Miracle-dz/UniFAR-FTUs huggingface dataset:
Association between CDKN1A gene rs1801270 polymorphisms and susceptibility to colorectal cancser in an Iranian population

Abstract CDKN1A gene is implicated in cell differentiation, development process, repair, apoptosis, senescence, migration, and tumorigenesis. Somatic alterations and polymorphisms may interfere in the function of CDKN1A, and this could affect the individual susceptibility to colorectal cancer (CRC). Here in, we evaluated the importance of single nucleotide polymorphic variants in codon 31 of CDKN1A (rs1801270: C > A) for the development of colorectal cancer in an Iranian population. A total of 150 CRC patients and 150 healthy controls were enrolled in this study. Genomic DNA was extracted from peripheral blood specimens. Genotypes were determined using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) assay. In CRC patients, the genotype frequencies detected were 90%, 8.0% and 2.0%2 for CC, AC and AA genotypes while the genotype frequencies in control group were 78%, 20.7% and 1.35% 1.35% for CC, AC and AA genotype, respectively. There were statistically significant differences in the distribution of CDKN1A rs1801270 genotypes and allele frequencies between colorectal cancer patients and healthy controls (p value = 0.021). Also, results indicated a significant negative association between AC genotype and risk of colorectal cancer occurrence. (Odds ratio (OR)=0.357; 95% confidence interval (CI)=0.168–0.760, p = 0.007). Our data suggest that the AC genotype may have a protective role in the development of CRC in an Iranian population.
Auxin-independent effects of apical dominance induce changes in phytohormones correlated with bud outgrowth

Abstract The inhibition of shoot branching by the growing shoot tip of plants, termed apical dominance, was originally thought to be mediated by auxin. Recently, the importance of the shoot tip sink strength during apical dominance has re-emerged with recent studies highlighting roles for sugars in promoting branching. This raises many unanswered questions on the relative roles of auxin and sugars in apical dominance. Here we show that auxin depletion after decapitation is not always the initial trigger of rapid cytokinin (CK) increases in buds that are instead correlated with enhanced sugars. Auxin may also act through strigolactones (SLs) which have been shown to suppress branching after decapitation, but here we show that SLs do not have a significant effect on initial bud outgrowth after decapitation. We report here that when sucrose or CK is abundant, SLs are less inhibitory during the bud release stage compared to during later stages and that SL treatment rapidly inhibits CK accumulation in pea (Pisum sativum) axillary buds of intact plants. After initial bud release, we find an important role of gibberellin (GA) in promoting sustained bud growth downstream of auxin. We are, therefore, able to suggest a model of apical dominance that integrates auxin, sucrose, SLs, CKs, and GAs and describes differences in signalling across stages of bud release to sustained growth.
Tumor-infiltrating lymphocytes and macrophages as a significant prognostic factor in biliary tract cancer

Background The impact of tumor-infiltrating lymphocytes (TILs) and tumor-associated macrophages (TAMs) on the prognosis of biliary tract cancer (BTC) is not completely understood. Therefore, in our study, we investigated the effects of the various immune cells infiltration in tumor microenvironment (TME). Methods A total of 130 patients with BTC who underwent surgical treatment at our institution were enrolled in this study. We retrospectively evaluated TILs and TAMs with immunohistochemical staining. Results With CD8-high, CD4-high, FOXP3-high, and CD68-low in TME as one factor, we calculated Immunoscore according to the number of factors. The high Immunoscore group showed significantly superior overall survival (OS) and recurrence-free survival (RFS) than the low Immunoscore group (median OS, 60.8 vs. 26.4 months, p = 0.001; median RFS not reached vs. 17.2 months, p < 0.001). Also, high Immunoscore was an independent good prognostic factor for OS and RFS (hazards ratio 2.05 and 2.41 and p = 0.01 and p = 0.001, respectively). Conclusions High Immunoscore group had significantly superior OS and RFS and was an independent good prognostic factor for OS and RFS.
Translation Between Unrelated Languages and Cultures, as Illustrated by Japanese-English Translation

