Miracle-dz/UniFAR-FTUs huggingface dataset:
Seasonal variations in gut microbiota of semiprovisioned rhesus macaques (Macaca mulatta) living in a limestone forest of Guangxi, China

Assessment of gut microbiota, used to explore ecological adaptation strategies and evolutionary potential of species, provides a new viewpoint to the conservation and management of endangered animals. In this research, the gut microbiota of a group of semiprovisioned rhesus macaques (Macaca mulatta) living in a limestone forest exhibiting seasonal changes in plant items were studied to investigate the adaptation strategies of these macaques to this specific habitat. The findings revealed significant seasonal changes in the diversity and composition of the rhesus macaques’ gut microbiota, which were higher in the rainy season than in the dry season. In the rainy season, Bacteroidetes (31.83 ± 16.14% vs. 19.91 ± 18.20%) were significantly increased and Prevotella (23.70 ± 15.33% vs. 15.40 ± 16.10%), UCG-002 (4.48 ± 3.16% vs. 2.18 ± 2.01%), and UCG-005 (4.22 ± 2.90% vs. 2.03 ± 1.82%) were more enriched at the genus level. In the dry season, Firmicutes significantly increased (71.84 ± 19.28% vs. 60.91 ± 16.77%), and Clostridium_sensu_stricto_1 (8.45 ± 9.72% vs. 4.76 ± 6.64%), Enterococcus (10.17 ± 13.47% vs. 0.69 ± 2.36%), and Sarcina (4.72 ± 7.66% vs. 2.45 ± 4.71%) were more enriched at the genus level. These differences in gut microbiota may be due to seasonal variations in plant items in these habitats alongside changes in the provisioned foods from tourists. Additionally, deterministic processes predominate the assembly of the macaque’s gut microbiota community. This indicates that the animal’s high reliance on natural plants and provisioned foods increased the impact of deterministic processes. This study concludes that a balance between provisioned foods and natural plants might be vital in shaping the gut microbiota in the macaques. Furthermore, the dynamic adjustment in gut microbiota might be a physiological mechanism for the macaques in response to the seasonal variations in the ecological factors and food provision.
Immunological risk factors for sepsis-associated delirium and mortality in ICU patients

Background A major challenge in intervention of critical patients, especially sepsis-associated delirium (SAD) intervention, is the lack of predictive risk factors. As sepsis and SAD are heavily entangled with inflammatory and immunological processes, to identify the risk factors of SAD and mortality in the intensive care unit (ICU) and determine the underlying molecular mechanisms, the peripheral immune profiles of patients in the ICU were characterized. Methods This study contains a cohort of 52 critical patients who were admitted to the ICU of the First Affiliated Hospital of Jinan University. Comorbidity, including sepsis and SAD, of this cohort was diagnosed and recorded. Furthermore, peripheral blood samples were collected on days 1, 3, and 5 of admission for peripheral immune profiling with blood routine examination, flow cytometry, ELISA, RNA-seq, and qPCR. Results The patients with SAD had higher mortality during ICU admission and within 28 days of discharge. Compared with survivors, nonsurvivors had higher neutrophilic granulocyte percentage, higher CRP concentration, lower monocyte count, lower monocyte percentage, lower C3 complement level, higher CD14loCD16+ monocytes percentage, and higher levels of IL-6 and TNFα. The CD14hiCD16- monocyte percentage manifested favorable prediction values for the occurrence of SAD. Differentially expressed genes between the nonsurvival and survival groups were mainly associated with immune response and metabolism process. The longitudinal expression pattern of SLC2A1 and STIMATE were different between nonsurvivors and survivors, which were validated by qPCR. Conclusions Nonsurvival critical patients have a distinct immune profile when compared with survival patients. CD14hiCD16- monocyte prevalence and expression levels of SLC2A1 and STIMATE may be predictors of SAD and 28-day mortality in ICU patients.
Reduced serum magnesium is associated with the occurrence of diabetic macular edema in patients with diabetic retinopathy: A retrospective study

