bluuebunny/crossref_metadata_2025 huggingface dataset:
Overview of Analytical Methods for Evaluating Tinidazole
Authors: Pereira Sousa Jean Carlos , Kogawa Ana Carolina
Published: November 2022

Background

Tinidazole (TIN) has amoebicidal, giardicidal, antifungal, and antimicrobial activities. It is marketed in the form of tablets. Analytical methods to assess the quality of TIN-based products are essential for correct pharmacotherapy.

Objective

The objective of this review is to show an overview of the existing analytical methods for evaluating TIN, according to the quality control (QC) analysis routine and green analytical chemistry (GAC).

Results

Official compendia show a method for evaluating TIN in tablets by nonaqueous titration, which has limitations (materials on the mg scale using solvents considered not recommended and harmful). The literature shows some analytical methods for evaluating TIN, both physicochemical and microbiological. The most used physicochemical method is UV (41%), and second is HPLC (28%). Among the microbiological methods, agar diffusion and turbidimetric methods are equally divided. The most studied matrix is TIN tablets (73%), and the most used solvent is methanol.

Conclusions

The literature shows space for the development of analytical methods according to GAC for evaluating TIN, optimizing time, resources, and materials, reducing waste generation, and opting for less aggressive reagents, solvents, and diluents.

Highlights

This review shows the status of analytical methods, both physicochemical and microbiological, for the analysis of TIN in pharmaceutical matrix, in the context of routine analysis of the chemical-pharmaceutical industries and of GAC.
Gas coal delamination recognition method based on the Fisher discriminant function of trace element characteristics
Authors: Pan Hui , Zhou Wei , Chen Dezhong , Zhang Hongling , Han Yunchun
Published: November 2022

Numerous geological factors will affect determining the well bottom position by well depth during the construction of coalbed methane wells, resulting in inaccurate results. By using the trace element characteristics of coal samples to determine the source layer of coal samples, it is possible to avoid making incorrect assumptions. The groove method was used in this study to collect 40 gas coal samples from seven gas coal seams in Dingji Mine, which were then sealed and stored. The contents of 40 different trace elements were analyzed in the samples, and the types and content characteristics of trace elements in each coal seam were determined preliminarily through content distribution map analysis. Simultaneously, the SPSS analysis software was used to analyze the 1600 trace element test data from various coal seams, and cluster analysis was performed using the average link method between classes. The clustering tree diagram was created, and the discrimination was calculated using the distance between classes and samples. This study analyzed the typical explanatory variables and established the Fisher discriminant function for coal seam identification. Accordingly, identifying gas coal stratification requires only measuring the concentrations of nine trace elements (typical explanatory variables) in the coal seam being discriminated against. This method can be used in Dingji mine to determine the final hole horizon of surface coalbed methane wells and eliminates the risk of accidentally exposing coal seams during the excavation of an underground roadway.
A ‘wiring diagram’ for sink strength traits impacting wheat yield potential
Authors: Slafer Gustavo A , Foulkes M John , Reynolds Matthew P , Murchie Erik H , Carmo-Silva Elizabete , Flavell Richard , Gwyn Jeff , Sawkins Mark , Griffiths Simon
Published: November 2022

Identifying traits for improving sink strength is a bottleneck to increasing wheat yield. The interacting processes determining sink strength and yield potential are reviewed and visualized in a set of ‘wiring diagrams’, covering critical phases of development (and summarizing known underlying genetics). Using this framework, we reviewed and assembled the main traits determining sink strength and identified research gaps and potential hypotheses to be tested for achieving gains in sink strength. In pre-anthesis, grain number could be increased through: (i) enhanced spike growth associated with optimized floret development and/or a reduction in specific stem–internode lengths and (ii) improved fruiting efficiency through an accelerated rate of floret development, improved partitioning between spikes, or optimized spike cytokinin levels. In post-anthesis, grain, sink strength could be augmented through manipulation of grain size potential via ovary size and/or endosperm cell division and expansion. Prospects for improving spike vascular architecture to support all rapidly growing florets, enabling the improved flow of assimilate, are also discussed. Finally, we considered the prospects for enhancing grain weight realization in relation to genetic variation in stay-green traits as well as stem carbohydrate remobilization. The wiring diagrams provide a potential workspace for breeders and crop scientists to achieve yield gains in wheat and other field crops.
Intravenous immunoglobulin for chronic residual peripheral neuropathy in microscopic polyangiitis: A multicentre randomised double-blind trial
Authors: Arimura Yoshihiro , Sobue Gen , Hattori Naoki , Takashima Hiroshi , Harigai Masayoshi , Nagata Koichi , Makino Hirofumi
Published: November 2022

Objectives

We conducted a Phase 3, multicentre, randomised, double-blind, placebo-controlled, parallel-group trial to evaluate the efficacy and safety of intravenous immunoglobulin (IVIg) in patients with glucocorticoid-refractory neuropathy associated with microscopic polyangiitis.

Methods

Patients received immunoglobulin or placebo intravenously for 5 consecutive days at baseline and after 4 weeks. The IVIg and placebo groups received IVIg and placebo, respectively, after 8 weeks. The primary and major secondary end-points were the least squares mean of the change in the manual muscle test (MMT) sum score after 8 and 4 weeks, respectively.

