Miracle-dz/UniFAR-FTUs huggingface dataset:
Influence of Temperature and Backslopping Time on the Microbiota of a Type I Propagated Laboratory Wheat Sourdough Fermentation

ABSTRACT Sourdough fermentation is a cereal fermentation that is characterized by the formation of stable yeast/lactic acid bacteria (LAB) associations. It is a unique process among food fermentations in that the LAB that mostly dominate these fermentations are heterofermentative. In the present study, four wheat sourdough fermentations were carried out under different conditions of temperature and backslopping time to determine their effect on the composition of the microbiota of the final sourdoughs. A substantial effect of temperature was observed. A fermentation with 10 backsloppings (once every 24 h) at 23°C resulted in a microbiota composed of Leuconostoc citreum as the dominant species, whereas fermentations at 30 and 37°C with backslopping every 24 h resulted in ecosystems dominated by Lactobacillus fermentum. Longer backslopping times (every 48 h at 30°C) resulted in a combination of Lactobacillus fermentum and Lactobacillus plantarum. Residual maltose remained present in all fermentations, except those with longer backslopping times, and ornithine was found in almost all fermentations, indicating enhanced sourdough-typical LAB activity. The sourdough-typical species Lactobacillus sanfranciscensis was not found. Finally, a nonflour origin for this species was hypothesized.
Microbial mannan inhibits bacterial killing by macrophages: a possible pathogenic mechanism for Crohn's disease.

BACKGROUND & AIMS Crohn's disease (CD) is mimicked by inherited phagocyte disorders and is associated with circulating antibodies against yeast mannan (anti-Saccharomyces cerevisiae antibody; ASCA). We speculated that mannans might impair phagocyte function. METHODS S cerevisiae mannan was assessed for its effects on human peripheral blood neutrophils, adherent monocytes, and monocyte-derived macrophages (MDM). RESULTS Mannan caused dose-related increased survival of CD Escherichia coli HM605 within adherent monocytes from 24% +/- 10.5% (control) to 114% +/- 22.7% with mannan 1 mg/mL at 2 hours (mean +/- SEM, n = 9; P = .0002). Electron microscopy showed E coli HM605 surviving and probably replicating within macrophage vesicles. Mannan (1 mg/mL) inhibited the respiratory burst in neutrophils and monocytes (both P = .002) and bacterial killing within MDM (P < .001). E coli survival was increased within macrophages from TLR4(-/-) (126% +/- 3.5% survival at 2 hours) and MyD88(-/-) (134.8% +/- 6.5%) mice compared with wild-type mice (both P < .0001). Mannan had no additional effect, showing that TLR4 and MyD88 are involved in bacterial killing by macrophages and its inhibition by mannan. Putative CD-associated micro-organisms were screened for the ASCA mannan epitope by Galanthus nivalis lectin (GNA) blotting. ASCA epitope was expressed by Candida albicans and Mycobacterium paratuberculosis but not by Mycobacterium tuberculosis or E coli. Supernatants from M paratuberculosis culture inhibited killing of E coli HM605 by adherent human monocytes and murine macrophages. The inhibitory activity was removed by GNA-affinity chromatography. CONCLUSIONS Suppression of mucosal phagocyte function by microbial mannans, possibly of Mycobacterial origin, may contribute to CD pathogenesis.
Specific induction of macrophage inflammatory protein 1‐α in glial cells of Sandhoff disease model mice associated with accumulation of N‐acetylhexosaminyl glycoconjugates

