Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of molecular subtypes and a prognostic signature based on chromatin regulators related genes in prostate cancer

The clinical and molecular phenotypes of prostate cancer (PCa) exhibit substantial heterogeneity, ranging from indolent to metastatic disease. In this study, we aimed to identify PCa subtypes and construct a gene signature that can predict the recurrence-free survival (RFS) of PCa patients based on chromatin regulators genes (CRGs). Strikingly, we identified two heterogeneous subtypes with distinct clinical and molecular characteristics. Furthermore, by performing differential analysis between the two CRGs subtypes, we successfully constructed a gene signature to predict PCa prognosis. The signature, comprising four genes (MXD3, SSTR1, AMH and PPFIA2), was utilized to classify PCa patients into two risk groups; the high-risk group was characterized by poor prognosis and more aggressive clinical features. Moreover, we investigated the immune profile, mutation landscape and molecular pathways in each of the groups. Additionally, drug-susceptibility testing was performed to explore sensitive drugs for high-risk patients. Furthermore, we found that MXD3 downregulation suppressed the proliferation of PCa cell lines in vitro. Overall, our results highlight the signature based on CRGs as a powerful tool for predicting RFS of PCa patients, as well as an indicator for personalized treatment of those patients.
Chemical abundances of the LMC cluster Hodge 11 and its surrounding field

Abstract We have obtained high-resolution VLT/FLAMES spectra of a number of giants in the LMC cluster Hodge 11 and the surrounding field. We present results of a detailed model-atmosphere abundance analysis for a variety of elements, including Fe, Ca, Ti, Si, Sc, Ni and Cr.
Changes in the structure, perfusion, and function of the hippocampus in type 2 diabetes mellitus

Objective This study aims to explore the changes in the structure, perfusion, and function of the bilateral hippocampus in type 2 diabetes mellitus (T2DM) applying multimodal MRI methods, hoping to provide reliable neuroimaging evidence for the diagnosis of hippocampus-related brain injury in T2DM. Methods We recruited 30 T2DM patients and 45 healthy controls (HCs), on which we performed 3D T1-weighted images, resting-state functional MRI (rs-fMRI), arterial spin labeling (ASL) sequences, and a series of cognitive tests. Then, we compared the differences of two groups in the cerebral blood flow (CBF) value, amplitude of low-frequency fluctuation (ALFF) value, fractional ALFF (fALFF) value, coherence-based regional homogeneity (Cohe-ReHo) value, and degree centrality (DC) values of the bilateral hippocampus. Results In the T2DM group, the bilateral hippocampal volumes and the CBF value of the right hippocampus were lower than those in the HCs, while the ALFF value, fALFF value, and Cohe-ReHo value of the bilateral hippocampus were higher than those in the HCs. Correlation analysis showed that fasting blood glucose (FBG) was negatively correlated with the residuals of left hippocampal volume (r = −0.407, P = 0.025) and right hippocampal volume (r = −0.420, P = 0.021). The residual of the auditory-verbal learning test (AVLT) (immediate) score was positively correlated with the residual of right hippocampal volume (r = 0.369, P = 0.045). Conclusion This study indicated that the volume and perfusion of the hippocampus are decreased in T2DM patients that related to chronic hyperglycemia. Local spontaneous neural activity and coordination are increased in the hippocampus of T2DM patients, possibly as an adaptive compensation for cognitive decline.
Incident factors in Andalusian university dropout: A qualitative approach from the perspective of higher education students

