| 1. |
- Beal, Jacob, et al.
(författare)
-
Robust estimation of bacterial cell count from optical density
- 2020
-
Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
-
Tidskriftsartikel (refereegranskat)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.
|
|
| 2. |
- Klionsky, Daniel J., et al.
(författare)
-
Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
-
Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
-
Forskningsöversikt (refereegranskat)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.
|
|
| 3. |
- Sampson, Joshua N., et al.
(författare)
-
Analysis of Heritability and Shared Heritability Based on Genome-Wide Association Studies for 13 Cancer Types
- 2015
-
Ingår i: Journal of the National Cancer Institute. - : Oxford University Press (OUP). - 0027-8874 .- 1460-2105. ; 107:12
-
Tidskriftsartikel (refereegranskat)abstract
- Background: Studies of related individuals have consistently demonstrated notable familial aggregation of cancer. We aim to estimate the heritability and genetic correlation attributable to the additive effects of common single-nucleotide polymorphisms (SNPs) for cancer at 13 anatomical sites. Methods: Between 2007 and 2014, the US National Cancer Institute has generated data from genome-wide association studies (GWAS) for 49 492 cancer case patients and 34 131 control patients. We apply novel mixed model methodology (GCTA) to this GWAS data to estimate the heritability of individual cancers, as well as the proportion of heritability attributable to cigarette smoking in smoking-related cancers, and the genetic correlation between pairs of cancers. Results: GWAS heritability was statistically significant at nearly all sites, with the estimates of array-based heritability, h(l)(2), on the liability threshold (LT) scale ranging from 0.05 to 0.38. Estimating the combined heritability of multiple smoking characteristics, we calculate that at least 24% (95% confidence interval [CI] = 14% to 37%) and 7% (95% CI = 4% to 11%) of the heritability for lung and bladder cancer, respectively, can be attributed to genetic determinants of smoking. Most pairs of cancers studied did not show evidence of strong genetic correlation. We found only four pairs of cancers with marginally statistically significant correlations, specifically kidney and testes (rho = 0.73, SE = 0.28), diffuse large B-cell lymphoma (DLBCL) and pediatric osteosarcoma (rho = 0.53, SE = 0.21), DLBCL and chronic lymphocytic leukemia (CLL) (rho = 0.51, SE = 0.18), and bladder and lung (rho = 0.35, SE = 0.14). Correlation analysis also indicates that the genetic architecture of lung cancer differs between a smoking population of European ancestry and a nonsmoking Asian population, allowing for the possibility that the genetic etiology for the same disease can vary by population and environmental exposures. Conclusion: Our results provide important insights into the genetic architecture of cancers and suggest new avenues for investigation.
|
|
| 4. |
- Liu, Lizheng, et al.
(författare)
-
A Design of Autonomous Error-Tolerant Architectures for Massively Parallel Computing
- 2018
-
Ingår i: IEEE Transactions on Very Large Scale Integration (vlsi) Systems. - : Institute of Electrical and Electronics Engineers (IEEE). - 1063-8210 .- 1557-9999. ; 26:10, s. 2143-2154
-
Tidskriftsartikel (refereegranskat)abstract
- The massively parallel computing systems composed of many processors are connected on chips, which will become more and more complex and unreliable. This paper presents an error-tolerant design based on the autonomous error-tolerant (AET) architecture that aims to have a self-repairing capability. A nearby error sensing mechanism is designed to discover faults, and an active evolution scheme is studied to handle unrecoverable errors. A circuit backup switching mechanism is proposed to bypass the failed nodes. The board-level prototype is implemented based on dual-core embedded processors. The analysis shows that the error-tolerant capability of the proposed architecture is better than the conventional multimodular redundant system when the failure rate of a single core is less than 0.7. In the AET test system consisting of 16 processors, the error-tolerant capability is verified. The results show that the relative variation of the overall performance of the AET system will not be changed due to the high reliability requirements of the system. Through experimental comparison, under the premise that the architecture of AET and the triple modular redundancy method are basically consistent in reliability, whether on the logical-level error tolerant or on the physical-level error tolerant, the former has lower power consumption.
|
|
| 5. |
- Pan, Xiong-Fei, et al.
