Miracle-dz/UniFAR-FTUs huggingface dataset:
Strategies to investigate and mitigate collider bias in genetic and Mendelian randomisation studies of disease progression

Genetic studies of disease progression can be used to identify factors that may influence survival or prognosis, which may differ from factors which influence on disease susceptibility. Studies of disease progression feed directly into therapeutics for disease, whereas studies of incidence inform prevention strategies. However, studies of disease progression are known to be affected by collider (also known as index event) bias since the disease progression phenotype can only be observed for individuals who have the disease. This applies equally to observational and genetic studies, including genome-wide association studies and Mendelian randomization analyses. In this paper, our aim is to review several statistical methods that can be used to detect and adjust for index event bias in studies of disease progression, and how they apply to genetic and Mendelian Randomization studies using both individual and summary-level data. Methods to detect the presence of index event bias include the use of negative controls, a comparison of associations between risk factors for incidence in individuals with and without the disease, and an inspection of Miami plots. Methods to adjust for the bias include inverse probability weighting (with individual-level data), or Slope-hunter and Dudbridge index event bias adjustment (when only summary-level data are available). We also outline two approaches for sensitivity analysis. We then illustrate how three methods to minimise bias can be used in practice with two applied examples. Our first example investigates the effects of blood lipid traits on mortality from coronary heart disease, whilst our second example investigates genetic associations with breast cancer mortality.
Vocal fold injury models in rats: a literature review on techniques and methodology

This study reviewed the current literature on technical aspects regarding controlled vocal fold injuries in the rat model. Data from PubMed, Embase, and Scopus database for English language literature was collected to identify methodological steps leading to a controlled surgical injury of the rat vocal fold. Inclusion criteria: full disclosure of anesthesia protocol, positioning of the rat for surgery, vocal fold visualization method, instrumentation for vocal fold injury, vocal fold injury type. Articles with partial contribution were evaluated and separately included due to the limited number of original methodologies. 724 articles were screened, and eleven articles were included in the analysis. Anesthesia: ketamine hydrochloride and xylazine hydrochloride varied in dose from 45 mg/kg and 4.5 mg/kg to 100 mg/kg and 10 mg/kg. Visualization: The preferred method was the 1.9 mm, 25–30 degree endoscopes. The widest diameter endoscope used was 2.7 mm with a 0 or 30 degree angle of view. Instruments for lesion induction range from 18 to 31G needles, microscissors, micro forceps to potassium titanyl phosphate, and blue light lasers. Injury types: vocal fold stripping was the main injury type, followed by vocal fold scarring and charring. One article describes scaffold implantation with injury to the superior aspect of the vocal fold. Rats are good candidates for in vivo larynx and vocal folds research. A more standardized approach should be considered regarding the type of vocal fold injury to ease data comparison.
A framework to integrate innovations in invasion science for proactive management

Invasive alien species (IAS) are a rising threat to biodiversity, national security, and regional economies, with impacts in the hundreds of billions of U.S. dollars annually. Proactive or predictive approaches guided by scientific knowledge are essential to keeping pace with growing impacts of invasions under climate change. Although the rapid development of diverse technologies and approaches has produced tools with the potential to greatly accelerate invasion research and management, innovation has far outpaced implementation and coordination. Technological and methodological syntheses are urgently needed to close the growing implementation gap and facilitate interdisciplinary collaboration and synergy among evolving disciplines. A broad review is necessary to demonstrate the utility and relevance of work in diverse fields to generate actionable science for the ongoing invasion crisis. Here, we review such advances in relevant fields including remote sensing, epidemiology, big data analytics, environmental DNA (eDNA) sampling, genomics, and others, and present a generalized framework for distilling existing and emerging data into products for proactive IAS research and management. This integrated workflow provides a pathway for scientists and practitioners in diverse disciplines to contribute to applied invasion biology in a coordinated, synergistic, and scalable manner.
WIND TUNNEL INVESTIGATION AND ANALYSIS OF THE SM701 AIRFOIL

