bluuebunny/crossref_metadata_2025_split huggingface dataset:
MazEF-rifampicin interaction suggests a mechanism for rifampicin induced inhibition of persisters
Authors: Alexander Cyrus , Guru Ankeeta , Pradhan Pinkilata , Mallick Sunanda , Mahanandia Nimai Charan , Subudhi Bharat Bhushan , Beuria Tushar Kant 
Published: September 2020

Abstract
Background: Persistence is a natural phenomenon whereby a subset of a population of isogenic bacteria either grow slow or become dormant conferring them with the ability to withstand various stresses including antibiotics. In a clinical setting bacterial persistence often leads to the recalcitrance of various infections increasing the treatment time and costs. Additionally, some studies also indicate that persistence can also pave way for the emergence of resistant strains. In a laboratory setting this persistent phenotype is enriched in nutritionally deprived environments. Consequently, in a batch culture the late stationary phase is enriched with persistent bacteria. The mechanism of persister cell formation and its regulation is not well understood. Toxin-antitoxins (TA) systems have been implicated to be responsible for bacterial persistence and rifampicin is used to treat highly persistent bacterial strains. The current study tries to explore a possible interaction between rifampicin and the MazEF TA system that furthers the former’s success rate in treating persistent bacteria. Results: In the current study we found that the population of bacteria in the death phase of a batch culture consists of metabolically inactive live cells resembling persisters, which showed higher membrane depolarization as compared to the log phase bacteria. We also observed an increase in the expression of the MazEF TA modules in this phase. Since rifampicin is used to kill the persisters, we assessed the interaction of rifampicin with MazEF complex. We showed that rifampicin moderately interacts with MazEF complex with 1:1 stoichiometry.Conclusion: Our study suggests that the interaction of rifampicin with MazEF complex might play an important role in inhibition of persisters.
Feasibility of remote digital monitoring using wireless Bluetooth monitors, the Smart AngelTM&nbsp;app and an original web platform for patients following outpatient surgery: A prospective observational pilot study.
Authors: Chevallier Thierry , Buzancais Gautier , Occean Bob-valery , Rataboul Pierre , Boisson Christophe , simon natacha , Lannelongue Ariane , Chaniaud Noemie , Gricourt Yann , Lefrant Jean-Yves , cuvillon philippe 
Published: September 2020

Abstract
Background Remote monitoring of mean arterial blood pressure (MAP), heart rate (HR) or oxygen saturation (SpO2) remains a challenge in outpatient surgery. This study evaluates a new digital technology (Smart AngelTM) for remotely monitoring hemodynamic data in real time: data transmitted from the patient's home to a central server, using a dedicated web-based software package.Methods Adults scheduled for elective outpatient surgery were prospectively enrolled. In the first 5 postoperative days, patients completed a self-report questionnaire (pain, comfort, nausea, vomiting) and recorded SpO2, HR and MAP via two wireless Bluetooth monitors connected to a 4G tablet to transmit the data to a website, in real time, using Smart AngelTM software. Before transmission to the website, these data were also self-reported by the patient on a paper form. The primary outcome was the proportion of variables (self-monitored physiological data + questionnaire scores) correctly transmitted to the hospital via the system compared with the paper version. On Day 5, a system usability scale survey (SUS score 1-100) was also attributed.Results From May 2018 to September 2018, data were available for 29 out of 30 patients enrolled (1 patient was not discharged from hospital after surgery). The remote monitoring technology recorded 2038 data items (62%) compared with 2656 (82%) items recorded on the paper form (p=0.001). The most common errors with the remote technology were software malfunctioning when starting the MAP monitor and malfunctioning between the tablet and the Bluetooth monitor. No serious adverse events were noted. The SUS score for the system was 85 (68-93) for 26 patients.Conclusion This work evaluates the ability of a pilot system for monitoring remote physiological data using digital technology after ambulatory surgery and highlights the digital limitations of this technology. Technological improvements are required to reduce malfunctioning (4G access, transmission between apps).Trial registration: ClinicalTrials.gov (NCT03464721) (March 8, 2018)
Ethnobotanical knowledge on non-conventional food and medicinal plants in Rio Cajari Extractivist Reserve, Amazon, Brazil
Authors: Filho Galdino Xavier de Paula , Ribeiro Adivair Freitas , Moraes Alcidete Flexa , Penha Willis Freitas , Borges Wardsson Lustrino , Santos Ricardo Henrique Silva 
Published: September 2020

