Miracle-dz/UniFAR-FTUs huggingface dataset:
Toward clinical understanding of aristolochic acid upper-tract urothelial carcinoma

A cluster of patients poisoned by herbal medicine in the 1990s revealed that aristolochic acid (AA) causes kidney failure and upper tract urothelial carcinoma (UTUC). Recent research demonstrated that this was not an isolated incident; on the contrary, AA exposure is widespread in East Asia. This editorial highlights research by Lu and colleagues that investigates clinical characteristics of AA and non-AA UTUCs from 90 patients in Beijing based on the AA mutational signature. The study also detected AA mutations in non-tumor tissue of AA exposed patients and showed that AA mutations can be detected in urine, which might form the basis for non-invasive tests for AA exposure.
Does Duration Off Respiratory Support Prior to Discharge from NICU Predict Hospital Readmission among Extremely Low Gestational Age Neonates?

Abstract Objective Our objective was to determine if the duration off respiratory support prior to discharge home from the neonatal intensive care unit (NICU) would impact hospital readmission rates among extremely low gestational age neonates (ELGAN). Study Design In this retrospective chart review, we examined readmission rates for ELGAN admitted to the Montefiore–Weiler NICU between 2013 and 2015. Results Of 140 infants born at <29 weeks' gestational age, 30 (21%) of these infants were subsequently readmitted within 90 days, primarily for respiratory complaints. Readmitted infants were born at an earlier gestational age (median = 26 weeks; interquartile range [IQR]: 24–27 weeks) compared to infants who did not require readmission (median = 27 weeks; IQR: 25-28 weeks), p = 0.03. Birth weights were smaller among infants who required readmission, 800 ± 248 g compared to 910 ± 214 g (p = 0.02). Infants with Hispanic ethnicity and those discharged during the spring season were likely to be readmitted. Duration off respiratory support prior to discharge did not predict 90-day readmission rates. Lower gestational age and birth weight were associated with higher rates of readmissions after NICU discharge. Conclusion Duration off and invasiveness of respiratory support prior to discharge did not predict risk of 90-day readmission nor did discharge during months with traditionally higher prevalence of respiratory viruses.
The Role of Mechanoperception in Plant Cell Wall Integrity Maintenance

The plant cell walls surrounding all plant cells are highly dynamic structures, which change their composition and organization in response to chemical and physical stimuli originating both in the environment and in plants themselves. They are intricately involved in all interactions between plants and their environment while also providing adaptive structural support during plant growth and development. A key mechanism contributing to these adaptive changes is the cell wall integrity (CWI) maintenance mechanism. It monitors and maintains the functional integrity of cell walls by initiating adaptive changes in cellular and cell wall metabolism. Despite its importance, both our understanding of its mode of action and knowledge regarding the molecular components that form it are limited. Intriguingly, the available evidence implicates mechanosensing in the mechanism. Here, we provide an overview of the knowledge available regarding the molecular mechanisms involved in and discuss how mechanoperception and signal transduction may contribute to plant CWI maintenance.
Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly.

Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared to bacteria and eukaryotes. Here, we use parallel high-resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large-scale latitudinal, climatic (nemoral to arctic), and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea-specific sequencing revealed that freshwater archaeal diversity could be partly explained by lake variables associated with nutrient status. Combined with deterministic co-occurrence patterns this finding suggests that ecological drift is overridden by environmental sorting, as well as other deterministic processes such as biogeographic and evolutionary history, leading to lake-specific archaeal biodiversity. Acetoclastic, hydrogenotrophic and methylotrophic methanogens as well as ammonia-oxidizing archaea were frequently detected across the lakes. Archaea-specific sequencing also revealed representatives of Woesearchaeota and other phyla of the DPANN superphylum. This study adds to our understanding of the ecological range of key archaea in freshwaters and links these taxa to hypotheses about processes governing biogeochemical cycles in lakes.
The dual role of c‐src in cell‐to‐cell transmission of α‐synuclein