A wind tururel test was performed on a two-dimensional model of the SM701 airfoil designed for use on World Class gliders. The test covered a range of Reynolds Number conditions from one million to 2.5 million. Aerodynamic forces and moments were measured with an extemal balance. Wake-rake measurements of the two dimensional drag were also made. Flow visualization techniques provided information on transition from laminar to turbulent flow. Post stall conditions were examined for both positive and negative angles of attack. Llft, drag, and pitching moment were analyzed and comparisons made with numerical predictions. The model was designed, constructed, and the test conducted by students at Texas A&M University.
Ultrahigh-Throughput Screening of High-β-Xylosidase-Producing Penicillium piceum and Investigation of the Novel β-Xylosidase Characteristics

A droplet-based microfluidic ultrahigh-throughput screening technology has been developed for the selection of high-β-xylosidase-producing Penicillium piceum W6 from the atmospheric and room-temperature plasma-mutated library of P. piceum. β-xylosidase hyperproducers filamentous fungi, P. piceum W6, exhibited an increase in β-xylosidase activity by 7.1-fold. A novel β-D-xylosidase was purified from the extracellular proteins of P. piceum W6 and designated as PpBXL. The optimal pH and temperature of PpBXL were 4.0 and 70 °C, respectively. PpBXL had high stability an acidic pH range of 3.0–5.0 and exhibited good thermostability with a thermal denaturation half-life of 10 days at 70 °C. Moreover, PpBXL showed the bifunctional activities of α-L-arabinofuranosidase and β-xylosidase. Supplementation with low-dose PpBXL (100 μg/g substrate) improved the yields of glucose and xylose generated from delignified biomass by 36–45%. The synergism between PpBXL and lignocellulolytic enzymes enhanced delignified biomass saccharification, increased the Xyl/Ara ratio, and decreased the strength of hydrogen bonds.
TFAM loss induces nuclear actin assembly upon mDia2 malonylation to promote liver cancer metastasis

The mechanisms underlying cancer metastasis remain poorly understood. Here, we report that TFAM deficiency rapidly and stably induced spontaneous lung metastasis in mice with liver cancer. Interestingly, unexpected polymerization of nuclear actin was observed in TFAM‐knockdown HCC cells when cytoskeleton was examined. Polymerization of nuclear actin is causally linked to the high‐metastatic ability of HCC cells by modulating chromatin accessibility and coordinating the expression of genes associated with extracellular matrix remodeling, angiogenesis, and cell migration. Mechanistically, TFAM deficiency blocked the TCA cycle and increased the intracellular malonyl‐CoA levels. Malonylation of mDia2, which drives actin assembly, promotes its nuclear translocation. Importantly, inhibition of malonyl‐CoA production or nuclear actin polymerization significantly impeded the spread of HCC cells in mice. Moreover, TFAM was significantly downregulated in metastatic HCC tissues and was associated with overall survival and time to tumor recurrence of HCC patients. Taken together, our study connects mitochondria to the metastasis of human cancer via uncovered mitochondria‐to‐nucleus retrograde signaling, indicating that TFAM may serve as an effective target to block HCC metastasis.
Tanshinone IIA enhances the ovarian reserve and attenuates ovarian oxidative stress in aged mice

