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| 2. |
- Beal, Jacob, et al.
(author)
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Robust estimation of bacterial cell count from optical density
- 2020
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In: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Journal article (peer-reviewed)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 3. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 4. |
- Wang, Guo-dong, et al.
(author)
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The genomics of selection in dogs and the parallel evolution between dogs and humans
- 2013
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In: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 4, s. 1860-
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Journal article (peer-reviewed)abstract
- The genetic bases of demographic changes and artificial selection underlying domestication are of great interest in evolutionary biology. Here we perform whole-genome sequencing of multiple grey wolves, Chinese indigenous dogs and dogs of diverse breeds. Demographic analysis show that the split between wolves and Chinese indigenous dogs occurred 32,000 years ago and that the subsequent bottlenecks were mild. Therefore, dogs may have been under human selection over a much longer time than previously concluded, based on molecular data, perhaps by initially scavenging with humans. Population genetic analysis identifies a list of genes under positive selection during domestication, which overlaps extensively with the corresponding list of positively selected genes in humans. Parallel evolution is most apparent in genes for digestion and metabolism, neurological process and cancer. Our study, for the first time, draws together humans and dogs in their recent genomic evolution.
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| 5. |
- Chen, I-Hua, et al.
(author)
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Internet addiction and psychological distress among Chinese schoolchildren before and during the COVID-19 outbreak : A latent class analysis
- 2021
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In: Journal of Behavioral Addictions. - : AKADEMIAI KIADO ZRT. - 2062-5871 .- 2063-5303. ; 10:3, s. 731-746
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Journal article (peer-reviewed)abstract
- Background and aims: The present longitudinal study examined the changes in problematic internet use (problematic smartphone use, problematic social media use, and problematic gaming) and changes in COVID-19-related psychological distress (fear of COVID-19 and worry concerning COVID-19) across three time-points (before the COVID-19 outbreak, during the initial stages of the COVID-19 outbreak, and during the COVID-19 outbreak recovery period). Methods: A total of 504 Chinese schoolchildren completed measures concerning problematic internet use and psychological distress across three time points. Latent class analysis (LCA) was used to classify participants into three groups of problematic internet use comprising Group 1 (lowest level), Group 2 (moderate level), and Group 3 (highest level). Results: Statistical analyses showed that as problematic use of internet-related activities declined among Group 3 participants across the three time points, participants in Group 1 and Group 2 had increased problematic use of internet-related activities. Although there was no between-group difference in relation to worrying concerning COVID-19 infection, Groups 2 and 3 had significantly higher levels of fear of COVID-19 than Group 1 during the COVID-19 recovery period. Regression analysis showed that change in problematic internet use predicted fear of COVID-19 during the recovery period. Conclusion: The varied levels of problematic internet use among schoolchildren reflect different changing trends of additive behaviors during COVID-19 outbreak and recovery periods.
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| 6. |
- Dalal, Koustuv, 1969-, et al.
(author)
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Knowledge and attitudes towards childhood injury prevention : a study of parents in Shanghai, China
- 2012
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In: HealthMed. - Sarajevo, Bosnia & Herzegovina : DRUNPP. - 1840-2291 .- 1986-8103. ; 6:11, s. 3783-3789
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Journal article (peer-reviewed)abstract
- Childhood injuries are a major problem worldwide. The study explored the parents' knowledge and attitudes towards childhood injury prevention in relation to theirsocioeconomic status. The study also tried to compare parents' perceptions of cause and place of child injury with actual cause and place of injury. This was a cross sectional study of 986 randomly selected parents whose children (3-6 years old) were enrolled at selected kindergartens in a 'Safe Community' in Shanghai, China. Chi-square tests and bar diagrams were used. Almost all parents (97%) thought that injury was a serious problem for their children. Around half of the parents thought that child injuries could be prevented while almost one-third (29%) of parents indicated that there were risk factors in the living environment of their children. Parental perceptions of cause of injuries and place of injuries significantly differed from that of the reality. Parents identified the most common barriers of childhood injury prevention: lack of parental attention (41.6%), environment (35.6%) and children's risky behavior (22.7%). The difference between parental opinions and reality illustrated that parents had incorrect knowledge of childhood injuries, which might lead to incorrect foci of prevention programs.Before tackling environmental modifications to prevent child injuries, policy makers should focus on rectifying parents' incorrect perceptions and on modifying their attitudes as key players. It is important to first raise awareness about childhood injury prevention among the parents for appropriate intervention strategies.
