Miracle-dz/UniFAR-FTUs huggingface dataset:
Factors influencing recurrence of stage I–III rectal cancer in regional Australia

As treatments for rectal cancer improve with developments in surgical techniques, radiotherapy and chemotherapy, the nature of recurrences are evolving. We used a comprehensive database of a large Australian population with stage I–III rectal adenocarcinoma to identify timing and prognostic significance of recurrences, and factors associated with risk of developing recurrent disease.
Neohesperidin attenuates obesity by altering the composition of the gut microbiota in high‐fat diet‐fed mice

Obesity and related metabolic disorders are associated with intestinal microbiota dysbiosis, disrupted intestinal barrier, and chronic inflammation. Neohesperidin (Neo), a natural polyphenol abundant in citrus fruits, is known for its preventative and therapeutic effects on numerous diseases. Here, we report that Neo administration attenuates weight gain, low‐grade inflammation, and insulin resistance in mice fed high‐fat diet (HFD). Also, Neo administration substantially restores gut barrier damage, metabolic endotoxemia, and systemic inflammation. Sequencing of 16S rRNA genes in fecal samples revealed that Neo administration reverses HFD‐induced intestinal microbiota dysbiosis: an increase in the diversity of gut microbiota and alteration in the composition of intestinal microbiota (particularly in the relative abundances of Bacteroidetes and Firmicutes). Furthermore, systemic antibiotic treatment abolishes the beneficial effects of Neo in body weight control, suggesting that the effect of Neo on obesity attenuation largely depends on the gut microbiota. More importantly, we demonstrate that the impact of Neo on the regulation of obesity could be transferred from Neo‐treated mice to HFD‐fed mice via fecal microbiota transplantation. Collectively, our data highlight the efficacy of Neo as a prebiotic agent for attenuating obesity, implying a potential mechanism for gut microbiota mediated the beneficial effect of Neo.
Periodontal Disease, Tooth Loss, and Risk of Serrated Polyps and Conventional Adenomas

Growing data indicate an association between periodontal disease and the development of cancer. However, the evidence for colorectal cancer has been inconsistent and longitudinal study examining its precursor lesions is lacking. We prospectively collected information on periodontal disease and number of tooth loss in the Nurses' Health Study (1992–2002) and the Health Professionals Follow-up Study (1992–2010). Polyp diagnosis was acquired via self-reported questionnaires and confirmed through review of medical records. We used logistic regression to calculate the multivariate-adjusted ORs and 95% confidence intervals (CI) with adjustment for smoking and other known risk factors for periodontal disease and colorectal cancer. In this study, we included 17,904 women and 24,582 men. We documented 2,336 cases of serrated polyps and 4,102 cases of conventional adenomas among 84,714 person-endoscopies throughout follow-up. The ORs of serrated polyps and conventional adenomas comparing individuals with and without periodontal disease were 1.17 (95% CI, 1.06–1.29) and 1.11 (95% CI, 1.02–1.19), respectively. Compared with participants without tooth loss, those who lost ≥4 teeth had 20% (OR, 1.20; 95% CI, 1.03–1.39) greater risk of serrated polyps (Ptrend 0.01). Among never smokers, similar associations with periodontal disease were observed for both serrated polyps (OR, 1.20; 95% CI, 1.02–1.41) and conventional adenomas (OR, 1.12; 95% CI, 1.00–1.26). History of periodontal disease and possibly higher number of tooth loss may modestly increase the risk of developing colorectal precursor lesions. Our findings advance our understanding of the interplay between oral health, microbiome, and early colorectal carcinogenesis.
Survival of Newcastle disease virus (NDV) strain V 4 - UPM coated on three grains offal and exposed to room temperature