Results

A total of 37 patients were randomised into two groups (IVIg [19] and placebo [18]). The least squares mean for the change in the MMT sum score was 9.02 for IVIg and 6.71 for placebo (difference 2.32, 95% confidence interval −2.60 to 7.23, p = .345) after 8 weeks and 6.81 and 2.83 (difference 3.99, 95% confidence interval −1.22 to 9.19, p = .129), respectively, after 4 weeks. There were no new safety concerns for IVIg.

Conclusions

MMT sum scores improved with IVIg compared with placebo after 8 weeks of dosing and two courses of treatment, but the differences were not statistically significant, and the results showed no clear efficacy of IVIg in this patient population. No new safety concerns were raised.
Which Way?Indigenous-led Smoking Cessation Care: Knowledge, Attitudes and Practices of Aboriginal and Torres Strait Islander Health Workers and Practitioners – A National Cross-sectional Survey
Authors: Kennedy Michelle , Longbottom Hayley , Mersha Amanual , Maddox Raglan , Briscoe Karl , Hussein Paul , Bacon Shanell , Bar-Zeev Yael
Published: November 2022

Introduction

Tobacco is the leading preventable cause of morbidity and mortality for Aboriginal and Torres Strait Islander people. Accordingly, the provisions of culturally safe and effective smoking cessation strategies are crucial. While previous research has suggested Aboriginal Health Workers/Practitioners are well placed to provide smoking cessation care, no research to date has explored the workforce knowledge, attitudes and practices in offering best practice cessation care.

Methods

A cross-sectional study was conducted among Aboriginal Health Workers/Practitioners from June to September 2021. Descriptive and inferential statistics were conducted to examine participant characteristics, provision of smoking cessation care, and explore the factors associated with smoking cessation care.

Results

Out of 1052 registered Aboriginal Health Workers/Practitioners, 256 participants completed the full survey (24.3%). Smoking cessation counseling was always provided by 41.9%; provided some of the time by 42.4%, and never provided by 12.9%. Combination NRT and Quitline referral were always offered by 23.1% and 44.9% of participants, respectively. Those that received training, felt smoking cessation care was part of their role, and were based in Aboriginal Community Controlled Health Organization were significantly more likely to offer best practice smoking cessation care.

Conclusion

Aboriginal Health Workers/Practitioners and Aboriginal Community Controlled Health Organizations play a critical role in delivering high quality, evidence based and culturally safe care to Aboriginal and Torres Strait Islander people. Aboriginal Health Workers/Practitioners are well placed to offer smoking cessation care. Ongoing funding and implementation of a targeted smoking cessation workforce with appropriate training and resources are urgently required.

Implications

Aboriginal Health Workers/Practitioners are well placed to offer culturally safe, best practice smoking cessation care. However, due to the magnitude and complexity of Aboriginal Health Workers/Practitioners roles, it is challenging for smoking cessation care to be consistently and feasibly integrated into usual care. Acknowledging Australia’s National Preventative Health Strategy target of 27% or less Aboriginal and Torres Strait Islander people smoking by 2030, urgent investment and resourcing must be directed to building a skilled workforce to support quitting and maintaining smokefree behaviors, ensuring equitable access to smoking cessation care for Aboriginal and Torres Strait Islander peoples.
Antipsychotic Use and Risk of Low-Energy Fractures in People With Schizophrenia: A Nationwide Nested Case-Control Study in Finland
Authors: Solmi Marco , Lähteenvuo Markku , Correll Christoph U , Tanskanen Antti , Tiihonen Jari , Taipale Heidi
Published: November 2022

Background

Low-energy fractures (LEF) are more frequent in people with schizophrenia than the general population, and the role of prolactin-increasing antipsychotics is unknown.

Study design

We conducted a nested case-control study using Finnish nationwide registers (inpatient, specialized outpatient care, prescription drug purchases). We matched each person with schizophrenia aged 16–85 years and incident LEF (cases) with 5 age/sex/illness duration-matched controls with schizophrenia, but no LEF. We investigated the association between cumulative exposure (duration, and Defined Daily Doses, DDDs) to prolactin-increasing/sparing antipsychotics and LEF. Adjusted conditional logistic regression analyses were performed. Sensitivity analyses were conducted.

Study results

Out of 61 889 persons with schizophrenia between 1972 and 2014, we included 4960 cases. Compared with 24 451 controls, 4 years or more of exposure to prolactin-increasing antipsychotics was associated with increased risk of LEF (adjusted odds ratio (aOR) from aOR = 1.22, 95%CI = 1.09–1.37 to aOR = 1.38, 95%CI = 1.22–1.57, for 4–<7/>13 years of exposure, respectively), without a significant association for prolactin-sparing antipsychotics. All cumulative doses higher than 1000 DDDs of prolactin-increasing antipsychotics were associated with LEF (from aOR = 1.21, 95%CI = 1.11–1.33, 1000–<3000 DDDs, to aOR = 1.64, 95%CI = 1.44–1.88, >9000 DDDs). Only higher doses of prolactin-sparing antipsychotics reached statistical significance (aOR = 1.24, 95%CI = 1.01–1.52, 6000–<9000 DDDs, aOR = 1.45, 95%CI = 1.13–1.85, >9000 DDDs). Sensitivity analyses confirmed the main analyses for prolactin-increasing antipsychotics. For prolactin-sparing antipsychotics, significant associations were limited to extreme exposure, major LEF, older age group, and males.