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| 7. |
- Hsu, Ya-Ching, et al.
(author)
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Methadone concentrations in blood, plasma, and oral fluid determined by isotope-dilution gas chromatography-mass spectrometry
- 2013
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In: Analytical and Bioanalytical Chemistry. - : Springer Verlag (Germany). - 1618-2642 .- 1618-2650. ; 405:12, s. 3921-3928
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Journal article (peer-reviewed)abstract
- Methadone (MTD) is widely used for detoxification of heroin addicts and also in pain management programs. Information about the distribution of methadone between blood, plasma, and alternative specimens, such as oral fluid (OF), is needed in clinical, forensic, and traffic medicine when analytical results are interpreted. We determined MTD and its metabolite 2-ethylidene-1,5-dimethyl-3,3-diphenylpyrrolidine (EDDP) in blood, plasma, blood cells, and OF by gas chromatography-mass spectrometry (GC-MS) after adding deuterium-labeled internal standards. The analytical limits of quantitation for MTD and EDDP by this method were 20 and 3 ng/mL, respectively. The amounts of MTD and EDDP were higher in plasma (80.4 % and 76.5 %) compared with blood cells (19.6 % and 23.5 %) and we found that repeated washing of blood cells with phosphate-buffered saline increased the amounts in plasma (93.6 % and 88.6 %). Mean plasma/blood concentration ratios of MTD and EDDP in spiked samples (N = 5) were 1.27 and 1.21, respectively. In clinical samples from patients (N = 46), the concentrations of MTD in plasma and whole blood were highly correlated (r = 0.92, p andlt; 0.001) and mean (median) plasma/blood distribution ratios were 1.43 (1.41). The correlations between MTD in OF and plasma (r = 0.46) and OF and blood (r = 0.52) were also statistically significant (p andlt; 0.001) and the mean OF/plasma and OF/blood distribution ratios were 0.55 and 0.77, respectively. The MTD concentration in OF decreased as salivary pH increased (more basic). These results will prove useful in clinical and forensic medicine when MTD concentrations in alternative specimens are compared and contrasted.
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| 8. |
- Huang, Wen-Yi, et al.
(author)
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Effectiveness of using calligraphic activity to treat people with schizophrenia : a randomized controlled trial in Southern Taiwan
- 2022
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In: THERAPEUTIC ADVANCES IN CHRONIC DISEASE. - : Sage Publications. - 2040-6223 .- 2040-6231. ; 13
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Journal article (peer-reviewed)abstract
- Background: Prior research has shown preliminary evidence that calligraphy activity improves various body functions and decreases severity of psychotic symptoms in individuals with schizophrenia. However, major limitations of earlier studies include small and heterogeneous samples. The current large-scale randomized controlled trial examined effects of calligraphy activity on cognition (including attention), emotions, psychotic symptoms, quality of life, and mood in people with schizophrenia. Methods: One-hundred-and-fifty patients with schizophrenia were randomly allocated to the treatment group (receiving calligraphy activity) or the control group (receiving general activity), both of which lasted for 24weeks (70 minutes per session; one session per week). Assessments were conducted at pretest, posttest, and three-month follow-up. The Montreal Cognitive Assessment, Chu's Attention Test, Depression, Anxiety, and Stress Scale, Positive and Negative Syndrome Scale, World Health Questionnaire on the Quality of Life-Brief Form, and Visual Analogue Scale were used. Results: Improved cognition and attention were found in both groups, although no group effects were shown. The treatment group appeared to show lower severity of positive symptoms at follow-up than posttest, whereas the control group appeared to show the opposite pattern. Improved mood was found in the treatment group. Conclusion: This study provides evidence regarding effects of calligraphy activity on increasing cognition and potentially decreasing severity of positive symptoms in patients with schizophrenia. Calligraphy activity can be incorporated in clinical occupational therapy and may be provided to supplement medication treatment.
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| 9. |
- Mei, Wang Shu, et al.
