Miracle-dz/UniFAR-FTUs huggingface dataset:
Advanced radiotherapy technique in hepatocellular carcinoma with portal vein thrombosis: Feasibility and clinical outcomes

Background In Thailand, individuals with hepatocellular carcinoma (HCC) who develop portal vein tumor thrombosis (PVTT) have a restricted treatment option because to the extent of the disease, poor underlying liver function, and non-coverage of immuno/targeted therapy. Radiotherapy (RT) plays an increasingly important function in these patients. To investigate the feasibility, efficacy, and adverse event rates, we performed a retrospective analysis of patients with HCC with PVTT who underwent 3-dimensional conformal radiation (3DCRT), intensity-modulated radiation (IMRT), volumetric-modulated radiotherapy (VMAT), and stereotactic body radiotherapy (SBRT) in a single—institution. Objectives To examine clinical results in terms of overall survival (OS), local control (LC), response of primary tumor and PVTT, hepatic and gastrointestinal adverse reaction, and prognosis variables for OS and LC. Materials and methods Between July 2007 and August 2019, non-metastatic HCC with PVTT patients treated with RT were retrospectively reviewed and evaluated. Results The analysis included data from 160 patients. The mean age of the patients was 60.8 years ((95% CI 58.2–62.0). The median diameter of the tumor was 7.7 cm (range: 1–24.5). 85 (54.5%) individuals had PVTT in the main or first branch. At 1.8–10 Gy per fraction, the mean biologically effective dose (BED) as α/β ratio of 10 was 49.6 (95% CI 46.7–52.5) Gy10. The median survival time was 8.3 (95% CI 6.1–10.3) months. Survival rates at one and two years were 39.6% and 17.1%, respectively. Estimated incidence of local failure using competing risk analysis were 24% and 60% at 1 and 2 years, respectively. The overall response rate was 74%, with an 18.5 percent complete response rate. In multivariate analysis, tumor size, overall response, and radiation dose were all significant prognostic variables for OS. Hepatic unfavorable events of grade 3 and 4 were for 14.1% of the total. There was no occurrences of grade 3–4 gastrointestinal toxicity, either acute or late. Additionally, there were no treatment-related mortality. Conclusions Advanced RT is regarded as a safe and effective therapeutic option for HCC with PVTT. Overall survival was clearly related to tumor size, radiation dose, and tumor/PVTT response. Individuals with BED 56 Gy10 had significantly better overall survival than patients with BED 56 Gy10. A prospective randomized trial is required to validate these outcomes in order to corroborate these findings.
Effect of food source availability in the salivary gland transcriptome of the unique burying beetle Nicrophorus pustulatus (Coleoptera: Silphidae)

Nicrophorus is a genus of beetles that bury and transform small vertebrate carcasses into a brood ball coated with their oral and anal secretions to prevent decay and that will serve as a food source for their young. Nicrophorus pustulatus is an unusual species with the ability to overtake brood of other burying beetles and whose secretions, unlike other Nicrophorus species, has been reported not to exhibit antimicrobial properties. This work aims to better understand how the presence or absence of a food source influences the expression of genes involved in the feeding process of N. pustulatus. To achieve that, total RNA was extracted from pooled samples of salivary gland tissue from N. pustulatus and sequenced using an Illumina platform. The resulting reads were used to assemble a de novo transcriptome using Trinity. Duplicates with more than 95% similarity were removed to obtain a “unigene” set. Annotation of the unigene set was done using the Trinotate pipeline. Transcript abundance was determined using Kallisto and differential gene expression analysis was performed using edgeR. A total of 651 genes were found to be differentially expressed, including 390 upregulated and 261 downregulated genes in fed insects compared to starved. Several genes upregulated in fed beetles are associated with the insect immune response and detoxification processes with only one transcript encoding for the antimicrobial peptide (AMP) defensin. These results confirm that N. pustulatus does not upregulate the production of genes encoding AMPs during feeding. This study provides a snapshot of the changes in gene expression in the salivary glands of N. pustulatus following feeding while providing a well described transcriptome for the further analysis of this unique burying beetle.
A Review on Therapeutic Effects of Labisia pumila on Female Reproductive Diseases