Abstract Background Tanshinone IIA (TSA), a major lipophilic component extracted from the roots of Salvia miltiorrhiza Bunge, has been widely used in China for its various biological activities. However, its effect on ovarian reserve in aged mice was not studied elsewhere. Objectives This study aimed to explore the effect of TSA on the ovarian reserve of aged mice as well as young mice. Forty weeks old mice (N = 40) were considered as aged group compared to 4 weeks old mice (N = 40), and these groups were subdivided into four subgroups (N = 10) to receive different doses of TSA (0, 10, 20, and 40 μg/g/day). Methods The effect of TSA was evaluated by counting follicular number by histological examination. Basal serum levels of FSH, LH, E2, and anti‐Mullerian hormone (AMH) were measured by ELISA. Moreover, the expression levels of antioxidant genes (CAT, Nrf2, GPX1), gap junction (Cx37), ERK1/2, and Smad5 family gene were examined at both mRNA (qPCR) and protein levels (western blot). Results Follicular number, level of AMH and E2, and the expression of CAT, Nrf2, and GPX1 genes increased significantly (p < 0.05) in aged mice administrated with medium (20 μg/g/day) and high (40 μg/g/day) doses of TSA, whereas FSH and LH levels were significantly low compared to low dose (10 μg/g/day) and control (0 μg/g/day) aged subgroups. However, we did not observe any effect of all doses of TSA on young mice. Conclusions Administration of TSA with medium and high doses up‐regulates the expression of antioxidative genes, reduces the oxidative injury, increases levels of AMH, and E2 levels that are relatively comparable to those in young mice, and consequently results in a healthy oocyte development.
PHYSIOLOGICAL WORKLOAD OF WORKERS EMPLOYED DURING MOTOR-MANUAL TIMBER HARVESTING IN YOUNG ALDER STANDS IN DIFFERENT SEASONS

Objectives: This study examined the physiological strain experienced by workers employed in motor-manual timber harvesting performed in winter and summer, and the applicability of heart rate indices for estimating energy expenditure. Material and Methods: The heart rates (HR) of 2 teams consisting of 2 persons working simultaneously during felling and forwarding, in both winter and summer, were measured. Heart rate at work (HRwork), resting heart rate (HRrest), relative heart rate (%HRR), ratio of working heart rate to resting heart rate, and 50% level were used to estimate the physiological workload in particular jobs. The HRindex (HRwork/HRrest) equation was used to estimate the energy expenditure (EE). Results: For all jobs, significantly higher physiological workload and energy expenditure were recorded during winter. Conclusions: The season significantly affects the physiological workload during logging operations. If there is no possibility of harvesting wood in summer, in order to limit the workload of workers during winter activity, attention should be paid to the proper organization of work and selection of workers.
Streptococcus pasteurianus‐induced valvular endocarditis and sepsis in a puerperal emperor tamarin (Saguinus imperator)

Streptococcus pasteurianus is associated with endocarditis and sepsis in humans. A puerperal emperor tamarin died, and necropsy showed a bacterial endocarditis with sepsis. DNA sequencing from the paraffinized heart tissue was compatible with S. pasteurianus. S. pasteurianus could be an important agent associated with sepsis in tamarins.
The efficacy and safety of alpelisib in breast cancer: A real-world analysis

Published trials of alpelisib + fulvestrant demonstrate efficacy and high rates of adverse effects as a first-line treatment option for metastatic breast cancer and as an option after cyclin-dependent kinase 4 and 6 inhibitors (CDK4/6i). The purpose of this analysis is to determine the real-world efficacy and safety of this regimen in heavily pretreated patients. This is a retrospective cohort analysis evaluating patients receiving alpelisib + fulvestrant for hormone receptor positive (HR+), human epidermal growth factor receptor 2 negative (HER2-) metastatic breast cancer who previously received ≤ 2 lines of therapy in the metastatic setting and those who previously received ≥ 3 lines of therapy in the metastatic setting. Adverse effects, specifically hyperglycemia, rash, and diarrhea, were reported for the entire population. Thirty-three patients were included in this analysis. Progression-free survival (PFS), overall survival, time to change in therapy, and time to discontinuation were similar in the two groups. Forty-nine percent of patients discontinued alpelisib + fulvestrant due to progression of disease, and 27% of patients discontinued treatment due to adverse effects. Hyperglycemia, rash, and diarrhea occurred at high rates: 66.7%, 45.5%, and 72.7%, respectively. All three of these adverse effects required hospitalizations and pharmacological treatment. This analysis demonstrates that the outcomes of alpelisib + fulvestrant were worse in the real-world salvage setting in HR+, HER2- metastatic breast cancer as compared to the front-line setting. The real-world tolerability of this regimen is still of great concern.
Different Alternatives to Improve Rheological and Textural Characteristics of Fermented Goat Products - A Review

