Miracle-dz/UniFAR-FTUs huggingface dataset:
Validation and efficacy of ‘pure’ venous lymph node flap in a rat lymphoedema model

The venous lymph node flap (vLNF) is regarded as an arterialized or ‘pure’ venous flap, subject to which type of vessel provides blood supply to the flap. However, whether the vLNF drainage function is maintainable or sufficient for the treatment of lymphoedema is yet to be elucidated. In this study, the venous flow‐through lymph node flaps or ‘pure’ vLNF was investigated in a rat's tail (lymphoedema model), and the therapeutic effect was analysed to clarify its potential value for the treatment of lymphoedema. The subjects (rats) were divided into three groups, the experimental group (‘pure’ vLNF group), the control group (lymphoedema group), and the baseline group. The tail circumference and diameter were recorded for 5 weeks after the operation. Five weeks after surgery, the lymphatic drainage function was evaluated using indocyanine green (ICG) lymphography, while the skin thickness and collagen layer were assessed by histological analysis. The average diameter and circumference of the experimental group were significantly shorter than the control group (p < 0.01). When comparing ICG lymphography within the three groups, the baseline group showed that the ICG entered the inguinal lymph node and appeared in the liver while the ICG still accumulated in the oedematous tail with no fluorescence emerging in other parts of the rat's body, in the control group. In the experimental group, the ICG entered the vLNF via the flap junction with the rat's tail and fluorescence emerging in the rat's liver. When comparing the three groups above with the control group, the experimental group's skin and collagen layer thickness were significantly improved (p < 0.01). Lymphatic recanalization was shown to appear between ‘pure’ vLNF and the recipient area. Moreover, vLNF was shown to drain lymph fluid via the venous system, thus relieved swelling and fibrosis of the lymphoedematous tissue. Consequently, this could represent a new potential surgical approach for the treatment of lymphoedema.
Microbial necromass in cropland soils: A global meta‐analysis of management effects

Microbial necromass is a large and persistent component of soil organic carbon (SOC), especially under croplands. The effects of cropland management on microbial necromass accumulation and its contribution to SOC have been measured in individual studies but have not yet been summarized on the global scale. We conducted a meta‐analysis of 481‐paired measurements from cropland soils to examine the management effects on microbial necromass and identify the optimal conditions for its accumulation. Nitrogen fertilization increased total microbial necromass C by 12%, cover crops by 14%, no or reduced tillage (NT/RT) by 20%, manure by 21%, and straw amendment by 21%. Microbial necromass accumulation was independent of biochar addition. NT/RT and straw amendment increased fungal necromass and its contribution to SOC more than bacterial necromass. Manure increased bacterial necromass higher than fungal, leading to decreased ratio of fungal‐to‐bacterial necromass. Greater microbial necromass increases after straw amendments were common under semi‐arid and in cool climates in soils with pH <8, and were proportional to the amount of straw input. In contrast, NT/RT increased microbial necromass mainly under warm and humid climates. Manure application increased microbial necromass irrespective of soil properties and climate. Management effects were especially strong when applied during medium (3–10 years) to long (10+ years) periods to soils with larger initial SOC contents, but were absent in sandy soils. Close positive links between microbial biomass, necromass and SOC indicate the important role of stabilized microbial products for C accrual. Microbial necromass contribution to SOC increment (accumulation efficiency) under NT/RT, cover crops, manure and straw amendment ranged from 45% to 52%, which was 9%–16% larger than under N fertilization. In summary, long‐term cropland management increases SOC by enhancing microbial necromass accumulation, and optimizing microbial necromass accumulation and its contribution to SOC sequestration requires site‐specific management.
In silico analysis of substitution mutations in the β-globin gene in Turkish population of β-thalassemia