Conclusions

Long-term exposure to prolactin-increasing antipsychotics at any dose, and high cumulative doses of prolactin-sparing antipsychotics is associated with significantly increased odds of LEF. Monitoring and addressing hyperprolactinemia is paramount in people with schizophrenia receiving prolactin-increasing antipsychotics.
A longitudinal investigation of sleep hygiene as a mediator linking parental warmth with adolescent sleep
Authors: Richardson Cele E , Magson Natasha R , Oar Ella L , Fardouly Jasmine , Johnco Carly J , Freeman Justin Y A , Rapee Ronald M
Published: November 2022

Study Objectives

Parental warmth in adolescence protects sleep in early adulthood, yet the nature, directions, and mechanisms of this association across adolescence are unknown. This study examined parental warmth, adolescent sleep hygiene and sleep outcomes (morning/eveningness, school night sleep duration, and daytime sleepiness) across five annual waves, spanning four years, using a cross-lagged panel design.

Methods

Adolescents and one primary caregiver (96% mothers) completed questionnaires assessing parental warmth (child- and parent-report) and adolescent sleep hygiene and sleep (child-report), across five annual waves: Wave 1 (N = 531, Mage = 11.18, SD = 0.56, 51% male), Wave 2 (N = 504, Mage = 12.19, SD = 0.53, 52% male), Wave 3 (N = 478, Mage = 13.19, SD = 0.53, 52% male), Wave 4 (N = 440, Mage = 14.76, SD = 0.47, 51% male), and Wave 5 (N = 422, Mage = 15.75, SD = 0.49, 51% male).

Results

Greater child-reported parental warmth was indirectly associated with better adolescent sleep (greater morningness, longer school night sleep duration, less sleepiness) through healthier sleep hygiene. The inverse was also often observed. Warmth had a direct relationship with sleep duration and sleepiness, independent of sleep hygiene. Parent-reported parental warmth did not predict, nor was predicted by child-reported adolescent sleep.

Conclusions

Parental warmth may protect against developmental changes in adolescent sleep, partially by improving sleep hygiene practices. Similarly, inadequate adolescent sleep may negatively impact parental warmth via deteriorating sleep hygiene. Sleep hygiene emerged as a key mechanism for protecting adolescent sleep and parent-child relationships.
Structural plasticity of motor cortices assessed by voxel-based morphometry and immunohistochemical analysis following internal capsular infarcts in macaque monkeys
Authors: Matsuda Kohei , Nagasaka Kazuaki , Kato Junpei , Takashima Ichiro , Higo Noriyuki
Published: November 2022

Compensatory plastic changes in the remaining intact brain regions are supposedly involved in functional recovery following stroke. Previously, a compensatory increase in cortical activation occurred in the ventral premotor cortex (PMv), which contributed to the recovery of dexterous hand movement in a macaque model of unilateral internal capsular infarcts. Herein, we investigated the structural plastic changes underlying functional changes together with voxel-based morphometry (VBM) analysis of magnetic resonance imaging data and immunohistochemical analysis using SMI-32 antibody in a macaque model. Unilateral internal capsular infarcts were pharmacologically induced in 5 macaques, and another 5 macaques were used as intact controls for immunohistochemical analysis. Three months post infarcts, we observed significant increases in the gray matter volume (GMV) and the dendritic arborization of layer V pyramidal neurons in the contralesional rostral PMv (F5) as well as the primary motor cortex (M1). The histological analysis revealed shrinkage of neuronal soma and dendrites in the ipsilesional M1 and several premotor cortices, despite not always detecting GMV reduction by VBM analysis. In conclusion, compensatory structural changes occur in the contralesional F5 and M1 during motor recovery following internal capsular infarcts, and the dendritic growth of pyramidal neurons is partially correlated with GMV increase.
Value of dynamic metabolic curves and artificial neural network prediction models based on 18F-FDG PET/CT multiphase imaging in differentiating nonspecific solitary pulmonary lesions: a pilot study
Authors: Luo Yongjun , Li Jicheng , Huang Lele , Han Yuping , Tian Xiaoxue , Ma Wanjun , Wang Lu , Liu Jiangyan , Zhou Junlin
Published: November 2022

Objective

To investigate the value of dynamic metabolic curves and artificial neural network prediction models based on 18F-FDG PET multiphase imaging in differentiating nonspecific solitary pulmonary lesions.

Methods

This study enrolled 71 patients with solitary pulmonary lesions (48 malignant and 23 benign lesions) who underwent multiphase 18F-fluorodeoxyglucose (18F-FDG)-PET/CT imaging. We recorded information on age, sex and uniformity of FDG uptake, measured standardized uptake value, metabolic tumor volume and total lesion glycolysis at various time points, and calculated individual standardized uptake values, retention index (RI) and slope of metabolic curve. Variables with high diagnostic efficiency were selected to fit dynamic metabolic curves for various lesions and establish different artificial neural network prediction models.

