Miracle-dz/UniFAR-FTUs huggingface dataset:
The Yin and Yang of the Bone Marrow Microenvironment: Pros and Cons of Mesenchymal Stromal Cells in Acute Myeloid Leukemia

Mesenchymal stromal cells (MSCs) have, for a long time, been recognized as pivotal contributors in the set up and maintenance of the hematopoietic stem cell (HSC) niche, as well as in the development and differentiation of the lympho-hematopoietic system. MSCs also have a unique immunomodulatory capacity, which makes them able to affect, both in vitro and in vivo, the function of immune cells. These features, namely the facilitation of stem cell engraftment and the inhibition of lymphocyte responses, have both proven essential for successful allogeneic stem cell transplantation (allo-SCT), which remains the only curative option for several hematologic malignancies. For example, in steroid-refractory acute graft-vs. host disease developing after allo-SCT, MSCs have produced significant results and are now considered a treatment option. However, more recently, the other side of the MSC coin has been unveiled, because of their emerging role in creating a protective and immune-tolerant microenvironment able to support the survival of leukemic cells and affect the response to therapies. In this light, it has been proposed that the failure of current treatments to efficiently override the stroma-mediated protection of leukemic cells accounts for the high rate of relapse in acute myeloid leukemia, at least in part. In this review, we will focus on emerging microenvironment-driven mechanisms conferring a survival advantage to leukemic cells overt physiological HSCs. This body of evidence increasingly highlights the opportunity to consider tumor-microenvironment interactions when designing new therapeutic strategies.
An Analysis of Clinical Characteristics of Rare Bilateral Cerebral Peduncular Infarction

Objective: To investigate the anatomical characteristics, clinical manifestations, and imaging features of bilateral cerebral peduncular infarction. Methods: A retrospective analysis was performed on 11 patients diagnosed with bilateral cerebral peduncular infarction in the Affiliated Hospital of Xuzhou Medical University from December 2014 to December 2018. Their clinical and imaging features were analyzed and summarized in combination with the relevant national and international literature. Results: Among all the patients, there were eight cases with a history of hypertension, four cases with a history of diabetes mellitus, and four cases with a history of smoking. Conscious disturbance was observed in nine cases, quadriplegia in seven cases, pseudobulbar paralysis in three cases, and ataxia in one case. Brain magnetic resonance (MR) scans of bilateral cerebral peduncles showed patchy abnormal shadows with a hypointense signal on T1-weighted imaging (T1WI) and apparent diffusion coefficient (ADC) and hyperintense signal on T2-weighted imaging (T2WI), fluid-attenuated inversion recovery (FLAIR), and diffusion-weighted imaging (DWI). Computed tomography angiography (CTA) scans of head and neck showed severe stenosis or occlusion of vertebral artery, basilar artery, or posterior cerebral artery. All the patients received standardized treatment for cerebral infarction. Six patients died while five were left disabled. Conclusion: Bilateral cerebral peduncle infarction may be related to cerebral perfusion insufficiency caused by the stenosis or occlusion of vertebrobasilar artery and its branches. The main clinical manifestations are locked-in syndrome and persistent vegetative state. The specific imaging feature of “Mickey Mouse ear”-like infarction is associated with a poor prognosis.
Drug Discovery and Repurposing Inhibits a Major Gut Pathogen-Derived Oncogenic Toxin

Objective: The human intestinal microbiome plays an important role in inflammatory bowel disease (IBD) and colorectal cancer (CRC) development. One of the first discovered bacterial mediators involves Bacteroides fragilis toxin (BFT, also named as fragilysin), a metalloprotease encoded by enterotoxigenic Bacteroides fragilis (ETBF) that causes barrier disruption and inflammation of the colon, leads to tumorigenesis in susceptible mice, and is enriched in the mucosa of IBD and CRC patients. Thus, targeted inhibition of BFT may benefit ETBF carrying patients. Design: By applying two complementary in silico drug design techniques, drug repositioning and molecular docking, we predicted potential BFT inhibitory compounds. Top candidates were tested in vitro on the CRC epithelial cell line HT29/c1 for their potential to inhibit key aspects of BFT activity, being epithelial morphology changes, E-cadherin cleavage (a marker for barrier function) and increased IL-8 secretion. Results: The primary bile acid and existing drug chenodeoxycholic acid (CDCA), currently used for treating gallstones, cerebrotendinous xanthomatosis, and constipation, was found to significantly inhibit all evaluated cell responses to BFT exposure. The inhibition of BFT resulted from a direct interaction between CDCA and BFT, as confirmed by an increase in the melting temperature of the BFT protein in the presence of CDCA. Conclusion: Together, our results show the potential of in silico drug discovery to combat harmful human and microbiome-derived proteins and more specifically suggests a potential for retargeting CDCA to inhibit the pro-oncogenic toxin BFT.
Management of Pest Insects and Plant Diseases by Non-Transformative RNAi