Newcastle disease virus (NDV) strain V4-UPM was investigated for its viability when coated on different grains offal following exposure to room temperature (RT) (21-27°C) for 8 weeks and using residual infectivity titration at weekly intervals in chick embryos as a measure of viability. The grains (maize, sorghum and millet) used for the study were processed to produce the offal which was dried in the sun before and at RT under a gentle air current after coating with virus. The time duration taken for the infectivity of the virus to drop below the minimum immunizing dose (MID) (log10 EID50/g≥ 6.0) was compared for virus suspensions containing additive (2% gelatin) and without additive. Results showed that the virus coated onto the carrier foods offal without additive remained stable at  MID value for 3 weeks (millet), 3.5 weeks (sorghum) and 5 weeks (maize) and with additive for 5.2 weeks (sorghum), 5 weeks (millet) and 6 weeks (maize) at RT. Thus, V4-UPM was found in this study to be stable even without additive for a minimum of 3 weeks on one of the grains offal, a reasonable time for the food vaccine to reach remote areas of most villages. It is concluded that the waste byproducts of any of these foods could be suitable as carriers for food-based vaccination of rural chickens in Nigeria.
Surveillance of HIV-1 transmitted integrase strand transfer inhibitor resistance in the UK

Abstract Background HIV treatment guidelines have traditionally recommended that all HIV-positive individuals are tested for evidence of drug resistance prior to starting ART. Testing for resistance to reverse transcriptase inhibitors and PIs is well established in routine care. However, testing for integrase strand transfer inhibitor (InSTI) resistance is less consistent. Objectives To inform treatment guidelines by determining the prevalence of InSTI resistance in a national cohort of recently infected individuals. Patients and methods Recent (within 4 months) HIV-1 infections were identified using a Recent Infection Testing Algorithm of new HIV-1 diagnoses in the UK. Resistance-associated mutations (RAMs) in integrase, protease and reverse transcriptase were detected by ultradeep sequencing, which allows for the sensitive estimation of the frequency of each resistant variant in a sample. Results The analysis included 655 randomly selected individuals (median age = 33 years, 95% male, 83% MSM, 78% white) sampled in the period 2014 to 2016 and determined to have a recent infection. These comprised 320, 138 and 197 samples from 2014, 2015 and 2016, respectively. None of the samples had major InSTI RAMs occurring at high variant frequency (≥20%). A subset (25/640, 3.9%) had major InSTI RAMs occurring only as low-frequency variants (2%–20%). In contrast, 47/588 (8.0%) had major reverse transcriptase inhibitor and PI RAMs at high frequency. Conclusions Between 2014 and 2016, major InSTI RAMs were uncommon in adults with recent HIV-1 infection, only occurring as low-frequency variants of doubtful clinical significance. Continued surveillance of newly diagnosed patients for evidence of transmitted InSTI resistance is recommended to inform clinical practice.
Accuracy of a neural net classification of closely-related species of microfossils from a sparse dataset of unedited images

Identification of biologic objects in images is a major source of biodiversity data. Currently this is done by scarce taxonomic experts and data is thus limited in scope and reproducibility. Automated identification in fields such as plankton research or micropaleontology, where enormous numbers of objects are available, would significantly improve data quantity and quality, particularly in applied studies of environmental and climate change. We describe a machine learning workflow based on the MobileNet convolutional network. The software can identify closely related species of radiolarians, a morphologically challenging group of microfossils, and from complete species populations (not only ideal specimens) as they are normally identified in standard transmitted light microscope preparations. Multiple, partial focus, depth of field limited images were obtained for each fossil specimen from multiple radiolarian microslides. Images were normalized and in one test also cropped to remove most systematic slide-linked image biases (e. g. type of background particles) that could be used by a classifier as non-taxonomic clues to species assignment. An average of 60 specimens per species for 16 species in two distinct clusters of closely related forms (9 species in the Antarctissa group and 7 species in the genus Cycladophora) were used to train and test the system. An overall average classification accuracy of ca 73% was achieved, and for some species >85%. Using a cutoff for specimens with classifier-calculated low certainty values boosts overall accuracy close to 90%, but at the cost of ca 1/3 reduction in identifiable specimens. This latter accuracy is close to the reproducibility of human experts, albeit with more unidentifiable specimens. The most important constraint to broader use is the time and effort needed by taxonomic experts to collect and label images to be used in training, as many species in these diverse biotas are rare, and the numbers of taxonomic experts available are very limited.
Characterisation of Porcine Peroxisome Proliferator-Activated Receptors γ1 and γ2: Detection of Breed and Age Differences in Gene Expression

