Miracle-dz/UniFAR-FTUs huggingface dataset:
Torque teno virus load as marker of rejection and infection in solid organ transplantation – A systematic review and meta‐analysis

Balancing immunosuppression to prevent rejection in solid organ transplant (SOT) recipients remains challenging. Torque teno virus (TTV), a commensal non‐pathogenic virus, has been proposed as marker of functional immunity: higher loads correspond to over‐immunosuppression, and lower loads to under‐immunosuppression. This review offers an overview of the current evidence of the association between TTV‐load and infection and rejection after SOT. A systematic literature search strategy, deposited in the PROSPERO registry, resulted in 548 records. After screening, 23 original and peer‐reviewed articles were assessed investigating the association between TTV‐load, infection and/or rejection in SOT. The Quality in Prognostic Studies (QUIPS)‐tool was used to assess the risk of bias. Meta‐analysis with random‐effects was performed on results with similar outcomes and exposure measures. Most of the included studies involved retrospective cohorts in which the TTV‐load was measured longitudinally, within the first 2 years post‐transplantation. Infection outcomes differed between studies and included viral, bacterial, parasitic and fungal infections. Rejection was defined by biopsy confirmation or initiation of rejection treatment. Twelve out of 16 studies reported an association between high TTV‐load and infections, whereas 13 out of 15 reported an association between low TTV‐load and rejection. Meta‐analysis showed an increased risk of infection (OR: 1.16, 95% CI: 1.03–1.32; HR: 1.05, 95% CI: 0.97–1.14) and a decreased risk of rejection (OR: 0.90, 95% CI: 0.87–0.94; HR: 0.74, 95% CI: 0.71–0.76) per 1 log TTV‐load increase. The qualitative assessment showed varying risks of bias in the included studies. This systematic review and meta‐analysis indicates that blood TTV‐load measured within the first 2 years after SOT is associated with the risk of infection or allograft rejection, although substantial risk of bias in the studies included warrant cautious interpretation. The results in this review provide a rationale for larger, prospective, studies into TTV as marker of infection and rejection after SOT.
Developmental validation of the Microreader Group Y Direct ID System: A novel six‐dye typing system with 54 Y‐chromosomal loci for forensic application

Y‐chromosome, as a gender‐determined biological marker, is inherited only between fathers and sons. The Y‐chromosome short tandem repeats (Y‐STRs) play an essential role in paternity lineage tracing as well as sexual assault cases. The Microreader Group Y Direct ID System as a six‐dye multiplex amplification kit, including 53 Y‐STR and one Y‐Indel locus, would improve performance and aid in obtaining more information through a greater number of loci with high polymorphism. In the present study, to verify the accuracy and efficiency of the kit, developmental validation was conducted by investigating sensitivity, species specificity, PCR inhibition, male–male and male–female mixtures, and reproducibility. The kit was tested using 311 male samples from Han and Qiang populations in Sichuan Province. The results showed that this kit had fairly high power for forensic discrimination (Han: haplotype diversity [HD] = 1, Qiang: HD = 0.999944). Additionally, 44 confirmed father–son pairs were also genotyped, among which 69 distinct haplotypes could be obtained. These father–son pairs cannot be distinguished by commonly used Y‐STR panels, indicating that adding these extra Y‐STRs to a single panel can achieve better discrimination performance. Collectively, the Microreader Group Y Direct ID System is robust and informative for forensic applications.
Integrating morphology and physiology of the key endocrine organ during tadpole development: The interrenal gland

