Miracle-dz/UniFAR-FTUs huggingface dataset:
An End-to-end Approach to Semantic Segmentation with 3D CNN and Posterior-CRF in Medical Images

Fully-connected Conditional Random Field (CRF) is often used as post-processing to refine voxel classification results by encouraging spatial coherence. In this paper, we propose a new end-to-end training method called Posterior-CRF. In contrast with previous approaches which use the original image intensity in the CRF, our approach applies 3D, fully connected CRF to the posterior probabilities from a CNN and optimizes both CNN and CRF together. The experiments on white matter hyperintensities segmentation demonstrate that our method outperforms CNN, post-processing CRF and different end-to-end training CRF approaches.
Oestrogen Inhibits VEGF Expression And Angiogenesis In Triple-Negative Breast Cancer By Activating GPER-1

Triple-negative breast cancer (TNBC) is the most malignant type of breast cancer with ample vascularisation and high vascular endothelial growth factor (VEGF) expression. The sex steroid hormone oestrogen is involved in several cellular activities associated with TNBC regulation. However, the role of oestrogen in VEGF expression and angiogenesis in TNBC remains unclear. In this study, we found that treatment with 17β-oestradiol (E2) inhibited VEGF mRNA and protein expression in the TNBC cell lines MDA-MB-468 and MDA-MB-436. To further elaborate on the phenomenon of E2-regulated angiogenesis, we showed that conditioned medium from the TNBC cell line MDA-MB-468 treated with E2 inhibits the tube formation ability of human umbilical vein endothelial cells (HUVECs). Additionally, the G-protein-coupled oestrogen receptor-1 (GPER-1)-specific agonist G-1 has a function similar to that of E2. While G-15, the selective antagonist of GPER-1, notably reversed the inhibitory effects of E2 and G-1 on VEGF expression and tube formation, suggesting that GPER-1 is involved in the E2-induced angiogenesis suppression in TNBC cells. Moreover, E2 inhibited in vivo tumour growth and angiogenesis and reduced the expression levels of VEGF, NF-κB/p65, STAT3, and the endothelial marker CD34 in MDA-MB-468 xenograft tumours. Our findings provide important evidence that E2 can inhibit VEGF expression and angiogenesis in TNBC by activating GPER-1, offering additional insight into tumour angiogenesis and targets for drug intervention in TNBC.
Social factors relating to depression among older people in Japan: analysis of longitudinal panel data from the AGES project

Abstract Objectives: Preventing the onset of depression among older people in Japan requires clarifying the social determinants of depression by using longitudinal data, while also taking biological and psychological factors into account. Identification of such determinants may enable more active intervention through social policy. We aimed to reveal the social factors related to depression in Japan’s older people and consider associated policy implications. Method: Panel data obtained from a longitudinal survey (Wave 1 to Wave 2) of 3464 elderly subjects, aged 65 years or more, as part of the Aichi Gerontological Evaluation Study (AGES) project was employed. The outcome variable was depression, as evaluated by the Geriatric Depression Scale. Frequency of meeting with friends, social support, hobbies, participation in organizations, life events, illness, self-rated health, instrumental activities of daily living, and sense of coherence were entered as explanatory variables within a logit model for each gender. Results: Of the subjects without mental illness or depression at Wave 1, 14% had become depressed by Wave 2. In both men and women, life events predicted increased odds of depression, while sense of coherence predicted reduced odds. The frequency of meeting with friends, hobbies, and self-rated health predicted reduced odds of depression in men, while age predicted increased odds in women. Conclusion: Overall, social interaction is important for preventing depression in Japan, and that the establishment of a system capable of promoting social interaction and providing care to the elderly during life events may be a useful social policy approach to preventing depression.
Exploring the Perceived Barriers to Following a Mediterranean Style Diet in Childbearing Age: A Qualitative Study

A considerable amount of research has focused on interventions in pregnancy to promote health in current and future generations. This has yielded inconsistent results and focus has turned towards improving health in the preconception period. Promotion of healthy dietary patterns similar to a Mediterranean diet in the preconception years has been suggested as a dietary strategy to prevent maternal obesity and optimize offspring health. However, it is uncertain whether adoption is acceptable in women of childbearing age. This qualitative study aims to investigate the perceived barriers to following a Mediterranean diet in women of childbearing age. Semi-structured focus groups were used to generate deep insights to be used to guide the development of a future intervention. Nulliparous women aged between 20 and 47 years were recruited (n = 20). Six focus groups were digitally audio recorded and transcribed verbatim by the researcher. Thematic analysis was used to analyze data, which occurred in parallel with data collection to ascertain when data saturation was reached. Five core themes were identified: Mediterranean diet features, perceived benefits, existing dietary behavior and knowledge, practical factors, and information source. The present study highlights that a Mediterranean diet is acceptable to childbearing-aged women, and the insights generated will be helpful in developing an intervention to promote Mediterranean diet adoption.
A Comparative Quantitative LC-MS/MS Profiling Analysis of Human Pancreatic Adenocarcinoma, Adjacent-Normal Tissue, and Patient-Derived Tumour Xenografts