Abstract Beta-thalassemia is a genetic blood disorder represented by anomalies in hemoglobin’s beta chain production. Most hemoglobin defects are a result of mutations of the structural β-globin gene. Many diseases, including β-thalassemia, benefit from computational studies that aid researchers in investigating the association of genotype and phenotype. In this study, the alanine substitution mutations of the β-globin protein sub-units in the Turkish population (Hb Ankara, Hb Siirt and Hb Izmir) and the effects of those mutations on the β-globin protein structure and performance are examined using molecular dynamics simulation. While Hb Ankara variant showed a non-conservative mutation, Hb Siirt and Hb Izmir showed a semi-conservative mutation. RMSF values of Hb Siirt, between residues 95 and 99, were higher than wild-type and the other mutant proteins. The residues of Hb Ankara showed lower fluctuation compared to the other structures. The mean ROG values were 1.47 nm, 1.46 nm, 1.49 nm and 1.48 and the average number of the hydrogen bonds were 92, 100, 99, and 89 for Hb Ankara, Hb Siirt and Hb Izmir, respectively. Moreover, a significant increase in overall motion in Hb Siirt was observed based on PCA analysis. Hb Siirt substitution mutation might cause an effect in β-globin proteins which could impact the protein function. This indicates a major role on beta globin subunit’s stability for alanine on 27th position. However, Hb Ankara and Hb Izmir variants may act as a silent mutation, since these two mutations did not show a large change in the dynamics of the protein. Communicated by Ramaswamy H. Sarma
Radial Basis Functions: Theory and Implementations: Preface

Preface 1. Introduction 2. Summary of methods and applications 3. General methods for approximation and interpolation 4. Radial basis function approximation on infinite grids 5. Radial basis functions on scattered data 6. Radial basis functions with compact support 7. Implementations 8. Least squares methods 9. Wavelet methods with radial basis functions 10. Further results and open problems Appendix Bibliography Index.
Expressive Power and Data Complexity of Nonrecursive Logic Programming

We characterize the expressiveness and data complexity of nonrecursive logic programming. Our main results show that nonrecursive logic programming has the same expressive power as nonrecursive Datalog with negation (under a natural representation of inputs). Thus, the use of recursive data structures, namely trees, in nonrecursive Datalog: gives no gain in the expressive power. It also follows from our results that nonrecursive logic programming, like nonrecursive Datalog:, has polynomial data complexity. This contrasts with a huge di erence between these query languages in the program complexity. y Copyright c Evgeny Dantsin and Andrei Voronkov, 1998. This technical report and other technical reports in this series can be obtained at http://www.csd. uu.se/papers/reports.html or at ftp://ftp.csd. uu.se/pub/papers/reports. Some reports can be updated, check one of these addresses for the latest version. yEvgeny Dantsin is partially supported by grants from TFR, INTAS and RFBR. Andrei Voronkov is partially supported by TFR grants. Evgeny Dantsin and Andrei Voronkov. Expressive power and data complexity 1
OnabotulinumtoxinA effects on trigeminal nociceptors

Background OnabotulinumtoxinA (onabotA) is approved globally for prevention of chronic migraine; however, the classical mechanism of action of onabotA in motor and autonomic neurons cannot fully explain the effectiveness of onabotulinumtoxinA in this sensory neurological disease. We sought to explore the direct effects of onabotulinumtoxinA on mouse trigeminal ganglion sensory neurons using an inflammatory soup-based model of sensitization. Methods Primary cultured trigeminal ganglion neurons were pre-treated with inflammatory soup, then treated with onabotulinumtoxinA (2.75 pM). Treated neurons were used to examine transient receptor potential vanilloid subtype 1 and transient receptor potential ankyrin 1 cell-surface expression, calcium influx, and neuropeptide release. Results We found that onabotulinumtoxinA cleaved synaptosomal-associated protein-25 kDa in cultured trigeminal ganglion neurons; synaptosomal-associated protein-25 kDa cleavage was enhanced by inflammatory soup pre-treatment, suggesting greater uptake of toxin under sensitized conditions. OnabotulinumtoxinA also prevented inflammatory soup-mediated increases in TRPV1 and TRPA1 cell-surface expression, without significantly altering TRPV1 or TRPA1 protein expression in unsensitized conditions. We observed similar inhibitory effects of onabotulinumtoxinA on TRP-mediated calcium influx and TRPV1- and TRPA1-mediated release of calcitonin gene-related peptide and prostaglandin 2 under sensitized, but not unsensitized control, conditions. Conclusions Our data deepen the understanding of the sensory mechanism of action of onabotulinumtoxinA and support the notion that, once endocytosed, the cytosolic light chain of onabotulinumtoxinA cleaves synaptosomal-associated protein-25 kDa to prevent soluble N-ethylmaleimide-sensitive factor attachment protein receptor-mediated processes more generally in motor, autonomic, and sensory neurons.
Inhibition of antiapoptotic BCL-2 proteins with ABT-263 induces fibroblast apoptosis, reversing persistent pulmonary fibrosis

