Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical characteristics and outcomes of 17 cases of inflammatory myofibroblastic tumor at a University Hospital in China

The aim of the present study was to explore the clinical and pathological characteristics, diagnosis, and treatment of inflammatory myofibroblastic tumor (IMT). A total of 17 patients with IMT diagnosed between July 2010 and February 2020 were included in the present study, and the clinical characteristics, pathological features, treatment and prognosis were analyzed retrospectively. The cohort consisted of 17 participants, including 12 men and 5 women, with a mean age of 34.76 years. The most common locations of tumors were the bronchi and the lungs (9 cases, including 1 case involving the mediastinum), followed by the colon and bladder (2 cases each), and the omentum majus, mesocolon, stomach and peritoneal cavity (1 case each). Immunohistochemical staining demonstrated that the tumor cells exhibited positive staining for anaplastic lymphoma kinase p80 (13/17), smooth muscle actin (12/17), cytokeratin pan (6/17), vimentin (5/17) and desmin (4/17). The follow-up time was 18–114 months. A patient with epithelial inflammatory myofibroblast sarcoma (EIMS) succumbed to the disease, 1 case was lost to follow-up, 2 cases relapsed and the other 13 cases were considered cured. IMTs may be malignant or low-grade. EIMS is a rare and invasive variant of IMT. The clinical and imaging manifestations are often unique and vary among individuals. Once confirmed by pathology, radical surgery should be the first choice of treatment.
Co-mining: Self-Supervised Learning for Sparsely Annotated Object Detection

Object detectors usually achieve promising results with the supervision of complete instance annotations. However, their performance is far from satisfactory with sparse instance annotations. Most existing methods for sparsely annotated object detection either re-weight the loss of hard negative samples or convert the unlabeled instances into ignored regions to reduce the interference of false negatives. We argue that these strategies are insufficient since they can at most alleviate the negative effect caused by missing annotations. In this paper, we propose a simple but effective mechanism, called Co-mining, for sparsely annotated object detection. In our Co-mining, two branches of a siamese network predict the pseudo-label sets for each other. To enhance multi-view learning and better mine unlabeled instances, the original image and corresponding augmented image are used as the inputs of two branches of the siamese network, respectively. Co-mining can serve as a general training mechanism applied to most of modern object detectors. Experiments are performed on MS COCO dataset with three different sparsely annotated settings using two typical frameworks: anchor-based detector RetinaNet and anchor-free detector FCOS. Experimental results show that our Co-mining with RetinaNet achieves 1.4%∼2.1% improvements compared with different baselines and surpasses existing methods under the same sparsely annotated setting.
Lactobacillus plantarum 06CC2 reduces hepatic cholesterol levels and modulates bile acid deconjugation in Balb/c mice fed a high‐cholesterol diet

Abstract Previous study suggested that dietary intake of Lactobacillus plantarum 06CC2 (LP06CC2) isolated from Mongolian dairy products showed various health beneficial effects. Here, the effect of LP06CC2 on the cholesterol metabolism in mice fed a cholesterol‐loaded diet was evaluated. Cholesterol and LP06CC2 were incorporated into the AIN93G‐based diet to evaluate the effect on cholesterol metabolism in Balb/c mice. Serum and liver cholesterol levels were significantly increased in mice fed a cholesterol‐loaded diet whereas the LP06CC2 ingestion suppressed the increase of liver cholesterol. LP06CC2 suppressed the increase of the hepatic damage indices. The increase of the cecal content and fecal butyrate were observed in mice fed LP06CC2. The analysis of bile acids clearly showed that LP06CC2 increased their deconjugation indicating the decrease of bile acid absorption. The protein expression of hepatic Cyp7A1 was also suppressed by LP06CC2 in mice fed cholesterol. Finally, in vitro studies showed that LP06CC2 had the most potent ability to deconjugate bile acids using glycocholate among the tested probiotic lactic acid bacteria isolated from Mongolian dairy products. Taken together, LP06CC2 is a promising microorganism for the reduction of the cholesterol pool via modulation of bile acid deconjugation.
Influences of the Culturing Media in the Virulence and Cell Wall of Sporothrix schenckii, Sporothrix brasiliensis, and Sporothrix globosa