Parkinson's disease (PD) is characterized by the loss of dopaminergic neurons located in the substantia nigra pars compacta and the presence of proteinaceous inclusions called Lewy bodies and Lewy neurites in numerous brain regions. Increasing evidence indicates that Lewy pathology progressively involves additional regions of the nervous system as the disease advances, and the prion‐like propagation of α‐synuclein (α‐syn) pathology promotes PD progression. Accordingly, the modulation of α‐syn transmission may be important for the development of disease‐modifying therapies in patients with PD. Here, we demonstrate that α‐syn fibrils induce c‐src activation in neurons, which depends on the FcγRIIb‐SHP‐1/‐2‐c‐src pathway and enhances signals for the uptake of α‐syn into neurons. Blockade of c‐src activation inhibits the uptake of α‐syn and the formation of Lewy body‐like inclusions. Furthermore, the blockade of c‐src activation also inhibits the release of α‐syn via activation of autophagy. The brain‐permeable c‐src inhibitor, saracatinib, efficiently reduces α‐syn propagation into neighboring regions in an in vivo model system. These results suggest a new therapeutic target against progressive PD.
The Protective Effects of 2’-Fucosyllactose Against E. Coli O157 Infection Are Mediated by the Regulation of Gut Microbiota and the Inhibition of Pathogen Adhesion

As the richest component in human milk oligosaccharides (HMOs), 2’-fucosyllactose (2’-FL) can reduce the colonization of harmful microbiota in vivo, thus lowering the risk of infection; however, the mechanism for this is still unclear. In this study, a model of Escherichia coli O157 infection in healthy adult mice was established to explore the effect of 2’-FL intervention on E. coli O157 colonization and its protective effects on mice. The results showed that 2’-FL intake reduced E. coli O157 colonization in mice intestine by more than 90% (p < 0.001), and it also reduced intestinal inflammation, increased the content of fecal short-chain fatty acids, and enhanced intestinal barrier function. These beneficial effects were attributed to the increased expression of mucins such as MUC2 (increased by more than 20%, p < 0.001), and inhibition of E. coli O157 cell adhesion (about 30% reduction, p < 0.001), and were associated with the modulation of gut microbiota composition. 2’-FL significantly increased the abundance of Akkermansia, a potential probiotic, which may represent the fundamental means by which 2’-FL enhances the expression of mucin and reduces the colonization of harmful bacteria. The current study may support the use of 2’-FL in the prevention of foodborne pathogen infections in human.
The Use of Living Mulches for Weed Management in Hot Pepper and Okra

ABSTRACT The study evaluated white clover (Trifolium rapens), red clover (T. pratencis), perennial ryegrass (Lolium pratense) and canola (Brassica napus) as living mulches for weed management in hot pepper (Capsicum annum) and okra (Abelmoschus esculentus). Perennial rye-grass and white clover provided the best weed control. Weed control was similar when living mulches were newly planted in the spring (NP) or in the previous year and overwintered (OW). In the NP treatment, weeds were suppressed similarly both in the tilled crop rows and within the mulch. Yields of okra and hot pepper were greatest in the conventional tillage (CT). Mowing of living mulches improved hot pepper yields in red clover but not okra yields.
Diel activity patterns of juvenile Atlantic salmon in rivers with summer water temperature near the temperature-dependent suppression of diurnal activity

Direct day and night underwater observations of juvenile Atlantic salmon Salmo salar during summer and autumn showed a duality in response to temperature between 7 and 11° C for young-of-the-year (YOY) Atlantic salmon. They were predominantly diurnal in early summer and nocturnal in late summer although water temperatures were similar. Post-YOY Atlantic salmon did not show a strong response to temperature as they were mostly nocturnal during the study period. It is suggested that the difference in activity patterns between YOY and post-YOY Atlantic salmon can be explained by size-dependent trade-off between growth and predation risk.
The use of ICD codes to identify IBD subtypes and phenotypes of the Montreal classification in the Swedish National Patient Register