Results

There were no significant differences in the retention index, metabolic tumor volume, total lesion glycolysis or sex between benign and malignant lesions; standardized uptake values, the slopes of five metabolic curves, uniformity of FDG uptake, and age showed significant differences. Dynamic metabolic curves for various solitary pulmonary lesions exhibited characteristic findings. Model-1 was established using metabolic parameters with high diagnostic efficacy (area under the curve, 83.3%). Model-2 was constructed as Model-1 + age (area under the curve, 86.7%), whereas Model-3 was established by optimizing Model-2 (area under the curve, 86.0%).

Conclusions

Dynamic metabolic curves showed varying characteristics for different lesions. Referring to these findings in clinical work may facilitate the differential diagnosis of nonspecific solitary pulmonary lesions. Establishing an artificial neural network prediction model would further improve diagnostic efficiency.
Examining real-world Alzheimer’s disease heterogeneity using neuroanatomical normative modelling
Authors: Loreto Flavia , Verdi Serena , Kia Seyed Mostafa , Duvnjak Aleksandar , Hakeem Haneen , Fitzgerald Anna , Patel Neva , Lilja Johan , Win Zarni , Perry Richard , Marquand Andre F. , Cole James H. , Malhotra Paresh
Published: November 2022

Alzheimer’s disease (AD) has been traditionally associated with episodic memory impairment and medial temporal lobe atrophy. However, recent literature has highlighted the existence of atypical forms of AD, presenting with different cognitive and radiological profiles. Failure to appreciate the heterogeneity of AD in the past has led to misdiagnoses, diagnostic delays, clinical trial failures and risks limiting our understanding of the disease. AD research requires the incorporation of new analytic methods that are as free as possible from the intragroup homogeneity assumption underlying case-control approaches according to which patients belonging to the same group are comparable to each other. Neuroanatomical normative modelling is a promising technique allowing for modelling the variation in neuroimaging profiles and then assessing individual deviations from the respective distribution. Here, neuroanatomical normative modelling was applied for the first time to a real-worldclinicalcohort of Alzheimer’s disease patients (n=86) who had a positive amyloid PET scan and a T1-weighted MR performed as part of their diagnostic workup. The model indexed normal cortical thickness distributions using a separate healthy reference dataset (n= 33,072), employing hierarchical Bayesian regression to predict cortical thickness per region using age and sex. Transfer learning was used to recalibrate the normative model on avalidation cohort(n=20) of scanner-matched cognitively normal individuals. Brain heterogeneity was quantified asz-scoresat each of the 148 ROIs generated within each AD patient. Z-scores < -1.96 defined as outliers. Clinical features including disease severity, presenting phenotypes and comorbidities were collected from health records to explore their association with outlier profiles. Amyloid quantification was performed using an automated PET-only driven method to examine the association between amyloid burden and outliers.

The total number of individual outliers (total outlier count) in biomarker-confirmed AD clinical patients ranged between 1 and 120 out of 148 (median 21.5). The superior temporal sulcus was the region with the highest count of outliers (60%) in AD patients. The mean proportion of outliers was higher in the temporal (31.5%) than in the extratemporal (19.1%) regions and up to 20% of patients had no temporal outliers. We found higher mean outlier count in patients with non-amnestic phenotypes, at more advanced disease stages and without depressive symptoms. Amyloid burden was negatively associated with outlier count. This study corroborates the heterogeneity of brain atrophy in AD and provides evidence that this approach can be used to explore anatomo-clinical correlations at an individual level.
The Utility of a Bayesian Predictive Model to Forecast Neuroinvasive West Nile Virus Disease in the United States, 2022
Authors: McCarter Maggie S. J. , Self Stella , Dye-Braumuller Kyndall C. , Lee Christopher , Li Huixuan , Nolan Melissa S.
Published: November 2022

Arboviruses (arthropod-borne-viruses) are an emerging global health threat that are rapidly spreading as climate change, international business transport, and landscape fragmentation impact local ecologies. Since its initial detection in 1999, West Nile virus (WNV) has shifted from being a novel to an established arbovirus in the United States. Subsequently, more than 25,000 cases of West Nile Neuro-invasive Disease (WNND) have been diagnosed, cementing WNV as an arbovirus of public health importance. Given its novelty in the United States, high-risk ecologies are largely underdefined making targeted population-level public health interventions challenging. Using the Centers for Disease Control and Prevention ArboNET WNV data from 2000 – 2021, this study aimed to predict WNND human cases at the county level for the contiguous US states using a spatio-temporal Bayesian negative binomial regression model. The model includes environmental, climatic, and demographic factors, as well as the distribution of host species. An integrated nested LaPlace approximation (INLA) approach was used to fit our model. To assess model prediction accuracy, annual counts were withheld, forecasted, and compared to observed values. The validated models were then fit to the entire dataset for 2022 predictions. This proof-of-concept mathematical, geospatial modelling approach has proven utility for national health agencies seeking to allocate funding and other resources for local vector control agencies tackling WNV and other notifiable arboviral agents.
Common anti-platelet therapies modulate procoagulant phospholipids in arterial disease
Authors: Protty Majd B , Tyrrell Victoria J , Hajeyah Ali A , Morgan Bethan , Li Yong , Choudhury Anirban , Mitra Rito , Bosanquet David , Poole Alastair W , Yousef Zaheer , Collins Peter W , O’Donnell Valerie B
Published: November 2022