Sporothrix schenckii, Sporothrix brasiliensis, and Sporothrix globosa are etiological agents of sporotrichosis, a human subcutaneous mycosis. Although the protocols to evaluate Sporothrix virulence in animal models are well described, the cell preparation before inoculation is not standardized, and several culturing media are used to grow yeast-like cells. Here, we found that carbon or nitrogen limitation during fungal cell preparation negatively impacted the ability of S. schenckii and S. brasiliensis to kill Galleria mellonella larvae, but not S. globosa. The fungal growth conditions associated with the short median survival of animals were accompanied by increased hemocyte countings, phenoloxidase activity, and cytotoxicity. The fungal growth under carbon or nitrogen limitation also affected the cell wall composition of both S. schenckii and S. brasiliensis and showed increased exposure of β-1,3-glucan at the cell surface, while those growing conditions had a minimal impact on the S. globosa wall, which had higher levels of this polysaccharide exposed on the wall regardless of the culture condition. This polysaccharide exposure was linked to the increased ability of insect hemocytes to uptake fungal cells, suggesting that this is one of the mechanisms behind the lower virulence of S. globosa or cells from the other species grown in carbon or nitrogen limitation.
Injuries in female and male elite Korean rowing athletes: an epidemiological study

Abstract This study aimed to determine the patterns of injury associated with training activities in elite South Korean rowing athletes training for the Olympic Games. Data were prospectively collected between 2010 and 2019 at the Korea National Training Center in South Korea. Three sports medicine doctors assessed athletes, and the data were stratified according to sex, rowing style, weight class, site of injury, and severity of injury. The groups were compared using the c 2 test. The 95 % confidence interval with Poisson rates and exact Poisson test were used for comparison of rates. In total 514 injuries were recorded during the study period, with an average of 2.86 injuries per athlete annually; among these, over half (57.8 %) were mild injuries. Most injuries occurred in the lower extremities (42.0 %), followed by the trunk (30.2 %), the upper extremities (24.9 %), and the head and neck area (2.9 %). Weight class was significantly associated with severity of injury in all rowing athletes (p < 0.001), for both male and female rowing athletes (p = 0.006 and p = 0.014, respectively). Lightweight male athletes demonstrated higher incidence rate of injury than open-weight male athletes (p < 0.001). On the contrary, lightweight female athletes demonstrated lower incidence rates of injury than open-weight female athletes (p < 0.001). These findings on the incidence of training injuries and patterns based on rowing styles, sexes, and weight classes may elucidate the circumstances leading to injuries in elite Korean rowing athletes. Furthermore, these findings may contribute to the development of programs to enhance athletic performance and reduce the incidence of sports injuries.
Nanoparticle System Based on Amino-Dextran as a Drug Delivery Vehicle: Immune-Stimulatory CpG-Oligonucleotide Loading and Delivery

The aim of this study is to prepare and characterize an amino-dextran nanoparticle (aDNP) platform and investigate two loading strategies for unmethylated cytosine-phosphate-guanine (CpG) oligonucleotide. aDNP was prepared by desolvation of amino-dextran followed by the chemical crosslinking of amino groups. Size, surface charge, and surface morphology of aDNP was determined by dynamic light scattering and transmission electron microscopy. CpG was either loaded onto aDNP by adsorption (CpG-adsorbed-aDNP) or conjugated to aDNP (CpG-conjugated-aDNP). In vitro cytokine production by bone marrow-derived dendritic cells (BMDCs) was measured by flow cytometry. aDNPs size and zeta potential could be controlled to produce uniform particles in the size range of 50 to 300 nm, surface charge of −16.5 to +14 mV, and were spherical in shape. Formulation control parameters investigated included the anti-solvent, water-to-anti-solvent ratio, level of amine functionality of dextran, and the molar ratio of glutaraldehyde to amine. aDNP could be lyophilized without additional cryoprotectant. Unloaded cationic aDNP (+13 mV) showed acceptable in vitro hemolysis. Unloaded and CpG-loaded aDNPs showed no cytotoxicity on BMDCs. CpG-loaded nanoparticles stimulated cytokine production by BMDCs, the level of cytokine production was higher for CpG-conjugated-aDNP compared to CpG-absorbed-aDNP. aDNP is a promising new drug delivery platform as its offers versatility in loading and tuning of particle properties.
Loss of MUNC18‐1 leads to retrograde transport defects in neurons