Serum magnesium levels have been reported to reflect the risk of diabetic retinopathy (DR); however, the effect of serum magnesium level on diabetic macular edema (DME) remains unclear. Here, we investigated the association between the serum magnesium levels and DME in patients with DR. Patients with DR were recruited between January 2018 and June 2021. A total of 519 such patients were included in this study. All patients underwent a standardized clinical ophthalmic examination by an experienced ophthalmologist, and an assay was conducted to determine the serum magnesium concentration. Compared with the non-DME group, the DME group had a higher proportion of insulin use and a higher level of serum ischemia-modified albumin and fasting plasma glucose. The serum magnesium and calcium levels were lower in the DME group than in the non-DME group (P < 0.05). Higher magnesium levels were negatively associated with DME after adjustment for relevant covariates. Compared with the participants in the lowest magnesium quartile, those in the fourth quartile showed a significantly lower risk of DME after adjustment [odds ratio (OR), 0.294; 95% confidence interval, 0.153–0.566; P < 0.0001]. Considering the potentially different effects of serum magnesium on the development of DME in patients with DR based on age, DR staging and insulin use, stratified analysis was performed by considering these factors. Among insulin-using patients with non-proliferative DR who were < 66 years of age, those in the third and fourth quartile of serum magnesium were less likely to develop DME than those in the lowest quartile of serum magnesium [OR (95% CI), 0.095 (0.014–0.620), 0.057 (0.011–0.305); P = 0.014, 0.001]. Overall, a higher serum magnesium level was associated with a lower risk of DME in patients with DR. Furthermore, patients with DR who used insulin were more likely to develop DME. Long-term studies on oral magnesium supplements are needed to determine whether maintaining the serum magnesium levels in a higher physiological range can reduce the risk of DME in patients with DR.
Global distribution of electrostatic electron cyclotron harmonic waves observed on THEMIS

A global, statistical analysis of electrostatic electron cyclotron harmonic (ECH) waves is performed using THEMIS wave data. Our results confirm the high occurrence of <1 mV/m ECH emissions throughout the outer magnetosphere (L > 5). The strongest (≥1 mV/m) ECH waves are enhanced during geomagnetically disturbed periods, and are mainly confined close to the magnetic equator (∣λ∣ < 3°) over the region L ≤ 10 in the night and dawn MLT sector. ECH wave intensities within 3° ≤ ∣λ∣ < 6° are generally much weaker but not negligible especially for L < ∼12 on the midnight side. Furthermore, the occurrence rates and variability of moderately intense (≥0.1 mV/m) ECH emissions suggest that ECH wave scattering could contribute to diffuse auroral precipitation in the outer (L > 8) magnetosphere where chorus emissions are statistically weak.
Computational surface partial differential equations

Surface partial differential equations model several natural phenomena; for example in uid mechanics, cell biology and material science. The domain of the equations can often have complex and changing morphology. This implies analytic techniques are unavailable, hence numerical methods are required. The aim of this thesis is to design and analyse three methods for solving different problems with surface partial differential equations at their core. First, we define a new finite element method for numerically approximating solutions of partial differential equations in a bulk region coupled to surface partial differential equations posed on the boundary of this domain. The key idea is to take a polyhedral approximation of the bulk region consisting of a union of simplices, and to use piecewise polynomial boundary faces as an approximation of the surface and solve using isoparametric finite element spaces. We study this method in the context of a model elliptic problem. The main result in this chapter is an optimal order error estimate which is confirmed in numerical experiments. Second, we use the evolving surface finite element method to solve a Cahn- Hilliard equation on an evolving surface with prescribed velocity. We start by deriving the equation using a conservation law and appropriate transport formulae and provide the necessary functional analytic setting. The finite element method relies on evolving an initial triangulation by moving the nodes according to the prescribed velocity. We go on to show a rigorous well-posedness result for the continuous equations by showing convergence, along a subsequence, of the finite element scheme. We conclude the chapter by deriving error estimates and present various numerical examples. Finally, we stray from surface finite element method to consider new unfitted finite element methods for surface partial differential equations. The idea is to use a fixed bulk triangulation and approximate the surface using a discrete approximation of the distance function. We describe and analyse two methods using a sharp interface and narrow band approximation of the surface for a Poisson equation. Error estimates are described and numerical computations indicate very good convergence and stability properties.
Kahoot, is it fun or unfun? Gamifying vocabulary learning to boost exam scores, engagement, and motivation