University dropout is currently one of the main challenges faced by government bodies and state and regional universities. Both personal and institutional reasons can be identified as root causes of university dropout. On a personal level, students accumulate experiences of academic failure that lead them to reflect on the possibility of continuing their studies, while from an institutional point of view, failure can be attributed to educational deficits, reputation, and quality parameters of the university institution itself. Even though more and more universities have educational policies aimed at reducing dropout rates, the dropout figures continue to rise, which shows that this is a complex problem due to the number of variables involved. The main objective of this study is to analyze the factors that influence university dropout among Andalusian students. The methodology is qualitative through a focus group with the participation of 12 students who dropped out of their academic studies in education science degrees at the University of Malaga (Spain). The study population corresponds to students who formalized their enrollment in the first year of the degree in the 2021/22 academic year. The content analysis followed a deductive category development model. The results reveal that the factors that explain the educational abandonment of the students, who are the object of this research, are identification with studies that did not meet their initial expectations, the use of traditionalist methodologies, the development of work activity, and the economic difficulties in covering the costs derived from university education. The main conclusion include the importance of designing educational policies in line with the reality and needs of the students, the use of innovative methodologies that increase the degree of motivation of the students, as well as studying dropouts from a holistic perspective, considering the multiple variables that influence its origin.
Elucidating afferent-driven presynaptic inhibition of primary afferent input to spinal laminae I and X

Although spinal processing of sensory information greatly relies on afferent-driven (AD) presynaptic inhibition (PI), our knowledge about how it shapes peripheral input to different types of nociceptive neurons remains insufficient. Here we examined the AD-PI of primary afferent input to spinal neurons in the marginal layer, lamina I, and the layer surrounding the central canal, lamina X; two nociceptive-processing regions with similar patterns of direct supply by Aδ- and C-afferents. Unmyelinated C-fibers were selectively activated by electrical stimuli of negative polarity that induced an anodal block of myelinated Aβ/δ-fibers. Combining this approach with the patch-clamp recording in an ex vivo spinal cord preparation, we found that attenuation of the AD-PI by the anodal block of Aβ/δ-fibers resulted in the appearance of new mono- and polysynaptic C-fiber-mediated excitatory postsynaptic current (EPSC) components. Such homosegmental Aβ/δ-AD-PI affected neurons in the segment of the dorsal root entrance as well as in the adjacent rostral segment. In their turn, C-fibers from the L5 dorsal root induced heterosegmental AD-PI of the inputs from the L4 Aδ- and C-afferents to the neurons in the L4 segment. The heterosegmental C-AD-PI was reciprocal since the L4 C-afferents inhibited the L5 Aδ- and C-fiber inputs, as well as some direct L5 Aβ-fiber inputs. Moreover, the C-AD-PI was found to control the spike discharge in spinal neurons. Given that the homosegmental Aβ/δ-AD-PI and heterosegmental C-AD-PI affected a substantial percentage of lamina I and X neurons, we suggest that these basic mechanisms are important for shaping primary afferent input to the neurons in the spinal nociceptive-processing network.
Development of a Chinese werewolf deception database

Although it is important to accurately detect deception, limited research in this area has been undertaken involving Asian people. We aim to address this gap by undertaking research regarding the identification of deception in Asians in realistic environments. In this study, we develop a Chinese Werewolf Deception Database (C2W2D), which consists of 168 video clips (84 deception videos and 84 honest videos). A total of 1,738,760 frames of facial data are recorded. Fifty-eight healthy undergraduates (24 men and 34 women) and 26 drug addicts (26 men) participated in a werewolf game. The development of C2W2D is accomplished based on a “werewolf” deception game paradigm in which the participants spontaneously tell the truth or a lie. Two synced high-speed cameras are used to capture the game process. To explore the differences between lying and truth-telling in the database, descriptive statistics (e.g., duration and quantity) and hypothesis tests are conducted using action units (AUs) of facial expressions (e.g., t-test). The C2W2D contributes to a relatively sizable number of deceptive and honest samples with high ecological validity. These samples can be used to study the individual differences and the underlying mechanisms of lies and truth-telling between drug addicts and healthy people.
Neurofilament Light Chain serum levels after Hypoxia-Ischemia in a newborn piglet model