Loss of the exocytic Sec1/MUNC18 protein MUNC18‐1 or its target‐SNARE partners SNAP25 and syntaxin‐1 results in rapid, cell‐autonomous and unexplained neurodegeneration, which is independent of their known role in synaptic vesicle exocytosis. cis‐Golgi abnormalities are the earliest cellular phenotypes before degeneration occurs. Here, we investigated whether loss of MUNC18‐1 causes defects in intracellular membrane transport pathways in primary murine neurons that may explain neurodegeneration. Electron, confocal and super resolution microscopy confirmed that loss of MUNC18‐1 expression results in a smaller cis‐Golgi. In addition, we now show that medial‐Golgi and the trans‐Golgi Network are also affected. However, stacking and cisternae ultrastructure of the Golgi were normal. Overall, ultrastructure of null mutant neurons was remarkably normal just hours before cell death occurred. By synchronizing protein trafficking by conditional cargo retention in the endoplasmic reticulum using selective hooks (RUSH) and immunocytochemistry, we show that anterograde Endoplasmic Reticulum‐to‐Golgi and Golgi exit of endogenous and exogenous proteins were normal. In contrast, loss of MUNC18‐1 caused reduced retrograde Cholera Toxin B‐subunit transport from the plasma membrane to the Golgi. In addition, MUNC18‐1‐deficiency resulted in abnormalities in retrograde TrkB trafficking in an antibody uptake assay. We conclude that MUNC18‐1 deficient neurons have normal anterograde but reduced retrograde transport to the Golgi. The impairments in retrograde pathways suggest a role of MUNC18‐1 in endosomal SNARE‐dependent fusion and provide a plausible explanation for the observed Golgi abnormalities and cell death in MUNC18‐1 deficient neurons.
Spatial dependence of soil organic carbon mass and its relationship to soil series and topography

Concern about the global increase in atmospheric CO2 has focussed attention on C sequestration in soil and the influence of management practices on soil organic C (OC) stocks. Evaluation of management practices is required at scales comparable to farm management units, which encompass heterogeneous soils and different landforms. The objectives of this study were to describe the spatial dependence of soil OC mass in two adjacent fields with contrasting tillage practices on Black Chernozemic soils using geostatistics and relate it to topographic features and soil series. Mass of OC was measured for a surface layer, the A horizon and solum. The spatial dependence of OC mass was at a scale commensurate with topographic variation. Spatial analysis generally corroborated description of the sampling site by soil series, which represented differences in drainage as influenced by slope-position and redistribution of water across the landscape. Soil series alone or grouped by drainage class, therefore, provided a f.
Alive and Well: Encouraging Long Term Health Habits Through Implementation of Student Driven Wellness Programs in Medical Schools