Pancreatic ductal adenocarcinoma (PDAC) is one of the deadliest cancers worldwide; it develops in a relatively symptom-free manner, leading to rapid disease progression and metastasis, leading to a 5-year survival rate of less than 5%. A lack of dependable diagnostic markers and rapid development of resistance to conventional therapies are among the problems associated with management of the disease. A better understanding of pancreatic tumour biology and discovery of new potential therapeutic targets are important goals in pancreatic cancer research. This study describes the comparative quantitative LC-MS/MS proteomic analysis of the membrane-enriched proteome of 10 human pancreatic ductal adenocarcinomas, 9 matched adjacent-normal pancreas and patient-derived xenografts (PDXs) in mice (10 at F1 generation and 10 F2). Quantitative label-free LC-MS/MS data analysis identified 129 proteins upregulated, and 109 downregulated, in PDAC, compared to adjacent-normal tissue. In this study, analysing peptide MS/MS data from the xenografts, great care was taken to distinguish species-specific peptides definitively derived from human sequences, or from mice, which could not be distinguished. The human-only peptides from the PDXs are of particular value, since only human tumour cells survive, and stromal cells are replaced during engraftment in the mouse; this list is, therefore, enriched in tumour-associated proteins, some of which might be potential therapeutic or diagnostic targets. Using human-specific sequences, 32 proteins were found to be upregulated, and 113 downregulated in PDX F1 tumours, compared to primary PDAC. Differential expression of CD55 between PDAC and normal pancreas, and expression across PDX generations, was confirmed by Western blotting. These data indicate the value of using PDX models in PDAC research. This study is the first comparative proteomic analysis of PDAC which employs PDX models to identify patient tumour cell-associated proteins, in an effort to find robust targets for therapeutic treatment of PDAC.
A Concept of an Adaptive Luminaire with Variable Luminous Intensity Distribution

The article presents an innovative concept of adaptive luminaire with variable luminous intensity distribution. It enables adjustment of photometric characteristic of luminaire to variable arrangement of the facility, including the quantitative regulation of luminous flux and spatial distribution. A solution presented in this paper was developed as part of a research project titled “Development of the Intelligent Light Distribution System SOLLS ACTIVE SKY” and is the subject of patent application. The authors present the results of simulation tests in terms of the possibility of obtaining different luminous intensity distribution and lighting parameters on the working plane, with variable position relative to the arrangement of the luminaires. The use of a luminaire with variable luminous intensity distribution as part of an adaptive lighting system allows for quick and cost-free introduction of changes in the lighting of selected functional zones inside the facility. It is possible to adjust the lighting in case of changes in the size or position of the working plane, while the position of luminaire is constant.
Developing Predictive or Prognostic Biomarkers for Charged Particle Radiotherapy

The response to radiotherapy can vary greatly among individuals, even though advances in technology allow for the highly localized placement of therapeutic doses of radiation to a tumor. This variability in patient response to radiation is biologically driven, but the individuality of tumor and healthy tissue biology are not used to create individual treatment plans. Biomarkers of radiosensitivity, whether intrinsic or from hypoxia, would move radiation oncology from precision medicine to precise, personalized medicine. Charged particle radiotherapy allows for even greater dose conformity, but the biological advantages of charged particle radiotherapy have not yet been cultivated. The development of biomarkers that would drive biologically based clinical trials, identify patients for whom charged particles are most appropriate, or aid in particle-selection strategies could be envisioned with appropriate biomarkers. Initially, biomarkers for low-linear energy transfer (LET) radiation responses should be tested against charged particles. Biomarkers of tumor radioresistance to low-LET radiations could be used to identify patients for whom the enhanced relative biological effectiveness (RBE) of charged particles would be more effective compared with low-LET radiations and those for whom specific DNA-repair inhibitors, in combination with charged particles, may also be appropriate. Furthermore, heavy charged particles can overcome the radioresistance of hypoxic tumors when used at the appropriate LET. Biomarkers for hypoxia could identify hypoxic tumors and, in combination with imaging, define hypoxic regions of a tumor for specific ion selection. Moreover, because of the enhanced RBE for charged particles, the risk for adverse healthy tissue effects may be greater, even though charged particles have greater tumor conformality. There are many validated healthy-tissue biomarkers available to test against charged particle exposures. Lastly, newer biological techniques, as well as newer bioinformatic and computational methods, are rapidly changing the landscape for biomarker identification, validation, and clinical trial design.
Vegetation type and grazing intensity jointly shape grazing effects on grassland biodiversity