(author)
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Elderly injury prevention perspectives : a qualitative study of elderly people in different socioeconomic strata within a Safe Community in Shanghai
- 2012
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In: HealthMed. - Sarajevo, Bosnia & Herzegovina : DRUNNP. - 1840-2291 .- 1986-8103. ; 6:12, s. 4170-4178
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Journal article (peer-reviewed)abstract
- Injuries represent an important cause of health problems among elderly people. The study has explored the perspectives and ideas of elderly people from different socioeconomic groups in terms of their injury-related issues. This paper examines a Safe Community accredited by the WHO Community Safety program. The community has three different residential sections labeled as Section-A, Section-B and Section-C, representing high, medium and low socioeconomic status of the residents respectively. Three focus group discussions (FGDs) were organized from three residential sections separately with 8 to 12 elderly people (>60years) in each group. Elderly people from Section-A were more concerned about emotional abuse whilst those from Sections B and C thought that fall and traffic injuries were most common injures. In Section-A, the most frequent risk factors were age, mental status and other people's unsafe behavior. In Section-B risk factors were age, environment and safety procedures. In Section-C, risk factors were environments, age and disease. For injury prevention, the elderly in A and B Sections thought that education should be improved while in C Section they emphasized environmental improvements. The perspectives and needs in terms of injury prevention among elderly people from different socioeconomic levels were not the same. When local governments develop their injury prevention plans and strategies, those differences should be considered.
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| 10. |
- Nie, Huizhen, et al.
(author)
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The short isoform of PRLR suppresses the pentose phosphate pathway and nucleotide synthesis through the NEK9-Hippo axis in pancreatic cancer
- 2021
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In: Theranostics. - : Ivyspring International Publisher. - 1838-7640. ; 11:8, s. 3898-3915
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Journal article (peer-reviewed)abstract
- Prolactin binding to the prolactin receptor exerts pleiotropic biological effects in vertebrates. The prolactin receptor (PRLR) has multiple isoforms due to alternative splicing. The biological roles and related signaling of the long isoform (PRLR-LF) have been fully elucidated. However, little is known about the short isoform (PRLR-SF), particularly in cancer development and metabolic reprogramming, a core hallmark of cancer. Here, we reveal the role and underlying mechanism of PRLR-SF in pancreatic ductal adenocarcinoma (PDAC). Methods: A human PDAC tissue array was used to investigate the clinical relevance of PRLR in PDAC. The in vivo implications of PRLR-SF in PDAC were examined in a subcutaneous xenograft model and an orthotopic xenograft model. Immunohistochemistry was performed on tumor tissue obtained from genetically engineered KPC (KrasG12D/+; Trp53R172H/+; Pdx1-Cre) mice with spontaneous tumors. 13C-labeled metabolite measures, LC-MS, EdU incorporation assays and seahorse analyses were used to identify the effects of PRLR-SF on the pentose phosphate pathway and glycolysis. We identified the molecular mechanisms by immunofluorescence, coimmunoprecipitation, proximity ligation assays, chromatin immunoprecipitation and promoter luciferase activity. Public databases (TCGA, GEO and GTEx) were used to analyze the expression and survival correlations of the related genes. Results: We demonstrated that PRLR-SF is predominantly expressed in spontaneously forming pancreatic tumors of genetically engineered KPC mice and human PDAC cell lines. PRLR-SF inhibits the proliferation of PDAC cells (AsPC-1 and BxPC-3) in vitro and tumor growth in vivo. We showed that PRLR-SF reduces the expression of genes in the pentose phosphate pathway (PPP) and nucleotide biosynthesis by activating Hippo signaling. TEAD1, a downstream transcription factor of Hippo signaling, directly regulates the expression of G6PD and TKT, which are PPP rate-limiting enzymes. Moreover, NEK9 directly interacts with PRLR-SF and is the intermediator between PRLR and the Hippo pathway. The PRLR expression level is negatively correlated with overall survival and TNM stage in PDAC patients. Additionally, pregnancy and lactation increase the ratio of PRLR-SF:PRLR-LF in the pancreas of wild-type mice and subcutaneous PDAC xenograft tumors. Conclusion: Our characterization of the relationship between PRLR-SF signaling, the NEK9-Hippo pathway, PPP and nucleotide synthesis explains a mechanism for the correlation between PRLR-SF and metabolic reprogramming in PDAC progression. Strategies to alter this pathway might be developed for the treatment or prevention of pancreatic cancer.
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