Miracle-dz/UniFAR-FTUs huggingface dataset:
The Potential Role of Matrix Metalloproteinases 8 and 9 and Myeloperoxidase in Predicting Outcomes of Bacterial Meningitis of Childhood

Background Matrix metalloproteinases (MMPs) and myeloperoxidase (MPO) contribute to the inflammatory cascade in the cerebrospinal fluid (CSF) during bacterial meningitis. We determined levels of MPO, MMP-8, MMP-9, and tissue inhibitor of metalloproteinase- (TIMP-) 1 in the CSF of children with bacterial meningitis and investigated how these inflammatory mediators relate to each other and to the disease outcomes. Methods Clinical data and the diagnostic CSF samples from 245 children (median age eight months) with bacterial meningitis were obtained from a clinical trial in Latin America in 1996–2003. MMP-9 levels in the CSF were assessed by zymography, while MMP-8, MPO, and TIMP-1 concentrations were determined with immunofluorometric and enzyme-linked immunosorbent assays. Results MPO correlated positively with MMP-8 (rho 0.496, P < 0.001) and MMP-9 (rho 0.153, P = 0.02) but negatively with TIMP-1 (rho -0.361, P < 0.001). MMP-8 emerged as the best predictor of disease outcomes: a CSF MMP-8 concentration above the median increased the odds of death 4.9-fold (95% confidence interval 1.8–12.9). Conclusions CSF MMP-8 presented as an attractive prognostic marker in children with bacterial meningitis.
Differential Expression of IFN-γ, IL-10, TLR1, and TLR2 and Their Potential Effects on Downgrading Leprosy Reaction and Erythema Nodosum Leprosum

Leprosy reactions are acute immunological events that occur during the evolution of chronic infectious disease causing neural damage and disabilities. A study using blood samples of 17 leprosy reaction patients and 17 reaction-free was carried out by means of associations between antigens, receptors, and expression of cytokines, using path analysis providing new insights into the immunological mechanisms involved in triggering leprosy reactions. Toll-like receptors (TLR) such as TLR1 and TLR2, presented balanced expression in the reaction-free multibacillary (MB) group (TLR1: 1.01 ± 0.23, TLR2: 1.22 ± 0.18; p = 0.267). On the other hand, downgrading type 1 reaction (T1R) (TLR1: 1.24 ± 0.17, TLR2: 2.88 ± 0.37; p = 0.002) and erythema nodosum leprosum (ENL) (TLR1: 1.93 ± 0.17, TLR2: 2.81 ± 0.15; p = 0.004) revealed an unbalance in relation to the expression of these receptors. When the path analysis was approached, it was noted that interleukin 10 (IL-10) expression showed a dependence relation with phenolic glycolipid I (PGL-I) in downgrading T1R (direct effect = 0.503 > residual effect = 0.364), whereas in ENL, such relationship occurred with lipoarabinomannan (LAM) (direct effect = 0.778 > residual effect = 0.280). On the contrary, in the reaction-free leprosy group, interferon-gamma (IFN-γ) levels were dependent on the association between TLR2 and TLR1 (0.8735). The high TLR2 expression associated with IL-10 levels, in the leprosy reaction groups, may be hypothetically related to the formation of TLR2/2 homodimers and/or TLR2/6 heterodimers linked to evasion mechanisms in downgrading reactions and pathophysiology of ENL.
Handgrip Strength Cut-Off Values for the Undernutrition Risk Screening among Elderly Men and Women in Bosnia and Herzegovina

