Miracle-dz/UniFAR-FTUs huggingface dataset:
In silico analysis identified miRNA-based therapeutic agents against glioblastoma multiforme

MicroRNAs (miRNAs or miRs) contribute to the development of various malignant neoplasms, including glioblastoma multiforme (GBM). The present study aimed to explore the pathogenesis of GBM and to identify latent therapeutic agents for patients with GBM, based on an in silico analysis. Gene chips that provide miRNA expression profiling in GBM were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed miRNAs (DEMs) were also determined via the RobustRankAggreg algorithm. The target genes of DEMs were predicted and then intersected with GBM-associated genes that were collected from the Gene Expression Profiling Interactive Analysis. Gene Oncology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of the overlapping genes were then performed. Simultaneously, a connectivity map (CMap) analysis was performed to screen for potential therapeutic agents for GBM. A total of 10 DEMs (hsa-miR-196a, hsa-miR-10b, hsa-miR-196b, hsa-miR-18b, hsa-miR-542-3p, hsa-miR-129-3p, hsa-miR-1224-5p, hsa-miR-876-3p and hsa-miR-770-5p) were obtained from three GEO gene chips (GSE25631, GSE42657 and GSE61710). Then, 1,720 target genes of the 10 miRNAs and 4,185 differently expressed genes in GBM were collected. By intersecting the aforementioned gene clusters, the present study identified 390 overlapping genes. GO and KEGG analyses of the 390 genes demonstrated that these genes were involved in certain cancer-associated biological functions and pathways. Eight genes [(GTPase NRas (NRAS), calcium/calmodulin-dependent protein kinase type II subunit Gamma (CAMK2G), platelet-derived growth factor receptor alpha (PDGFRA), calmodulin 3 (CALM3), cyclin-dependent kinase 6 (CDK6), calcium/calmodulin-dependent protein kinase type II subunit beta (CAMK2B), retinoblastoma-associated protein (RB1) and protein kinase C beta type (PRKCB)] that were centralized in the glioma pathway were selected for CMap analysis. Three chemicals (W-13, gefitinib and exemestane) were identified as putative therapeutic agents for GBM. In summary, the present study identified three miRNA-based chemicals for use as a therapy for GBM. However, more experimental data are needed to verify the therapeutic properties of these latent drugs in GBM.
Influence of bone meal degelatinisation and calcium source and particle size on broiler performance, bone characteristics and digestive and plasma alkaline phosphatase activity

ABSTRACT 1. The current experiment was performed to elucidate the effects of degelatinised bone meal (DBM) in combination with different particle sizes of limestone or oyster shell on broiler performance, bone characteristics and digestive and plasma alkaline phosphatase (ALP) activity. 2. Treatments were applied as a 3 × 3 factorial arrangement with three sources of P (DCP, bone meal and DBM) and three particle sizes (50, 100 and 200 µm) of limestone. Chickens were given either DCP or DBM with oyster shell (523 µm), resulting in a total of 11 treatments with 5 replicates of 8 chicks. 3. Performance criteria were measured weekly. Tibia strength, ash, calcium (Ca) and phosphorus (P) content and plasma P and Ca concentration along with plasma and intestinal alkaline phosphatase (ALP) activity and P digestibility were measured on d 14 and 28. 4. Body weight and FCR were improved in chicks which were fed DBM or oyster shell in comparison to the DCP and limestone respectively (P ≤ 0.05). Performance was influenced (P ≤ 0.05) by particle size; with coarser particles BW and feed intake were increased (P ≤ 0.05). Tibia shear force and P content were reduced (P ≤ 0.001), whereas tibia shear energy, length, ash and Ca content were increased by substitution of DCP with DBM or bone meal (P ≤ 0.001; P ≤ 0.05). A significant difference was observed in the tibia length between the chicks fed oyster shell or limestone with different particles (P ≤ 0.05). Plasma P concentration was reduced in chicks were fed with DBM, bone meal and lower limestone particle size. Intestinal ALP activity was increased (P ≤ 0.001) in chicks which were fed DBM, bone meal, oyster shell or coarse particles of limestone. The P digestibility in chicks fed bone meal was lower than that of those fed DBM or DCP (P ≤ 0.01). Overall, gelatin removal from bone meal improved broiler bone characteristics through the P digestibility and intestinal ALP activity enhancement.
Waveguiding and SERS Simplified Raman Spectroscopy on Biological Samples