Purpose A lack of coping mechanisms has been linked to increased rates of anxiety, depression, and imposter syndrome among medical students. In response, schools have been searching for methods to negate these results through wellness programs focused on student life. Methods A survey comprised of three multiple choice questions was disseminated amongst first year basic science medical students to determine their current state of well-being and potential interest in an educational course focused on wellness. Questions inquired about students’ current coping strategies and their interest in engaging in wellness focused activities. Participants’ responses were then used to create a Well-being selective. The course design was centered around a small points reward system in order to promote autonomous decision making and encourage balance of body, mind, and spirit. Results/Discussion Initial survey data suggests student interest in the creation of a wellness centered selective. Students engaged in a diverse array of activities to support the whole of their being. By tracking student choices of activities to engage in and feedback sent to the selective director, the selective design is being adapted to fit the needs of the student body. Conclusion Through promotion of on and off-campus extracurricular activities, the Well-being selective offers a non-threatening and self-paced approach to a balanced mind, body, and spirit. In this selective, students participate in diverse activities that support health and life balance, ranging from sunset group yoga to local botany. Student feedback suggests that through the selective they have experienced increased community engagement and support during their basic sciences medical education.
The Influence of Nitrogen Application Level on Eating Quality of the Two Indica-Japonica Hybrid Rice Cultivars

Indica-japonica hybrid rice cultivars show great yield potential but poor eating quality and require more nitrogen (N) input relative to japonica rice. However, the effect of N levels on the eating quality of indica-japonica hybrid rice is little known. A field experiment was carried out to investigate the effects of four N levels on two indica-japonica hybrid rice cultivars (Yongyou12 and Yongyou17) differing in eating quality. The results showed that the contents of amylose chains and water-insoluble storage proteins, especially prolamin, increased largely under a high N level, leading to deterioration of the rice-eating quality, although a low N level (100 N kg/ha) had a less negative effect on the eating quality. Moreover, both of the indica-japonica hybrids had high ratios of inferior grains (IG), and the ratio of IG increased with the N level. Grain weight and the immature ratio of IG were reduced and increased with the N level, respectively, which are also factors for deterioration of the eating quality. The two cultivars differed greatly in the responses of eating quality to the N level, with Yongyou17 being more sensitive than Yongyou12. The current results indicated that a high N level deteriorates the eating quality of indica-japonica hybrid rice mainly due to a large increase of IG.
Instance-Sensitive Algorithms for Pure Exploration in Multinomial Logit Bandit

Motivated by real-world applications such as fast fashion retailing and online advertising, the Multinomial Logit Bandit (MNL-bandit) is a popular model in online learning and operations research, and has attracted much attention in the past decade. In this paper, we give efficient algorithms for pure exploration in MNL-bandit. Our algorithms achieve instance-sensitive pull complexities. We also complement the upper bounds by an almost matching lower bound.
First Whole Transcriptome RNAseq on CHD8 Haploinsufficient Patient and Meta-Analyses Across Cellular Models Uncovers Likely Key Pathophysiological Target Genes

In 2019, we confirmed that the haploinsufficiency of CHD8 does indeed cause the novel syndromic neurodevelopmental disease we first discovered a dozen years before. Here, we report the first whole transcriptome RNAseq gene expression profiling for a patient with this new syndrome, as a preliminary exploration of potential pathophysiological mechanisms. We compared our patient transcriptome profile with that of all publicly available RNAseq datasets from human cellular models including neuronal progenitor cells, neurons and organoids. We compared differential gene expression profiles overall and conducted phenotype-informed data filtration based on the characteristic syndrome presentation. We found that concordance among differential gene expression profiles was poor across all datasets. Nevertheless, remarkably, we show that the patient blood differential gene expression profile most resembled that of the neuronal cell model, a finding that encourages further transcriptome profiling using patient blood samples. In addition, our custom phenotype-informed analyses yielded important, differentially expressed syndrome pathophysiology target genes. Finally, we note that genes dysregulated due to CHD8 heterozygous deletion are linked to known neurological as well as oncological pathways.
Emerging Role of Extracellular Vesicles in Immune Regulation and Cancer Progression