(författare)
-
Circulating fatty acids and risk of gestational diabetes mellitus : prospective analyses in China
- 2021
-
Ingår i: European Journal of Endocrinology. - : Bioscientifica. - 0804-4643 .- 1479-683X. ; 185:1, s. 87-97
-
Tidskriftsartikel (refereegranskat)abstract
- Objective: We aimed to examine prospective associations between circulating fatty acids in early pregnancy and incident gestational diabetes mellitus (GDM) among Chinese pregnant women.Methods: Analyses were based on two prospective nested case-control studies conducted in western China (336 GDM cases and 672 matched controls) and central China (305 cases and 305 matched controls). Fasting plasma fatty acids in early pregnancy (gestational age at enrollment: 10.4 weeks(s.d., 2.0)) and 13.2 weeks (1.0), respectively) were determined by gas chromatography-mass spectrometry, and GDM was diagnosed based on the International Association of Diabetes in Pregnancy Study Groups criteria during 24-28 weeks of gestation. Multiple metabolic biomarkers (HOMA-IR (homeostatic model assessment for insulin resistance), HbA1c, c-peptide, high-sensitivity C-reactive protein, adiponectin, leptin, and blood lipids) were additionally measured among 672 non-GDM controls at enrollment.Results: Higher levels of saturated fatty acids (SFAs) 14:0 (pooled odds ratio, 1.41 for each 1-s.d. increase; 95% CI: 1.25, 1.59) and 16:0 (1.19; 1.05, 1.35) were associated with higher odds of GDM. Higher levels of n-6 polyunsaturated fatty acid (PUFA) 18:2n-6 were strongly associated with lower odds of GDM (0.69; 0.60, 0.80). In non-GDM pregnant women, higher SFAs 14:0 and 16:0 but lower n-6 PUFA 18:2n-6 were generally correlated with unfavorable metabolic profiles.Conclusions: We documented adverse associations of 14:0 and 16:0 but a protective association of 18:2n-6 with GDM among Chinese pregnant women. Our findings highlight the distinct roles of specific fatty acids in the onset of GDM.
|
|
| 6. |
- Wang, Fang, et al.
(författare)
-
Emerging contaminants: A One Health perspective
- 2024
-
Ingår i: Innovation. - 2666-6758. ; 5
-
Forskningsöversikt (refereegranskat)abstract
- Environmental pollution is escalating due to rapid global development that often prioritizes human needs over planetary health. Despite global efforts to mitigate legacy pollutants, the continuous introduction of new substances remains a major threat to both people and the planet. In response, global initiatives are focusing on risk assessment and regulation of emerging contaminants, as demonstrated by the ongoing efforts to establish the UN's Intergovernmental Science-Policy Panel on Chemicals, Waste, and Pollution Prevention. This review identifies the sources and impacts of emerging contaminants on planetary health, emphasizing the importance of adopting a One Health approach. Strategies for monitoring and addressing these pollutants are discussed, underscoring the need for robust and socially equitable environmental policies at both regional and international levels. Urgent actions are needed to transition toward sustainable pollution management practices to safeguard our planet for future generations.
|
|
| 7. |
- Zhang, Yin-Ping, et al.
(författare)
-
Cross-cultural adaptation and validation of the osteoporosis assessment questionnaire short version (OPAQ-SV) for Chinese osteoporotic fracture females
- 2016
-
Ingår i: Clinical Rheumatology. - : Springer. - 0770-3198 .- 1434-9949. ; 35:4, s. 1003-1010
-
Tidskriftsartikel (refereegranskat)abstract
- The Osteoporosis Assessment Questionnaire Short Version (OPAQ-SV) was cross-culturally adapted to measure health-related quality of life in Chinese osteoporotic fracture females and then validated in China for its psychometric properties. Cross-cultural adaptation, including translation of the original OPAQ-SV into Mandarin Chinese language, was performed according to published guidelines. Validation of the newly cross-culturally adapted OPAQ-SV was conducted by sampling 234 Chinese osteoporotic fracture females and also a control group of 235 Chinese osteoporotic females without fractures, producing robust content, construct, and discriminant validation results. Major categories of reliability were also met: the Cronbach alpha coefficient was 0.975, indicating good internal consistency; the test-retest reliability was 0.80; and principal component analysis resulted in a 6-factor structure explaining 75.847 % of the total variance. Further, the Comparative Fit Index result was 0.922 following the modified model confirmatory factor analysis, and the chi-squared test was 1.98. The root mean squared error of approximation was 0.078. Moreover, significant differences were revealed between females with fractures and those without fractures across all domains (p < 0.001). Overall, the newly cross-culturally adapted OPAQ-SV appears to possess adequate validity and reliability and may be utilized in clinical trials to assess the health-related quality of life in Chinese osteoporotic fracture females.
|
|
| 8. |
- Chong, Hui, et al.