Biomarkers detection at an ultra-low concentration in biofluids (blood, serum, saliva, etc.) is a key point for the early diagnosis success and the development of personalized therapies. However, it remains a challenge due to limiting factors like (i) the complexity of analyzed media, and (ii) the aspecificity detection and the poor sensitivity of the conventional methods. In addition, several applications require the integration of the primary sensors with other devices (microfluidic devices, capillaries, flasks, vials, etc.) where transducing the signal might be difficult, reducing performances and applicability. In the present work, we demonstrate a new class of optical biosensor we have developed integrating an optical waveguide (OWG) with specific plasmonic surfaces. Exploiting the plasmonic resonance, the devices give consistent results in surface enhanced Raman spectroscopy (SERS) for continuous and label-free detection of biological compounds. The OWG allows driving optical signals in the proximity of SERS surfaces (detection area) overcoming spatial constraints, in order to reach places previously optically inaccessible. A rutile prism couples the remote laser source to the OWG, while a Raman spectrometer collects the SERS far field scattering. The present biosensors were implemented by a simple fabrication process, which includes photolithography and nanofabrication. By using such devices, it was possible to detect cell metabolites like Phenylalanine (Phe), Adenosine 5-triphosphate sodium hydrate (ATP), Sodium Lactate, Human Interleukin 6 (IL6), and relate them to possible metabolic pathway variation.
Paternal Preconception Every-Other-Day Ethanol Drinking Alters Behavior and Ethanol Consumption in Offspring

Alcohol use disorder is a devastating disease with a complex etiology. Recent preclinical studies have revealed that paternal preconception chronic intermittent ethanol (EtOH) exposure via vaporized EtOH altered drinking behaviors and sensitivity to EtOH selectively in male offspring. In the current study, we used a voluntary oral route of paternal preconception EtOH exposure, i.e., intermittent every-other-day two-bottle choice drinking, and tested offspring for behavioral alterations. Fifteen EtOH drinking sires and 10 control sires were mated to EtOH naïve females to produce EtOH-sired and control-sired offspring. These offspring were tested using the elevated plus maze, open field, drinking in the dark, and unlimited access two-bottle choice assays. We found that paternal preconception every-other-day two-bottle choice drinking resulted in reduced EtOH consumption selectively in male offspring in the drinking in the dark assay compared to control-sired offspring. No differences were detected in either sex in the unlimited access two-bottle choice and elevated plus maze assays. Open field analysis revealed complex changes in basal behavior and EtOH-induced behaviors that were sex specific. We concluded that paternal preconception voluntary EtOH consumption has persistent effects that impact the next generation. This study adds to a growing appreciation that one’s behavioral response to EtOH and EtOH drinking behavior are impacted by EtOH exposure of the prior generation.
CropDeep: The Crop Vision Dataset for Deep-Learning-Based Classification and Detection in Precision Agriculture