Indirect development is widespread in anurans and is considered an ancestral condition. The metamorphosis of larvae into juveniles involves highly coordinated morphological, physiological, biochemical, and behavioral changes, promoted by the thyroid hormone and interrenal corticosteroids. Stress response to environmental changes is also mediated by corticosteroids, affecting the timing and rate of metamorphosis and leading to great developmental plasticity in tadpoles. Given the potential effect of interrenal gland ontogeny alterations on metamorphosis and the lack of studies addressing both the morphology and endocrinology of this gland in tadpoles, we present corticosterone (CORT) production and histological changes through the ontogeny of interrenal gland in the generalized pond‐type tadpole of Rhinella arenarum (Anura, Bufonidae). This species shows the highest concentration of whole‐body CORT by the early climax when drastic metamorphic changes begin. This is coincident with the morphological differentiation of steroidogenic cells and the formation of interrenal cords. By this stage, steroidogenic cells have a shrunken cytoplasm, with a significantly higher nucleus‐to‐cell diameter ratio. The lowest CORT concentration during premetamorphosis and late climax is associated with small undifferentiated cells with lipid inclusions surrounding large blood vessels between kidneys, and with cords of differentiated steroidogenic cells with a significantly lower nucleus‐to‐cell diameter ratio, respectively. Our study characterizes the morphological and physiological pattern of interrenal gland development, showing an association between certain histological and morphometric characteristics and CORT levels. Variations in this morpho‐physiological pattern should be considered when studying the phenotypic plasticity or variable growth rates of tadpoles.
Liquid ozone therapies for the treatment of epithelial wounds: A systematic review and meta‐analysis

Ozonated water and ozonated oils are emerging as potential therapies for wound care, but their efficacy has not been appropriately evaluated. The aim of this systematic review and meta‐analysis was to evaluate the therapeutic potential of topical ozone in the treatment of mammalian wounds. A structured search of five scientific databases returned a total of 390 unique studies. Of these, 22 studies were included in this review. Four studies provided enough data to be included in a meta‐analysis evaluating the time to complete wound healing. All studies were randomised controlled trials of humans or other mammalian animals that reported clinical signs of wound healing. Each study was critically analysed by a six‐point assessment of the risk of bias. Wounds treated with topical ozone had a greater reduction in wound size than similar wounds treated with controls or standard of care in all studies. Those treated with ozonated liquids also had a shorter time to wound healing by approximately one week. In conclusion, topical ozone contributed to enhanced wound healing in all studies. While additional human experiments would be helpful to quantify ozone's specific effects on wound healing compared to standard treatment, topical ozone should be considered as part of an overall wound management strategy.
A population‐based meta‐analysis of circulating GFAP for cognition and dementia risk

Expression of glial fibrillary acidic protein (GFAP), a marker of reactive astrocytosis, colocalizes with neuropathology in the brain. Blood levels of GFAP have been associated with cognitive decline and dementia status. However, further examinations at a population‐based level are necessary to broaden generalizability to community settings.
Distribution and predicted climatic refugia for a reef‐building cold‐water coral on the southeast US margin

Climate change is reorganizing the planet's biodiversity, necessitating proactive management of species and habitats based on spatiotemporal predictions of distributions across climate scenarios. In marine settings, climatic changes will predominantly manifest via warming, ocean acidification, deoxygenation, and changes in hydrodynamics. Lophelia pertusa, the main reef‐forming coral present throughout the deep Atlantic Ocean (>200 m), is particularly sensitive to such stressors with stark reductions in suitable habitat predicted to accrue by 2100 in a business‐as‐usual scenario. However, with new occurrence data for this species along with higher‐resolution bathymetry and climate data, it may be possible to locate further climatic refugia. Here, we synthesize new and published biogeographic, geomorphological, and climatic data to build ensemble, multi‐scale habitat suitability models for L. pertusa on the continental margin of the southeast United States (SEUS). We then project these models in two timepoints (2050, 2100) and four climate change scenarios to characterize the occurrence probability of this critical cold‐water coral (CWC) habitat now and in the future. Our models reveal the extent of reef habitat in the SEUS and corroborate it as the largest currently known essentially continuous CWC reef province on earth, and also predict abundance of L. pertusa to identify key areas, including those outside areas currently protected from bottom‐contact fishing. Drastic reductions in L. pertusa climatic suitability index emerged primarily after 2050 and were concentrated at the shallower end (<~550 m) of the regional distribution under the Gulf Stream main axis. Our results thus suggest a depth‐driven climate refuge effect where deeper, cooler reef sites experience lesser declines. The strength of this effect increases with climate scenario severity. Taken together, our study has implications for the regional and global management of this species, portending changes in the biodiversity reliant on CWC habitats and the critical ecosystem services they provide.
Volumetric Pancreas Segmentation on Computed Tomography: Accuracy and Efficiency of a Convolutional Neural Network Versus Manual Segmentation in 3D Slicer in the Context of Interreader Variability of Expert Radiologists