The goat’s milk is one of the main milk produced and consumed, which is also used in the production of a large variety of food (milk, fermented milk, cheese and others) and non-food products (medicines and cosmetics products). In addition, goat milk represents an excellent source of food to human nutrition, which has a distinct characteristic, such as the composition and size of casein micelles’ and fat globules structure. These peculiarities in the composition and structure of goat milk are responsible for the unique flavor and texture of goat’s milk and derivatives. Furthermore, these peculiarities are responsible for the easy digestion and absorption, besides the hypoallergenic, of goat milk when compared to cow milk. However, goat milk products present a lower hardness, adhesiveness, consistency, stability, extrusion force and a greater tendency to syneresis than cow and sheep milk products. Thus, the goat dairy industry encounters some challenges in relation to the rheological and texture characteristics of goat products. In this context, the aim of this review was to overview some strategies, including the addition of traditional and functional ingredients and new technological processes, applied in fermented goat milk to improve the rheological and textural characteristics.
Ongoing rabies outbreak in dogs of unprecedented scale and human cases in Nelson Mandela Bay Municipality, South Africa, up to 13 February 2022

More than 430 cases of rabies have been confirmed in dogs in the Nelson Mandela Bay Metropolitan Municipality of South Africa since July 2021. We describe the ongoing outbreak, its geographical spread and six related human deaths that have occurred. Further investigation of the outbreak and vaccination of the dog population is required. Raising awareness among healthcare providers, the public, and among international travellers planning to visit the region, is key for action to protect human and animal health.
Use of intravascular optical coherence tomography to confirm the diagnosis of a carotid web in a patient with recurrent ipsilateral embolic strokes and evaluate the response to stenting

A Carotid web (CaW) is defined as a focal shelf-like projection of non-atheromatous, fibrous tissue along the posterior wall of the carotid bulb. CaW are rare and commonly overlooked lesions increasingly recognized as a cause of stroke in otherwise healthy patients. Intravascular imaging modalities such as intravascular ultrasound and optical coherence tomography (OCT) have been proposed as an adjunct to digital subtraction angiography for the evaluation of CaW. However, the use of OCT in CaW has yet to be described. This report investigated the utility of OCT as an adjunct imaging modality in the evaluation of CaW morphology in a young patient with recurrent ischemic strokes.
Risk Factors for Carbapenem-resistant Pseudomonas aeruginosa Infection in Children

Background: Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is rapidly emerging as a life-threatening nosocomial infection. The study aimed to identify the risk factors for CRPA infection in children, especially antimicrobials use and invasive procedures. Methods: A retrospective study was conducted in the Children’s Hospital of Chongqing Medical University, which involved a cohort of patients with PA infection from January 2016 to December 2020. Patients were assigned to a carbapenem-susceptible PA group or to a CRPA group and matched using propensity-score matching. Univariate analysis and multivariate analysis were performed to estimate the risk factors of CRPA. Results: One-thousand twenty-five patients were included in the study but 172 children were analyzed. Several factors were associated with CRPA infection according to univariate analysis (P < 0.05), such as prior treatment with some antimicrobials and invasive procedures. However, only prior exposure to carbapenems (odds ratio [OR]: 0.102; confidence interval [CI]: 0.033–0.312; P < 0.001) and bronchoscopy (OR: 0.147; CI: 0.032–0.678; P = 0.014) during time at risk, previous invasive therapy in the last year (OR: 0.353; CI: 0.159–0.780; P = 0.013), and previous use of β-lactams/β-lactamase inhibitors within the last 90 days (OR: 0.327; CI: 0.121–0.884; P = 0.03) were considered independent risk factors by multivariate analysis. Conclusions: Those who had prior exposure to carbapenems and bronchoscopy were high-risk population to develop CRPA infection. The spread of CRPA could be influenced by invasive therapy, and we need pay attention to it. Moreover, we should take restrictions in the clinical use of carbapenems into account.
Social media and Web 2.0 for knowledge sharing in product design