Patients with progressive fibrosing interstitial lung diseases (PF-ILDs) carry a poor prognosis and have limited therapeutic options. A hallmark feature is fibroblast resistance to apoptosis, leading to their persistence, accumulation, and excessive deposition of extracellular matrix. A complex balance of the B cell lymphoma 2 (BCL-2) protein family controlling the intrinsic pathway of apoptosis and fibroblast reliance on antiapoptotic proteins has been hypothesized to contribute to this resistant phenotype. Examination of lung tissue from patients with PF-ILD (idiopathic pulmonary fibrosis and silicosis) and mice with PF-ILD (repetitive bleomycin and silicosis) showed increased expression of antiapoptotic BCL-2 family members in α–smooth muscle actin–positive fibroblasts, suggesting that fibroblasts from fibrotic lungs may exhibit increased susceptibility to inhibition of antiapoptotic BCL-2 family members BCL-2, BCL-XL, and BCL-W with the BH3 mimetic ABT-263. We used 2 murine models of PF-ILD to test the efficacy of ABT-263 in reversing established persistent pulmonary fibrosis. Treatment with ABT-263 induced fibroblast apoptosis, decreased fibroblast numbers, and reduced lung collagen levels, radiographic disease, and histologically evident fibrosis. Our studies provide insight into how fibroblasts gain resistance to apoptosis and become sensitive to the therapeutic inhibition of antiapoptotic proteins. By targeting profibrotic fibroblasts, ABT-263 offers a promising therapeutic option for PF-ILDs.
Testing demand homogeneity when error terms have an elliptically symmetric distribution

In this article, we show that the exact test for the homogeneity restriction developed by Laitinen (1978) is robust when the error terms have an elliptically symmetric distribution. The power performance of the test is also examined, assuming that the error terms have a multivariate t distribution. Our empirical example shows that the homogeneity restriction is not rejected at the 5% level by the exact test though it is rejected by the asymptotic Wald test.
Bacterial communities of Antarctic lichens explored by gDNA and cDNA 16S rRNA gene amplicon sequencing

Abstract Recently, lichens came once more into the scientific spotlight due to their unique relations with prokaryotes. Several temperate region lichen species have been thoroughly explored in this regard yet, the information on Antarctic lichens and their associated bacteriobiomes is somewhat lacking. In this paper, we assessed the phylogenetic structure of the whole and active fractions of bacterial communities housed by Antarctic lichens growing in different environmental conditions by targeted 16S rRNA gene amplicon sequencing. Bacterial communities associated with lichens procured from a nitrogen enriched site were very distinct from the communities isolated from lichens of a nitrogen depleted site. The former were characterized by substantial contributions of Bacteroidetes phylum members and the elusive Armatimonadetes. At the nutrient-poor site the lichen-associated bacteriobiome structure was unique for each lichen species, with chlorolichens being occupied largely by Proteobacteria. Lichen species with a pronounced discrepancy in diversity between the whole and active fractions of their bacterial communities had the widest ecological amplitude, hinting that the nonactive part of the community is a reservoir of latent stress coping mechanisms. This is the first investigation to make use of targeted metatranscriptomics to infer the bacterial biodiversity in Antarctic lichens.
Artiﬁcial Intelligence and Machine Learning Approaches to Facilitate Therapeutic Drug Management and Model-Informed Precision Dosing