Enzymatically oxygenated phospholipids (eoxPL) formed by lipoxygenases (LOX) and cyclooxygenase (COX) in platelets and leukocytes are pro-coagulant in multiple model systems. However, their generation in arterial thrombotic disease, and how their levels are modulated by common therapies is unknown. Here, eoxPL were first characterized in isolated platelets and leukocytes from an arterial vascular disease cohort, a healthy cohort administered low dose aspirin, and from retrieved human arterial thrombi. In both cohorts, aspirin reduced platelet COX-1-derived eoxPL, while elevating diacyl 12-LOX-derived eoxPL in males, through enhanced Lands’ cycle esterification. Conversely, P2Y12 inhibition reduced 12-LOX-derived eoxPL in leukocytes. Complex aspirin-dependent gender and seasonal effects on platelet eoxPL were seen in healthy subjects. Limb or coronary (STEMI) thrombi showed a platelet eoxPL signature while carotid thrombi had a white cell profile. Mice genetically lacking leukocyte 12/15-LOX, which are deficient in eoxPL, generated smaller carotid thrombi in vivo. In summary, pro-coagulant eoxPL generation is altered in human arterial vascular disease by commonly used cardiovascular therapies. These changes to the phospholipid composition of blood cells in humans at risk of thrombotic events may be clinically significant where the pro-coagulant membrane plays a central but poorly understood role in driving elevated thrombotic risk.

Key Points

eoxPL generation is altered in health and arterial vascular disease by aspirin or P2Y12 inhibitors, and shows gender and seasonal variation.

Aspirin regulates eoxPL by inhibiting cyclooxygenase and modulating Lands’ cycle.

The eoxPL profile of human arterial thrombi identifies platelet and leukocyte involvement.

Mice deficient in LOX-derived eoxPL form smaller arterial thrombiin vivo.
NEW EFFECTIVE METHOD OF SPERMATOZOA RECOVERY FROM SURGICALLY-RETRIEVED TESTICULAR AND EPIDIDYMAL SPECIMENS BY DIFFERENTIAL CENTRIFUGATION
Authors: Elena Zakharova
Published: November 2022

The newly proposed method of processing cell suspensions for spermatozoa recovery is based on differential centrifugation and allows obtaining male germ cells from biopsy samples and using them for fertilization, especially if they are critically low in number and conventional methods for sperm recovery do no work or are inefficient.
Michigan men’s diabetes project II: protocol for peer-led diabetes self-management education and long-term support in Black men
Authors: Hawkins Jaclynn , Sengupta Srijani , Kloss Katherine A. , Kurnick Katie , Ewen Alana , Nwawkwo Robin , Funnell Martha , Mitchell Jamie , Jones Lennette , Piatt Gretchen
Published: November 2022

Previous literature has indicated that Black men are twice as likely to develop type 2 diabetes compared to their non-Hispanic White counterparts and are also more likely to have associated complications. Furthermore, Black men have lower access to quality health care, and masculinity norms have been shown to hinder them from seeking the limited care that is available. In this study, we aim to investigate the effect of peer-led diabetes self-management education and long-term ongoing support on glycemic management. The first phase of our study will consist of modification of existing diabetes education content to be more appropriate for the population of interest, Then, in the second phase, we will conduct a randomized controlled trial to test the intervention. Participants randomized to the intervention arm will receive diabetes self-management education, structured diabetes self-management support, and a more flexible ongoing support period. Participants randomized to the control arm will receive diabetes self-management education. Diabetes self-management education will be taught by certified diabetes care and education specialists, while the diabetes self-management support and ongoing support period will be facilitated by fellow Black men with diabetes who will be trained in group facilitation, patient-provider communication strategies, and empowerment techniques. The third phase of this study will consist of post-intervention interviews and dissemination of findings to the academic community. The primary goal of our study is to determine whether long-term peer-led support groups in conjunction with diabetes self-management education are a promising solution to improve self-management behaviors and decrease A1C levels. We will also evaluate the retention of participants throughout the study, which has historically been an issue in clinical studies focused on the Black male population. Finally, the results from this trial will determine whether we can proceed to a fully-powered R01 trial or if other modifications of the intervention are necessary.

Trial Registration

Registered atClinicalTrials.govwith an ID ofNCT05370781on May 12, 2022
Oral mTOR Inhibition Limits And Reduces Actinic Keratosis And Cutaneous Squamous Cell Carcinoma In A UVB-Induced Mouse Model
Authors: Booty MG , Komalo B , Hosny A , Headland SE , Fernandez-Figueras MT , Nguyen AM , Cousin W , Heinrich J , Nicolaisen L , DeVay RM , White B , Elabd C
Published: November 2022