Abstract Two isoforms of peroxisome proliferator-activated receptor gamma (PPARγ) cDNAs, γ1 and γ2, have been isolated and characterised in swine. The relative expression of the two transcripts was studied by northern blot analysis using total RNA isolated from several porcine tissues taken at three different ages (day 1, after 5 weeks and at 100 kg weight). Hybridisation were carried out with two different probes, one binding to both PPARγ transcripts and the other being PPARγ2 specific. Strongest hybridisation signals with the PPARγ probe binding both variants were detected in adipose tissues and spleen at all three ages, whereas only faint or no signals were detected in other tissues. The tissue distribution pattern of PPARγ1 and γ2 suggests a modulation of tissue distribution for the two transcripts and obvious age and breed differences in gene expression in swine.
Temporomandibular disorders in Venezuelan and Italian adolescents

ABSTRACT Objective The aim of this research was to compare the prevalence of temporomandibular disorders (TMDs) among Venezuelan and Italian adolescents. Methods One hundred-seventeen Venezuelan and 138 Italian adolescents aged 11–18 years were examined according to the Diagnostic Criteria for TMDs (DC/TMD). Signs and symptoms were registered. Results TMD prevalence among Venezuelan adolescents (17.9%) was lower than that among Italian adolescents (29.7%) and was higher in females and in the 15–18 age group. Intra-articular disorders were the most frequent in Venezuelan (8.5%) and Italian adolescents (13.0%). Pain-associated disorders were more frequent in the 11–14 age group, while intra-articular disorders were more frequent in the 15–18 age group in both samples. Italian adolescents presented greater muscle pain and joint noise than Venezuelan adolescents. Conclusion TMD prevalence in Venezuelan adolescents was lower than that in Italian adolescents. This suggests the involvement of cultural and/or genetic factors in the etiology of these disorders.
Genetic Basis of Natural Variation in Spontaneous Grooming in Drosophila melanogaster

Spontaneous grooming behavior is a component of insect fitness. We quantified spontaneous grooming behavior in 201 sequenced lines of the Drosophila melanogaster Genetic Reference Panel and observed significant genetic variation in spontaneous grooming, with broad-sense heritabilities of 0.25 and 0.24 in females and males, respectively. Although grooming behavior is highly correlated between males and females, we observed significant sex by genotype interactions, indicating that the genetic basis of spontaneous grooming is partially distinct in the two sexes. We performed genome-wide association analyses of grooming behavior, and mapped 107 molecular polymorphisms associated with spontaneous grooming behavior, of which 73 were in or near 70 genes and 34 were over 1 kilobase from the nearest gene. The candidate genes were associated with a wide variety of gene ontology terms, and several of the candidate genes were significantly enriched in a genetic interaction network. We performed functional assessments of 29 candidate genes using RNA interference, and found that 11 affected spontaneous grooming behavior. The genes associated with natural variation in Drosophila grooming are involved with glutamate metabolism (Gdh) and transport (Eaat); interact genetically with (CCKLR-17D1) or are in the same gene family as (PGRP-LA) genes previously implicated in grooming behavior; are involved in the development of the nervous system and other tissues; or regulate the Notch and Epidermal growth factor receptor signaling pathways. Several DGRP lines exhibited extreme grooming behavior. Excessive grooming behavior can serve as a model for repetitive behaviors diagnostic of several human neuropsychiatric diseases.
Climate warming and reproduction in Chinese alligators