Objectives To determine the optimal cut-off points of handgrip strength (HGS) to identify the undernutrition risk among individuals older than 65 years of age in Bosnia and Herzegovina. Design Cross-sectional study. Setting Towns of Sarajevo, Foca, Rogatica, and Pale in Bosnia and Herzegovina. Participants 300 community-dwelling older adults and 146 nursing home residents. Comprehensive Geriatric multidimensional assessment (CGA) was carried out to evaluate general health, functional, and cognitive capabilities. Nutritional status and undernutrition risk were assessed by Mini Nutritional Assessment (MNA) and Seniors in the Community: risk evaluation for eating and nutrition, version II (SCREEN II). HGS was measured with a Smedley dynamometer. Results According to the classification of nutritional status by MNA, 42% of community-dwelling men and 39% of community-dwelling women were at undernutrition risk. The undernutrition risk was significantly higher among nursing home residing men (89%) and women (78%) (p < 0.001). When nutritional status was assessed by SCREEN II, 100% on nursing home residents, 86% of community-dwelling men and 80% of women were identified as having a high risk for undernutrition. Per MNA, HGS cut-off thresholds were 23.50 kgF (65–74 years) and 19.50 kgF (≥75 years) for men; 15.50 kgF (65–74 years) and 13.50 kgF (≥75 years) for women. Per SCREEN II, cut-points were 28.50 kgF (65–74 years) and 24.50 kgF (≥75 years) for men; 24.50 kgF (65–74 years), 19.50 kgF (≥75 years for women). Conclusion HGS can be a useful instrument to identify undernutrition risk among the elderly patients. This study provides threshold for men and women older than 65 years of age in Bosnia and Herzegovina.
Cyclin-Dependent Kinase Regulatory Subunit 2 Indicated Poor Prognosis and Facilitated Aggressive Phenotype of Hepatocellular Carcinoma

Cyclin-dependent kinase regulatory subunit 2 (CKS2) is a member of the cell cycle-dependent protein kinase subunit family, which is implicated as an oncogene in various malignancies. However, the clinical significance, oncogenic functions, and related mechanisms of CKS2 in hepatocellular carcinoma (HCC) remain largely unclear. In the present study, expression features and prognostic value of CKS2 were evaluated in the bioinformatic databases and HCC tissues. The effects of CKS2 on the malignant phenotypes of HCC cells were explored in vitro. According to the analyses of three bioinformatic databases, mRNA levels of CKS2 were elevated in HCC tissues compared with the normal tissues. Immunohistochemical assays found that high CKS2 expression was closely associated with liver cirrhosis (P = 0.019), poor differentiation (P = 0.02), portal vein invasion (P < 0.001), TNM stage (P = 0.019), tumor metastasis (P = 0.008), and recurrence (P = 0.003). The multivariate regression analyses suggested that CKS2 was an independent prognostic factor for overall survival (HR = 2.088, P = 0.014) and disease-free survival (HR = 2.511, P = 0.002) of HCC patients. Moreover, the bioinformatic analyses indicated that CKS2 might be associated with the malignant phenotypes in HCC progression. In addition, in vitro assays showed that CKS2 expression was higher in HCC cell lines than in normal liver cells. Knockdown of CKS2 remarkably repressed the proliferation, colony formation (P = 0.0003), chemoresistance, migration (P = 0.0047), and invasion (P = 0.0012) of HCC cells. Taken together, overexpression of CKS2 was significantly correlated with poor prognosis of HCC patients and the malignant phenotypes of HCC cells, suggesting that it was a novel prognostic biomarker and potential target of HCC.
Crotalus durissus ruruima Snake Venom and a Phospholipase A2 Isolated from This Venom Elicit Macrophages to Form Lipid Droplets and Synthesize Inflammatory Lipid Mediators

Viper snake Crotalus durissus ruruima (Cdr) is a subspecies found in northern area of Brazil. Among the snakes of Crotalus genus subspecies, the venom of Cdr presents highest level of crotoxin, which is the major component of Crotalus snake venoms, formed by two subunits (crotapotin and a phospholipase A2 named CBr) and presents potent neurotoxic activity. Curiously, the venom of C. d. ruruima (CdrV) is better neutralized by antibothropic than by anticrotalic serum, strongly suggesting that this venom has similarities with venom of Bothrops genus snakes with regard to the ability to induce inflammation. Macrophages are cells with a central role in inflammatory and immunological responses. Upon inflammatory stimuli, these cells exhibit increased numbers of lipid droplets, which are key organelles in the synthesis and release of inflammatory mediators. However, the effects of CdrV and CBr in macrophage functions are unknown. We herein investigated the ability of CdrV and CBr to activate macrophages with focus on the formation of lipid droplets (LDs), synthesis of lipid mediators, and mechanisms involved in these effects. The involvement of LDs in PGE2 biosynthesis was also assessed. Stimulation of murine macrophages with CdrV and CBr induced an increased number of LDs and release of prostanoids (PGE2, PGD2, and TXB2). Neither CdrV nor CBr induced the expression of COX-1 and COX-2 by macrophages. LDs induced by both CdrV and CBr are associated to PLIN2 recruitment and expression and were shown to be dependent on COX-1, but not COX-2 activity. Moreover, PGE2 colocalized to CdrV- and CBr-induced LDs, revealing the role of these organelles as sites for the synthesis of prostanoids. These results evidence, for the first time, the ability of a whole snake venom to induce formation of LDs and the potential role of these organelles for the production of inflammatory mediators during envenomation by Crotalus snakes.
Integrated Cognitive Architecture for Robot Learning of Action and Language