(författare)
-
Organo-ptii complexes for potent photodynamic inactivation of multi-drug resistant bacteria and the influence of configuration
- 2024
-
Ingår i: Advanced Science. - : John Wiley & Sons. - 2198-3844. ; 11:14
-
Tidskriftsartikel (refereegranskat)abstract
- PtII based organometallic photosensitizers (PSs) have emerged as novel potent photodynamic inactivation (PDI) reagents through their enhanced intersystem crossing (ISC) processes. Currently, few PtII PSs have been investigated as antibacterial materials, with relatively poor performances reported and with structure-activity relationships not well described. Herein, a pair of configurational isomers are reported of Bis-BODIPY (4,4-difluoro-boradizaindacene) embedded PtII PSs. The cis-isomer (cis-BBP) displayed enhanced 1O2 generation and better bacterial membrane anchoring capability as compared to the trans-isomer (trans-BBP). The effective PDI concentrations (efficiency > 99.9%) for cis-BBP in Acinetobacter baumannii (multi-drug resistant (MDR)) and Staphylococcus aureus are 400 nM (12 J cm−2) and 100 nM (18 J cm−2), respectively; corresponding concentrations and light doses for trans-BBP in the two bacteria are 2.50 µM (30 J cm−2) and 1.50 µM (18 J cm−2), respectively. The 50% and 90% minimum inhibitory concentration (MIC50 and MIC90) ratio of trans-BBP to cis-BBP is 22.22 and 24.02 in A. baumannii (MDR); 21.29 and 22.36 in methicillin resistant S. aureus (MRSA), respectively. Furthermore, cis-BBP displays superior in vivo antibacterial performance, with acceptable dark and photoinduced cytotoxicity. These results demonstrate cis-BBP is a robust light-assisted antibacterial reagent at sub-micromolecular concentrations. More importantly, configuration of PtII PSs should be an important issue to be considered in further PDI reagents design.
|
|
| 9. |
- Dimovska, Eleonora O. F., et al.
(författare)
-
Outcomes and quality of life in immediate one-stage versus two-stage breast reconstructions without an acellular dermal matrix : 17- years of experience.
- 2021
-
Ingår i: Journal of Surgical Oncology. - : John Wiley & Sons. - 0022-4790 .- 1096-9098. ; 124:4, s. 510-520
-
Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: Advantages of one-stage implant-based reconstructions include expedited surgery and recovery. This study aimed to investigate clinical and patient-reported outcomes in one-stage implant-based breast reconstructions without acellular dermal matrix (ADM).METHODS: A prospectively collected database from 2002 to 2018 was retrospectively reviewed. One-stage and two-stage groups were compared for demographics, implant properties, early complications (hematoma, seroma, poor wound healing, implant removal), late complications (skin necrosis, capsular contracture, implant exposure, implant rupture), revision procedures, and Breast-Q questionnaire outcomes.RESULTS: A total of 223 patients, 187 one-stage (84%) and 36 two-stage (16%) patients were recruited. At a mean follow-up of 124.9 and 92.5 months, respectively (p < .01), there were no differences in early (p = .85) or late (p = .23) complications or revision procedures (p = .12). Eighty patients (36%) returned the Breast-Q questionnaire (60 one-stage, 20 two-stage patients). There were no statistical differences in patient reported outcomes in breast well-being (p = .07), psychosocial well-being (p = .84), or sexual well-being (p = .78).CONCLUSIONS: One-stage implant-based breast reconstruction without an ADM is a viable reconstruction providing comparable outcomes to two-stage procedures, with the benefit of minimal complications, a shorter reconstructive journey, and satisfactory quality of life.
|
|
| 10. |
- Francis, Eamon C., et al.
(författare)
-
Nipple-sparing mastectomy with immediate breast reconstruction with a deep inferior epigastric perforator flap without skin paddle using delayed primary retention suture
- 2022
-
Ingår i: Journal of Surgical Oncology. - : John Wiley & Sons. - 0022-4790 .- 1096-9098. ; 125:8, s. 1202-1210
-
Tidskriftsartikel (refereegranskat)abstract
- Background This study investigated the outcomes of nipple-sparing mastectomy (NSM) with a deep inferior epigastric perforator (DIEP) flap using delayed primary retention suture (DPRS) to achieve superior breast esthetics.Methods Between December 2010 and March 2021, patients who underwent NSM with DIEP flap were inset with or without a skin paddle (using DPRS) as Group A or B, respectively. Demographics, operative findings, complications, BREAST-Q questionnaire, and Manchester scar scale were compared between two groups.Results Twelve patients underwent 12 unilateral reconstructions in Group A, while 12 patients underwent 13 DIEP flaps in Group B. There was no significant difference in demographics, ischemia time, flap-used weight and percentage, complications of hematoma, infection, re-exploration, partial flap loss, and total flap loss (All p > 0.05, respectively). At a mean 9 months of follow-up, the Breast-Q "Satisfaction with surgeon" domain was significant in Group B (p = 0.04). At a mean 12 months of follow-up, the overall Manchester scar scale of 10.3 in Group B was statistically superior to 12.6 in Group A (p = 0.04).Conclusions The NSM with a DIEP flap using DPRS is a reliable and straightforward technique. It can provide greater cosmesis of the reconstructed breast mound in a single-stage procedure.
|
|