Purpose This study aimed to compare accuracy and efficiency of a convolutional neural network (CNN)–enhanced workflow for pancreas segmentation versus radiologists in the context of interreader reliability. Methods Volumetric pancreas segmentations on a data set of 294 portal venous computed tomographies were performed by 3 radiologists (R1, R2, and R3) and by a CNN. Convolutional neural network segmentations were reviewed and, if needed, corrected (“corrected CNN [c-CNN]” segmentations) by radiologists. Ground truth was obtained from radiologists' manual segmentations using simultaneous truth and performance level estimation algorithm. Interreader reliability and model's accuracy were evaluated with Dice-Sorenson coefficient (DSC) and Jaccard coefficient (JC). Equivalence was determined using a two 1-sided test. Convolutional neural network segmentations below the 25th percentile DSC were reviewed to evaluate segmentation errors. Time for manual segmentation and c-CNN was compared. Results Pancreas volumes from 3 sets of segmentations (manual, CNN, and c-CNN) were noninferior to simultaneous truth and performance level estimation–derived volumes [76.6 cm3 (20.2 cm3), P < 0.05]. Interreader reliability was high (mean [SD] DSC between R2-R1, 0.87 [0.04]; R3-R1, 0.90 [0.05]; R2-R3, 0.87 [0.04]). Convolutional neural network segmentations were highly accurate (DSC, 0.88 [0.05]; JC, 0.79 [0.07]) and required minimal-to-no corrections (c-CNN: DSC, 0.89 [0.04]; JC, 0.81 [0.06]; equivalence, P < 0.05). Undersegmentation (n = 47 [64%]) was common in the 73 CNN segmentations below 25th percentile DSC, but there were no major errors. Total inference time (minutes) for CNN was 1.2 (0.3). Average time (minutes) taken by radiologists for c-CNN (0.6 [0.97]) was substantially lower compared with manual segmentation (3.37 [1.47]; savings of 77.9%–87% [P < 0.0001]). Conclusions Convolutional neural network–enhanced workflow provides high accuracy and efficiency for volumetric pancreas segmentation on computed tomography.
Topical therapy for pain management in malignant fungating wounds: A scoping review.

AIMS AND OBJECTIVES To map and synthesise the existing literature on topical therapies for malignant fungating wounds pain management and the gaps involved. BACKGROUND Most cancer patients with malignant fungating wounds suffer from wound-related pain, affecting their quality of life. Unfortunately, even though pain is a relevant symptom in cancer and palliative care, little is currently known about topical treatments' availability and impact on pain management. DESIGN A scoping review following JBI® methodology METHODS: Searches were performed in CINAHL, LILACS, Embase, Web of Science, PubMed, Cochrane, NICE, Scopus, JBISRIR and grey literature, in English, Portuguese and Spanish, with no time limit. Two authors independently reviewed all citations and a third was called in case of divergence, and studies in adults with malignant fungal wounds reporting topical pain interventions were included. In addition, a data extraction tool for synthesis and thematic analysis was developed. This study followed the PRISMA-ScR Checklist. RESULTS Seventy publications were selected from 796 records retrieved from databases. The studies mainly included non-systematic reviews and case studies with only six clinical trials. According to the narrative synthesis, twenty therapies were identified, including the use of wound dressings (58.6%), analgesic drugs (55.7%), topical antimicrobials (25.7%), skin barriers (15.7%), cryotherapy (5.7%) and negative pressure wound therapy (4.3%). Therapies were recommended to be applied to the wound bed or the periwound skin. In 68.5% of the studies, a standardised assessment for pain was not described. CONCLUSIONS Topical therapies applied to malignant fungating wounds or periwound areas had been examined for pain management. However, their effectiveness was analysed in a few interventional studies, indicating the need for further primary studies to inform evidence-based practice. IMPLICATION FOR PRACTICE Highlighted topical therapies for clinical practice consideration are opioids, anaesthetics and antimicrobials, with positive results described in randomised clinical trials. This study did not include patients.
Study on superconducting properties of CeIrIn5 thin films grown via pulsed laser deposition