Since the discovery of RNA interference (RNAi), scientists have made significant progress towards the development of this unique technology for crop protection. The RNAi mechanism works at the mRNA level by exploiting a sequence-dependent mode of action with high target specificity due to the design of complementary dsRNA molecules, allowing growers to target pests more precisely compared to conventional agrochemicals. The delivery of RNAi through transgenic plants is now a reality with some products currently in the market. Conversely, it is also expected that more RNA-based products reach the market as non-transformative alternatives. For instance, topically applied dsRNA/siRNA (SIGS – Spray Induced Gene Silencing) has attracted attention due to its feasibility and low cost compared to transgenic plants. Once on the leaf surface, dsRNAs can move directly to target pest cells (e.g., insects or pathogens) or can be taken up indirectly by plant cells to then be transferred into the pest cells. Water-soluble formulations containing pesticidal dsRNA provide alternatives, especially in some cases where plant transformation is not possible or takes years and cost millions to be developed (e.g., perennial crops). The ever-growing understanding of the RNAi mechanism and its limitations has allowed scientists to develop non-transgenic approaches such as trunk injection, soaking, and irrigation. While the technology has been considered promising for pest management, some issues such as RNAi efficiency, dsRNA degradation, environmental risk assessments, and resistance evolution still need to be addressed. Here, our main goal is to review some possible strategies for non-transgenic delivery systems, addressing important issues related to the use of this technology.
Crowd Control: Effects of Physical Crowding on Cargo Movement in Healthy and Diseased Neurons

High concentration of cytoskeletal filaments, organelles, and proteins along with the space constraints due to the axon’s narrow geometry lead inevitably to intracellular physical crowding along the axon of a neuron. Local cargo movement is essential for maintaining steady cargo transport in the axon, and this may be impeded by physical crowding. Molecular motors that mediate active transport share movement mechanisms that allow them to bypass physical crowding present on microtubule tracks. Many neurodegenerative diseases, irrespective of how they are initiated, show increased physical crowding owing to the greater number of stalled organelles and structural changes associated with the cytoskeleton. Increased physical crowding may be a significant factor in slowing cargo transport to synapses, contributing to disease progression and culminating in the dying back of the neuronal process. This review explores the idea that physical crowding can impede cargo movement along the neuronal process. We examine the sources of physical crowding and strategies used by molecular motors that might enable cargo to circumvent physically crowded locations. Finally, we describe sub-cellular changes in neurodegenerative diseases that may alter physical crowding and discuss the implications of such changes on cargo movement.
Modulating Activity in the Dorsolateral Prefrontal Cortex Changes Punishment in the 3-Player Prisoner’s Dilemma: A Transcranial Direct Current Stimulation Study

Altruistic punishment of social norm violations plays a crucial role in maintaining widespread cooperation in human societies, and punitive behavior has been suggested to be related to the activity level of the dorsolateral prefrontal cortex (DLPFC). This study used unilateral and bilateral transcranial direct current stimulation (tDCS) to investigate how modulating the activity of the DLPFC affects cooperation and punishment in a 3-player prisoner’s dilemma. We found that none of the unilateral stimulations changed the participants’ cooperation behaviors, while left anodal/right cathodal stimulation increased the participants’ cooperation. For punitive behavior, we found that all unilateral stimulations (i.e., right anodal, right cathodal, left anodal, left cathodal) and bilateral stimulations (i.e., right anodal/left cathodal, left anodal/right cathodal) significantly decreased the punishment imposed by the cooperators toward the defectors. In addition, right anodal stimulation significantly decreased the participant’s third-party punishment (TPP) imposed by the cooperators toward the defectors. The other three unilateral stimulations also significantly decreased the participant’s TPP imposed by the cooperators toward the defectors, but only when the punishment was revealed to the punished person. Our findings indicate that the mechanisms of selfishness and negative emotions suggested by previous studies probably interact with different stimulations: for anodal stimulations, the mechanism of negative emotions may overwhelm the mechanism of selfishness, while for cathodal stimulations, the mechanism of selfishness may be more dominant than the mechanism of negative emotions.
Coagulation FXIII-A Protein Expression Defines Three Novel Sub-populations in Pediatric B-Cell Progenitor Acute Lymphoblastic Leukemia Characterized by Distinct Gene Expression Signatures