Abstract Introduction: Whether data on International Classification of Diseases (ICD)-codes from the Swedish National Patient Register (NPR) correctly correspond to subtypes of inflammatory bowel disease (IBD) and phenotypes of the Montreal classification scheme among patients with prevalent disease is unknown. Materials and methods: We obtained information on IBD subtypes and phenotypes from the medical records of 1403 patients with known IBD who underwent biological treatment at ten Swedish hospitals and retrieved information on their IBD-associated diagnostic codes from the NPR. We used previously described algorithms to define IBD subtypes and phenotypes. Finally, we compared these register-generated subtypes and phenotypes with the corresponding information from the medical records and calculated positive predictive values (PPV) with 95% confidence intervals. Results: Among patients with clinically confirmed disease and diagnostic listings of IBD in the NPR (N = 1401), the PPV was 97 (96–99)% for Crohn’s disease, 98 (97–100)% for ulcerative colitis, and 8 (4–11)% for IBD-unclassified. The overall accuracy for age at diagnosis was 95% (when defined as A1, A2, or A3). Examining the validity of codes representing disease phenotype, the PPV was 36 (32–40)% for colonic Crohn’s disease (L2), 61 (56–65)% for non-stricturing/non-penetrating Crohn’s disease behaviour (B1) and 83 (78–87)% for perianal disease. Correspondingly, the PPV was 80 (71–89)% for proctitis (E1)/left-sided colitis (E2) in ulcerative colitis. Conclusions: Among people with known IBD, the NPR is a reliable source of data to classify most subtypes of prevalent IBD, even though misclassification commonly occurred in Crohn’s disease location and behaviour and also among IBD-unclassified patients.
Energetic relationships between field and laboratory woodchucks (Marmota monax) along a latitudinal gradient

Hibernation is a strategy for energy conservation during periods of low food availability, but has energetic costs associated with arousal and maintenance of core body temperature above ambient temperature. Animals hibernating at low ambient temperatures generally exhibit low metabolic rates and reduced body mass loss, but little is known how these energetic costs differ in a single species in varying environments and temperatures. Also, it is unknown how populations along an extreme latitudinal gradient may alter energetic costs in a common environment. We investigated three free-living populations of woodchucks (Marmota monax) along a latitudinal gradient in the United States. In addition, animals obtained from the same three field populations were studied in the laboratory under a “common garden experimental design” to determine whether trends in energetic costs would be maintained. Based on calculated metabolic rates and body mass loss, animals from the northern most latitude exhibited a significantly higher total energetic cost (mlO2/g) over the hibernation season, but a significantly lower cost per day, compared with animals from more southern latitudes. Results from laboratory animals showed similar trends to those found in the field. However, the calculated energetic costs of hibernation in the laboratory were less than the freeliving populations. Energetic cost was compared among the laboratory populations during a period when food was removed and ambient temperature was 5 °C. The southern latitude population was torpid the least amount of time and incurred the highest energetic cost. We conclude that latitude has a significant effect on the energetic costs of hibernation.
Modeling of Dough Mixing Profile Under Thermal and Nonthermal Constraint for Evaluation of Breadmaking Quality of Hard Spring Wheat Flour

ABSTRACT This research was initiated to investigate associations between flour breadmaking traits and mixing and empirical dough rheological properties under thermal stress. Thirty hard spring wheat flour samples were analyzed by a Mixolab standard procedure. Mixolab profiles were divided into six different stages, and torque measurements of individual stages were modeled by nonlinear curve fitting using a compound of two solution searching procedures, multidimensional unconstrained nonlinear minimization and genetic algorithm. Mixing patterns followed exponential equations. Dough torque patterns under heat constraint, specifically dough thermal weakening and pasting profiles, were described by a sigmoid logistic equation as a function of time. Dough stability during heating appeared important for bread loaf volume increase from significant correlations between bread loaf volume and parameters generated from models of a dough thermal weakening stage. Multivariate continuum regression was employed to calib.
Mycorrhizal and dark septate fungal associations in gingers and spiral gingers