We report the growth of CeIrIn5 thin films with different crystal orientations on a MgF2 (001) substrate using pulsed laser deposition technique. X-ray diffraction analysis showed that the thin films were either mainly a-axis-oriented (TF1) or a combination of a- and c-axis-oriented (TF2). The characteristic features of heavy-fermion superconductors, i.e. Kondo coherence and superconductivity, were clearly observed, where the superconducting transition temperature (T c) and Kondo coherence temperature (T coh) are 0.58 K and 41 K for TF1 and 0.52 K and 37 K for TF2, respectively. The temperature dependencies of the upper critical field (Hc 2) of both thin films and the CeIrIn5 single crystal revealed a scaling behavior, indicating that the nature of unconventional superconductivity has not been changed in the thin film. The successful synthesis of CeIrIn5 thin films is expected to open a new avenue for novel quantum phases that may have been difficult to explore in the bulk crystalline samples.
The natural cytotoxicity receptor genes in the family Felidae

Natural killer (NK) cells belong to the innate immune system. The germline‐encoded natural killer cell receptors represent activating and inhibitory receptors regulating multiple NK cell activities. The natural cytotoxicity receptors (NCRs) are activating natural cytotoxicity triggering receptors 1, 2, and 3 (NKp46, NKp44, and NKp30), encoded by the genes NCR1, NCR2, and NCR3, respectively. NCRs may be expressed in different cell types engaged in mechanisms of innate and adaptive immunity. The family Felidae, comprising the domestic cat and a wide variety of free‐ranging species represents a well‐suited model for biomedical and evolutionary studies. We characterized the NCR1, NCR2, and NCR3 genes in a panel of felid species. We confirmed the presence of potentially functional genes NCR1, NCR2, and NCR3 in all species. All three genes are conserved within the family and are similar to other phylogenetically related mammalian families. The NCR1 and NCR2 phylogenetic trees based on both nucleotide and protein sequences corresponded to the current zoological taxonomy, with some exceptions suggesting effects of different selection pressures in some species. Highly conserved NCR3 sequences did not allow a robust phylogenetic analysis. Most interspecific differences both at the nucleotide and protein level were found in NCR2. Within species, the most polymorphic CDS was detected in NCR1. Selection analyses indicated the effects of purifying selection on individual amino acid sites in all three genes. In stray cats, a rather high intraspecific diversity was observed.
Diagnosis of rectal cancer based on the Xception-MS network

Objective. Accurate T staging of rectal cancer based on ultrasound images is convenient for doctors to determine the appropriate treatment. To effectively solve the problems of low efficiency and accuracy of traditional methods for T staging diagnosis of rectal cancer, a deep-learning-based Xception-MS diagnostic model is proposed in this paper. Approach. The proposed diagnostic model consists of three steps. First, the model preprocesses rectal cancer images to solve the problem of data imbalance and deficiency of sample size, and reduces the risk of model overfitting. Second, a new Xception-MS network with stronger feature extraction capability, which is a combination of the Xception network and MS module, is proposed. The MS module is a new function module that can more effectively extract multi-scale information from rectal cancer images. In addition, to solve the deficiency of the small sample size of rectal cancer, the proposed network is combined with transfer learning technology. At last, the output layer of the network is modified, in which the global average pooling and a fully connected softmax layer are employed to replace the original ones, and then the rectal cancer 4 classification (T1, T2, T3, T4 staging) is output. Main results. Experiments of rectal cancer T staging are conducted on a dataset of 1078 rectal cancer images in 4 categories collected from the Department of Colorectal Surgery of the Third Affiliated Hospital of Kunming Medical University. The experimental results show that the accuracy, precision, recall and F1 values obtained by the model are 94.66%, 94.70%, 94.65%, and 94.67%, respectively. Significance. The experimental results show that our model is superior to the existing classification models, can effectively and automatically classify ultrasound images of rectal cancer, and can better assist doctors in the diagnosis of rectal cancer.
Conceptual framework for a digital organization