Abstract Working collaboratively with internal and external partners (suppliers, customers and internal stakeholders) has been at the epicentre of product design. Knowledge sharing has been well recognised in this context. However, there is limited research that has addressed the role of social media/Web 2.0 in facilitating knowledge sharing for sense- and decision-making within product design. To address this gap, this study draws on the resource-based view (RBV) of the firm and two vignettes that relate to ‘collaborative co-design’ and ‘collaborative design-to-order’. We illustrate the role of social media/Web 2.0 in building knowledge sharing capabilities for sense- and decision-making for internal and external partners during product design. Limitations and further research into the use of social media/Web 2.0 are also discussed.
Are dietary patterns becoming more processed? The effects of different dietary patterns on cognition: A review

Background: Identifying dietary patterns that promote healthy aging has become increasingly important due to changes in food processing and consumption of processed foods. Recently, the effects of these foods and unhealthy dietary patterns on cognitive function have become more widely recognized. Aim: The aim of this review is to discuss the association between various dietary patterns and cognition in older age, while also highlighting growing evidence that ultra processed food (UPF) may negatively impact healthy aging. Methods: We have performed a non-systematic literature review searches in Google Scholar electronic database with pre-defined terms relating to UPF, diet, dietary patterns, cognition and ageing. Results: The most prevalent diets in the literature include the Western, Mediterranean, Dietary Approach to Stop Hypertension (DASH), Mediterranean-DASH Intervention for Neurogenerative Delay (MIND), Japanese, Nordic, and plant-based diets. Based on the findings, higher intakes of fresh fruit and vegetables, wholegrains and oily fish are common components of dietary patterns that are positively associated with better cognitive function. In contrast, the characteristics of a Western style dietary pattern, consisting of high amounts of UPF's, are increasing in many countries even where the staple dietary pattern was identified as healthy (i.e. Japan). Conclusion: The consumption of UPF, classified by the NOVA food classification system as industrially manufactured foods containing high levels of starches, vegetable oils, sugar, emulsifiers, and foods additives, has a negative impact on the overall nutritional quality of individual diets.
Gradual domestication of root traits in the earliest maize from Tehuacán

Significance Despite their importance in supplying nutrients, root traits related to maize domestication are scarce. We used laser ablation tomography to characterize the root architecture and anatomy of 5,300-y-old maize specimens recovered from San Marcos (Tehuacán, Mexico), revealing exquisite preservation of their cellular organization. Outer cortical cells contained thick and lignified walls typical of extant maize adapted to hard soils. By contrast, the absence of seminal roots is only found in the maize ancestor, teosinte. Two genes important for seminal root development had mutations that could relate to their absence. Our results indicate that some traits related to drought adaptation were not fully present in the earliest maize from Tehuacán, providing clues to conditions prevailing during early maize cultivation.
Sequence variability of CatSper1 and TNP2 gene in indigenous and crossbred cattle in Bangladesh

Abstract CatSper1 and TNP2 genes are known to affect semen quality and fertility parameters, including sperm motility and maturation. However, studies are yet to examine the genes in indigenous and crossbred cattle in Bangladesh. Therefore, this study was conducted to determine the genetic variants of CatSper1 and TNP2 in indigenous and crossbred cattle in Bangladesh. Blood samples were collected from 130 indigenous and 70 crossbred (Holstein Friesian × indigenous) cattle. Nucleotide variation was evaluated by PCR-RFLP and sequencing. The results of the study showed that the indigenous cattle possessed only TT genotype (1.0), whereas the crossbreds possessed both TT (0.91) and CT (0.09) genotypes, which was validated by gene sequencing. Additionally, the CatSper1 was conserved in both the indigenous and crossbred cattle, suggesting good semen quality and fertility. However, the TNP2 was conserved in the indigenous breeds and mostly conserved in the crossbreds. The findings of this study reveal the diversity of CatSper1 and TNP2 genes in indigenous and crossbred cattle.