Associations of arbuscular mycorrhizal (AM) and dark septate endophyte (DSE) fungi with 38 ginger species (Zingiberaceae) and two spiral gingers (Costaceae) were investigated. All species were mycorrhizal, and the status of 35 gingers and one spiral ginger has been investigated for the first time. The extent of AM colonization and the root length colonized by AM structures varied significantly among species. AM structures were also observed in non-root portions such as scale leaves. Arbuscular mycorrhizae were of either Arum-type or intermediate- type; AM-type is reported for the first time in 37 species. Spores of 16 morphotypes belonging to 4 genera (Glomus, Acaulospora, Scutellospora, Racocetra) were identified from the rhizosphere soil. DSE colonization was found in 22 gingers and 2 spiral gingers. Twenty-two plant species are reported as hosts of DSE fungi for the first time. The extent of total AM and DSE colonization was not correlated.
Comparison of ultrasound-guided thermal ablation and conventional thyroidectomy for benign thyroid nodules: a systematic review and meta-analysis

Abstract Objective To compare the safety and efficacy of ultrasound-guided thermal ablation and conventional thyroidectomy for benign thyroid nodules (TNs) by performing a systematic review and meta-analysis. Methods We searched PubMed, Embase, Web of Science and Cochrane Library databases for clinical trials from the date of their inception to 1 April 2019. Two investigators independently examined the trials to select qualified studies, extracted relevant information and assessed the risk of bias according to the Cochrane Collaboration checklist (Oxford, UK). The primary study outcomes were safety (hoarseness, hypothyroidism and postoperative pain) and efficacy (symptom improvement, postoperative cosmetic effects and hospitalization time). This study is registered with PROSPERO (CRD42019125643). Results Seven studies involving 1289 patients were included. The results demonstrated that the incidences of hoarseness [odds ratio (OR) 0.33, 95% confidence interval (95% CI) (0.14, 0.79)], hypothyroidism [risk difference (RD) −0.31, 95% CI (−0.34, −0.28)] and postoperative pain [OR 0.35, 95% CI (0.25, 0.49)] were lower, and the hospitalization time was shorter [standard mean difference (SMD) −4.01, 95% CI (−4.22, −3.81)], in the thermal ablation group than in the conventional thyroidectomy group, and postoperative cosmetic effects were better [relative risk (RR) ratio 1.12, 95% CI (1.01, 1.24)] (p < 0.05). For symptom improvement, the difference was not statistically significant. Conclusions This study shows that for benign TNs, ultrasound-guided thermal ablation may have potential advantages in terms of safety, cosmetic effects and shorter hospitalization time compared with conventional thyroidectomy, while symptom improvement is the same.
Emergence of simian foamy viruses in humans: facts and unanswered questions

A large proportion of viral pathogens that have emerged in humans are considered to have originated in animals. Simian viral infections of humans represent an increasing public health concern. This is well illustrated by retroviruses such as HIV-1/2 and human T-cell lymphotropic virus (HTLV)-1, which have a unique ability to cross species, adapt to a new host and spread. In this short review, we will present the currently available data on the transmission of the simian foamy retroviruses (SFVs) to humans. Indeed, recent data indicate the presence of these exogenous retroviruses, of the Spumaretrovirinae subfamily and of the Spumavirus genus, in individuals occupationally exposed to nonhuman primates (animal caretaker, veterinarian, zoo worker) and in individuals having contact with apes and monkeys, such as hunters in Central Africa. The main unanswered questions concerning the natural history of such SFVs in humans, for instance, their magnitude and geographical distribution, their interhuman transmissi.
T helper 2 inflammatory markers are associated with recurrence in chronic rhinosinusitis with nasal polyps after endoscopic sinus surgery.