Purpose: Innovative technologies are forcing companies to incorporate digitization more into their value creation processes in order to remain competitive long-term. A transformation to a digital organization is therefore required. Aim of the paper is to identify which key components should be covered during the transformation to a digital organization and should therefore be part of a conceptual framework. The conceptual framework will help companies achieving a holistic transformation into a digital organization. Methodology: Based on an analysis of the literature, the key components necessary to successfully transition to digital organization are identified. The relevance of these core topics are then examined with the help of expert interviews. Based on the results, a conceptual framework for a holistic transformation into a digital organization is developed. Findings: Six key components are identified for the framework, which represent the basic requirements for the transformation into the digital organization. Furthermore, drivers as well as challenges are shown that companies have to overcome in the digital transformation. Originality: Scientifically sound concepts that include a holistic approach to transformation into a digital organization have, until now, lacked the scientific methods used to collect the content. The development of our framework has a scientifically grounding.
Data in Brief Transcriptome and H3K27 tri-methylation pro ﬁ ling of Ezh2-de ﬁ cient lung epithelium

The adaptation of the lungs to air breathing at birth requires the ﬁ ne orchestration of different processes to con- plays a critical role in lung lineage speci ﬁ cation and survival at birth. We performed a genome-wide tran- scriptome study combined with a genome-wide analysis of the distribution of H3K27 tri-methylation marks to interrogate the role of Ezh2 in lung epithelial cells. Lung cells isolated from Ezh2-de ﬁ cient and control mice at embryonic day E16.5 were sorted into epithelial and mesenchymal populations based on EpCAM expression. This enabled us to dissect the transcriptional and epigenetic changes induced by the loss of Ezh2 speci ﬁ cally in the lung epithelium.Herewe providea detaileddescription ofthe analysis
Statistical estimation of haemodynamic parameters in optical coherence tomography

Abstract of thesis entitled: “Statistical Estimation of Haemodynamic Parameters in Optical Coherence Tomography” Submitted by: CHAN, Chun Wang Aaron For the degree of Doctor of Philosophy at The University of Hong Kong in September 2014.of thesis entitled: “Statistical Estimation of Haemodynamic Parameters in Optical Coherence Tomography” Submitted by: CHAN, Chun Wang Aaron For the degree of Doctor of Philosophy at The University of Hong Kong in September 2014. Optical coherence tomography (OCT) is an imaging modality analogous to ultrasound. By using the interference properties of light, one may image to micrometer resolutions using interferometric methods. Most modern systems can acquire A-scans at kHz to MHz speeds, and are capable of real-time 3D imaging. OCT has been used extensively in ophthalmology and has been used in angiography to quantify blood flow. The aim of this research has been to develop statistically optimal estimators for blood flow estimation to take advantage of these hardware advances. This is achieved through a deeper understanding of the noise characteristics of OCT. Through mathematical derivations and simulations, the noise characteristics of OCT Doppler and flow imaging were accurately modelled as additive white noise and multiplicative decorrelation noise. Decorrelation arises due to relative motion of tissue relative to the OCT region of interest and adversely affects Doppler estimation. From these models maximum likelihood estimators (MLEs) that statistically outperform the commonly used Kasai autocorrelation estimator were derived. The Cramer-Rao lower bound (CRLB), which gives the theoretical lowest estimator variance for an unbiased estimator was derived for different noise regimes. It is shown that the AWGN MLE achieves the CRLB for additive white noise dominant conditions, and the decorrelation noise MLE achieves the CRLB under more general noise conditions. The use of computational algorithms that enhance the capabilities of OCT are demonstrated. This shows that this approach for determining parametric estimators may be used in a more general medical imaging context. In addition, the use of decorrelation as a measure of speed is explored, as it is itself proportional to flow speed. An abstract of exactly 265 words.