Actinic keratosis (AK) is a skin disease that is characterized by clinical and subclinical cutaneous lesions in sun-exposed areas. It is a considerable burden due to its high occurrence in middle-aged and older populations, as well as its propensity to progress to invasive cutaneous squamous cell carcinoma. The mammalian target of rapamycin (mTOR) pathway is critical in carcinogenesis and tumor development, and it has been shown to be over-activated during skin tumorigenesis, particularly upon ultraviolet (UV) radiation exposure, the key risk factor for AK. However, the ability of mTOR inhibitors to treat AK is not well documented. Herein, we evaluated the effect of oral mTOR inhibitorsin vitroandin vivoand found that mTOR inhibitors lower keratinocyte cell proliferationin vitroand both clear and prevent AK and cutaneous squamous cell carcinoma (cSCC) in a UV-B induced SKH1 hairless mouse model of disease. mTOR inhibition reduced the number and size of skin lesions and the frequency of cSCC, resulting in a considerable reduction in disease severity. mTOR inhibition prevented lesion occurrence in areas of field cancerization, without affecting epidermal thickness, keratinocyte proliferationin vivo, or the presence of p53+ cells. Our findings indicate that, when appropriately dosed, oral mTOR inhibitors provide a safe home-based systemic treatment alternative with significant benefits to patients over current topical treatment options.
Machine-learning based detection of adventitious microbes in T-cell therapy cultures using long read sequencing
Authors: Strutt James P. B. , Natarajan Meenubharathi , Lee Elizabeth , Teo Denise Bei Lin , Sin Wei-Xiang , Cheung Faye Ka-Wai , Chew Marvin , Thazin Khaing , Barone Paul W. , Wolfrum Jacqueline M. , Williams Rohan B. H. , Rice Scott A. , Springs Stacy L.
Published: November 2022

Assuring that cell therapy products are safe before releasing them for use in patients is critical. Currently, compendial sterility testing for bacteria and fungi can take 7-14 days. The goal of this work was to develop a rapid untargeted approach for the sensitive detection of microbial contaminants at low abundance from low volume samples during the manufacturing process of cell therapies. We developed a long-read sequencing methodology using Oxford Nanopore Technologies MinION platform with 16S and 18S amplicon sequencing to detect USP<71> organisms and other microbial species. Reads are classified metagenomically to predict the microbial species. We used an extreme gradient boosting machine learning algorithm (XGBoost) to first assess if a sample is contaminated and second, determine whether the predicted contaminant is correctly classified or misclassified. The model was used to make a final decision on the sterility status of the input sample. An optimised experimental and bioinformatics pipeline starting from spiked species through to sequenced reads allowed for the detection of microbial samples at 10 CFU / mL using metagenomic classification. Machine learning can be coupled with long read sequencing to detect and identify sample sterility status and microbial species present in T-cell cultures, including the USP<71> organisms to 10 CFU / mL.

Importance

This research presents a novel method for rapidly and accurately detecting microbial contaminants in cell therapy products, which is essential for ensuring patient safety. Traditional testing methods are time-consuming, taking 7-14 days, while our approach can significantly reduce this time. By combining advanced long read Nanopore sequencing techniques and machine learning, we can effectively identify the presence and types of microbial contaminants at low abundance levels. This breakthrough has the potential to improve the safety and efficiency of cell therapy manufacturing, leading to better patient outcomes and a more streamlined production process.
Assessing the impact of pedigree quality on the validity of quantitative genetic parameter estimates
Authors: Mawass Walid , Milot Emmanuel
Published: November 2022

Investigating the evolutionary dynamics of complex traits in nature requires the accurate assessment of their genetic architecture. Using a quantitative genetic (QG) modeling approach (e.g., animal model), relatedness information from a pedigree combined with phenotypic measurements can be used to infer the amount of additive genetic variance in traits. However, pedigree information from natural systems is not perfect and might contain errors or be of low quality. Published sensitivity analyses revealed a limited impact of expected error rates on parameter estimates. However, natural systems will differ in many respects (e.g., mating system, data availability, pedigree structure), thus it can be inappropriate to generalize outcomes from one system to another. French-Canadian (FC) genealogies are extensive and deep-rooted (up to 9 generations in this study) making them ideal to study how the quality and properties (e.g., errors, completeness) of pedigrees affect QG estimates. We conducted simulation analyses to infer the reliability of QG estimates using FC pedigrees and how it is impacted by genealogical errors and variation in pedigree structure. Broadly, results show that pedigree size and depth are important determinants of precision but not of accuracy. While the mean genealogical entropy (based on missing links) seems to be a good indicator of accuracy. Including a shared familial component into the simulations led to on average a 46% overestimation of the additive genetic variance. This has crucial implications for evolutionary studies aiming to estimate QG parameters given that many traits of interest, such as life history, exhibit important non-genetic sources of variation.
Mutual Annotation-Based Prediction of Protein Domain Functions with Domain2GO
Authors: Ulusoy Erva , Doğan Tunca
Published: November 2022

Motivation

Identifying unknown functional properties of proteins is an important task for understanding their roles in both health and disease states. The domain composition of a protein can reveal critical information in this context, as domains are structural and functional units that dictate how the protein should act at the molecular level. The expensive and time-consuming nature of wet-lab experimental approaches prompted researchers to develop computational strategies for predicting biomolecular functions. Biological ontologies, such as the Gene Ontology (GO), which provide a standardized vocabulary of information about biological entities, are frequently employed in protein function prediction.