Intelligence has been considered as the major challenge in promoting economic potential and production efficiency of precision agriculture. In order to apply advanced deep-learning technology to complete various agricultural tasks in online and offline ways, a large number of crop vision datasets with domain-specific annotation are urgently needed. To encourage further progress in challenging realistic agricultural conditions, we present the CropDeep species classification and detection dataset, consisting of 31,147 images with over 49,000 annotated instances from 31 different classes. In contrast to existing vision datasets, images were collected with different cameras and equipment in greenhouses, captured in a wide variety of situations. It features visually similar species and periodic changes with more representative annotations, which have supported a stronger benchmark for deep-learning-based classification and detection. To further verify the application prospect, we provide extensive baseline experiments using state-of-the-art deep-learning classification and detection models. Results show that current deep-learning-based methods achieve well performance in classification accuracy over 99%. While current deep-learning methods achieve only 92% detection accuracy, illustrating the difficulty of the dataset and improvement room of state-of-the-art deep-learning models when applied to crops production and management. Specifically, we suggest that the YOLOv3 network has good potential application in agricultural detection tasks.
Childhood sexual abuse and attachment insecurity: Associations with child psychological difficulties.

Childhood sexual abuse (CSA) is considered an important public health concern that can derail the developmental course of children. Given that children rely upon their attachment figures when they experience upsetting events, attachment organization may play a critical role in predicting victims' adaptation to CSA. To date, no studies have delineated the unique and interactive contributions of these two risk factors in the prediction of psychopathology. The aims of this study were to examine attachment in CSA victims and a comparison group and to assess the contributions of each risk factor to child psychological difficulties. Participants included 111 children aged 7-13, of whom 43 were CSA victims. Children completed an attachment interview and reported on their depressive symptoms. Their mothers reported on children's externalizing symptoms, internalizing symptoms, dissociation, and sexualized behavior. Our key findings showed that child victims of CSA were more likely to be classified as having insecure and disorganized attachment. Further, insecure attachment was the primary factor associated with higher self-reported depressive symptoms in all children and that CSA was associated with more parent-reported child externalizing problems, sexualizing problems, and dissociation. (PsycINFO Database Record (c) 2019 APA, all rights reserved).
Congruence of Reproductive Goals and Fertility-Related Attitudes of Adolescent and Young Adult Males and Their Parents After Cancer Treatment.

Purpose: Approximately half of all males experience fertility impairment after cancer treatment, which can diminish quality of life. Parents are often responsible for sharing health-related information, and parental recommendation strongly impacts fertility-related decisions; yet it remains unclear whether adolescents and young adults' (AYAs) and their parents' fertility-related goals/attitudes align. This study examined parent-AYAs congruence on fertility-related attitudes and (grand) parenthood goals during survivorship, and if parents were aware of their sons' parenthood goals and reproductive concerns. Methods: Males (15-25 years) and their parents were recruited within 1-8 years of completing cancer treatment. Based on the Health Belief Model, AYAs (N = 38), mothers (N = 33), and fathers (N = 24) reported on parenthood goals, perceived benefits/barriers of fertility testing/preservation, perceived susceptibility/severity of infertility, and fertility knowledge. Analyses included Pearson's correlations and paired-sample t-tests. Results: More than 80% of mothers, fathers, and AYAs desired future (grand) children. Mother-son dyads had differences in fertility knowledge (p = 0.037), and father-son dyads differed in parenthood goals (p = 0.024). AYAs perceived more fertility-related barriers than their mothers (p = 0.014) and fathers (p = 0.006). AYA survivors were less likely to report they could accept a life without a biological child compared with their mothers (p = 0.009) and fathers (p = 0.024). Conclusions: These findings suggest some similarities, yet important differences between male AYA survivors' and their parents' attitudes toward fertility and parenthood. As infertility is common in this population, and is associated with uncertainty and distress, these findings underscore the need for family-centered fertility-related interventions at the time of cancer diagnosis and throughout survivorship.
Connecting Ears to Eye Muscles: Evolution of a ‘Simple' Reflex Arc