Simple Summary Accumulating evidence has reported that extracellular vesicles secreted by different tumor microenvironment cells can interfere with the host immune system. These vesicles transmit the signals in the tumor microenvironment that affect the proliferation, apoptosis, activation, and, metabolism of immune cells such as dendritic cells, T cells, macrophages, and natural killer cells, creating a pro-tumoral environment for tumor progression and survival. In this review, we summarize the recent literature on the function of extracellular vesicles derived from tumor cells and immune cells in regulating the critical processes associated with cancer progression. Besides, we also provide insights on how the extracellular vesicles are employed as diagnostic and prognostic biomarkers and drug carriers in cancer. Abstract The development of effective therapies for cancer treatment requires a better understanding of the tumor extracellular environment and a dynamic interaction between tumor cells, the cells of the immune system, and the tumor stroma. Increasing evidence suggests that extracellular vesicles play an important role in this interaction. Extracellular vesicles are nanometer-sized membrane-bound vesicles secreted by various types of cells that facilitate intracellular communication by transferring proteins, various lipids, and nucleic acids, especially miRNAs, between cells. Extracellular vesicles play discrete roles in the immune regulatory functions, such as antigen presentation, and activation or suppression of immune cells. Achieving therapeutic intervention through targeting of extracellular vesicles is a crucial area of research now. Thus, a deeper knowledge of exosome biology and the molecular mechanism of immune regulation is likely to provide significant insight into therapeutic intervention utilizing extracellular vesicles to combat this dreadful disease. This review describes the recent updates on immune regulation by extracellular vesicles in cancer progression and possible use in cancer therapy.
Identification and simultaneous determination of glycyrrhizin, formononetin, glycyrrhetinic acid, liquiritin, isoliquiritigenin, and licochalcone A in licorice by LC-MS/MS

Summary A new liquid chromatography-tandem mass spectrometry (LC-MS/MS) method was developed and validated for simultaneous determination of glycyrrhizin, formononetin, glycyrrhetinic acid, liquiritin, isoliquiritigenin, and licochalcone A in licorice. An Eclipse Plus C18 column (I.D. 4.6 × 100 mm, 3.5 μm particle size; Agilent) was used in the analysis. Electrospray ionization (ESI)-tandem interface in the negative mode was performed, and multiple reaction monitoring (MRM) was employed with the precursor multiple reaction monitoring production combination for the determination of six analytes. The average recoveries ranged from 98.30% to 100.13% with relative standard deviations (RSDs) ≤ 1.95%, and limits of detection (LODs) ranged from 2.1 to 3.6 pg. The applicability of this analytical approach was confirmed by the successful analysis of six samples. The results indicated that the established method was validated, sensitive, and reliable for the determination of six analytes in licorice.
Characterization of commercial poultry farms in Mexico: Towards a better understanding of biosecurity practices and antibiotic usage patterns

Mexico is one of the world’s major poultry producing countries. Two significant challenges currently facing the poultry industry are the responsible and judicious use of antimicrobials, and the potential occurrence of infectious disease outbreaks. For example, repeated outbreaks of highly pathogenic avian influenza virus subtype H7N3 have occurred in poultry since its first detection in Mexico in 2012. Both of these challenges can be addressed through good husbandry practices and the application of on-farm biosecurity measures. The aims of this study were: (i) to assess the biosecurity measures practiced across different types of poultry farms in Mexico, and (ii) to collect information regarding antimicrobial usage. A cross-sectional study was carried out through on-farm interviews on 43 poultry farms. A multiple correspondence analysis was performed to characterize the farms based on their pattern of biosecurity practices and antimicrobial usage. Three clusters of farms were identified using an agglomerative hierarchical cluster analysis. In each cluster, a specific farm type was predominant. The biosecurity measures that significantly differentiated the visited farms, thus allowing their clusterization, were: the use of personal protective equipment (e.g. face masks, hair caps, and eye protection), the requirement for a hygiene protocol before and after entering the farm, the use of exclusive working clothes by staff and visitors, footbath presence at the barn entrance, and the mortality disposal strategy. The more stringent the biosecurity measures on farms within a cluster, the fewer the farms that used antimicrobials. Farms with more biosecurity breaches used antimicrobials considered critically important for public health. These findings could be helpful to understand how to guide strategies to reinforce compliance with biosecurity practices identified as critical according to the farm type. We conclude by providing certain recommendations to improve on-farm biosecurity measures.