Background: Leukemic B-cell precursor (BCP) lymphoblasts were identified as a novel expression site for coagulation factor XIII subunit A (FXIII-A). Flow cytometry (FC) revealed three distinct expression patterns, i.e., FXIII-A negative, FXIII-A dim, and FXIII-A bright subgroups. The FXIII-A negative subgroup was significantly associated with the “B-other” genetic category and had an unfavorable disease outcome. Methods: RNA was extracted from bone marrow lymphoblasts of 42 pediatric patients with BCP-acute lymphoblastic leukemia (ALL). FXIII-A expression was determined by multiparameter FC. Genetic diagnosis was based on conventional cytogenetic method and fluorescence in situ hybridization. Affymetrix GeneChip Human Primeview array was used to analyze global expression pattern of 28,869 well-annotated genes. Microarray data were analyzed by Genespring GX14.9. 1 software. Gene Ontology analysis was performed using Cytoscape 3.4. 0 software with ClueGO application. Selected differentially expressed genes were validated by RT-Q-PCR. Results: We demonstrated, for the first time, the general expression of F13A1 gene in pediatric BCP-ALL samples. The intensity of F13A1 expression corresponded to the FXIII-A protein expression subgroups which defined three characteristic and distinct gene expression signatures detected by Affymetrix oligonucleotide microarrays. Relative gene expression intensity of ANGPTL2, EHMT1 FOXO1, HAP1, NUCKS1, NUP43, PIK3CG, RAPGEF5, SEMA6A, SPIN1, TRH, and WASF2 followed the pattern of change in the intensity of the expression of the F13A1 gene. Common enhancer elements of these genes revealed by in silico analysis suggest that common transcription factors may regulate the expression of these genes in a similar fashion. PLAC8 was downregulated in the FXIII-A bright subgroup. Gene expression signature of the FXIII-A negative subgroup showed an overlap with the signature of “B-other” samples. DFFA, GIGYF1, GIGYF2, and INTS3 were upregulated and CD3G was downregulated in the “B-other” subgroup. Validated genes proved biologically and clinically relevant. We described differential expression of genes not shown previously to be associated with pediatric BCP-ALL. Conclusions: Gene expression signature according to FXIII-A protein expression status defined three novel subgroups of pediatric BCP-ALL. Multiparameter FC appears to be an easy-to-use and affordable method to help in selecting FXIII-A negative patients who require a more elaborate and expensive molecular genetic investigation to design precision treatment.
Genome-Wide Association Studies for Cerebrospinal Fluid Soluble TREM2 in Alzheimer’s Disease

Alzheimer’s disease (AD) is the most common form of dementia. Rare variants in triggering receptor expressed on myeloid cells 2 (TREM2) have been identified as risk factors for AD. Soluble TREM2 (sTREM2) in the cerebrospinal fluid (CSF) is a potential and novel biomarker of neuroinflammation implicated in the onset and progression of AD. To explore the roles of CSF sTREM2 on the pathogenesis of AD, we performed genome-wide association studies (GWAS) by using the data from Alzheimer’s Disease Neuroimaging Initiative (ADNI). We found CSF sTREM2 levels were elevated with the disease stages, but there was no significant difference between that of AD patients and normal participants. CSF sTREM2 was positively correlated with CSF total tau and phosphorylated-tau levels (ρ > 0.35, p < 1e-06; ρ > 0.32, p < 1e-05, respectively) for all disease states. We identified the most significant CSF sTREM2 related locus was rs7232 (FDR = 3.01e-08), a missense variant in MS4A6A gene of chromosome 11. Moreover, we also detected rs7232 was highly associated with MS4A6A gene expression (FDR = 1.37e-18). In addition, our pathway analysis for our significant GWAS results showed that biological processes for regulation of viruses and immune response were highly overrepresented or enriched. Our study suggests that CSF sTREM2 plays an informative role in AD progression. Moreover, CSF sTREM2 and AD is highly related to viral infections and immune response.
Common Neural System for Sentence and Picture Comprehension Across Languages: A Chinese–Japanese Bilingual Study