Sandhoff disease is a lysosomal storage disease caused by simultaneous deficiencies of β‐hexosaminidase A (HexA; αβ) and B (HexB; ββ), due to a primary defect of the β‐subunit gene (HEXB) associated with excessive accumulation of GM2 ganglioside (GM2) and oligosaccharides with N‐acetylhexosamine residues at their non‐reducing termini, and with neurosomatic manifestations. To elucidate the neuroinflammatory mechanisms involved in its pathogenesis, we analyzed the expression of chemokines in Sandhoff disease model mice (SD mice) produced by disruption of the murine Hex β‐subunit gene allele (Hexb–/–). We demonstrated that chemokine macrophage inflammatory protein‐1 α (MIP‐1α) was induced in brain regions, including the cerebral cortex, brain stem and cerebellum, of SD mice from an early stage of the pathogenesis but not in other systemic organs. On the other hand, little changes in other chemokine mRNAs, including those of RANTES (regulated upon activation, normal T expressed and secreted), MCP‐1 (monocyte chemotactic protein‐1), SLC (secondary lymphoid‐tissue chemokine), fractalkine and SDF‐1 (stromal derived factor‐1), were detected. Significant up‐regulation of MIP‐1α mRNA and protein in the above‐mentioned brain regions was observed in parallel with the accumulation of natural substrates of HexA and HexB. Immunohistochemical analysis revealed that MIP‐1α‐immunoreactivity (IR) in the above‐mentioned brain regions of SD mice was co‐localized in Iba1‐IR‐positive microglial cells and partly in glial fibrillary acidic protein (GFAP)‐IR‐positive astrocytes, in which marked accumulation of N‐acetylglucosaminyl (GlcNAc)‐oligosaccharides was observed from the presymptomatic stage of the disease. In contrast, little MIP‐1α‐IR was observed in neurons in which GM2 accumulated predominantly. These results suggest that specific induction of MIP‐1α might coincide with the accumulation of GlcNAc‐oligosaccharides due to a HexB deficiency in resident microglia and astrocytes in the brains of SD mice causing their activation and acceleration of the progressive neurodegeneration in SD mice.
Characterization of Two Autographa californica Nucleopolyhedrovirus Proteins, Ac145 and Ac150, Which Affect Oral Infectivity in a Host-Dependent Manner

ABSTRACT The genome of the baculovirus Autographa californica nuclear polyhedrosis virus (AcMNPV) contains two homologues, orf145 and orf150, of the Heliothis armigera Entomopoxvirus (HaEPV) 11,000-kDa gene. Polyclonal antibodies raised against the Ac145 or Ac150 protein were utilized to demonstrate that they are expressed from late to very late times of infection and are within the nuclei of infected Sf-21 cells. Transmission electron microscopy coupled with immunogold labeling of Ac145 found this protein within the nucleus in areas of nucleocapsid assembly and maturation, along with some association with the enveloped bundles of virions within the developing occlusion bodies (OBs). Ac150 was found to be mainly associated with enveloped bundles of virions within OBs and also with those not yet occluded. Both Ac145 and Ac150 were found to be present in budded virus as well as OBs. Both orf145 and orf150 were deleted from the AcMNPV genome, singly or together, and these deletion mutants were assessed for oral infectivity both in Trichoplusia ni and Heliothis virescens larvae. Deletion of Ac145 led to a small but significant drop in infectivity (sixfold) compared to wild-type (wt) AcMNPV for T. ni but not for H. virescens. Deletion of Ac150 alone had no effect on infectivity of the virus for either host. However, deletion of both Ac145 and Ac150 gave a recombinant virus with a drastic (39-fold) reduction in infectivity compared to wt virus for H. virescens. Intrahemocoelic injection of budded virus from the double-deletion virus into H. virescens larvae is as infectious to this host as wt budded virus, indicating that Ac145 and Ac150 play a role in primary oral infection of AcMNPV, the extent of which is host dependent.
Contributions to the herpetofauna of the Albertine Rift: Two new species of chameleon (Sauria: Chamaeleonidae) from an isolated montane forest, south eastern Democratic Republic of Congo.

Two new species of chameleons from the genera Rhampholeon and Kinyongia are described from an isolated montane forest remnant situated toward the southern end of the Albertine Rift bordering Lake Tanganyika. The closest known localities of species from these genera are 200km and 400km to the north respectively, separated by large intervening tracts of lowland savannah and Brachystegia (Miombo) woodland - habitats not normally inhabited by species of these genera. Rhampholeon hattinghi sp. nov. and Kinyongia mulyai sp. nov. bear superficial resemblances to previously described species (Rh. boulengeri Steindachner and K. adolfifriderici (Sternfeld)). Rhampholeon hattinghi sp. nov. has a relatively smooth supra-orbital ridge, deep axillary but absent inguinal mite pockets, prominent white spots on the base of the tail and a uniquely derived hemipenal morphology with billowing parasulcal evaginations. Like K. adolfifriderici, Kinyongia mulyai sp. nov. is devoid of a rostral appendage but differs in having a longer and narrower head, a higher upper labial scale count and by the absence of a dorsal crest in the male. To place these new chameleons within the context of their respective genera, Bayesian and maximum likelihood phylogenetic analyses were carried out utilising two mitochondrial (ND2 and 16S) and one nuclear marker (RAG1). Both chameleons were found to have morphological features that distinguish them from other congeners. Based on phylogenetic analysis they are clearly separate evolutionary lineages and are described as new species.
Use and misuse of antibiotics in Latin America.