Background: Therapeutic drug monitoring (TDM) and model-informed precision dosing (MIPD) have greatly bene ﬁ tted from computational and mathematical advances over the past 60 years. Furthermore, the use of arti ﬁ cial intelligence (AI) and machine learning (ML) approaches for supporting clinical research and support is increasing. However, AI and ML applications for precision dosing have been evaluated only recently. Given the capability of ML to handle multidimensional data, such as from electronic health records, opportunities for AI and ML applications to facilitate TDM and MIPD may be advantageous. Methods: This review summarizes relevant AI and ML approaches to support TDM and MIPD, with a speci ﬁ c focus on recent applications. The opportunities and challenges associated with this integration are also discussed. Results: Various AI and ML applications have been evaluated for precision dosing, including those related to concentration or exposure prediction, dose optimization, population pharmacokinetics and pharmacodynamics, quantitative systems pharmacology, and MIPD system development and support. These applications provide an opportunity for ML and pharmacometrics to operate in an integrated manner to provide clinical decision support for precision dosing. Conclusions: Although the integration of AI with precision dosing is still in its early stages and is evolving, AI and ML have the potential to work harmoniously and synergistically with pharmaco-metric approaches to support TDM and MIPD. Because data are increasingly shared between institutions and clinical networks and aggregated into large databases, these applications will continue to grow. The successful implementation of these approaches will depend on cross-ﬁ eld collaborations among clinicians and experts in informatics
On the boundary integral method for the rebounding bubble

The formation of a toroidal bubble towards the end of the bubble collapse stage in the neighbourhood of a solid boundary has been successfully studied using the boundary integral method. The further evolution (rebound) of the toroidal bubble is considered with the loss of system energy taken into account. The energy loss is incorporated into a mathematical model by a discontinuous jump in the potential energy at the minimum volume during the short collapse–rebound period accompanying wave emission. This implementation is first tested with the spherically oscillating bubble system using the theoretical Rayleigh–Plesset equation. Excellent agreement with experimental data for the bubble radius evolution up to three oscillation periods is obtained. Secondly, the incorporation of energy loss is tested with the motion of an oscillating bubble system in the neighbourhood of a rigid boundary, in an axisymmetric geometry, using a boundary integral method. Example calculations are presented to demonstrate the possibility of capturing the peculiar entity of a counterjet, which has been reported only in recent experimental studies.
Fungal bioaerosols as an occupational hazard

Purpose of review Over the past 40 years, the circumstances where fungal bioaerosols are major issues have shifted because of changes in the industrial sector from mainly agriculture to operations, including composting, cannabis production and forestry in hot humid conditions. Changes in the design and operation of nonindustrial workplaces meant that mould and dampness became major issues that are just being reduced. This review attempts to frame that history offers a perspective on the current thinking on mechanisms and provide potentially useful sources of information for physicians and their patients. Recent findings The major impact of fungal exposures is not only from their allergens but also from an array of Danger-Associated Molecular Pattern molecules, possibly the most important of which is the type of glucan found in moulds that grow in damp buildings, wood chips and crops, that is beta 1, 3 D glucan in triple helical form. Located in lung epithelia, the dectin receptor is exquisitely sensitive to this compound. Except in some agricultural workplaces, low molecular weight secondary metabolites often mischaracterized as mycotoxins play little, if any, role on population health. Summary There has been a convergence in thinking between the allergy and industrial hygiene communities as well as government agencies on mould and occupational health. This has led to some useful strategies for better managing these issues as well as increasing consumer awareness.
Uniqueness of Maximum Likelihood Estimators for a Backup System in a Condition-Based Maintenance

A parameter estimation problem for a backup system in a condition-based maintenance is considered. We model a backup system by a hidden, three-state continuous time Markov process. Data are obtained through condition monitoring at discrete time points. Maximum likelihood estimates of the model parameters are obtained using the EM algorithm. We establish conditions under which there is no more than one limitation in the parameter space for any sequence derived by the EM algorithm.
Establishment of reference intervals for hematological parameters of adult population in the western region of Saudi Arabia