The Labisia pumila (LP) is a traditional plant that is locally known as Kacip Fatimah, Selusuh Fatimah, or Pokok Ringgang by the Malaysian indigenous people. It is believed to facilitate their childbirth, treating their postchild birth and menstrual irregularities. The water extract of LP has shown to contain bioactive compounds such as flavonoids, ascorbic acid, β-carotene, anthocyanin, and phenolic acid, which contribute extensive antioxidant, anti-inflammatory, antimicrobial, and antifungal. The LP ethanolic extract exhibits significant estrogenic effects on human endomentrial adenocarcinoma cell in estrogen-free basal medium and promoting an increase in secretion of alkaline phosphate. Water based has been used for many generations, and studies had reported that it could displace in binding the antibodies and increase the estradiol production making it similar to esterone and estradiol hormone. LP extract poses a potential and beneficial aspect in medical and cosmeceutical applications. This is mainly due to its phytoestrogen properties of the LP. However, there is a specific functionality in the application of LP extract, due to specific functional group in phytoconstituent of LP. Apart from that, the extraction solvent is important in preparing the LP extract as it poses some significant and mild side effects towards consuming the LP extracts. The current situation of women reproductive disease such as postmenopausal syndrome and polycystic ovary syndrome is increasing. Thus, it is important to find ways in alternative treatment for women reproductive disease that is less costly and low side effects. In conclusion, these studies proven that LP has the potential to be an alternative way in treating female reproductive related diseases such as in postmenopausal and polysystic ovarian syndrome women.
The effect of pre-harvest shielding and spraying on yield, scab incidence, phenolic compounds and fruit qualityin organic apple production

Demand of organic apples is increasing but the yield is low due to apple scab disease. The aim of the present study was to investigate the effect of exposing three apple (Malus domestica Borkh.) cultivars ‘Red Elstar’, ‘Rubens’ and ‘Santana’ to different pre-harvest treatments in the orchard during the growing season 2014. Treatments were (i) untreated (control), (ii) sprayed with sulphur and potassium bicarbonate (sprayed), (iii) sprayed with sulphur and potassium bicarbonate and from fruit set supplemented with an extract of Acadian algae (sprayed + Acadian), and (iv) trees covered with a rain shield (shielded). The yield was recorded for every treatment. The incidence and severity of apple scab in the harvested fruits was evaluated. In addition, the content of 7 different phenols in apple peel was determined using HPLC. Further, the quality of apple fruits in relation to physio-chemical parameters was investigated. Results showed that all pre-harvest treatments reduced scab disease where shielding provided the best control: The rain shield reduced scab severity by 85-100 % in the three cultivars compared to the control and meanwhile increased the marketable yield of apple fruits. Control apples contained a significantly higher concentration of total phenols compared to apples receiving a treatment. Pre-treated apples had lower firmness, contained less total soluble solids and acids and had a higher sugar/acid ratio compared to control. It was concluded that shielding of apples showed to be a promising tool to diminish the presence of apple scab, increase yield and positively affect the eating quality at harvest.
Ozone‐induced changes in the murine lung extracellular vesicle small RNA landscape