Developmental and evolutionary data from vertebrates are beginning to elucidate the origin of the sensorimotor pathway that links gravity and motion detection to image-stabilizing eye movements - the vestibulo-ocular reflex (VOR). Conserved transcription factors coordinate the development of the vertebrate ear into three functional sensory compartments (graviception/translational linear acceleration, angular acceleration and sound perception). These sensory components connect to specific populations of vestibular and auditory projection neurons in the dorsal hindbrain through undetermined molecular mechanisms. In contrast, a molecular basis for the patterning of the vestibular projection neurons is beginning to emerge. These are organized through the actions of rostrocaudally and dorsoventrally restricted transcription factors into a ‘hodological mosaic' within which coherent and largely segregated subgroups are specified to project to different targets in the spinal cord and brain stem. A specific set of these regionally diverse vestibular projection neurons functions as the central element that transforms vestibular sensory signals generated by active and passive head and body movements into motor output through the extraocular muscles. The large dynamic range of motion-related sensory signals requires an organization of VOR pathways as parallel, frequency-tuned, hierarchical connections from the sensory periphery to the motor output. We suggest that eyes, ears and functional connections subserving the VOR are vertebrate novelties that evolved into a functionally coherent motor control system in an almost stereotypic organization across vertebrate taxa.
Functional Characterization of OXYL, A SghC1qDC LacNAc-specific Lectin from The Crinoid Feather Star Anneissia Japonica

We identified a lectin (carbohydrate-binding protein) belonging to the complement 1q(C1q) family in the feather star Anneissia japonica (a crinoid pertaining to the phylum Echinodermata). The combination of Edman degradation and bioinformatics sequence analysis characterized the primary structure of this novel lectin, named OXYL, as a secreted 158 amino acid-long globular head (sgh)C1q domain containing (C1qDC) protein. Comparative genomics analyses revealed that OXYL pertains to a family of intronless genes found with several paralogous copies in different crinoid species. Immunohistochemistry assays identified the tissues surrounding coelomic cavities and the arms as the main sites of production of OXYL. Glycan array confirmed that this lectin could quantitatively bind to type-2 N-acetyllactosamine (LacNAc: Galβ1-4GlcNAc), but not to type-1 LacNAc (Galβ1-3GlcNAc). Although OXYL displayed agglutinating activity towards Pseudomonas aeruginosa, it had no effect on bacterial growth. On the other hand, it showed a significant anti-biofilm activity. We provide evidence that OXYL can adhere to the surface of human cancer cell lines BT-474, MCF-7, and T47D, with no cytotoxic effect. In BT-474 cells, OXYL led to a moderate activation of the p38 kinase in the MAPK signaling pathway, without affecting the activity of caspase-3. Bacterial agglutination, anti-biofilm activity, cell adhesion, and p38 activation were all suppressed by co-presence of LacNAc. This is the first report on a type-2 LacNAc-specific lectin characterized by a C1q structural fold.
Clinical impact of Internet-based tools to guide therapeutic decisions for mantle cell lymphoma

Abstract Mantle cell lymphoma (MCL) is a rare cancer with diverse management options. Although clinical practice guidelines have become ubiquitous across medicine, the utility of guidelines for MCL management is limited by provider awareness and the lack of a definitive standard of care. We sought to determine whether expert recommendations, delivered as an online decision support tool, impacted practitioners’ therapeutic decisions with MCL. Participants were more likely than the experts to select aggressive regimens for both newly diagnosed and relapsed/refractory MCL. After seeing the expert recommendations, participants revealed that the expert opinion impacted their treatment choices in 103 of 365 clinical scenarios, suggesting that online decision support tools may increase the number of clinicians making treatment decisions for patients with MCL that are concordant with expert consensus recommendations.
Identifying Behavioral Phenotypes and Heterogeneity in Heart Valve Surface Endothelium