Some common characteristics that distinguish antibiotic use in Latin America are a high incidence of infections that are treatable with antibiotics, extensive use and frequent misuse of antibiotics, and frequent self-medication and nonprofessional prescription in the outpatient setting. Community-acquired organisms are generally more antibiotic-resistant in Latin America than in more-industrialized countries. Antibiotics also are used extensively in hospitals, largely for surgical prophylaxis and for nosocomial infections, which occur more frequently (in 15%-20%) in hospitalized patients. Prophylactic use of antibiotics is largely inappropriate--i.e., indiscriminate, inopportune, and prolonged. A frequent outcome of this inappropriate use is the occurrence of nosocomial infections due to strains that are much more drug resistant than those encountered in industrialized countries. The great number of pharmaceutical products available, and the lack of stringent policies regarding drug sales and advertising often result in pressure to prescribe and in confusion not only among the public at large but among physicians themselves. Coordinated efforts to educate health care professionals, campaigns against self-medication, stricter rules for drug sales and advertising, and restricted use of certain antibiotics in hospitals may contribute to rational antibiotic use.
Behavioral Oscillation in Priming: Competing Perceptual Predictions Conveyed in Alternating Theta-Band Rhythms

The brain constantly creates perceptual predictions about forthcoming stimuli to guide perception efficiently. Abundant studies have demonstrated that perceptual predictions modulate sensory activities depending on whether the actual inputs are consistent with one particular prediction. In real-life contexts, however, multiple and even conflicting predictions might concurrently exist to be tested, requiring a multiprediction coordination process. It remains largely unknown how multiple hypotheses are conveyed and harmonized to guide moment-by-moment perception. Based on recent findings revealing that multiple locations are sampled alternatively in various phase of attentional rhythms, we hypothesize that this oscillation-based temporal organization mechanism may also underlie the multiprediction coordination process. To address the issue, we used well established priming paradigms in combination with a time-resolved behavioral approach to investigate the fine temporal dynamics of the multiprediction harmonization course in human subjects. We first replicate classical priming effects in slowly developing trends of priming time courses. Second, after removing the typical priming patterns, we reveal a new theta-band (∼4 Hz) oscillatory component in the priming behavioral data regardless of whether the prime was masked. Third, we show that these theta-band priming oscillations triggered by congruent and incongruent primes are in an out-of-phase relationship. These findings suggest that perceptual predictions return to low-sensory areas not continuously but recurrently in a theta-band rhythm (every 200–300 ms) and that multiple predictions are dynamically coordinated in time by being conveyed in different phases of the theta-band oscillations to achieve dissociated but temporally organized neural representations.
Clinical responses to a mega-dose of vitamin D3 in infants and toddlers with vitamin D deficiency rickets.

OBJECTIVES Was to investigate the effect of treatment with an IM injection, a mega dose of vitamin D3 (10,000 IU/kg) on the clinical, biochemical and radiological parameters of 40 rachitic children with vitamin D deficiency (VDD) over a period of 3 months. DESIGN In this prospective study we evaluated the clinical, biochemical and radiological responses of an IM injection of cholecalciferol (10,000 IU/kg) for 3 months. RESULTS At presentation, the most frequent manifestations were enlarged wrist joints, hypotonia, irritability, cranial bossing, wide anterior fontanel, bow legs, delayed teething and walking and Harrison's sulcus with chest rosaries. Short stature (length SDS < -2) was recorded in 30% of patients. Craniotabes and hypocalcemic tetany were the least common presentations. In VDD children the most frequent biochemical abnormality was high alkaline phosphatase (ALP) (100%), followed by low phosphate (PO(4)) (75%) and low calcium (Ca) (12.5%). One month after treatment, serum Ca, PO(4) and 25(OH)D concentrations were normal. Three months after the injection, serum level of ALP and parathormone (PTH) decreased to normal. The majority of patients (87.5%) had serum 25(OH)D level >or= 20 ng/ml, but some (12.5%) had level <20 ng/ml. Hypercalcemia was not recorded in any patient during the 3-month-period. Significant cure of all symptoms and signs related to vitamin D deficiency had been achieved in all children. Leg bowing showed significant improvement in all patients but was still evident in one third. Complete healing of the radiological evidence of rickets was achieved in 95% of all children. CONCLUSION An IM injection of a mega dose of cholecalciferol is a safe and effective therapy for treatment of VDD rickets in infants and toddlers with normalization of all the biochemical parameters and healing of radiological manifestations. Measurement of serum 25(OH)D level is highly recommended in all short children with a clear need for a general vitamin D supplementation for all infants and young children in Qatar.
Depression, craving, and substance use following a randomized trial of mindfulness-based relapse prevention.