In language learning environments, technology is rapidly manipulated to encourage engagement, promote autonomy, and boost motivation. Many instructors have initiated to exploit online platforms and tools as a more engaging alternative to conventional activities. One of the engaging, and enjoyable games is Kahoot. The purpose of this study is to perceive the course content of Kahoot in the classroom to increase exam scores in vocabulary, and boost student engagement, and motivation. In addition, this study also explored the issues encountered by students in vocabulary learning through Kahoot. The impact of gamification on student achievement was assessed using quantitative and qualitative methods on the first-year students of the English department (N = 82). The findings revealed that incorporating Kahoot for teaching vocabulary effectively allows learners to expand a deeper understanding of vocabulary and course concepts indicated by exam scores improvement. This method also has a positive impact on student engagement as well as motivation. Furthermore, rigorous future research is needed to fully understand Kahoot’s efficacy and to improve pedagogy in the vocabulary classroom.
Outcomes of atherectomy in treating severely calcified coronary lesions in patients with reduced left ventricular ejection fraction: A systematic review and meta-analysis

Background Severely calcified coronary lesions with reduced left ventricular (LV) function result in worse outcomes. Atherectomy is used in treating such lesions when technically feasible. However, there is limited data examining the safety and efficacy of atherectomy without hemodynamic support in treating severely calcified coronary lesions in patients with reduced left ventricular ejection fraction (LVEF). Objective To evaluate the clinical outcomes of atherectomy in patient with reduced LVEF. Methods We searched PubMed, Cochrane CENTRAL Register and ClinicalTrials.gov (inception through July 21, 2021) for studies evaluating the outcomes of atherectomy in patients with severe LV dysfunction. We used random-effect model to calculate risk ratio (RR) with 95% confidence interval (CI). The endpoints were in-hospital and long term all-cause mortality, cardiac death, myocardial infarction (MI), and target vessel revascularization (TVR). Results A total of 7 studies consisting of 2,238 unique patients were included in the analysis. The median follow-up duration was 22.4 months. The risk of in-hospital all-cause mortality using atherectomy in patients with severely reduced LVEF compared to the patients with moderate reduced or preserved LVEF was [2.4vs. 0.5%; RR:5.28; 95%CI 1.65–16.84; P = 0.005], the risk of long term all-cause mortality was [21 vs. 8.8%; RR of 2.84; 95% CI 1.16–6.95; P = 0.02]. In-hospital TVR risk was 2.0 vs. 0.6% (RR: 4.15; 95% CI 4.15–15.67; P = 0.04) and long-term TVR was [6.0 vs. 9.9%; RR of 0.75; 95% CI 0.39–1.42; P = 0.37]. In-hospital MI was [7.1 vs. 5.4%; RR 1.63; 95% CI 0.91–2.93; P = 0.10], long-term MI was [7.5 vs. 5.7; RR 1.74; 95%CI 0.95–3.18; P = 0.07). Conclusion Our meta-analysis suggested that the patients with severely reduced LVEF when using atherectomy devices experienced higher risk of clinical outcomes in the terms of all-cause mortality and cardiac mortality. As we know that the patients with severely reduced LVEF are inherently at increased risk of adverse clinical outcomes, this information should be considered hypothesis generating and utilized while discussing the risks and benefits of atherectomy in such high risk patients. Future studies should focus on the comparison of outcomes of different atherectomy devices in such patients. Adjusting for the inherent mortality risk posed by left ventricular dysfunction may be a strategy while designing a study.
Duration of oral contraceptive use relates to cognitive performance and brain activation in current and past users