Inhalation exposure to ozone (O3) causes adverse respiratory health effects that result from airway inflammation, a complex response mediated in part by changes to airway cellular transcriptional programs. These programs may be regulated by microRNAs transferred between cells (e.g., epithelial cells and macrophages) via extracellular vesicles (EV miRNA). To explore this, we exposed female C57BL/6J mice to filtered air (FA), 1, or 2 ppm O3 by inhalation and collected bronchoalveolar lavage fluid (BALF) 21 h later for markers of airway inflammation, EVs, and EV miRNA. Both concentrations of O3 significantly increased markers of inflammation (neutrophils), injury (total protein), and the number of EV‐sized particles in the BALF. Imagestream analysis indicated a substantial portion of particles was positive for canonical EV markers (CD81, CD51), and Siglec‐F, a marker of alveolar macrophages. Using high‐throughput small RNA sequencing, we identified several differentially expressed (DE) BALF EV miRNAs after 1 ppm (16 DE miRNAs) and 2 ppm (99 DE miRNAs) O3 versus FA exposure. O3 concentration‐response patterns in EV miRNA expression were apparent, particularly for miR‐2137, miR‐126‐3p, and miR‐351‐5p. Integrative analysis of EV miRNA expression and airway cellular mRNA expression identified EV miR‐22‐3p as a candidate regulator of transcriptomic responses to O3 in airway macrophages. In contrast, we did not identify candidate miRNA regulators of mRNA expression data from conducting airways (predominantly composed of epithelial cells). In summary, our data show that O3 exposure alters EV release and EV miRNA expression, suggesting that further investigation of EVs may provide insight into their effects on airway macrophage function and other mechanisms of O3‐induced respiratory inflammation.
Mutations at a split codon in the GTPase-encoding domain of OPA1 cause dominant optic atrophy through different molecular mechanisms

Abstract Exonic (i.e. coding) variants in genes associated with disease can exert pathogenic effects both at the protein and mRNA level, either by altering the amino acid sequence or by affecting pre-mRNA splicing. The latter is often neglected due to the lack of RNA analyses in genetic diagnostic testing. In this study we considered both pathomechanisms and performed a comprehensive analysis of nine exonic nucleotide changes in OPA1, which is the major gene underlying autosomal dominant optic atrophy (DOA) and is characterized by pronounced allelic heterogeneity. We focused on the GTPase-encoding domain of OPA1, which harbors most of the missense variants associated with DOA. Given that the consensus splice sites extend into the exons, we chose a split codon, namely codon 438, for our analyses. Variants at this codon are the second most common cause of disease in our large cohort of DOA patients harboring disease-causing variants in OPA1. In silico splice predictions, heterologous splice assays, analysis of patient’s RNA when available, and protein modeling revealed different molecular outcomes for variants at codon 438. The wildtype aspartate residue at amino acid position 438 is directly involved in the dimerization of OPA1 monomers. We found that six amino acid substitutions at codon 438 (i.e. all substitutions of the first and second nucleotide of the codon) destabilized dimerization while only substitutions of the first nucleotide of the codon caused exon skipping. Our study highlights the value of combining RNA analysis and protein modeling approaches to accurately assign patients to future precision therapies.
Oxygen sensing, anaesthesia and critical care: a narrative review

In 2019, the scientists who discovered how cells sense and adapt to oxygen availability were awarded the Nobel Prize. This elegant sensing pathway is conserved throughout evolution, and it underpins the physiology and pathology that we, as clinicians in anaesthesia and critical care, encounter on a daily basis. The purpose of this review is to bring hypoxia‐inducible factor, and the oxygen‐sensing pathway as a whole, to the wider clinical community. We describe how this unifying mechanism was discovered, and how it orchestrates diverse changes such as erythropoiesis, ventilatory acclimatisation, pulmonary vascular remodelling and altered metabolism. We explore the lessons learnt from genetic disorders of oxygen sensing, and the wider implications in evolution of all animal species, including our own. Finally, we explain how this pathway is relevant to our clinical practice, and how it is being manipulated in new treatments for conditions such as cancer, anaemia and pulmonary hypertension.
MRI and CT in the follow-up after irreversible electroporation of small renal masses.