Abstract In the Palaearctic steppe zone, overgrazing was identified as one of the key drivers of declining grassland biodiversity, which underlines the necessity of the functional evaluation of increased grazing pressure on grassland vegetation. We tested the following hypotheses: (a) The effect of grazing intensity on species and functional diversity is strongly dependent on grassland type. (b) The magnitude of diet selectivity of grazers decreases with increasing grazing intensity. (c) Increasing grazing intensity increases evenness and functional evenness of the subjected grasslands. We analyzed vegetation patterns in four types of grasslands (Dry alkali short‐grass steppes, Dry loess steppes, Non‐alkali wet and Alkali wet grasslands) along an intensity gradient of beef cattle grazing at 73 sites in Hungary. Species richness, Shannon diversity, evenness, and four leaf traits were analyzed. We calculated community‐weighted means for each single trait, and multi‐trait functional richness, functional evenness, and divergence for all leaf traits. All species and functional diversity metrics were significantly affected by the grassland type, except leaf dry matter content. The effect of interaction between grazing intensity and grassland type was also significant for functional richness, functional evenness, community‐weighted means of leaf area, and for species richness and evenness. An upward trend of specific leaf area was detected in all grasslands with the highest scores for the overgrazed sites, but the change was also grassland type dependent. The detected trend suggests that with increased intensity the overall selectivity of grazing decreased. We found that evenness was affected but functional evenness was not affected by grazing intensity. Functional evenness scores were more related to the grassland type than to changes in grazing intensity, and displayed a high variability. We stress that one‐size‐fits‐all strategies cannot be recommended and actions should be fine‐tuned at least at the level of grassland type.
The effects of warming and nitrogen addition on ecosystem respiration in a Tibetan alpine meadow: The significance of winter warming

Abstract In recent decades, global warming has become an indisputable fact on the Tibetan Plateau. Alpine ecosystems are very sensitive to global warming, and the impact may depend on the degree of atmospheric nitrogen (N) deposition. The previous studies have paid more attention to year‐round warming, but the effect of winter warming has been unstudied. In this study, a manipulative experiment was conducted, consisting of warming and N addition. It was carried out since 2010 in an alpine meadow, and three types of warming treatments were set up: no warming (NW), year‐round (YW), and winter warming (WW). Warming significantly increased air and soil temperature, but decreased soil moisture. Under no N addition, YW showed significantly decreased ecosystem respiration (Reco) in 2012, and WW decreased Reco in 2014. Under N addition, neither YW nor WW had significant effects on Reco, indicating that N addition compensated the negative effect of warming on Reco. Annually, YW and WW decreased ecosystem carbon (C) emissions, and the extent of the reduction was even larger under WW. Under no N addition, both YW and WW significantly decreased aboveground biomass. Moreover, especially under no N, YW and WW significantly decreased soil inorganic N. WW also had negative effects on soil microbial biomass C. Structure equation modeling showed that soil moisture was the most important factors controlling Reco, and soil inorganic N content and microbial biomass C could explain 46.6% and 16.8% of the variation of Reco. The findings indicate that soil property changes under warming had substantial effects on ecosystem C efflux. The inhibitory effects of winter warming on ecosystem C efflux were mainly attributed to the decline of soil N and microbial biomass. Thus, the effects of winter warming on ecosystem C emissions in this semiarid alpine meadow are not as serious as expected and largely depend on N deposition.
Th17 response in patients with cervical cancer

Persistent infection by high-risk human papillomavirus (HR-HPV) is the main risk factor for uterine cervical cancer (UCC). However, viral infection alone is not sufficient for the development and progression of premalignant cervical lesions for cancer. In previous years it has been suggested that the adaptive immune response triggered by the differentiation of naïve helper T cells in Th17 cells may serve an important role in disease development. It has been hypothesized that Th17 cells may be involved in the promotion of UCC, as high levels of interleukin 17 (IL17) expression have been detected in the mucosa of the uterine cervix of patients affected by the disease. However, the role of Th17 cells in the tumor development and progression remains unclear. It is believed that the immune response of the Th17 type during persistent infection of the genital tract with HR-HPV triggers chronic inflammation with a long duration with the production of IL17 and other pro-inflammatory cytokines, creating a favorable environment for tumor development. These cytokines are produced by immune system cells in addition to tumor cells and appear to function by modulating the host immune system, resulting in an immunosuppressive response as opposed to inducing an effective protective immune response, thus contributing to the growth and progression of the tumor. In the present review, the latest advances are presented about the function of Th17 cells and the cytokines produced by them in the development and progression of UCC.
Catheter ablation of atrial fibrillation: current status, techniques, outcomes and challengesCatheter ablation of atrial fibrillation: current status, techniques, outcomes, and challenges.