Previous studies indicate effects of oral contraceptive (OC) use on spatial and verbal cognition. However, a better understanding of the OC effects is still needed, including the differential effects of androgenic or anti-androgenic OC use and whether the possible impact persists beyond the OC use. We aim to investigate the associations of OC use duration with spatial and verbal cognition, differentiating between androgenic and anti-androgenic OC. Using functional magnetic resonance imaging (MRI), we scanned a group of 94 past and current OC-users in a single session. We grouped current OC users (N=53) and past OC users with a natural cycle (N=41) into androgenic and anti-androgenic user. Effects of OC use duration were observed for current use and after discontinuation. Duration of OC use was reflected only in verbal fluency performance but not navigation: The longer the current OC use, the less words were produced in the verbal fluency task. During navigation, deactivation in the caudate and postcentral gyrus was duration-dependent in current androgenic OC users. Only during the verbal fluency task, duration of previous OC use affects several brain parameters, including activation of the left putamen and connectivity between right-hemispheric language areas (i.e., right inferior frontal gyrus and right angular gyrus). The results regarding performance and brain activation point towards stronger organizational effects of OCs on verbal rather than spatial processing. Irrespective of the task, a duration-dependent connectivity between the hippocampus and various occipital areas was observed. This could suggest a shift in strategy or processing style with long-term contraceptive use during navigation/verbal fluency. The current findings suggest a key role of the progestogenic component of OCs in both tasks. The influence of OC use on verbal fluency remains even after discontinuation which further points out the importance of future studies on OC effects and their reversibility.
Prevalence of potentially inappropriate medications and association with comorbidities in older adults with diabetes in an outpatient visitation setting

Aims Potentially inappropriate medications had been found associated with adverse drug events such as falls, emergency department admissions and hospital readmissions. There is lack of information about the prevalence of potentially inappropriate medications and associated chronic conditions in older patients with diabetes in China. This study aimed to assess the prevalence of potentially inappropriate medications in older adults with diabetes in an outpatient visitation setting and the association with polypharmacy due to comorbidities. Materials and methods This was a 3-year repeated cross-sectional study which conducted in outpatient setting of 52 hospitals in Shenzhen, China, using 2019 Beers criteria. The prevalence of potentially inappropriate medications, polypharmacy and comorbidities in older adults with diabetes in an outpatient setting was expressed as percentages. Logistic models were used to investigate the association between potentially inappropriate medication exposure and age, sex, polypharmacy and comorbidities. Results Among the 28,484 older adults with diabetes in 2015, 31,757 in 2016 and 24,675 in 2017, the prevalence of potentially inappropriate medications was 43.2%, 44.88% and 42.40%, respectively. The top five potentially inappropriate medications were diuretics (20.56%), benzodiazepines (13.85%), androgens (13.18%), non-steroidal anti-inflammatory drugs (12.94%) and sulfonylureas (6.23%). After adjustment for age and polypharmacy, the probability of potentially inappropriate medication exposure was associated with chronic gastrointestinal diseases, followed by osteoarthritis and rheumatoid arthritis, chronic pulmonary disease, chronic kidney disease, tumor, dementia, chronic liver disease, hypertension, cardiovascular disease, cerebrovascular disease and hyperlipemia. Conclusion Potentially inappropriate medications were common in older patients with diabetes in an outpatient visitation setting. Higher probability of potentially inappropriate medication exposure was associated with the comorbidity chronic gastrointestinal diseases as well as osteoarthritis and rheumatoid arthritis. To ensure that iatrogenic risks remain minimal for older adults with diabetes, the clinical comorbidities should be considered.
Spatiotemporal trends of black walnut forest stocking under climate change

Basal area is a key measure of forest stocking and an important proxy of forest productivity in the face of climate change. Black walnut (Juglans nigra) is one of the most valuable timber species in North America. However, little is known about how the stocking of black walnut would change with differed bioclimatic conditions under climate change. In this study, we projected the current and future basal area of black walnut. We trained different machine learning models using more than 1.4 million tree records from 10,162 Forest Inventory and Analysis (FIA) sample plots and 42 spatially explicit bioclimate and other environmental attributes. We selected random forests (RF) as the final model to estimate the basal area of black walnut under climate change because RF had a higher coefficient of determination (R2), lower root mean square error (RMSE), and lower mean absolute error (MAE) than the other two models (XGBoost and linear regression). The most important variables to predict basal area were the mean annual temperature and precipitation, potential evapotranspiration, topology, and human footprint. Under two emission scenarios (Representative Concentration Pathway 4.5 and 8.5), the RF model projected that black walnut stocking would increase in the northern part of the current range in the USA by 2080, with a potential shift of species distribution range although uncertainty still exists due to unpredictable events, including extreme abiotic (heat, drought) and biotic (pests, disease) occurrences. Our models can be adapted to other hardwood tree species to predict tree changes in basal area based on future climate scenarios.
Strong inflammatory signatures in the neutrophils of PAMI syndrome