Heart valvular endothelial cells (VECs) are distinct from vascular endothelial cells (ECs), but have an uncertain context within the spectrum of known endothelial phenotypes, including lymphatic ECs (LECs). Profiling the phenotypes of the heart valve surface VECs would facilitate identification of a proper seeding population for tissue-engineered valves, as well as elucidate mechanisms of valvular disease. Porcine VECs and porcine aortic ECs (AECs) were isolated from pig hearts and characterized to assess known EC and LEC markers. A transwell migration assay determined their propensity to migrate toward vascular endothelial growth factor, an angiogenic stimulus, over 24 h. Compared to AECs, Flt-1 was expressed on almost double the percentage of VECs, measured as 74 versus 38%. The expression of angiogenic EC markers CXCR4 and DLL4 was >90% on AECs, whereas VECs showed only 35% CXCR4+ and 47% DLL4+. AECs demonstrated greater migration (71.5 ± 11.0 cells per image field) than the VECs with 30.0 ± 15.3 cells per image field (p = 0.032). In total, 30% of VECs were positive for LYVE1+/Prox1+, while these markers were absent in AECs. In conclusion, the population of cells on the surface of heart valves is heterogeneous, consisting largely of nonangiogenic VECs and a subset of LECs. Previous studies have indicated the presence of LECs within the interior of the valves; however, this is the first study to demonstrate their presence on the surface. Identification of this unique endothelial mixture is a step forward in the development of engineered valve replacements as a uniform EC seeding population may not be the best option to maximize transplant success.
The Shape of Mitochondrial Dysfunction in Down Syndrome

Oxidative stress (OS) and mitochondrial dysfunction (MD) have been extensively studied and defined as therapeutic targets in Down syndrome (DS). Though originally associated to individual genes located in supernumerary chromosome 21, OS and MD metabolic compromises appear to be linked to whole genome functionally defined transcriptional fingerprints that further exacerbate the contribution of critical genes in DS–AD pathology. As the main ROS generator, mitochondrial complex double‐membrane organization, tightly regulated fission/fusion dynamics, and involvement in critical pathways, makes it particularly vulnerable to functional alterations. Consequently, mitochondrial network morphology depends on its metabolic state and has been used as an indicator of cellular homeostasis. Initial qualitative categorization, suitable for sparse arranged fragments analysis, were proven to be ineffective to measure network connectivity and replaced by innovative tools that involve the transformation of raw images to linear skeletons. These manipulations allowed the development of a new generation of structural parameters, such as mean degree value (MDV). Alterations in DS mitochondrial networks include increased frequency of aberrant morphologies, shorter mitochondrial fragments, and significantly lower mitochondrial network connectivity. Similar structural and functional mitochondrial defects are common to other neurodegenerative diseases, such as Parkinson disease and Prion disease, and to a progeroid syndrome like HGPS. Therapeutic interventions aimed to either increase mitochondrial biogenesis or diminish OS using mitochondrial‐targeted antioxidants, successfully restored mitochondrial activity and structural organization, confirming the strong correlation between network form and function.
Diagnostic accuracy of established central auditory processing test batteries in patients with documented brain lesions.

PURPOSE The sensitivity, specificity, and efficiency of commonly used behavioral central auditory processing tests and test batteries were determined for 20 individuals with known lesions of the central auditory nervous system (CANS) and related auditory symptoms. RESEARCH DESIGN Twenty-nine individuals with no known neurological involvement served as the control group. Both groups were administered dichotic digits (DD), competing sentences (CS), frequency patterns (FP), and low-pass filtered speech (FS) tests. DATA ANALYSIS Diagnostic indices for individual tests and test batteries comprised of two, three, or four tests were calculated both using a lax criterion in which failure on only one test in a battery led to a positive diagnosis and using a strict criterion in which failure on all tests in the battery was necessary to trigger a positive diagnosis. RESULTS The test battery providing the best balance between sensitivity and specificity varied as a function of criterion. The two-test DD-FP battery using a strict criterion demonstrated the best balance. CONCLUSIONS Limitations of particular tests, the advantages of larger test batteries to more broadly examine multiple auditory processes, the degree to which the present results can be generalized clinically to populations without known brain lesions, and other clinical considerations are discussed.