Aim Neurofilament light Chain (NfL) is a promising brain injury biomarker which may assist diagnosis and prognostication in hypoxic-ischemic encephalopathy (HIE). The aim of this study was to investigate serum NfL levels after hypoxia-ischemia (HI) in a newborn piglet model. Second, to characterize the influence of sex, weight, and treatment with remote ischemic postconditioning (RIPC) on NfL and the correlation between NfL, brain imaging and histologic brain injury. Methods We used serum from 48 newborn piglets of both sexes subjected to 45 min of global HI, and 4 sham piglets. Blood was collected pre-HI, 2 h post-HI and 72 h post-HI. NfL was measured by single-molecule array (Simoa™). We analysed the temporal profile of NfL after HI, and correlations between NfL, magnetic resonance spectroscopy brain Lac/NAA ratios and histologic brain injury 72 h after HI. Results Median (IQR) NfL levels were: pre-HI: 66 pg/ml (45–87), 2 h post-HI: 105 pg/ml (77–140), and 72 h post-HI: 380 pg/ml (202–552). The increase in NfL after HI was statistically significant (p < 0.0001, mixed-effects ANOVA). Median NfL levels in sham animals were 41.4 pg/ml at baseline and 92.4 pg/ml at 72 h (p = 0.11, paired t-test). Neither sex, nor treatment with RIPC influenced NfL levels. Weight had a small, not biologically important, influence. NfL levels at 72 h were moderately correlated with histologic brain injury and brain Lac/NAA ratios. NfL 72 h post-HI > 330 pg/ml had a sensitivity of 89% (95% CI, 57%–99%) and a specificity of 52% (95% CI, 34%–69%) for predicting basal ganglia Lac/NAA ratio in the highest quartile. NfL 72 h post-HI > 445 pg/ml had a sensitivity of 90% (95% CI, 60%–99%) and a specificity of 74% (95% CI, 58%–86%) for predicting cortical brain histopathology injury in the highest quartile. Conclusion NfL increased after HI, with the largest values at 72 h post-HI. Early NfL was sensitive but not very specific, whereas NfL at 72 h was both highly sensitive and specific for exposure to moderate-severe HI in this model of HI-induced brain injury. This was supported by a moderate correlation of NfL at 72 h with brain Lac/NAA ratio and histopathology.
The gene regulatory network of Staphylococcus aureus ST239-SCCmecIII strain Bmb9393 and assessment of genes associated with the biofilm in diverse backgrounds

Introduction Staphylococcus aureus is one of the most prevalent and relevant pathogens responsible for a wide spectrum of hospital-associated or community-acquired infections. In addition, methicillin-resistant Staphylococcus aureus may display multidrug resistance profiles that complicate treatment and increase the mortality rate. The ability to produce biofilm, particularly in device-associated infections, promotes chronic and potentially more severe infections originating from the primary site. Understanding the complex mechanisms involved in planktonic and biofilm growth is critical to identifying regulatory connections and ways to overcome the global health problem of multidrug-resistant bacteria. Methods In this work, we apply literature-based and comparative genomics approaches to reconstruct the gene regulatory network of the high biofilm-producing strain Bmb9393, belonging to one of the highly disseminating successful clones, the Brazilian epidemic clone. To the best of our knowledge, we describe for the first time the topological properties and network motifs for the Staphylococcus aureus pathogen. We performed this analysis using the ST239-SCCmecIII Bmb9393 strain. In addition, we analyzed transcriptomes available in the literature to construct a set of genes differentially expressed in the biofilm, covering different stages of the biofilms and genetic backgrounds of the strains. Results and discussion The Bmb9393 gene regulatory network comprises 1,803 regulatory interactions between 64 transcription factors and the non-redundant set of 1,151 target genes with the inclusion of 19 new regulons compared to the N315 transcriptional regulatory network published in 2011. In the Bmb9393 network, we found 54 feed-forward loop motifs, where the most prevalent were coherent type 2 and incoherent type 2. The non-redundant set of differentially expressed genes in the biofilm consisted of 1,794 genes with functional categories relevant for adaptation to the variable microenvironments established throughout the biofilm formation process. Finally, we mapped the set of genes with altered expression in the biofilm in the Bmb9393 gene regulatory network to depict how different growth modes can alter the regulatory systems. The data revealed 45 transcription factors and 876 shared target genes. Thus, the gene regulatory network model provided represents the most up-to-date model for Staphylococcus aureus, and the set of genes altered in the biofilm provides a global view of their influence on biofilm formation from distinct experimental perspectives and different strain backgrounds.
Application and trend of bioluminescence imaging in metabolic syndrome research