The manner in which humans learn, plan, and decide actions is a very compelling subject. Moreover, the mechanism behind high-level cognitive functions, such as action planning, language understanding, and logical thinking, has not yet been fully implemented in robotics. In this paper, we propose a framework for the simultaneously comprehension of concepts, actions, and language as a first step toward this goal. This can be achieved by integrating various cognitive modules and leveraging mainly multimodal categorization by using multilayered multimodal latent Dirichlet allocation (mMLDA). The integration of reinforcement learning and mMLDA enables actions based on understanding. Furthermore, the mMLDA, in conjunction with grammar learning and based on the Bayesian hidden Markov model (BHMM), allows the robot to verbalize its own actions and understand user utterances. We verify the potential of the proposed architecture through experiments using a real robot.
Properdin: A Novel Target for Neuroprotection in Neonatal Hypoxic-Ischemic Brain Injury

Background: Hypoxic-ischemic (HI) encephalopathy is a major cause of neonatal mortality and morbidity, with a global incidence of 3 per 1,000 live births. Intrauterine or perinatal complications, including maternal infection, constitute a major risk for the development of neonatal HI brain damage. During HI, inflammatory response and oxidative stress occur, causing subsequent cell death. The presence of an infection sensitizes the neonatal brain, making it more vulnerable to the HI damage. Currently, therapeutic hypothermia is the only clinically approved treatment available for HI encephalopathy, however it is only partially effective in HI alone and its application in infection-sensitized HI is debatable. Therefore, there is an unmet clinical need for the development of novel therapeutic interventions for the treatment of HI. Such an alternative is targeting the complement system. Properdin, which is involved in stabilization of the alternative pathway convertases, is the only known positive regulator of alternative complement activation. Absence of the classical pathway in the neonatal HI brain is neuroprotective. However, there is a paucity of data on the participation of the alternative pathway and in particular the role of properdin in HI brain damage. Objectives: Our study aimed to validate the effect of global properdin deletion in two mouse models: HI alone and LPS-sensitized HI, thus addressing two different clinical scenarios. Results: Our results indicate that global properdin deletion in a Rice-Vannucci model of neonatal HI and LPS-sensitized HI brain damage, in the short term, clearly reduced forebrain cell death and microglial activation, as well as tissue loss. In HI alone, deletion of properdin reduced TUNEL+ cell death and microglial post-HI response at 48 h post insult. Under the conditions of LPS-sensitized HI, properdin deletion diminished TUNEL+ cell death, tissue loss and microglial activation at 48 h post-HI. Conclusion: Overall, our data suggests a critical role for properdin, and possibly also a contribution in neonatal HI alone and in infection-sensitized HI brain damage. Thus, properdin can be considered a novel target for treatment of neonatal HI brain damage.
Transcriptomic and Network Analysis Highlight the Association of Diabetes at Different Stages of Alzheimer’s Disease

Alzheimer’s disease (AD) and type 2 diabetes (T2D) are among the most prevalent chronic diseases affecting the aging population. Extensive research evidence indicates that T2D is a well-established risk factor for AD; however, the molecular mechanisms underlying this association have not been fully elucidated. Furthermore, how T2D may contribute to the progression of AD is a subject of extensive investigation. In this study, we compared the blood transcriptome of patients with mild cognitive impairment (MCI), AD, and advanced AD to those afflicted with T2D to unveil shared and unique pathways and potential therapeutic targets. Blood transcriptomic analyses revealed a positive correlation between gene expression profiles of MCI, AD, and T2D in seven independent microarrays. Interestingly, gene expression profiles from women with advanced AD correlated negatively with T2D, suggesting sex-specific differences in T2D as a risk factor for AD. Network and pathway analysis revealed that shared molecular networks between MCI and T2D were predominantly enriched in inflammation and infectious diseases whereas those networks shared between overt AD and T2D were involved in the phosphatidylinositol 3-kinase and protein kinase B/Akt (PI3K-AKT) signaling pathway, a major mediator of insulin signaling in the body. The PI3K-AKT signaling pathway became more significantly dysregulated in the advanced AD and T2D shared network. Furthermore, endocrine resistance and atherosclerosis pathways emerged as dysregulated pathways in the advanced AD and T2D shared network. Interestingly, network analysis of shared differentially expressed genes between children with T2D and MCI subjects identified forkhead box O3 (FOXO3) as a central transcriptional regulator, suggesting that it may be a potential therapeutic target for early intervention in AD. Collectively, these results suggest that T2D may be implicated at different stages of AD through different molecular pathways disrupted during the preclinical phase of AD and more advanced stages of the disease.
Sheep Are Susceptible to the Bovine Adapted Transmissible Mink Encephalopathy Agent by Intracranial Inoculation and Have Evidence of Infectivity in Lymphoid Tissues