Most writing on translation is based on Indo-European languages, which are not only linguistically related but also share a similar cultural background. In an attempt to counter this eurocentric bias, we shall discuss some aspects of Japanese-English translation, focussing especially on differences in paragraph and discourse structure and on cultural factors. The aim is to demonstrate that linguistic typology and sociocultural distance need to be taken into account in translation theory and practice. We conclude that in order to avoid misunderstanding, at times the translator of unrelated languages used in different communicative frameworks may have to step beyond what is normally regarded as the role of the translator into a role approaching that of an editor. Translation between ethnolinguistically divergent systems may contribute to translation studies by highlighting problem areas that are less evident elsewhere.
Vacuum gaps in pulsar magnetospheres.

We show, by giving several explicit examples, that a charge-separated magnetosphere about a star can have vacuum voids within it. These can range from the small polar ''gaps'' discussed by Ruderman and Sutherland to being so large that the charge particles are confined to a disk or even a ring about the central object. Insofar as the pulsar problem is concerned, the possible existence of such structuring appears to remove one of the outstanding roadblocks to the construction of self-consistent models.
The Gynandropsis gynandra genome provides insights into whole-genome duplications and the evolution of C4 photosynthesis in Cleomaceae

Abstract Gynandropsis gynandra (Cleomaceae) is a cosmopolitan leafy vegetable and medicinal plant, which has also been used as a model to study C4 photosynthesis due to its evolutionary proximity to C3 Arabidopsis (Arabidopsis thaliana). Here, we present the genome sequence of G. gynandra, anchored onto 17 main pseudomolecules with a total length of 740 Mb, an N50 of 42 Mb and 30,933 well-supported gene models. The G. gynandra genome and previously released genomes of C3 relatives in the Cleomaceae and Brassicaceae make an excellent model for studying the role of genome evolution in the transition from C3 to C4 photosynthesis. Our analyses revealed that G. gynandra and its C3 relative Tarenaya hassleriana shared a whole-genome duplication event (Gg-α), then an addition of a third genome (Th-α, +1×) took place in T. hassleriana but not in G. gynandra. Analysis of syntenic copy number of C4 photosynthesis-related gene families indicates that G. gynandra generally retained more duplicated copies of these genes than C3T. hassleriana, and also that the G. gynandra C4 genes might have been under positive selection pressure. Both whole-genome and single-gene duplication were found to contribute to the expansion of the aforementioned gene families in G. gynandra. Collectively, this study enhances our understanding of the polyploidy history, gene duplication and retention, as well as their impact on the evolution of C4 photosynthesis in Cleomaceae.
Fifty years on: How we uncovered the unique bioenergetics of brown adipose tissue

Exactly 50 years ago, I was a post‐doc in the laboratory of Olov Lindberg in Stockholm measuring fatty acid oxidation by mitochondria isolated from thermogenic brown adipose tissue, when we noticed a curious nonlinearity in the respiration rate. This initiated a convoluted chain of experiments revealing that the mitochondria were textbook demonstrations of the then novel and highly controversial “chemiosmotic hypothesis” of Peter Mitchell and that thermogenesis was regulated by a proton short‐circuit, mediated by a 32 kDa “uncoupling protein,” UCP1, activated by fatty acid. This review is a personal account of the research into the bioenergetics of isolated brown adipocytes and isolated mitochondria, which led, after fifteen years of investigation, to what is still accepted as the “canonical” UCP1‐mediated mechanism of nonshivering thermogenesis, uniting whole animal physiology with mitochondrial bioenergetics.
Time and sequence of the replacement of the deciduous by the permanent dentition in dogs and its applicability for age estimation