Abstract
Background: Information on the knowledge, management and ways of using food and medicinal plants by traditional populations, family farmers and Brazilian native population in the Amazon is essential to guarantee the sovereignty of these groups. The objective of this study was to evaluate the diversity, knowledge and ways of using non-conventional food and medicinal plants in traditional communities in a protected area in the Brazilian Amazon. Methods: This study was conducted using semi-structured interviews applied to local respondents. Fifty-six residents were interviewed in 26 communities. The Indices of Use Value (UVI) and relative frequency of species citation (Fr) were evaluated; also, their diversity and equitability using the Shannon- Wiener (H’) Pielou (J’) indices, respectively. The species were listed according to their family, scientific name, popular names, categories of use, propagation environment, growth habit, medicinal indications, domestication status, production cycle, and herbarium registration. Results: A total of 269 species of both non-conventional food and medicinal plants were identified, distributed in 84 botanical families, 198 genera, in addition to 13 unidentified species. The Arecaceae and Lamiaceae families had the highest species richness (11 and 7, respectively). Eryngium foetidum L. (Apiaceae) and Ipomoea batatas L. (Convolvulaceae) presented the highest relative citation frequencies (19.7 and 19.3, respectively) and the highest index of use value of the species (0.94 and 0.92, respectively). The Shannon-Wiener (H’) and Pielou (J’) diversity indices were considered high (5.02 and 0.9, respectively). Conclusions: It was observed that the studied species are consumed daily by the population of this protected area. In the environment in which these families are found, of geographical isolation and distance from urban centers, these species become the only food and medicinal resources, therefore, being fundamental to the sovereignty of these families.
Endosomal Dysfunction in iPSC-Derived Neural Cells from Parkinson’s Disease Patients with VPS35 D620N
Authors: Bono Keiko , Miyauchi-Hara Chikako , Sumi Shunsuke , Oka Hisayoshi , Iguchi Yasuyuki , Okano Hirotaka James 
Published: September 2020

Abstract
Mutations in the Vacuolar protein sorting 35 (VPS35) gene have been linked to familial Parkinson’s disease (PD), PARK17. VPS35 is a key component of the retromer complex, which plays a central role in endosomal trafficking. However, whether and how VPS35 deficiency or mutation contributes to PD pathogenesis remain unclear. Here, we analyzed human induced pluripotent stem cell (iPSC)-derived neurons from PD patients with the VPS35 D620N mutation and addressed relevant disease mechanisms. In the disease group, dopaminergic (DA) neurons underwent extensive apoptotic cell death. The movement of Rab5a- or Rab7a-positive endosomes was slower, and the endosome fission and fusion frequencies were lower in the PD group than in the healthy control group. Interestingly, vesicles positive for cation-independent mannose 6-phosphate receptor transported by retromers were abnormally localized in glial cells derived from patient iPSCs. Furthermore, we found a-synuclein accumulation in TH positive DA neurons. Our results demonstrate the induction of cell death, endosomal dysfunction and a-synuclein accumulation in neural cells of the PD group. PARK17 patient-derived iPSCs provide an excellent experimental tool for understanding the pathophysiology underlying PD.
Stagewise resolution of temperature-dependent embryonic and postembryonic development in the cowpea seed beetle Callosobruchus maculatus (F.)
Authors: Kutcherov Dmitry 
Published: September 2020