PSTPIP1 (proline-serine-threonine phosphatase-interactive protein 1)–associated myeloid-related proteinemia inflammatory (PAMI) syndrome is a rare autoinflammatory disease caused by heterozygous gain-of-function mutation in PSTPIP1. As one of the PSTPIP1-associated inflammatory diseases (PAIDs), neutropenia is a distinct manifestation to separate PAMI syndrome from other PAIDs. This study aimed to investigate the potential role of neutrophils and inflammatory signatures in the pathogenesis of PAMI. PAMI neutrophils displayed markedly increased production of interleukin-1β (IL-1β) and IL-18 by enzyme linked immunosorbent assay (ELISA) assay and intracellular cytokine staining. ASC speck formation and lactic dehydrogenase (LDH) release are also increased in patient neutrophils suggesting elevated pyrin inflammasome activation followed by upregulated cell death in PAMI neutrophils. RNA sequencing result showed strong inflammatory signals in both nuclear-factor kappa B (NF-κB) pathway and interferon (IFN) pathway in patient neutrophils. This study highlighted that elevated proinflammatory cytokines IL-1β and IL-18, increased pyrin inflammasome activation, and upregulation of NF-κB and IFN signaling pathways in neutrophils play important roles in pathogenicity of PAMI syndrome.
Mycobacterium avium subsp. paratuberculosis and Hashimoto’s thyroiditis: Is MAP the trigger?

Hashimoto’s thyroiditis (HT) is an autoimmune disorder of the thyroid gland that can cause hypothyroidism. As HT is a multifactorial disorder, activation of immune responses in genetically predisposed individuals exposed to some environmental factors can contribute to it. Microorganisms, as environmental factors, including Mycobacterium avium ssp. paratuberculosis (MAP) by molecular mimicry, can be important in this autoimmune disorder. This study aimed to investigate the association between MAP and HT. This case–control study included 110 participants consisting of 60 HT patients and 50 healthy controls (HCs). Blood samples were collected. Nested PCR of the IS900 gene determined the presence of MAP DNA. The enzyme-linked immunosorbent assay (ELISA) was designed to identify antibodies (Abs) against the MAP3865c epitope, which has a homologous sequence with ZnT8 in the sera. The demographic information of all participants was recorded. Anti-TG, anti-TPO, TSH, anemia, and ruminant exposure were higer in HT patients than in the HCs (p < 0.05). MAP IS900 was detected significantly more in the patients (46.6% consisting of 30, 8.3, and 8.3% in clinical, subclinical, and unknown) than in the HCs (14%). The sera showed a remarkable frequency of reactivity against MAP3865c in the patients (38.3%) in comparison to the HCs (10%) (p = 0.0001). Furthermore, a significantly higher rate of livestock contact and traditional dairy consumption was found in individuals with MAP or anti-MAP3865c Abs positive result (p < 0.05). This study suggests a possible link between MAP and HT. These findings indicated that MAP frequency was not statistically different in the severity of HT and its shift into the clinical and subclinical forms; therefore, it could be assumed that MAPs are the initiators of the process. The results imply on a possible zoonosis transmission route of MAP from livestock products to humans. Further research is needed to confirm these results in larger groups of HT patients.
Role of airway epithelial cell miRNAs in asthma

The airway epithelial cells and overlying layer of mucus are the first point of contact for particles entering the lung. The severity of environmental contributions to pulmonary disease initiation, progression, and exacerbation is largely determined by engagement with the airway epithelium. Despite the cellular cross-talk and cargo exchange in the microenvironment, epithelial cells produce miRNAs associated with the regulation of airway features in asthma. In line with this, there is evidence indicating miRNA alterations related to their multifunctional regulation of asthma features in the conducting airways. In this review, we discuss the cellular components and functions of the airway epithelium in asthma, miRNAs derived from epithelial cells in disease pathogenesis, and the cellular exchange of miRNA-bearing cargo in the airways.