The Chinese alligator Alligator sinensis is a critically endangered species endemic to China, and one of the most endangered crocodilian species in the world. Like many other reptiles, important aspects of alligator biology such as foraging, timing of hibernation, breeding and the sex ratio of offspring are all affected by temperature variation. We examined the effects of long‐term temperature change on oviposition dates and clutch sizes of the Chinese alligator in a semi‐natural facility in southern China. Our study focused on two captive generations including an old breeding generation captured from the wild and a generation composed of their F1 offspring. Median oviposition date shifted to earlier in the year and mean clutch size was larger for both generations as the monthly mean air temperature in April increased over the 19 years of data collection. We observed a mean advance in oviposition date of 10 days for the old breeding generation from 1987 to 2005 and 8 days for both generations from 1991 to 2005. Correspondingly, clutch sizes for the two generations also increased during this period. There were no differences in median oviposition dates and clutch sizes between the two generations from 1991 to 2005. Our results suggest that Chinese alligators have responded to increasing global temperatures. Our findings also suggest that recent increasing global temperatures have the potential to have a substantial effect on Chinese alligator populations in the wild, thus prompting an urgent need for field monitoring of the effects of global warming on this endangered alligator species.
Role of the central autonomic nervous system intrinsic functional organisation and psychosocial factors in primary microvascular angina and Takotsubo syndrome

Introduction and objective Dysfunctional central autonomic nervous system network (CAN) at rest may result in aberrant autonomic responses to psychosocial stressors. We hypothesised that patients with primary microvascular angina (MVA) or Takotsubo syndrome (TTS) would exhibit a peculiar functional organisation of the CAN, potentially associated with psychological patterns. Methods Patients underwent a psychosocial evaluation: a clinical diagnostic interview, Millon Clinical Multiaxial Inventory III, State-Trait Anxiety Inventory form Y and Short Form 36 Health Survey (SF-36). The strength of intrinsic functional connectivity (FC) between various nodes of the CAN was investigated using cerebral resting state functional MRI (RS-fMRI). Results We evaluated 50 (46 women) stable patients: 16 patients with MVA, 17 patients with TTS and 17 patients with previous acute myocardial infarction (AMI). Compared with AMI, patients with MVA showed a lower (higher impairment) SF-36 Body-Pain score (p 0.046) and a higher SF-36 Mental-Health score (p 0.039). Patients with TTS showed the strongest FC between two nodes of the CAN (sympathetic midcingulate cortex and parasympathetic primary motor area) (F 6.25, p 0.005) using RS-fMRI. Conclusions The study implements an innovative collaborative research among cardiologists, neuroscientists and psychiatrists (‘Neuro-psycho-heart Team’). MVA showed a discrepancy between the highest level of self-reported body pain and the best mental health score, which might suggest a mechanism of somatisation. TTS exhibited an increased functional integration between two areas of the CAN involved in interoceptive pain awareness and negative emotional status. We implemented an innovative research collaboration among cardiologists, neuroscientists and psychiatrists. These data are hypothesis generating and suggest potential prospective investigations on pathophysiology and implementation of psychotherapy and stress-reducing techniques as therapeutic strategies. Trial registration number NCT02759341.
Heritability of Oral Microbiota and Immune Responses to Oral Bacteria

Maintaining a symbiotic oral microbiota is essential for oral and dental health, and host genetic factors may affect the composition or function of the oral microbiota through a range of possible mechanisms, including immune pathways. The study included 836 Swedish twins divided into separate groups of adolescents (n = 418) and unrelated adults (n = 418). Oral microbiota composition and functions of non-enzymatically lysed oral bacteria samples were evaluated using 16S rRNA gene sequencing and functional bioinformatics tools in the adolescents. Adaptive immune responses were assessed by testing for serum IgG antibodies against a panel of common oral bacteria in adults. In the adolescents, host genetic factors were associated with both the detection and abundance of microbial species, but with considerable variation between species. Host genetic factors were associated with predicted microbiota functions, including several functions related to bacterial sucrose, fructose, and carbohydrate metabolism. In adults, genetic factors were associated with serum antibodies against oral bacteria. In conclusion, host genetic factors affect the composition of the oral microbiota at a species level, and host-governed adaptive immune responses, and also affect the concerted functions of the oral microbiota as a whole. This may help explain why some people are genetically predisposed to the major dental diseases of caries and periodontitis.
Does conception spontaneously or with ART affect postpartum parenting behaviors?