OBJECTIVE A strong relation between negative affect and craving has been demonstrated in laboratory and clinical studies, with depressive symptomatology showing particularly strong links to craving and substance abuse relapse. Mindfulness-based relapse prevention (MBRP), shown to be efficacious for reduction of substance use, uses mindfulness-based practices to teach alternative responses to emotional discomfort and lessen the conditioned response of craving in the presence of depressive symptoms. The goal in the current study was to examine the relation between measures of depressive symptoms, craving, and substance use following MBRP. METHOD Individuals with substance use disorders (N = 168; mean age 40.45 years, SD = 10.28; 36.3% female; 46.4% non-White) were recruited after intensive stabilization, then randomly assigned to either 8 weekly sessions of MBRP or a treatment-as-usual control group. Approximately 73% of the sample was retained at the final 4-month follow-up assessment. RESULTS Results confirmed a moderated-mediation effect, whereby craving mediated the relation between depressive symptoms (Beck Depression Inventory) and substance use (Timeline Follow-Back) among the treatment-as-usual group but not among MBRP participants. MBRP attenuated the relation between postintervention depressive symptoms and craving (Penn Alcohol Craving Scale) 2 months following the intervention (f(2) = . 21). This moderation effect predicted substance use 4 months following the intervention (f(2) = . 18). CONCLUSION MBRP appears to influence cognitive and behavioral responses to depressive symptoms, partially explaining reductions in postintervention substance use among the MBRP group. Although results are preliminary, the current study provides evidence for the value of incorporating mindfulness practice into substance abuse treatment and identifies a potential mechanism of change following MBRP.
Fluoroquinolone-associated tendon-rupture: a summary of reports in the Food and Drug Administration’s adverse event reporting system

Objective: To review and summarize reports of tendon rupture associated with each fluoroquinolone (FQ) currently marketed in the United States (US), as reported to the FDA’s Adverse Event Reporting System (FAERS). Methods: FAERS data were reviewed for reports of tendon rupture associated with each FQ from their respective approval date through September 2012. Disproportional reporting signal detection was estimated using empirical Bayes geometric mean (EBGM) with 95% confidence intervals (CI). Results: There were 2495 FAERs reports of tendon rupture associated with currently approved FQs. Most FAERS reports were associated with levofloxacin (n = 1555) followed by ciprofloxacin (n = 606) and moxifloxacin (n = 230). Signal detection results for FQs were as follows: levofloxacin (EBGM = 55.2, 95% CI = 52.3 – 58.0), ciprofloxacin (EBGM = 20.0, 95% CI = 18.2 – 21.6), moxifloxacin (EBGM = 13.3, 95% CI = 11.7 – 15.1), norfloxacin (EBGM = 9.6, 95% CI = 6.5 – 13.5), ofloxacin (EBGM = 8.2, 95%CI = 6.3 – 10.2) and gemifloxacin (EBGM = 1.9, 95% CI = 0.7 – 4.5). The mean age of affected individuals was 59.6 ± 5.1 years. Corticosteroids were administered concomitantly with FQs in 21.2% of cases. Conclusion: As noted in boxed warnings, FQ use is associated with increased tendon rupture risk. Risk factors for FQ associated tendon rupture include use in the elderly, and in patients with concomitant corticosteroids. Further monitoring may be needed due to antibiotic overuse and marketing of newer FQs.
Interaction of CED-6/GULP, an Adapter Protein Involved in Engulfment of Apoptotic Cells with CED-1 and CD91/Low Density Lipoprotein Receptor-related Protein (LRP)*