While common semantic representations for individual words across languages have been identified, a common meaning system at sentence-level has not been determined. In this study, fMRI was used to investigate whether an across-language sentence comprehension system exists. Chinese–Japanese bilingual participants (n = 32) were asked to determine whether two consecutive stimuli were related (coherent) or not (incoherent) to the same event. Stimuli were displayed with three different modalities (Chinese written sentences, Japanese written sentences, and pictures). The behavioral results showed no significant difference in accuracy and response times among the three modalities. Multi-voxel pattern analysis (MVPA) of fMRI data was used to classify the semantic relationship (coherent or incoherent) across the stimulus modalities. The classifier was first trained to determine coherency within Chinese sentences and then tested with Japanese sentences, and vice versa. A whole-brain searchlight analysis revealed significant above-chance classification accuracy across Chinese and Japanese sentences in the supramarginal gyrus (BA 40), extending into the angular gyrus (BA 39) as well as the opercular (BA 44) and triangular (BA 45) parts of the inferior frontal gyrus in the left hemisphere (cluster-level FWE corrected p < 0.05). Significant above-chance classification accuracy was also found across Japanese sentences and pictures in the supramarginal (BA 40) and angular gyrus (BA 39). These results indicate that a common meaning system for sentence processing across languages and modalities exists, and it involves the left inferior parietal gyrus.
Photodynamic Therapy Based on Graphene and MXene in Cancer Theranostics

Cancer is one of the leading causes of death in the world. Therefore, the development of new advanced and targeted strategies in cancer research for early diagnosis and treatment has become essential to improve diagnosis outcomes and reduce therapy side effects. Graphene and more recently, MXene, are the main representatives of the family of two-dimensional (2D) materials and are widely studied as multimodal nanoplatforms for cancer diagnostics and treatment, in particular leveraging their potentialities as photodynamic therapeutic agents. Indeed, due to their irreplaceable physicochemical properties, they are virtuous allies for photodynamic therapy (PDT) in combination with bioimaging, photothermal therapy, as well as drug and gene delivery. In this review, the rapidly progressing literature related to the use of these promising 2D materials for cancer theranostics is described in detail, highlighting all their possible future advances in PDT.
Characterization of the Genome Feature and Toxic Capacity of a Bacillus wiedmannii Isolate From the Hydrothermal Field in Okinawa Trough

The Bacillus cereus group is frequently isolated from soil, plants, food, and other environments. In this study, we report the first isolation and characterization of a B. cereus group member, Bacillus wiedmannii SR52, from the hydrothermal field in the Iheya Ridge of Okinawa Trough. SR52 was isolated from the gills of shrimp Alvinocaris longirostris, an invertebrate species found abundantly in the ecosystems of the hydrothermal vents, and is most closely related to B. wiedmannii FSL W8-0169. SR52 is aerobic, motile, and able to form endospores. SR52 can grow in NaCl concentrations up to 9%. SR52 has a circular chromosome of 5,448,361 bp and a plasmid of 137,592 bp, encoding 5,709 and 189 genes, respectively. The chromosome contains 297 putative virulence genes, including those encoding enterotoxins and hemolysins. Fourteen rRNA operons, 107 tRNAs, and 5 sRNAs are present in the chromosome, and 7 tRNAs are present in the plasmid. SR52 possesses 13 genomic islands (GIs), all on the chromosome. Comparing to FSL W8-0169, SR52 exhibits several streaking features in its genome, notably an exceedingly large number of non-coding RNAs and GIs. In vivo studies showed that following intramuscular injection into fish, SR52 was able to disseminate in tissues and cause mortality; when inoculated into mice, SR52 induced acute mortality and disseminated transiently in tissues. In vitro studies showed that SR52 possessed hemolytic activity, and the extracellular product of SR52 exhibited a strong cytotoxic effect. These results provided the first insight into the cytotoxicity and genomic feature of B. wiedmannii from the deep-sea hydrothermal environment.
Kinematic Analysis of Postural Stability During Ballet Turns (pirouettes) in Experienced and Novice Dancers