ABSTRACT Pregnancy and parenting may be psychologically more complex after assisted conception than after spontaneous conception. On the other hand, the literature demonstrates that mothers who conceived with ART comply with transition to parenting easily although they experience more problems in pregnancy and postpartum. This study aimed to compare postpartum parenting behaviors of women who conceived spontaneously or with ART. This descriptive, cross-sectional and comparative study was conducted between October 2017 and June 2018 in Dokuz Eylul University postpartum clinic with 50 spontaneous mother and 50 ART mothers. After a brief explanation of the study, the personal information form was applied to women and the parenting behaviours were observed by using Postpartum Parenting Behavior Scale. The total PPBS average score in the ART group was 5.40 ± 1.41 compared with 3.62 ± 2.24 in the comparison group. The ART mother displayed significantly a more positive attitude toward their infant than spontaneous mother (p = 0.00). Also, in six components of PPBS separately it was determined higher score in ART group, respectively (p = 0.04, p = 0.00, p = 0.00, p = 0.00, p = 0.00, p = 0.00). Mothers who were conceived with ART exhibit more positive parenting behaviors.
Seroprevalence of SARS-CoV-2–Specific Antibodies, Faroe Islands

We conducted a nationwide study of the prevalence of severe acute respiratory syndrome coronavirus 2 infection in the Faroe Islands. Of 1,075 randomly selected participants, 6 (0.6%) tested seropositive for antibodies to the virus. Adjustment for test sensitivity and specificity yielded a 0.7% prevalence. Our findings will help us evaluate our public health response.
Risk Prediction and New Prophylaxis Strategies for Thromboembolism in Cancer

In the general population, the incidence of thromboembolic events is 117 cases/100,000 inhabitants/year, while in cancer patient incidence, it is four-fold higher, especially in patients who receive chemotherapy and who are affected by pancreatic, lung or gastric cancer. At the basis of venous thromboembolism (VTE) there is the so-called Virchow triad, but tumor cells can activate coagulation pathway by various direct and indirect mechanisms, and chemotherapy can contribute to VTE onset. For these reasons, several studies were conducted in order to assess efficacy and safety of the use of anticoagulant therapy in cancer patients, both in prophylaxis setting and in therapy setting. With this review, we aim to record principal findings and current guidelines about thromboprophylaxis in cancer patients, with particular attention to subjects with additional risk factors such as patients receiving chemotherapy or undergoing surgery, hospitalized patients for acute medical intercurrent event and patients with central venous catheters. Nonetheless we added a brief insight about acute and maintenance therapy of manifested venous thromboembolism in cancer patients.
Clinical Experience with High-Dose Polymyxin B against Carbapenem-Resistant Gram-Negative Bacterial Infections—A Cohort Study

Population pharmacokinetic studies have suggested that high polymyxin B (PMB) doses (≥30,000 IU/kg/day) can improve bacterial kill in carbapenem-resistant Gram-negative bacteria (CR-GNB). We aim to describe the efficacy and nephrotoxicity of patients with CR-GNB infections prescribed high-dose PMB. A single-centre cohort study was conducted from 2013 to 2016 on septic patients with CR-GNB infection and prescribed high-dose PMB (~30,000 IU/kg/day) for ≥72 h. Study outcomes included 30-day mortality and acute kidney injury (AKI) development. Factors associated with AKI were identified using multivariable regression. Forty-three patients with 58 CR-GNB received high-dose PMB; 57/58 (98.3%) CR-GNB were susceptible to PMB. The median daily dose and duration of high-dose PMB were 32,051 IU/kg/day (IQR, 29,340–34,884 IU/kg/day) and 14 days (IQR, 7–28 days), respectively. Thirty-day mortality was observed in 7 (16.3%) patients. AKI was observed in 25 (58.1%) patients with a median onset of 8 days (IQR, 6–13 days). Higher daily PMB dose (aOR,1.01; 95% CI, 1.00–1.02) and higher number of concurrent nephrotoxins (aOR, 2.14; 95% CI; 1.03–4.45) were independently associated with AKI. We observed that a sizable proportion developed AKI in CR-GNB patients described high-dose PMB; hence, the potential benefits must be weighed against increased AKI risk. Concurrent nephrotoxins should be avoided to reduce nephrotoxicity.