PURPOSE Ablation plays a growing role in the treatment of small renal masses (SRMs) due to its nephron sparing properties and low invasiveness. Irreversible electroporation (IRE) has the potential, although still experimental, to overcome current limitations of thermal ablation. No prospective imaging studies exist of the ablation zone in the follow up after renal IRE in humans. Objectives are to assess computed tomography (CT) and magnetic resonance imaging (MRI) on the ablation zone volume (AZV), enhancement and imaging characteristics after renal IRE. METHODS Prospective phase 2 study of IRE in nine patients with ten SRMs. MRI imaging was performed pre-IRE, 1 week, 3 months, 6 months and 12 months after IRE. CT was performed pre-IRE, perioperatively (direct after ablation), 3 months, 6 months and 12 months after IRE. AZVs were assessed by two independent observers. Observer variation was analyzed. Evolution of AZVs, and relation between the needle configuration volume (NCV; planned AZV) and CT- and MRI volumes were evaluated. RESULTS Eight SRMs were clear cell renal cell carcinomas, one SRM was a papillary renal cell carcinoma and one patient had a non-diagnostic biopsy. On CT, median AZV increased perioperatively until 3 months post-IRE (respectively, 16.8 cm3 and 6.2 cm3) compared to the NCV (4.8 cm3). On MRI, median AZV increased 1-week post-IRE until 3 months post-IRE (respectively, 14.5 cm3 and 4.6 cm3) compared to the NCV (4.8 cm3). At 6 months the AZV starts decreasing (CT 4.8 cm3; MRI 3.0 cm3), continuing at 12 months (CT 4.2 cm3, MRI 1.1 cm3). Strong correlation was demonstrated between the planning and the post-treatment volumes. Inter-observer agreement between observers was excellent (CT 95% CI 0.82-0.95, MRI 95% CI 0.86-0.96). All SRMs appeared non-enhanced immediately after ablation, except for one residual tumour. Subtraction images confirmed non-enhancement on MRI in unclear enhancement cases (3/9). Directly after IRE, gas bubbles, perinephric stranding and edema were observed in all cases. CONCLUSION The AZV increases immediately on CT until 3 months after IRE. On MRI, the AZV increases at 1 week until 3 months post-IRE. At 6 months the AZV starts decreasing until 12 months post-IRE on both CT and MRI. Enhancement was absent post-IRE, except for one residual tumour. Gas bubbles, perinephric stranding and edema are normal findings directly post-IRE.
Rapid and Bihemispheric Reorganization of Neuronal Activity in Premotor Cortex after Brain Injury

Brain injuries cause hemodynamic changes in several distant, spared areas from the lesion. Our objective was to better understand the neuronal correlates of this reorganization in awake, behaving female monkeys. We used reversible inactivation techniques to “injure” the primary motor cortex, while continuously recording neuronal activity of the ventral premotor cortex in the two hemispheres, before and after the onset of behavioral impairments. Inactivation rapidly induced profound alterations of neuronal discharges that were heterogeneous within each and across the two hemispheres, occurred during movements of either the affected or nonaffected arm, and varied during different phases of grasping. Our results support that extensive, and much more complex than expected, neuronal reorganization takes place in spared areas of the bihemispheric cortical network involved in the control of hand movements. This broad pattern of reorganization offers potential targets that should be considered for the development of neuromodulation protocols applied early after brain injury. SIGNIFICANCE STATEMENT It is well known that brain injuries cause changes in several distant, spared areas of the network, often in the premotor cortex. This reorganization is greater early after the injury and the magnitude of early changes correlates with impairments. However, studies to date have used noninvasive brain imaging approaches or have been conducted in sedated animals. Therefore, we do not know how brain injuries specifically affect the activity of neurons during the generation of movements. Our study clearly shows how a lesion rapidly impacts neurons in the premotor cortex of both hemispheres. A better understanding of these complex changes can help formulate hypotheses for the development of new treatments that specifically target neuronal reorganization induced by lesions in the brain.
The conserved fertility factor SPACA4/Bouncer has divergent modes of action in vertebrate fertilization