BACKGROUND Despite maximum medical treatment and endoscopic sinus surgery (ESS), chronic rhinosinusitis with nasal polyps (CRSwNP) can require revision surgery. With a growing literature on the diversity of cytokine inflammation patterns in CRSwNP, an endotype-driven approach could lead to the identification of cytokine profiles that predict recurrence. METHODS A monocentric longitudinal study was carried out until June 2019 following CRSwNP patients who underwent surgery for the first time between December 2010 and January 2012. The biomarker profiles were established on blood and nasal secretions at the time of the first surgery (Interleukin (IL)-5, IgE, IgA, eosinophilic cationic protein (ECP) and eosinophilic- derived neurotoxin (EDN)). Profiles were compared between the patients still controlled by medical treatment and the patients requiring revision surgery during the course of the follow-up period. RESULTS Among the 48 patients initially enrolled in our study, 8 required revision surgery (16,7%). Clinical features (asthma, allergy, aspirin intolerance, active smoking) and levels of blood markers measured at the time of the first surgery were comparable between the 2 groups of patients. Levels of IL-5, IgE and ECP in nasal secretions were significantly increased in the group of patients needing revision surgery. CONCLUSIONS Based on simple approach of nasal secretions sampling, we showed that a predominant T helper 2 proteins expression profile can be associated with recurrent CRSwNP after ESS. Initial immunoprofiling in CRSwNP disease may contribute to better predict the therapeutic response to optimal medical and surgical treatment, and help define the role of innovative targeted treatment, beside corticosteroids and ESS.
Amphibian Population Declines in Latin America: A Synthesis 1

The loss of global amphibian biodiversity has been well documented in recent years. The greatest information from Latin America came from countries such as Costa Rica, Panama, Ecuador, and Puerto Rico. The five papers in this special section illustrate the critical status of Latin American amphibians and further demonstrate certain commonalities of amphibian population declines within the region. These studies provide a framework by which future research and management could proceed in all tropical regions.
FLAVONOIDS AND BIOLOGICAL ACTIVITIES OF CENTAUREA

Centaurea nerimaniae S. Kultur, an endemic species from the Turkish flora, distributed in south Anatolia (Icel Province) was investigated for its flavonoids and in vitro antioxidant, anti-cholinergic, anti-inflammatory and antibacterial activities. The phytochemical investigation of the plant led to the isolation of five flavonoids, identified as cirsimaritin, hispidulin, apigenin, isokaempferide and apigenin 7-O-glucoside. In addition to its ability to inhibit AChE and lipid peroxidation, induced by Fe/ascorbate system, scavenge DPPH radicals, and to reduce Fe to Fe, the extract showed strong COX-1 and COX-2 inhibitory and antimicrobial activities, suggesting that this plant could act as an antioxidant and anti-inflammatory agent against disorders, associated with oxidative damage, as well as an effective phytotherapeutic agent against some fungal and bacterial diseases.
Influence of boron in organic red clover (Trifolium pratense L.) seed production

The effect of boron (B) on flower development, nectar production, seed yield and germination in organic red clover was investigated in soils with <1 mg B kg−1. Different techniques for application of a liquid B product were studied in four field experiments in 2009–2011. The treatments were as follows: control (no B); three rates of B application to the soil at sowing; and three rates of B as foliar application in the harvest year. The effects of B application varied between the fields and included increased seed yield, seed weight of fifty inflorescences (IFs), number of florets IF−1 and nectar volume IF−1. The greatest effects on seed yield were found in treatments with low B rates. Boron application increased seed B concentration in only one experiment and had no effect on shoot B concentration. The percentage of seeds with normal germination increased with increasing seed B concentration (R2 = 0·73). Seed weight of fifty IFs and number of IFs m−2 increased with increasing shoot B concentration. Boron is therefore an important element for red clover seed production. Further knowledge on improving the B uptake of red clover plants is required to improve seed yield and quality.