Results

In this study, we proposed a new method called Domain2GO that predicts associations between protein domains and GO terms, thus redefining the problem as domain function prediction, using documented protein-level GO annotations together with proteins’ domain content. To obtain reliable associations, co-annotation patterns of domains and GO terms in the same proteins are examined using statistical resampling. An ablation study was conducted to compare the predictive performance of various implementations of Domain2GO, differing from each other by the utilized statistical measure (e.g., information theory inspired similarity measures and the ones calculated by the expectation-maximization algorithm). As a use-case study, examples selected from the finalized domain-GO term mappings were evaluated for their biological relevance via a literature review. Then, we applied the proposed method to predict presently unknown protein functions by propagating domain-associated GO terms to proteins annotated with these domains. For protein function prediction performance evaluation and comparison against other methods, we employed Critical Assessment of Function Annotation 3 (CAFA3) challenge datasets. The results demonstrated the high potential of Domain2GO, particularly for predicting molecular function and biological process terms, along with advantages such as producing interpretable results and having exceptionally low computational costs. The approach presented here can be extended to other ontologies and biological entities in order to investigate unknown relationships in complex and large-scale biological data.

Availability and implementation

The source code, datasets, results, and user instructions for Domain2GO are available athttps://github.com/HUBioDataLab/Domain2GO.
Mosquito bites and stages specific antibody responses againstPlasmodium falciparumin southern Ghana
Authors: Kwapong Sebastian Shine , Asare Kwame Kumi , Kusi Kwadwo Asamoah , Pappoe Faustina , Ndam Nicaise , Tahar Rachida , Poinsignon Anne , Amoah Linda Eva
Published: November 2022

Background

The human host elicits specific immune responses after exposure to various life stages of the malaria parasite as well as components of mosquito saliva injected into the host during a mosquito bite. This study describes differences in IgG responses against antigens derived from the sporozoite (PfCSP), asexual stage parasite (PfEBA175) and the gametocyte (Pfs230) in addition to anAnopheles gambiaesalivary gland antigen (gSG6-P1) in two communities in Ghana with similar blood stage malaria parasite prevalence.

Methodology

This study used archived plasma samples collected from an earlier cross-sectional study that enrolled volunteers aged from 6 months to 70 years from Simiw, peri-urban community (N=347) and Obom, rural community (N=291). An archived thick and thin blood smear for microscopy was used for the estimation ofPlasmodiumparasite density and species and DNA extraction from blood spots andP. falciparumconfirmation was performed using PCR. This study used the stored plasma samples to determine IgG antibody levels toPlasmodium falciparumandAnophelessalivary antigens using indirect ELISA.

Results

Individuals from Simiw had significantly higher levels of IgG against mosquito gSG6-P1 (median (95%CI)) (2.590 (2.452-2.783) ng/mL) compared to those from Obom (2.119 (1.957-2.345) ng/mL), p<0.0001. Both IgG responses against Pfs230proC (p=0.0006), and PfCSP (p=0.002) were significantly lower in volunteers from Simiw compared to the participants from Obom. The seroprevalence of PfEBA-175.5R (p=0.8613), gSG6-P1 (p=0.0704), PfCSP (p=0.7798) IgG were all similar in Obom and Simiw. However, Pfs230 seroprevalence was significantly higher at Obom compared to Simiw (p=0.0006). Spearman correlation analysis showed no significant association between IgG responses against gSG6-P1, PfCSP, Pfs230proC and PfEBA-175.5R and parasite density at both Obom and Simiw (p>0.05).

Conclusion

In conclusion, malaria transmission dynamics is highly complex. The similar malaria transmission intensity identified in the two communities resulted from a different combination of vector, environmental and host factors. With one community likely having a higher prevalence of uninfected mosquitoes and the other a larger reservoir of gametocyte carriers.
Organelle-specific photoactivation and dual-isotope labeling strategy reveals phosphatidylethanolamine metabolic flux
Authors: Simon Clémence , Asaro Antonino , Feng Suihan , Riezman Howard
Published: November 2022

Phosphatidylethanolamine metabolism plays essential roles in eukaryotic cells but has not been completely resolved due to its complexity. This is because lipid species, unlike proteins or nucleic acids, cannot be easily manipulated at the single molecule level or controlled with subcellular resolution, two of the key factors toward understanding their functions. Here, we use the organelle-targeting photoactivation method to study PE metabolism in living cells with a high spatiotemporal resolution. Containing predefined PE structures, we designed probes which can be selectively introduced to the ER or mitochondria to compare their metabolic products according to their subcellular localization. We combined photo-uncaging method with dual stable isotopic labeling to track PE metabolism in living cells by mass spectrometry analysis. Our results reveal that both mitochondrial- and ER-released PE participate in phospholipid remodeling, and that PE methylation can be detectable only under particular conditions. Thus, our method provides a framework to study phospholipid metabolism at subcellular resolution.
The Ribosome Maturation Factor Rea1 utilizes nucleotide independent and ATP-hydrolysis driven Linker remodelling for the removal of ribosome assembly factors
Authors: Busselez Johan , Koenig Geraldine , Klos Torben , Sosnowski Piotr , Marechal Nils , Gizardin-Fredon Hugo , Cianferani Sarah , Dominique Carine , Henry Yves , Henras Anthony , Schmidt Helgo
Published: November 2022