Abstract
Background: The thermal plasticity of life-history traits receives wide attention in the recent biological literature. Of all the temperature-dependent traits studied, developmental rates of ectotherms are especially often addressed, and yet surprisingly little is known about embryonic responses to temperature, including changes in the thermal thresholds and thermal sensitivity during early development. Even postembryonic development of many cryptically living species is understood superficially at best. Results: This study is the first to estimate the exact durations of developmental stages in the cowpea seed beetle C. maculatus from oviposition to adult emergence at five permissive constant temperatures from 20 to 32°C. Early embryonic development was tracked and documented by means of destructive sampling and subsequent confocal imaging of fluorescently stained specimens. Late embryonic and early larval development was studied with the use of destructive sampling and light microscopy. Well-resolved temporal series based on thousands of embryos allowed precise timing of the following developmental events: formation of the blastoderm; formation, elongation, and retraction of the germ band; dorsal closure; the onset and completion of sclerotization of the cuticle; hatching, and penetration of the first-instar larva into the cowpea seed. Pupation and adult eclosion were observed directly through an incision in the seed coat. The thermal phenotype of C. maculatus was found to vary in the course of ontogeny and different stages scaled disproportionately with temperature, but pitfalls and caveats associated with analyses of relative durations of individual stages are also briefly discussed. Conclusion: Disproportionate changes in developmental durations with temperature may have important implications when study design requires a high degree of synchronization among experimental embryos or when the occurrence of particular stages in the field is of interest, as well as in any other cases when development times need to be estimated with precision. This work provides one of the first examples of integration of embryological techniques with ecophysiological concepts and will hopefully motivate similar projects in the future. While experiments with Drosophila continue to be the main source of information on animal development, knowledge on other model species is instrumental to building a broader picture of developmental phenomena.
Comprehensive genetic testing combined with citizen science reveals a recently characterized ancient MC1R mutation is associated with partial recessive red phenotypes in dog
Authors: Anderson Heidi , Honkanen Leena , Ruotanen Päivi , Mathlin Julia , Donner Jonas 
Published: September 2020

Abstract
Background: The Melanocortin 1 Receptor (MC1R) plays a central role in regulation of coat color determination in dogs and is commonly referred to as the “E (extension) Locus”. Allelic variation of the MC1R gene is associated with coat color phenotypes EM (melanistic mask), EG (grizzle/domino) and e1-3 (recessive red) in dogs. In addition, a previous study of archeological dog specimens over 10,000 years of age identified a variant p.R301C in the MC1R gene that may have influenced coat color of early dogs.Results: Commercial genotyping of 11,750 dog samples showed the R301C variant of the MC1R gene was present in 35 breeds or breed varieties, at an allele frequency of 1.5% in the tested population. We detected no linkage disequilibrium between R301C and other tested alleles of the E locus. Based on current convention we propose that R301C should be considered a novel allele of the E locus, which we have termed eA for “e ancient red”. Phenotype analysis of owner-provided dog pictures reveals that the eA allele has an impact on coat color and is recessive to wild type E and dominant to the e alleles. In dominant black (KB/*) dogs it can prevent the expression of the K locus, and the expressed coat color is solely determined by the A locus. In the absence of dominant black, eA/eA and eA/e genotypes result in the coat color patterns referred to in their respective breed communities as domino in Alaskan Malamute and other Spitz breeds, grizzle in Chihuahua, and pied in Beagle.Conclusions: This study demonstrates a large genotype screening effort to identify the frequency and distribution of the MC1R R301C variant, one of the earliest mutations captured by canine domestication, and citizen science empowered characterization of its impact on coat color.
Combination of SB431542, Chir9901, and Bpv as a novel supplement in the culture of umbilical cord blood hematopoietic stem cells
Authors: Zarrabi Morteza , Afzal Elaheh , Asghari Mohammad Hassan , Ebrahimi Marzieh 
Published: September 2020