Atrial fibrillation (AF) is the most common human arrhythmia. Interventional treatment with catheter ablation is an established technique that is increasingly applied and has become one of the main treatment modalities in patients with AF. Ablation results in significant improvement of symptoms and the quality of life. There is as yet no clear evidence of any impact of the procedure on hard clinical endpoints, except in patients with heart failure, who seem to benefit significantly from ablation. The cornerstone of the procedure is the achievement of pulmonary vein isolation. Radiofrequency energy is the main applied energy source, but cryoballoon ablation has emerged as a safe and effective alternative to radiofrequency ablation. Additional ablation strategies and novel technical features have been proposed but without unequivocal proof of clinical benefit. The most promising of these seems to be substrate mapping of the left atrium with substrate modification in areas with low voltage as an adjunct to pulmonary vein isolation. Complication rates remain considerable despite accumulated experience and can be partly reduced by application of preventive measures.
A systematic review and meta-analysis

Background: Robot-assisted partial nephrectomy (RPN) and focal therapy (FT) have both been successfully employed in the management of small renal masses. However, despite this being the era of minimally invasive surgery, few comparative studies exist on RPN and FT. The aim of our study is to review perioperative, renal functional and oncologic outcomes of FT and RPN in cT1 renal masses. Methods: Literature published in Medline, EMBASE, and Cochrane Library databases up to April 22, 2018, was systematically searched. We included literature comparing outcomes of FT (radiofrequency ablation, cryoablation, microwave ablation, and irreversible electroporation) and RPN. Studies that reported only on laparoscopic partial nephrectomy or open partial nephrectomy, and review articles, editorials, letters, or cost analyses were excluded. In total, data from 1166 patients were included. Results: From 858 total articles, 7 nonrandomized, observational studies were included. Compared with RPN, FT was associated with a significantly lower decrease of estimated glomerular filtration rate (weighted mean difference [WMD] 8.06mL/min/1.73m; confidence interval [CI] 15.85 to 0.26; P = .04), and lower estimated blood loss (WMD 49.61mL; CI 60.78 to 38.45; P< .001). However, patients who underwent FT had a significantly increased risk of local recurrence (risk ratio [RR] 9.89; CI 4.24– 23.04; P< .001) and distant metastasis (RR 6.42; CI 1.70–24.33; P= .006). However, operative times, lengths of stay, and complication rates were revealed to be similar between FT and RPN. Conclusion:RPN has a substantial advantage in preventing cancer recurrence. However, in the era of minimally invasive surgery, FT has advantages in renal function preservation and less bleeding. Long-term follow-up for survival rates and comparative analysis of microwave ablation and irreversible electroporation are needed to extend FT for patients with significant morbidities and for those who need sufficient renal function preservation with minimal bleeding. Abbreviations: AUA = American Urological Association, CA = cryoablation, CI = confidence interval, CSS = cancer-specific survival, EBL = estimated blood loss, eGFR = estimated glomerular filtration rate, FT = focal therapy, IRE = irreversible electroporation, LPN = laparoscopic partial nephrectomy, mNOS =modified Newcastle–Ottawa scale, MWA =microwave ablation, OPN = open partial nephrectomy, OR = odds ratio, OS = overall survival, PN = partial nephrectomy, RFA = radiofrequency ablation, RPN = robot-assisted partial nephrectomy, RR = risk ratio, SRMs = small renal masses, WMD = weighted mean difference.
Videolaryngoscopy versus fiberoptic bronchoscope for awake intubation – a systematic review and meta-analysis of randomized controlled trials

Background Awake intubation with videolaryngoscopy (VL) is a novel method that is drawing more and more attention as an alternative to awake intubation with fiberoptic bronchoscope (FOB). This meta-analysis is designed to determine the performance of VL compared to the FOB for awake intubation. Methods The Cochrane Central Register of Controlled Trials, PubMed, Embase, and Web of science were searched from database inception until October 30, 2017. Randomized controlled trials comparing VL and FOB for awake intubation were selected. The primary outcome was the overall success rate. Rev-Man 5.3 software was used to perform the pooled analysis and assess the risk of bias for each eligible study. The GRADE system was used to assess the quality of evidence for all outcomes. Results Six studies (446 patients) were included in the review for data extraction. Pooled analysis did not show any difference in the overall success rate by using VL and FOB (relative risk [RR], 1.00; P=0.99; high-quality evidence). There was no heterogeneity among studies (I2=0). Subgroup analyses showed no differences between two groups through nasal (RR, 1.00; P=1.00; high-quality evidence) and oral intubations (RR, 1.00; P=0.98; high-quality evidence). The intubation time was shorter by using VL than by using FOB (mean difference, −40.4 seconds; P<0.01; low-quality evidence). There were no differences between groups for other outcomes (P>0.05). Conclusion For awake intubation, VL with a shorter intubation time is as effective and safe as FOB. VL may be a useful alternative to FOB.