Bioluminescence imaging is a non-invasive technology used to visualize physiological processes in animals and is useful for studying the dynamics of metabolic syndrome. Metabolic syndrome is a broad spectrum of diseases which are rapidly increasing in prevalence, and is closely associated with obesity, type 2 diabetes, nonalcoholic fatty liver disease, and circadian rhythm disorder. To better serve metabolic syndrome research, researchers have established a variety of animal models expressing luciferase, while also committing to finding more suitable luciferase promoters and developing more efficient luciferase-luciferin systems. In this review, we systematically summarize the applications of different models for bioluminescence imaging in the study of metabolic syndrome.
Macromolecular electronic device: Field-effect transistor with a polythiophene thin film

The first solid‐state field‐effect transistor has been fabricated utilizing a film of an organic macromolecule, polythiophene, as a semiconductor. The device characteristics have been optimized by controlling the doping levels of the polymer. The device is a normally off type and the source (drain) current can be modulated by a factor of 102–103 by varying the gate voltage. The carrier mobility and the transconductance have also been determined to be ∼10−5 cm2/V s and 3 nS, respectively, by means of electrical measurements.
Effects of continuous cropping Jiashi muskmelon on rhizosphere microbial community

Introduction The continuous cropping of crops can result in the deterioration of the soil environment and cause a decline in plant health and yield, which complicates agricultural production. However, the effects of continuous melon cropping on rhizospheric microbial communities remain poorly understood. Methods In this study, high-throughput absolute quantification 16S rRNA gene amplicon sequencing was employed to analyze the bacterial community structure of greenhouse rhizosphere soil from Jiashi muskmelon replanted for 0, 1, 2, and 3 years (CK, 1a, 2a, and 3a, respectively). Results The results showed that long- term continuous cropping caused significant changes in soil physicochemical properties. The bacterial absolute abundances increased, but the bacterial community richness and diversity were significantly lost (p < 0.05). The composition of bacterial community was more similar after 2 and 3 years of continuous cropping. The longer the continuous cropping years were, the greater the shift in the bacterial diversity and abundance. Analysis of potential functional components revealed that different bacterial groups were enriched in different continuous cropping years. The significant reduction of the taxa associated with nitrate reduction may be responsible for the loss of soil nitrogen in continuous cropping soil. Discussion In summary, continuous cropping had a significant impact on the bacterial community structure of Jiashi muskmelon rhizospheric soil, and these results will provide a reference for soil management and scientific fertilization of melon and other crops under a continuous cropping regime.
Editorial: Organ microenvironment in vascular formation, homeostasis and engineering

engineering technology to model and investigate stromal ﬁ broblast cell-EC interactions within the tumor microenvironment. Here they showed that ﬁ broblast secreted CXCL12 can reprogram the tumor microenvironment by potently inducing a leakier endothelium that is hospitable to angiogenesis and tumor cell intravasation
Advanced mycotoxin control and decontamination techniques in view of an increased aflatoxin risk in Europe due to climate change