This study investigated the influence of several covariates on the time and sequence of permanent dentition emergence following exfoliation of the deciduous teeth in puppies. The aim was to determine whether the emergence of permanent dentition can be used to assess whether a puppy that is traded across borders in the EU has reached the legally required minimum age of 15 weeks. The events were evaluated in a longitudinal study, with some cross‐sectional observations, of 440 puppies belonging to 82 breeds. No significant differences were found between the left and right sides of a puppy's dentition nor between male and female puppies. Breed size and skull type had a significant impact: both the appearance and the completion of tooth eruption occurred considerably later in small or toy breeds and brachycephalic skull type breeds. The sequence of emergence differed little between maxillary or mandibular quadrants or between breeds. The first emerging elements were the maxillary first premolars or first incisors or the mandibular first incisors. The emergence of a permanent tooth usually occurred within 3 days before or after exfoliation of its precursor, except for the canines, which demonstrated a wider tooth replacement interval. This study presents standards for age assessment based on the emergence of permanent dentition for breeds of different sizes, using median ages or cumulative emergence percentages. However, the legal age determination of puppies with an assumed age of 15 weeks cannot be performed based on permanent dentition emergence, as this occurred at a later age in a large proportion of dogs (at least 95%) in our studied population. The probability of being at least 15 weeks old when at least one maxillary tooth has emerged was at least 72.25%, depending on breed size.
Improved PML for the FDTD solution of wave-structure interaction problems

In a previous paper, an optimum perfectly matched layer has been designed for the finite-difference time-domain (FDTD) solution of wave-structure interaction problems. The present paper shows the results of subsequent investigations that were done with the intention of reducing the thickness of this optimum PML. Four improvements to the PML are presented. The resulting reductions of the thickness are discussed.
Short-Term Surgical Mission in Sub-Saharan Country, Experience of a Breast-Dedicated Team: Reviewing the Past and Stepping Toward the Last Mission

PURPOSE The present article aims to present the data of a Breast Cancer Team Short-Term Surgical Mission in Guinea-Bissau in the setting of the National Bissau Hospital, Hospital Nacional Simão Mendes, level A referral health structure. PATIENTS AND METHODS Patients with breast disease have been presented to our team for in loco consultation during the total of three missions in 1 year. We have observed a total of 97 female patients with age ranging from 12 to 70 years. We performed 21 excisional biopsies, five radical surgeries, and 28 needle biopsies. RESULTS There have been diagnosed 19 invasive breast cancer cases in stage IV, and in seven patients, the biopsy resulted in malignancy. On the recall consultation of the needle biopsied patients, just two returned and accepted the proposed treatment. Major issue has been the lack of trained pathology technicians for adequate sampling conditioning, a fact that led to a poor quality of 18 samples. CONCLUSION Access to surgical care is disparate across the world, and short-term surgical missions are often call-in action to deliver not only patient care but also local staff training. Complex disease management, such as cancer, may create several problems being conditioned by the lack of basic resources required. In Guinea-Bissau, a poor country with very few inhabitants, the need to implement an anticancer national strategy is urgent but seems feasible. Any action should prioritize local team training and enhance specialization. No external intervention can provide any long-term benefit for patients if they are detached from local health workers.
Dispersal of Magnetic Flux in the Quiet Solar Photosphere