Transmissible mink encephalopathy (TME) is a food borne prion disease. Epidemiological and experimental evidence suggests similarities between the agents of TME and L-BSE. This experiment demonstrates the susceptibility of four different genotypes of sheep to the bovine adapted TME agent by intracranial inoculation. The four genotypes of sheep used in this experiment had polymorphisms corresponding to codons 136, 154, and 171 of the prion gene: V136R154Q171/VRQ, VRQ/ARQ, ARQ/ARQ, and ARQ/ARR. All intracranially inoculated sheep without comorbidities (15/15) developed clinical signs and had detectable PrPSc by immunohistochemistry, western blot, and enzyme immunoassay (EIA). The mean incubation periods in sheep with bovine adapted TME correlated with their relative genotypic susceptibility. There was peripheral distribution of PrPSc in the trigeminal ganglion and neuromuscular spindles; however, unlike classical scrapie and C-BSE in sheep, sheep inoculated with the bovine TME agent did not have immunohistochemically detectable PrPSc in the lymphoid tissue. To rule out the presence of infectivity, the lymph nodes of two sheep genotypes, VRQ/VRQ, and ARQ/ARQ, were bioassayed in transgenic mice expressing ovine prion protein. Mice intracranially inoculated with retropharyngeal lymph node from a VRQ/VRQ sheep were EIA positive (3/17) indicating that sheep inoculated with the bovine TME agent harbor infectivity in their lymph nodes despite a lack of detection with conventional immunoassays. Western blot analysis demonstrated similarities in the migration patterns between bovine TME in sheep, the bovine adapted TME inoculum, and L-BSE. Overall, these results demonstrate that sheep are susceptible to the bovine adapted TME agent, and the tissue distribution of PrPSc in sheep with bovine TME is distinct from classical scrapie.
First-Principles Calculation of Physical Tensors of α-Diisopropylammonium Bromide (α-DIPAB) Molecular Ferroelectric Crystal

We report accurate calculations of tonsorial elements of α-Diisopropylammonium bromide (α-DIPAB) molecular ferroelectric crystal. In particular, elastic, piezoelectric and dielectric tensors were calculated using Vienna ab initio simulation package (VASP) within the framework of density functional (DFT) theory. The determination of above parameters allows an accurate description of the energy landscape for modeling of realistic devices at finite temperatures. We determine the major physical tensors in energy expansion of total energy per volume of un-deformed crystal to provide experimentalists with valuable information for designing and fabrication of pyroelectric detectors, capacitors, piezoelectric ferroelectric memories, display devices, electro-optic devices, and ultrasound transducers based on α-DIPAB. The spontaneous polarization P_s was calculated using Berry phase approach and found to be 22.64 μC⁄〖cm〗^2 in agreement with reported theoretical value. The dynamical Born effective charge tensor is reported for all atoms in the unit cell of α-DIPAB to get a deeper insight into the bonding network. The neighboring layers of DIPA molecules were found to be strongly crenelated due to the strong short-ranged electrostatic repulsion between Br sites in the DIPAB crystal structure. The organization of species in DIPA molecular layer as well as in the bromine “stitching” layer is essential for accurate calculation of DIPAB elastic properties. Having understood the actual network bonding in α-DIPAB, we calculated the components of the elastic moduli tensor. Our results indicate that a Young’s modulus of 10-180 GPa and a shear modulus of 4-26 GPa were found. Thus, α-DIPAB phase has a great potential to be a terrific candidate for flexible electronic device applications. The value of the principle component of electronic contribution to the static dielectric tensor of α-DIPAB is found to be ≈ 2.5, i.e. 50% smaller than that in typical perovskite-based ferroelectrics. Therefore, α-DIPAB is anticipated to exhibit creative materials' innovations. It offers highly customized features for specific applications, including insulation on polymer thick film conductive inks in the manufacture of membrane switches and flex circuits. Furthermore, clamped-ion piezoelectric tensor is calculated. Our results indicate a reasonable piezoelectric response of this polar crystal making it a low cost attractive candidate for piezoelectric applications.
Host Range and Symbiotic Effectiveness of N2O Reducing Bradyrhizobium Strains

