generally support higher fish densities than surrounding habitat types, although not all fish species benefit from hard-bottom habitats. Of the commercially important species, cod (Gadus morhua) was the most frequently studied species, with enhanced biomass, density, feeding, and spawning on hard-bottom habitats compared to unstructured habitats. Moreover, hard-bottom habitats appear to be of particular importance for spawning of herring (Clupea harengus). Collectively, data indicate that loss of hard-bottom habitats may translate into less-favourable conditions for spawning and biomass of diverse commercial species, including cod and herring. creator: Hugo Flávio creator: Rochelle Seitz creator: David Eggleston creator: Jon C. Svendsen creator: Josianne Støttrup uri: https://doi.org/10.7717/peerj.14681 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Flávio et al. title: The root enrichment of bacteria is consistent across different stress-resistant plant species link: https://peerj.com/articles/14683 last-modified: 2023-01-17 description: Bacteria, inhabiting around and in plant roots, confer many beneficial traits to promote plant growth and health. The secretion of root exudates modulates the nutritional state of the rhizosphere and root area, further selecting specific bacteria taxa and shaping the bacteria communities. Many studies of the rhizosphere effects have demonstrated that selection by the plant rhizosphere consistently enriches a set of bacteria taxa, and this is conserved across different plant species. Root selection effects are considered to be stronger than the rhizosphere selection effects, yet studies are limited. Here, we focus on the root selection effects across a group of 11 stress-resistant plant species. We found that the root selection consistently reduced the alpha diversity (represented by total number of observed species, Shannon’s diversity, and phylogenetic diversity) and altered the structure and composition of bacteria communities. Furthermore, root selection tended to enrich for clusters of bacteria genera including Pantoea, Akkermansia, Blautia, Acinetobacter, Burkholderia-Paraburkholderia, Novosphingobium, Massilia, Pseudomonas, Chryseobacterium, and Stenotrophomonas. Our study offers some basic knowledge for understanding the microbial ecology of the plant root, and suggests that several bacteria genera are of interest for future studies. creator: Feng Huang creator: Congyi Zhu creator: Minli Huang creator: Xiaobing Song creator: Aitian Peng uri: https://doi.org/10.7717/peerj.14683 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Huang et al. title: Solithromycin inhibits IL-13-induced goblet cell hyperplasia and MUC5AC, CLCA1, and ANO1 in human bronchial epithelial cells link: https://peerj.com/articles/14695 last-modified: 2023-01-17 description: Solithromycin is a novel fluoroketolide antibiotic belonging to the class of macrolide antibiotics. Activation of the interleukin (IL)-13 receptor leads to STAT6 activation and subsequent induction of SAM pointed domain containing ETS transcription factor (SPDEF), chloride channel accessory 1 (CLCA1), and anoctamin-1 (ANO1), all of which are associated with the induction of MUC5AC. We examined the effects of solithromycin on mucin production led by IL-13 signaling. Normal human bronchial epithelial cells were grown at the air-liquid interface with IL-13 with/without solithromycin for 14 days. Histochemical analysis was performed using hematoxylin and eosin staining and MUC5AC immunostaining. MUC5AC, SPDEF, CLCA1, and ANO1 mRNA expressions were examined using real-time polymerase chain reaction. Western blot analysis was performed to assess CLCA1 and ANO1 proteins, and phosphorylation of STAT6 and ERK. Solithromycin attenuated IL-13 induction of goblet cell hyperplasia and MUC5AC, CLCA1 and ANO1 mRNA and protein expression induced by IL-13, but had no effect on the phosphorylation of STAT6 and ERK. Our results indicate that solithromycin could attenuate goblet cell hyperplasia and MUC5AC induced by IL-13 through inhibition of CLCA1 and ANO1 mRNA and protein expression. However, much more information is required to clarify the molecular mechanisms underlying the inhibition of CLCA1 and ANO1 by solithromycin. creator: Yasuhiro Kimura creator: Masahiro Shinoda creator: Masaharu Shinkai creator: Takeshi Kaneko uri: https://doi.org/10.7717/peerj.14695 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2023 