We study the random walk of magnetic flux concentrations on two sequences of high-resolution magnetograms, observed with the Michelson Doppler Imager on board SOHO. The flux contained in the concentrations ranges from |Φ|=1018 Mx to |Φ|=1019 Mx, with an average of |Φ|=2.5×1018 Mx. Larger concentrations tend to move slower and live longer than smaller ones. On short timescales, the observed mean-square displacements are consistent with a random walk, characterized by a diffusion coefficient D(t<10 ks)=70-90 km2 s−1. On longer timescales, the diffusion coefficient increases to D(t>30 ks)=200-250 km2 s−1, approaching the measurements for a five-day set of Big Bear magnetograms, D≃250 km2 s−1. The transition between the low and large diffusion coefficients is explained with a model and simulations of the motions of test particles, subject to random displacements on both the granular and supergranular scales, simultaneously. In this model, the supergranular flow acts as a negligible drift on short timescale, but dominates the granular diffusion on longer timescales. We also investigate the possibility that concentrations are temporarily confined, as if they were caught in supergranular vertices, that form short-lived, relatively stable environments. The best agreement of model and data is found for step lengths of 0.5 and 8.5 Mm, associated evolution times of 14 minutes and 24 hr, and a confinement time of no more than a few hours. On our longest timescale, DSim(t>105)→285 km2 s−1, which is the sum of the small- and large-scale diffusion coefficients. Models of random walk diffusion on the solar surface require a larger value: DWang=600±200 km2 s−1. One possible explanation for the difference is a bias in our measurements to the longest lived, and therefore slower concentrations in our data sets. Another possibility is the presence of an additional, much larger diffusive scale.
The cost-effectiveness of exercise-based cardiac telerehabilitation intervention: a systematic review

INTRODUCTION Alternatives such as remotely delivered therapy in the home environment or telehealth represent an opportunity to increase overall cardiac rehabilitation (CR) utilization. Implementing alternatives into regular practice is the next step in development; however, the cost aspect is essential for policymakers. Limited economic budgets lead to cost-effectiveness analyses before implementation. They are appropriate in cases where there is evidence that the compared intervention provides a similar health benefit to usual care. This systematic review aimed to compare the cost-effectiveness of exercise-based telehealth CR interventions compared to standard exercise-based CR. EVIDENCE ACQUISITION PubMed and Web of Science databases were systematically searched up to August 2022 to identify randomized controlled trials assessing patients undergoing telehealth CR. The intervention was compared to standard CR protocols. The primary intent was to identify the cost-effectiveness. Interventions that met the criteria were home-based telehealth CR interventions delivered by information and communications technology (telephone, computer, internet, or videoconferencing) and included the results of an economic evaluation, comparing interventions in terms of cost-effectiveness, utility, costs and benefits, or cost-minimization analysis. The systematic review protocol was registered in the PROSPERO Registry (CRD42022322531). EVIDENCE SYNTHESIS Out of 1525 identified studies, 67 articles were assessed for eligibility, and, at the end of the screening process, 12 studies were included in the present systematic review. Most studies (92%) included in this systematic review found strong evidence that exercise-based telehealth CR is cost-effective. Compared to CBCR, there were no major differences, except for three studies evaluating a significant difference in average cost per patient and intervention costs in favor of telehealth CR. CONCLUSIONS Telehealth CR based on exercise is as cost-effective as CBCR interventions. Funding telehealth CR by third-party payers may promote patient participation to increase overall CR utilization. High-quality research is needed to identify the most cost-effective design.
Hierarchical generalised linear models: A synthesis of generalised linear models, random-effect models and structured dispersions

SUMMARY Hierarchical generalised linear models are developed as a synthesis of generalised linear models, mixed linear models and structured dispersions. We generalise the restricted maximum likelihood method for the estimation of dispersion to the wider class and show how the joint fitting of models for mean and dispersion can be expressed by two interconnected generalised linear models. The method allows models with (i) any combination of a generalised linear model distribution for the response with any conjugate distribution for the random effects, (ii) structured dispersion components, (iii) different link and variance functions for the fixed and random effects, and (iv) the use of quasilikelihoods in place of likelihoods for either or both of the mean and dispersion models. Inferences can be made by applying standard procedures, in particular those for model checking, to components of either generalised linear model. We also show by numerical studies that the new method gives an efficient estimation procedure for substantial class of models of practical importance. Likelihood-type inference is extended to this wide class of models in a unified way.
Accelerated ions ahead of earthward propagating dipolarization fronts