Turning is an important but difficult movement, often performed in ballet choreography. Understanding the postural sway during ballet turns is beneficial to both dancers and dance teachers alike. Accordingly, this study evaluated the postural sway angle during ballet turns in female novice and experienced ballet dancers by means of the inclination angle, determined from the center of mass (COM) and center of pressure (COP). Thirteen experienced dancers and 13 novice dancers performed ballet turns (pirouettes). The COM-COP inclination angle was measured during the preparatory, double-leg support, and single-leg support phases of the turn. The novice dancers exhibited significantly greater ranges of the COM-COP inclination angle in the anterior-posterior (AP) and medial-lateral (ML) directions during the preparatory (AP direction, p < 0.001; ML direction p = 0.035), double-leg support (AP direction p < 0.038; ML direction p = 0.011), and ending phases (AP direction p < 0.001; ML direction p = 0.024). Moreover, during the preparatory phase, the novice dancers failed to adjust their posture in a timely manner, and therefore showed overshooting errors. Finally, during the ending phase, the novice dancers showed a greater standard deviation of the COM-COP inclination angles and performed continual postural adjustments, leading to a less smooth movement than the experienced dancers. In conclusion, the novice dancers were suggested to focus on the COM-COP adjustment during both preparatory and ending phases.
Chromosome spreading of the (TTAGGG)n repeats in the Pipa carvalhoi Miranda-Ribeiro, 1937 (Pipidae, Anura) karyotype

Abstract Pipidae is a clade of Anura that diverged relatively early from other frogs in the phylogeny of the group. Pipids have a unique combination of morphological features, some of which appear to represent a mix of adaptations to aquatic life and plesiomorphic characters of Anura. The present study describes the karyotype of Pipa carvalhoi Miranda-Ribeiro, 1937, including morphology, heterochromatin distribution, and location of the NOR site. The diploid number of P. carvalhoi is 2n=20, including three metacentric pairs (1, 4, 8), two submetacentric (2 and 7), three subtelocentric (3, 5, 6), and two telocentric pairs (9 and 10). C-banding detected centromeric blocks of heterochromatin in all chromosome pairs and the NOR detected in chromosome pair 9, as confirmed by FISH using the rDNA 28S probe. The telomeric probes indicated the presence of interstitial telomeric sequences (ITSs), primarily in the centromeric region of the chromosomes, frequently associated with heterochromatin, suggesting that these repeats are a significant component of this region. The findings of the present study provide important insights for the understanding of the mechanisms of chromosomal evolution in the genus Pipa, and the diversification of the Pipidae as a whole.
Early Diagnosis of Mycoplasma pneumoniae in Children: Simultaneous Amplification and Testing (SAT) Is the Key

Objective: The effective diagnosis of Mycoplasma pneumoniae (MP) pneumonia (MPP) in children has been hampered by the difficulty of achieving an early diagnosis. The simultaneous amplification and testing (SAT) has the potential for early diagnosis of MP in children. Methods: Of the 1,180 children enrolled in this study, 169 were MPP antibody (Ab) seroconversion positive, 641 showed MPP positivity with a single Ab test, and 370 were MPP negative. Sera and pharyngeal swabs were collected for antibody testing and SAT detection, respectively, on admission. When the samples were Ab negative, the paired -Ab test was requested for MP 7 days later. Results: Using the Ab results as the diagnostic standard, the sensitivity, specificity, positive predictive values (PPV), and negative predictive values (NPV) for SAT were 72.8, 95.1, 97.0, and 61.5%, respectively. SAT had superior diagnostic value in the MPP group who had undergone Ab seroconversion (sensitivity: 82.2%; NPV: 92.1%) and in the short-course group also (sensitivity: 81.0%; NPV: 81.3%). Good agreement was observed between SAT and the paired-Ab results (kappa value = 0.79; P < 0.001), but there was a lack of consistency between SAT and the single-Ab test results on admission (kappa value = 0.54, P < 0.001). Conclusions: SAT is a rapid, sensitive, and specific method for MP diagnosis in pediatric patients. Our results indicate its value as an effective diagnostic tool for detecting MPP at the initial stage of an infection.