Aflatoxins are toxic secondary metabolites produced by Aspergillus spp. found in staple food and feed commodities worldwide. Aflatoxins are carcinogenic, teratogenic, and mutagenic, and pose a serious threat to the health of both humans and animals. The global economy and trade are significantly affected as well. Various models and datasets related to aflatoxins in maize have been developed and used but have not yet been linked. The prevention of crop loss due to aflatoxin contamination is complex and challenging. Hence, the set-up of advanced decontamination is crucial to cope with the challenge of climate change, growing population, unstable political scenarios, and food security problems also in European countries. After harvest, decontamination methods can be applied during transport, storage, or processing, but their application for aflatoxin reduction is still limited. Therefore, this review aims to investigate the effects of environmental factors on aflatoxin production because of climate change and to critically discuss the present-day and novel decontamination techniques to unravel gaps and limitations to propose them as a tool to tackle an increased aflatoxin risk in Europe.
Cassava yield gap—A model-based assessment in Nigeria

Introduction Cassava production is essential for food security in sub-Saharan Africa and serves as a major calorie-intake source in Nigeria. Estimating the yield gap in Nigeria is essential to indicate the most important limiting factors for production, and identify the yield gap hotspot areas. Secondly, these assessments may help set agendas in policy development and research prioritization where current information is scarce. Materials and methods Here, Wwe used a crop model, LINTUL5, calibrated for five different cassava varieties based on field experiments embedded into a modeling framework SIMPLACE to estimate potential, water- and nutrient (current) limited cassava yield gaps (YG) as affected by climate factors and contributing a better understanding of yield gaps and its potentials in 30 states of Nigeria. Results Our study shows that cumulative radiation and precipitation were the most significant factors associated with cassava yield variability (p < 0.01). The YG averaged across states was estimated as 18.2 Ton7ha-1, with a maximum of 31.2 Ton7ha-1 35 in Kano state. Across the states, nutrient limitation accounts for 55.3% of the total cassava yield gap, while the remaining 44.7% is attributed to water limitation. The highest untapped water-limited yields were estimated in the northern states, such as Bauchi, Gombe, and Sokoto, characterized by the short rainy season. Conclusion Our results showed that most northern states are better equipped to become leading cassava producers in Nigeria under adequate crop management practices involving irrigation and soil fertility enhancement. We reached this conclusion because the northern states usually receive the highest radiation from their characteristic reduced cloud cover, even Therefore, policy and management interventions can be prioritized in these areas. Conclusively, the current cassava yield levels can be increased by a factor of five by emphasizing nutrient and soil health management and irrigation, particularly in areas characterized by a shorter rainy season (Sudan Savanna) in Nigeria.
CK2β-regulated signaling controls B cell differentiation and function

Serine-Threonine kinase CK2 supports malignant B-lymphocyte growth but its role in B-cell development and activation is largely unknown. Here, we describe the first B-cell specific knockout (KO) mouse model of the β regulatory subunit of CK2. CK2βKO mice present an increase in marginal zone (MZ) and a reduction in follicular B cells, suggesting a role for CK2 in the regulation of the B cell receptor (BCR) and NOTCH2 signaling pathways. Biochemical analyses demonstrate an increased activation of the NOTCH2 pathway in CK2βKO animals, which sustains MZ B-cell development. Transcriptomic analyses indicate alterations in biological processes involved in immune response and B-cell activation. Upon sheep red blood cells (SRBC) immunization CK2βKO mice exhibit enlarged germinal centers (GCs) but display a limited capacity to generate class-switched GC B cells and immunoglobulins. In vitro assays highlight that B cells lacking CK2β have an impaired signaling downstream of BCR, Toll-like receptor, CD40, and IL-4R all crucial for B-cell activation and antigen presenting efficiency. Somatic hypermutations analysis upon 4-Hydroxy-3-nitrophenylacetyl hapten conjugated to Chicken Gamma Globulin (NP-CGG) evidences a reduced NP-specific W33L mutation frequency in CK2βKO mice suggesting the importance of the β subunit in sustaining antibody affinity maturation. Lastly, since diffuse large B cell lymphoma (DLBCL) cells derive from GC or post-GC B cells and rely on CK2 for their survival, we sought to investigate the consequences of CK2 inhibition on B cell signaling in DLBCL cells. In line with the observations in our murine model, CK2 inactivation leads to signaling defects in pathways that are essential for malignant B-lymphocyte activation.