[1] We report on the evolving ion distributions associated with the arrival of an earthward propagating dipolarization front in the near-Earth magnetotail using Time History of Events and Macroscale Interactions during Substorms (THEMIS). Ion distributions exhibit steady duskward anisotropy well before the front arrival, suggesting thin current sheet formation at ∼11 RE, during the growth phase of a moderate geomagnetic substorm. As the dipolarization front moves closer, an additional, earthward streaming ion population appears, resulting in an earthward velocity moment. This population eventually overwhelms the preexisting duskward anisotropy and merges with the earthward convecting bulk flow once the dipolarization front arrives. Test-particle simulations show that the observed ion evolution is consistent with a picture of ions reflected and accelerated by the approaching front and moving ahead of it.
Chatbot features for anxiety and depression: A scoping review

Chatbots can provide valuable support to patients in assessing and guiding management of various health problems particularly when human resources are scarce. Chatbots can be affordable and efficient on-demand virtual assistants for mental health conditions, including anxiety and depression. We review features of chatbots available for anxiety or depression. Six bibliographic databases were searched including backward and forwards reference list checking. The initial search returned 1302 citations. Post-filtering, 42 studies remained forming the final dataset for this scoping review. Most of the studies were from conference proceedings (62%, 26/42), followed by journal articles (26%, 11/42), reports (7%, 3/42), or book chapters (5%, 2/42). About half of the reviewed chatbots had functionality targeting both anxiety and depression (60%, 25/42), whereas 38% (16/42) targeted only depression, 38% (16/42) anxiety and the remaining addressed other mental health issues along with anxiety and depression. Avatars or fictional characters were rarely used in these studies only 26% (11/42) despite their increasing popularity. Mental health chatbots could benefit in helping patients with anxiety and depression and provide valuable support to mental healthcare workers, particularly when resources are scarce. Real-time personal virtual assistance fills in this gap. Their role in mental health care is expected to increase.
How do the skin barrier and microbiome adapt to the extra‐uterine environment after birth? Implications for the clinical practice

The multiple protective functions of the skin derive from the interactions between epithelial skin and immune cells as well as the commensal microbiota. Developed in the last trimester of intra‐uterine life, the skin barrier adapts dynamically after birth. Specific differences in the structure and physiology have been disclosed between infant and adult skin. The stratum corneum of infants is thinner and structured by thicker corneocytes with a more anisotropic surface in comparison to adult skin. Lower levels of the natural moisturizing factor and its constituents, together with the increased protease activity in the epidermis result in dry baby skin and ongoing adaptation of the desquamation to the extra‐uterine environment. Infant epidermis is characterized by an accelerated proliferation rate and clinically competent permeability barrier in term neonates, despite the higher baseline values of transepidermal water loss in infants. The skin surface of newborns is less acidic, which could increase susceptibility to diaper and atopic dermatitis. Immediately after birth, skin is colonized by commensal bacteria—a process dependent on the mode of delivery and of major importance for the maturation of the immune system. Skin bacterial diversity and dysbiosis have been related to different pathology such as atopic and seborrheic dermatitis. This paper focuses on the ongoing structural, functional and biochemical adaptation of the human skin barrier after birth. We discuss the interactions on the ‘skin barrier/ microbiota/ immune system’ axis and their role in the development of competent functional integrity of the epidermal barrier.
Activation of the NLRP1 inflammasome in human keratinocytes by the dsDNA mimetic poly(dA:dT)

Significance The potential of nucleic acids as therapeutics is now well appreciated with the widespread use of mRNA and adenovirus-based vaccines for COVID-19. RNA and DNA have potent immunostimulatory activities which can be harnessed for vaccine efficacy. While AIM2 and cGAS represent important sensors of cytosolic dsDNA, additional sensors of dsDNA also exist in cells. By studying inflammasome responses in human keratinocytes in response to poly(dA:dT), a widely used dsDNA mimetic, we defined a pathway that did not involve either AIM2 or cGAS-STING. Instead, we identify the NLRP1 inflammasome as a sensor for poly(dA:dT)-induced inflammation in the skin. These studies further our understanding of sensors of poly(dA:dT), helping explain the potent immunogenicity of this vaccine adjuvant in humans.