Kimura et al. title: Genome-wide identification and expression profile analysis of SWEET genes in Chinese jujube link: https://peerj.com/articles/14704 last-modified: 2023-01-17 description: The novel sugar transporter known as SWEET (sugars will eventually be exported transporter) is involved in the transport and distribution of photosynthesis products in plants. The SWEET protein is also involved in pollen development, nectar secretion, stress responses, and other important physiological processes. Although SWEET genes have been characterized and identified in model plants, such as Arabidopsis and rice, little is known about them in jujube. In this study, the molecular characteristics of the SWEET gene family in the Chinese jujube (Ziziphus jujuba Mill.) and their expression patterns in different organs, at different fruit developmental stages, and under abiotic stress were analyzed. A total of 19 ZjSWEET genes were identified in jujube through a genome-wide study; these were classified into four sub-groups based on their phylogenic relationships. The gene structure analysis of ZjSWEET genes showed that all the members had introns. The expression patterns of different ZjSWEET genes varied significantly in different organs (root, shoot, leave, flower, fruit), which indicated that ZjSWEETs play different roles in multiple organs. According to the expression profiles by quantitative real-time PCR analysis during fruit development, the expression levels of the two genes (ZjSWEET11, ZjSWEET18) gradually increased with the development of the fruit and reached a high level at the full-red fruit stage. A prediction of the cis-acting regulatory elements indicated that the promoter sequences of ZjSWEETs contained nine types of phytohormone-responsive cis-regulatory elements and six environmental factors. In addition, the expression profiles by quantitative real-time PCR analysis showed that some of the ZjSWEETs responded to environmental changes; ZjSWEET2 was highly induced in response to cold stress, and ZjSWEET8 was significantly up-regulated in response to alkali and salt stresses. This study showed that the functions of the ZjSWEET family members of jujube are different, and some may play an important role in sugar accumulation and abiotic stress in jujube. creator: Chong Yang creator: Xuan Zhao creator: Zhi Luo creator: Lihu Wang creator: Mengjun Liu uri: https://doi.org/10.7717/peerj.14704 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Yang et al. title: Nitrogen and potassium interactions optimized asynchronous spikelet filling and increased grain yield of japonica rice link: https://peerj.com/articles/14710 last-modified: 2023-01-17 description: Poor grain filling severely reduces rice yield. Fertilizers play a vital role in regulating grain filling, especially nitrogen (N) and potassium (K). In this field study we aimed to investigate the interactive effects of N and K on the asynchronous filling properties of superior and inferior spikelets of japonica rice. We looked at grain filling under three N rates (0, 90, and 180 kg N ha−1) and three K rates (0, 60, and 120 kg K2O ha−1) during 2020 and 2021. Across two years, the results showed that the combined use of N and K on superior and inferior spikelets significantly increased their weight by 1.29 mg and 2.31 mg, their maximum grain filling rate by 0.24 mg d−1 and 0.07 mg d−1, and their average grain filling rate by 0.21 mg d−1 and 0.06 mg d−1, respectively, in comparison with the control (N0K0) treatment. Likewise, K supply increased the average contribution rate of superior and inferior spikelets to yield by 9.1% and 10.0%, respectively. Correlation analysis showed that the grain filling rate of superior and inferior spikelets was an important factor in determining the spikelet weight, whereas the grain filling time was not. We also found that the 1,000-grain weight mainly increased after increasing the spikelets’ maximum grain filling rate and average grain filling rate. Collectively, these results illustrate that the combined use of N and K can optimize the asynchronous filling of superior and inferior spikelets and, in particular, enhance inferior spikelet weight with higher rice yield. creator: Weitao Xu creator: Jianming Li creator: Jiancheng Feng creator: Zhenzhu Shao creator: Yidan Huang creator: Wenfeng Hou creator: Qiang Gao uri: https://doi.org/10.7717/peerj.14710 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2022 Xu et al.