Emissions of the potent greenhouse gas N2O is one of the environmental problems associated with intensive use of synthetic N fertilizers, and novel N2O mitigation strategies are needed to minimize fertilizer applications and N2O release without affecting agricultural efficiencies. Increased incorporation of legume crops in agricultural practices offers a sustainable alternative. Legumes, in their symbiosis with nitrogen fixing bacteria, rhizobia, reduce the need for fertilizers and also respond to the need for increased production of plant-based proteins. Not all combinations of rhizobia and legumes result in efficient nitrogen fixation, and legume crops therefore often need to be inoculated with compatible rhizobial strains. Recent research has demonstrated that some rhizobia are also very efficient N2O reducers. Several nutritionally and economically important legumes form root nodules in symbiosis with bacteria belonging to Bradyrhizobium. Here, the host-ranges of fourteen N2O reducing Bradyrhizobium strains were tested on six legume hosts; cowpea, groundnut, mung bean, haricot bean, soybean, and alfalfa. The plants were grown for 35 days in pots in sterile sand supplemented with N-free nutrient solution. Cowpea was the most promiscuous host nodulated by all test strains, followed by groundnut (11 strains) and mungbean (4 strains). Three test strains were able to nodulate all these three legumes, while none nodulated the other three hosts. For cowpea, five strains increased the shoot dry weight and ten strains the shoot nitrogen content (pairwise comparison; p < 0.05). For groundnut the corresponding results were three and nine strains. The symbiotic effectiveness for the different strains ranged from 45 to 98% in cowpea and 34 to 95% in groundnut, relative to fertilized controls. The N2O reduction capacity of detached nodules from cowpea plants inoculated with one of these strains confirmed active N2O reduction inside the nodules. When released from senescent nodules such strains are expected to also act as sinks for N2O produced by denitrifying organisms in the soil microbial community. Our strategy to search among known N2O-reducing Bradyrhizobium strains for their N2-fixation effectiveness successfully identified several strains which can potentially be used for the production of legume inoculants with the dual capacities of efficacious N2-fixation and N2O reduction.
K5 Capsule and Lipopolysaccharide Are Important in Resistance to T4 Phage Attack in Probiotic E. coli Strain Nissle 1917

Rapidly growing antibiotic resistance among gastrointestinal pathogens, and the ability of antibiotics to induce the virulence of these pathogens makes it increasingly difficult to rely on antibiotics to treat gastrointestinal infections. The probiotic Escherichia coli strain Nissle 1917 (EcN) is the active component of the pharmaceutical preparation Mutaflor® and has been successfully used in the treatment of gastrointestinal disorders. Gut bacteriophages are dominant players in maintaining the microbial homeostasis in the gut, however, their interaction with incoming probiotic bacteria remains to be at conception. The presence of bacteriophages in the gut makes it inevitable for any probiotic bacteria to be phage resistant, in order to survive and successfully colonize the gut. This study addresses the phage resistance of EcN, specifically against lytic T4 phage infection. From various experiments we could show that (i) EcN is resistant toward T4 phage infection, (ii) EcN’s K5 polysaccharide capsule plays a crucial role in T4 phage resistance and (iii) EcN’s lipopolysaccharide (LPS) inactivates T4 phages and notably, treatment with the antibiotic polymyxin B which neutralizes the LPS destroyed the phage inactivation ability of isolated LPS from EcN. Combination of these identified properties in EcN was not found in other tested commensal E. coli strains. Our results further indicated that N-acetylglucosamine at the distal end of O6 antigen in EcN’s LPS could be the interacting partner with T4 phages. From our findings, we have reported for the first time, the role of EcN’s K5 capsule and LPS in its defense against T4 phages. In addition, by inactivating the T4 phages, EcN also protects E. coli K-12 strains from phage infection in tri-culture experiments. Our research highlights phage resistance as an additional safety feature of EcN, a clinically successful probiotic E. coli strain.