Abstract
Background: Small molecule compounds have been well recognized for their promising power in generation, expansion and maintenance of embryonic or adult stem cells. The aim of this study was to identify a novel combination of small molecules in order to optimize the ex vivo expansion of umbilical cord blood derived-CD34+ cells. Methods: Considering the most important signaling pathways involved in the self-renewal of hematopoietic stem cells, CB-CD34+ cells were expanded with cytokines in the presence of seven small molecules including SB, PD, Chir, Bpv, Pur, Pμ and NAM. Eliminativism approach was used to find the best combination of selected small molecules for effective ex vivo expansion of CD34+ cell. In each step, proliferation, self-renewal, and clonogenic potential of the expanded cells as well as expression of some hematopoietic stem cell related genes were studied. Finally, the engraftment potential of expanded cells was also examined by the mouse intra-uterine transplantation model. Results: Our data shows that simultaneous use of SB431542 (TGF-β inhibitor), Chir9901 (GSK3 inhibitor) and Bpv (PTEN inhibitor), resulted in a 50-fold increase in the number of CD34+CD38- cells. This was further reflected in approximately 3 times increase in clonogenic potential of the small molecule cocktail-expanded cells. These cells, also, showed a 1.5-fold higher engraftment potential in the peripheral blood of NMRI model of in utero transplantation. These results are in total conformity with up-regulation of HOXB4, GATA2 and CD34 marker gene as well as CXCR4 homing gene. Conclusion: Taken together, our findings introduce a novel combination of small molecules to improve the yield of existing protocols used in the expansion of hematopoietic stem cells.
Genome-wide identification and functional characterization of Camelina sativa WRKY gene family in response to abiotic stress
Authors: Song Yanan , Cui Hongli , Shi Ying , Xue Jinai , Ji Chunli , Zhang Chunhui , Yuan Lixia , Li Runzhi 
Published: September 2020

Abstract
Background: WRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, knowledge is limited for WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance against various stresses. Here, genome-wide characterization of WRKY proteins is performed to examine their gene-structures, phylogenetics, expressions, conserved motif organizations, and functional annotation to identify candidate WRKYs mediating regulation of stress resistance in camelina. Results: Total of 242 CsWRKY proteins encoded by 224 gene loci distributed uneven on chromosomes were identified, and classified into three groups via phylogenetic analysis according to their WRKY domains and zinc finger motifs. 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in C. sativa and Arabidopsis genomes as well as 282 pairs for C. sativa and B. napus, respectively. 137 segmental duplication events were observed but no tandem duplication in camelina genome. Ten major conserved motifs were examined, with WRKYGQK as the most conserved and several variants existed in many CsWRKYs. Expression analysis revealed that half more CsWRKY genes were expressed constitutively, and a set of them had a tissue-specific expression. Notably, 11 CsWRKY genes exhibited significantly expression changes in plant seedlings under cold, salt, and drought stress, respectively, having preferentially inducible expression pattern in response to the stress. Conclusions: The present described a detail analysis of CsWRKY gen family and their expression profiled in twelve tissues and under several stress conditions. Segmental duplication is the major force for large expansion of this gene family, and a strong purifying pressure happened for CsWRKY proteins evolutionally. CsWRKY proteins play important roles for plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms were found to be the key players possibly in mediating plant response to various stresses. Overall, our results provide a foundation for understanding roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance to stress as well as development of stress tolerance cultivars for Cruciferae crops.
Pregnancy vs. Paycheck: A qualitative study of patient’s experience with employment during pregnancy at high risk for preterm birth
Authors: Wheeler Sarahn M. , Massengale Kelley E. C. , Adewumi Konyin , Fitzgerald Thelma A. , Dombeck Carrie B. , Swezey Teresa , Swamy Geeta K. , Corneli Amy 
Published: September 2020