Significance We show that Bouncer’s homolog in mammals, SPACA4, is required for efficient fertilization in mice. In contrast to fish, in which Bouncer is required for female fertility, SPACA4 is expressed exclusively in the sperm and is required for male fertility. SPACA4 and Bouncer present an intriguing example of homologous proteins that both play key roles in reproduction yet diverged in terms of gene expression pattern and mode of action. Overall, our work identifies SPACA4 as an important sperm protein necessary for zona pellucida penetration during mammalian fertilization. Since human SPACA4 is also expressed exclusively in sperm, we anticipate that our findings in mice will have relevance to human biology. Fertilization is the fundamental process that initiates the development of a new individual in all sexually reproducing species. Despite its importance, our understanding of the molecular players that govern mammalian sperm–egg interaction is incomplete, partly because many of the essential factors found in nonmammalian species do not have obvious mammalian homologs. We have recently identified the lymphocyte antigen-6 (Ly6)/urokinase-type plasminogen activator receptor (uPAR) protein Bouncer as an essential fertilization factor in zebrafish [S. Herberg, K. R. Gert, A. Schleiffer, A. Pauli, Science 361, 1029–1033 (2018)]. Here, we show that Bouncer’s homolog in mammals, Sperm Acrosome Associated 4 (SPACA4), is also required for efficient fertilization in mice. In contrast to fish, in which Bouncer is expressed specifically in the egg, SPACA4 is expressed exclusively in the sperm. Male knockout mice are severely subfertile, and sperm lacking SPACA4 fail to fertilize wild-type eggs in vitro. Interestingly, removal of the zona pellucida rescues the fertilization defect of Spaca4-deficient sperm in vitro, indicating that SPACA4 is not required for the interaction of sperm and the oolemma but rather of sperm and the zona pellucida. Our work identifies SPACA4 as an important sperm protein necessary for zona pellucida penetration during mammalian fertilization.
RNA profiling of laser microdissected human trophoblast subtypes at mid-gestation reveals a role for cannabinoid signaling in invasion

ABSTRACT Human placental architecture is complex. Its surface epithelium, specialized for transport, forms by fusion of cytotrophoblast progenitors into multinucleated syncytiotrophoblasts. Near the uterine surface, these progenitors assume a different fate, becoming cancer-like cells that invade its lining and blood vessels. The latter process physically connects the placenta to the mother and shunts uterine blood to the syncytiotrophoblasts. Isolation of trophoblast subtypes is technically challenging. Upon removal, syncytiotrophoblasts disintegrate and invasive cytotrophoblasts are admixed with uterine cells. We used laser capture to circumvent these obstacles. This enabled isolation of syncytiotrophoblasts and two subpopulations of invasive cytotrophoblasts from cell columns and the endovascular compartment of spiral arteries. Transcriptional profiling revealed numerous genes, the placental or trophoblast expression of which was not known, including neurotensin and C4ORF36. Using mass spectrometry, discovery of differentially expressed mRNAs was extended to the protein level. We also found that invasive cytotrophoblasts expressed cannabinoid receptor 1. Unexpectedly, screening agonists and antagonists showed that signals from this receptor promote invasion. Together, these results revealed previously unseen gene expression patterns that translate to the protein level. Our data also suggested that endogenous and exogenous cannabinoids can affect human placental development.
EFNet: evidence fusion network for tumor segmentation from PET-CT volumes

Precise delineation of target tumor from positron emission tomography-computed tomography (PET-CT) is a key step in clinical practice and radiation therapy. PET-CT co-segmentation actually uses the complementary information of two modalities to reduce the uncertainty of single-modal segmentation, so as to obtain more accurate segmentation results. At present, the PET-CT segmentation methods based on fully convolutional neural network (FCN) mainly adopt image fusion and feature fusion. The current fusion strategies do not consider the uncertainty of multi-modal segmentation and complex feature fusion consumes more computing resources, especially when dealing with 3D volumes. In this work, we analyze the PET-CT co-segmentation from the perspective of uncertainty, and propose evidence fusion network (EFNet). The network respectively outputs PET result and CT result containing uncertainty by proposed evidence loss, which are used as PET evidence and CT evidence. Then we use evidence fusion to reduce uncertainty of single-modal evidence. The final segmentation result is obtained based on evidence fusion of PET evidence and CT evidence. EFNet uses the basic 3D U-Net as backbone and only uses simple unidirectional feature fusion. In addition, EFNet can separately train and predict PET evidence and CT evidence, without the need for parallel training of two branch networks. We do experiments on the soft-tissue-sarcomas and lymphoma datasets. Compared with 3D U-Net, our proposed method improves the Dice by 8% and 5% respectively. Compared with the complex feature fusion method, our proposed method improves the Dice by 7% and 2% respectively. Our results show that in PET-CT segmentation methods based on FCN, by outputting uncertainty evidence and evidence fusion, the network can be simplified and the segmentation results can be improved.