The ribosome maturation factor Rea1 (or Midasin) catalyses the removal of assembly factors from large ribosomal subunit precursors to promote their export from the nucleus to the cytosol. Rea1 consists of nearly 5000 amino-acid residues and belongs to the AAA+ protein family. It consists of a ring of six AAA+ domains from which the ≈ 1700 amino-acid residue linker emerges that is subdivided into stem, middle and top domains. A flexible and unstructured D/E rich region connects the linker top to a MIDAS (metal ion dependent adhesion site) domain, which is able to bind the assembly factor substrates. Despite its key importance for ribosome maturation, the Rea1 mechanism driving assembly factor removal is still poorly understood. Here we demonstrate that the Rea1 linker is essential for assembly factor removal. It rotates and swings towards the AAA+ ring following a complex remodelling scheme involving nucleotide independent as well as nucleotide dependent steps. ATP-hydrolysis is required to engage the linker with the AAA+ ring and ultimately with the AAA+ ring docked MIDAS domain. The interaction between the linker top and the MIDAS domain allows force transmission for assembly factor removal.
Cryo-EM structure of the chain-elongating E3 ligase UBR5
Authors: Hodáková Zuzana , Grishkovskaya Irina , Brunner Hanna L. , Bolhuis Derek L. , Belačić Katarina , Schleiffer Alexander , Kotisch Harald , Brown Nicholas G. , Haselbach David
Published: November 2022

UBR5 is a nuclear E3 ligase that ubiquitinates a vast range of substrates for proteasomal degradation. This HECT E3 ligase has recently been identified as an important regulator of oncogenes, e.g., MYC, but little is known about its structure or mechanisms of substrate engagement and ubiquitination. Here, we present the cryo-EM structure of the human UBR5, revealing a building block of an antiparallel dimer which can further assemble into larger oligomers. The large helical scaffold of the dimer is decorated with numerous protein-interacting motifs for substrate engagement. Using cryo-EM processing tools, we observe the dynamic nature of the domain movements of UBR5, which allows the catalytic HECT domain to reach engaged substrates. We characterise the proteasomal nuclear import factor AKIRIN2 as an interacting protein and propose UBR5 as an efficient ubiquitin chain elongator. This preference for ubiquitinated substrates permits UBR5 to function in several different signalling pathways and cancers. Together, our data expand on the limited knowledge of the structure and function of HECT E3s.
SEPepQuant enables comprehensive protein isoform characterization in shotgun proteomics
Authors: Dou Yongchao , Yi Xinpei , Olsen Lindsey K. , Zhang Bing
Published: November 2022

Shotgun proteomics is essential for protein identification and quantification in biomedical research, but protein isoform characterization is inhibited by the extensive number of peptides shared across proteins, hindering our understanding of protein isoform regulation and their roles in normal and disease biology. We systematically assess the challenge and opportunities of shotgun proteomics-based protein isoform characterization usingin silicoand experimental data, and then present SEPepQuant, a graph theory-based approach to enable isoform characterization. Using published data from one induced pluripotent stem cell study and two human hepatocellular carcinoma studies, we demonstrate the ability of SEPepQuant in addressing the key limitations of existing methods, providing more comprehensive proteome characterization, identifying hundreds of isoform-level regulation events, and facilitating streamlined cross-study comparisons. Our analysis provides solid evidence to support a widespread role of protein isoform regulation in normal and disease processes, and SEPepQuant has broad applications to biological and translational research.
IGF2BP2 is Induced by Stress in the Heart and Mediates Dilated Cardiomyopathy
Authors: Krumbein Miriam , Oberman Froma , Cinnamon Yuval , Golomb Mordechai , May Dalit , Vainer Gilad , Belzer Vitali , Meir Karen , Fridman Irina , Haybaeck Johannes , Poelzl Gerhard , Kehat Izhak , Beeri Ronen , Kessler Sonja , Yisraeli Joel K.
Published: November 2022

The IGF2BP family of RNA binding proteins consists of three paralogs that regulate intracellular RNA localization, RNA stability, and translational control. Although IGF2BP1 and 3 are oncofetal proteins, IGF2BP2 expression is maintained in many tissues, including the heart, into adulthood. Previous studies indicated that IGF2BP2 is upregulated in cardiomyocytes during cardiac stress and remodelling and returns to normal levels in recovering hearts. These results raise the possibility that IGF2BP2 might play an adaptive role during cardiac stress and recovery. Using a conditional, inducible transgenic mouse line, we found that enhanced expression of an IGF2BP2 transgene in newborn or adult hearts leads to dilated cardiomyopathy (DCM) and death within 3-4 weeks. Downregulation of the transgene after 2 weeks, however, rescues these mice, with complete recovery by 12 weeks. Hearts overexpressing IGF2BP2 downregulate sarcomeric and mitochondrial proteins and have fragmented mitochondria and elongated, thinner sarcomeres. Consistent with these results, IGF2BP2 is upregulated in patients with DCM or after myocardial infarction. These results suggest that IGF2BP2 may be an attractive target for therapeutic intervention in DCM.