Abstract
Background: Pregnant women with a history of preterm birth are at risk for recurrence, often requiring frequent prenatal visits for close monitoring and/or preventive therapies. Employment demands can limit uptake and adherence to recommended monitoring and preterm birth prevention therapies. Method: We conducted a qualitative descriptive study using in-depth interviews (IDIs) of pregnant women with a history of preterm birth. IDIs were conducted by trained qualitative interviewers following a semi-structured interview guide focused on uncovering barriers and facilitators to initiation of prenatal care, including relevant employment experiences, and soliciting potential interventions to improve prompt prenatal care initiation. The IDIs were analyzed via applied thematic analysis. Results: We described the interview findings that address women’s employment experiences. The current analysis includes 27 women who are majority self-described as non-Hispanic Black (74%) and publically insured (70%). Participants were employed in a range of professions; food services, childcare and retail were the most common occupations. Participants described multiple ways that being pregnant impacted their earning potential, ranging from voluntary work-hour reduction, involuntary duty hour reductions by employers, truncated promotions, and termination of employment. Participants also shared varying experiences with workplace accommodations to their work environment and job duties based on their pregnancy. Some of these accommodations were initiated by a collaborative employee/employer discussion, others were initiated by the employer’s perception of safe working conditions in pregnancy, and some accommodations were based on medical recommendations. Participants described supportive and unsupportive employer reactions to requests for accommodations. Conclusions: Our findings provide novel insights into women’s experiences balancing a pregnancy at increased risk for preterm birth with employment obligations. While many women reported positive experiences, the most striking insights came from women who described negative situations that ranged from challenging to potentially unlawful. Many of the findings suggest profound misunderstandings likely exist at the patient, employer and clinical provider level about the laws surrounding employment in pregnancy, safe employment responsibilities during pregnancy, and the range of creative accommodations that often allow for continued workplace productivity even during high risk pregnancy.
Global Optimization Of A Numerical Two-Layer Model Using Observed Data: A Case Study Of The 2018 Sunda Strait Tsunami
Authors: Pakoksung Kwanchai , Suppasri Anawat , Abdul Muhari , Syamsidik Syamsidik , Imamura Fumihiko 
Published: September 2020

Abstract
Following the eruption of Mount Anak Krakatau, a considerable landslide occurred on the southwestern part of the volcano and, upon entering the sea, generated a large tsunami within the Sunda Strait, Indonesia, on 22 December 2018. This tsunami traveled ~5 km across the strait basin and inundated the shorelines of Sumatra and Java with a vertical runup reaching 13 m. Following the event, observed field data, GPS measurements of the inundation, and multibeam echo soundings of the bathymetry within the strait were collected and publicly provided. Using this dataset, numerical modeling of the tsunami was conducted using the two-layer (soil and water) TUNAMI-N2 model based on a combination of landslide sources and bathymetry data. The two-layer model was implemented to nest the grid system using a finest grid size of 20 m. To constrain the unknown landslide parameters, the differential evolution (DE) global optimization algorithm was applied, which resulted in a parameter set that minimized the deviation from the measured bathymetry after the event. The DE global optimization procedure was effective at determining the landslide parameters for the model with the minimum deviation from the measured seafloor. The lowest deviation from the measured bathymetry was obtained for the best-fitting parameters: a maximum landslide thickness of 301.2 m and a landslide time of 10.8 minutes. The landslide volume of 0.182 km3 estimated by the best-fitting parameters shows that the tsunami flow depth could have reached 3-10 m along the shore with a K value of 0.89, although the simulated flow depths were underestimated in comparison with the observation data. According to the waveforms, the general wave pattern was well reproduced at tide gauges during the event. A large number of objective function evaluations were necessary to locate the minimum with the DE procedure to fix the grid cell size to 20 m; this limited the accuracy of the obtained parameter values for the two-layer model. Moreover, considering the generalizations in the modeling of landslide movements, the impact landslide time and thickness must be carefully calculated to obtain a suitable accuracy.