Background Most of hematology laboratories in Saudi Arabia utilize the reference intervals (RIs) provided by instrument manufacturers. This study aimed to define RIs of hematological parameters for adult population in the western region of Saudi Arabia and to explore their specific features from an international perspective. Method This study was conducted according to the harmonized protocol of IFCC Committee on RIs and Decision Limits. Blood samples collected from 409 healthy Saudi males and females adults were analyzed for complete blood count (CBC) by using Cell-Dyn Sapphire analyzer and for iron profile by using Architect analyzers. The needs for RIs partitioned by sex and age was based on standard deviation ratio (SDR) and/or bias ratio (BR). RIs were derived parametrically with/without application of the latent abnormal values exclusion method (LAVE). Results Based on thresholds of SDR≥0.4 and/or BR≥0.57, RIs were partitioned by sex for red-blood cell count, hemoglobin, hematocrit, red cell distribution width, erythrocyte sedimentation rate, iron, transferrin, ferritin, eosinophil, platelet, plateletcrit, etc. Partitioning by age was not necessary for any of the analytes. LAVE procedure caused appreciable changes in RI limits for most erythrocyte and iron parameters but not for leukocyte parameters. Comparable to other non-IFCC studies on CBC RIs, the RBC and hematocrit (Ht) ranges have shifted to a higher side in both genders. After applying the LAVE method, the male and female RIs for Hb were 4.56 to 6.22 ×106/μL and 3.94 to 5.25 ×106/μL respectively while RIs for Ht were 40.2 to 52.0% and 33.6 to 44.5% respectively. Conclusion LAVE method contributed to reducing the influence of latent anemia in deriving RIs for erythrocyte related parameters. Using the up-to-date methods, the RIs of CBC determined specifically for Saudis will help to improve the interpretation of test results in medical decision making.
Epidemiology of herpes simplex virus type 1 and genital herpes in Australia and New Zealand: systematic review, meta-analyses and meta-regressions

Abstract Herpes simplex virus type 1 (HSV-1) infection is a lifelong infection that is acquired primarily orally and during childhood. We aimed to characterise HSV-1 epidemiology in Australia and New Zealand. HSV-1-related data as recent as 6 December 2021 were systematically reviewed, synthesised and reported, following PRISMA guidelines. Pooled mean seroprevalence and proportions of HSV-1 detection in genital ulcer disease (GUD) and in genital herpes were calculated using random-effects meta-analyses. Meta-regressions were also conducted. HSV-1 measures were retrieved from 21 eligible publications. Extracted HSV-1 measures included 13 overall seroprevalence measures (27 stratified) in Australia, four overall proportions of HSV-1 detection in clinically diagnosed GUD (four stratified) in Australia, and ten overall proportions of HSV-1 detection in laboratory-confirmed genital herpes (26 stratified) in Australia and New Zealand. Pooled mean seroprevalence among healthy adults in Australia was 84.8% (95% confidence interval (CI) 74.3–93.1%). Pooled mean seroprevalence was 70.2% (95% CI 47.4–88.7%) among individuals <35 years of age and 86.9% (95% CI 79.3–93.0%) among individuals ≥35 years. Seroprevalence increased by 1.05-fold (95% CI 1.01–1.10) per year. Pooled mean proportion of HSV-1 detection in GUD was 8.2% (95% CI 0.4–22.9%). Pooled mean proportion of HSV-1 detection in genital herpes was 30.5% (95% CI 23.3–38.3%), and was highest in young individuals. Proportion of HSV-1 detection in genital herpes increased by 1.04-fold (95% CI 1.00–1.08) per year. Included studies showed heterogeneity, but 30% of the heterogeneity in seroprevalence and 42% of the heterogeneity in proportion of HSV-1 detection in genital herpes were explained in terms of epidemiological factors. HSV-1 seroprevalence is higher in Australia than in other Western countries. HSV-1 epidemiology in Australia and New Zealand appears to be transitioning towards less oral acquisition in childhood, but more genital acquisition among youth.