The prompt clearance of cells undergoing apoptosis is critical during embryonic development, normal tissue turnover, as well as inflammation and autoimmunity. The molecular details of the engulfment of apoptotic cells are not fully understood.ced-6 and its human homologue gulp, encode an adapter protein, whose function in engulfment is highly evolutionarily conserved; however, the upstream and downstream components of CED-6 mediated signaling are not known. Recently, ced-1 has been shown to encode a transmembrane protein on phagocytic cells, with two functional sequence motifs in its cytoplasmic tail that are important for engulfment. In this study, using a combination of biochemical approaches and yeast two-hybrid analysis, we present evidence for a physical interaction between GULP/CED-6 and one of the two motifs (NPXY motif) in the cytoplasmic tail of CED-1. The phosphotyrosine binding domain of GULP was necessary and sufficient for this interaction. Since the precise mammalian homologue of CED-1 is not known, we undertook a database search for human proteins that contain the motifs shown to be important for CED-1 function and identified CD91/LRP (low density lipoprotein receptor-related protein) as one candidate. Interestingly, recent studies have also identified CD91/LRP as a receptor involved in the phagocytosis of apoptotic cells in mammals. The GULP phosphotyrosine binding domain was able to specifically interact with one specific NPXY motif in the CD91 cytoplasmic tail. During these studies we have also identified the mouse GULP sequence. These studies suggest a physical link between CED-1 or CD91/LRP and the adapter protein CED-6/GULP during engulfment of apoptotic cells and further elucidate the pathway suggested by the genetic studies.
PHOTODYNAMIC ACTION IN Stentor coeruleus SENSITIZED BY ENDOGENOUS PIGMENT STENTORIN

Abstract— Stentorin acts as the photoreceptor for the step‐up photophobic and negative phototactic responses in Stentor coeruleus. The chromophore of stentorin appears to be hypericin which is linked to apoprotein. In addition to the photomovement responses of the organism, S. coeruleus was found to be photodynamically sensitive to light absorbed by the hypericin chromophore, as the apparent action spectrum for the photodynamic killing matches the absorption spectrum of stentorin. The protective effect of β‐carotene and crocetin on the photodynamic killing of S. coeruleus suggests that singlet oxygen generated by the stentorin‐sensitization plays an important role, according to the so‐called Type II mechanism of photosensitization. The generation of singlet oxygen via hypericin triplet was confirmed by in vitro photooxidation of tryptophan as a substrate. The photodynamic killing was more effective in deuterium oxide than in H2O in both the photosensitization by stentorin (endogenous) and added hypericin (exogenous). These results are consistent with the involvement of singlet oxygen in the photodynamic killing of S. coeruleus.
Targeting Prostaglandin E2 Receptors as an Alternative Strategy to Block Cyclooxygenase-2-dependent Extracellular Matrix-induced Matrix Metalloproteinase-9 Expression by Macrophages*

COX-2-dependent prostaglandin (PG) E2 synthesis regulates macrophage MMP expression, which is thought to destabilize atherosclerotic plaques. However, the administration of selective COX-2 inhibitors paradoxically increases the frequency of adverse cardiovascular events potentially through the loss of anti-inflammatory prostanoids and/or disturbance in the balance of pro- and anti-thrombotic prostanoids. To avoid these collateral effects of COX-2 inhibition, a strategy to identify and block specific prostanoid-receptor interactions may be required. We previously reported that macrophage engagement of vascular extracellular matrix (ECM) triggers proteinase expression through a MAPKerk1/2-dependent increase in COX-2 expression and PGE2 synthesis. Here we demonstrate that elicited macrophages express the PGE2 receptors EP1–4. When plated on ECM, their expression of EP2 and EP4, receptors linked to PGE2-induced activation of adenylyl cyclase, is strongly stimulated. Forskolin and dibutryl cyclic-AMP stimulate macrophage matrix metalloproteinase (MMP)-9 expression in a dose-dependent manner. However, an EP2 agonist (butaprost) has no effect on MMP-9 expression, and macrophages from EP2 null mice exhibited enhanced COX-2 and MMP-9 expression when plated on ECM. In contrast, the EP4 agonist (PGE1-OH) stimulated macrophage MMP-9 expression, which was inhibited by the EP4 antagonist ONO-AE3-208. When compared with COX-2 silencing by small interfering RNA or inhibition by celecoxib, the EP4 antagonist was as effective in inhibiting ECM-induced proteinase expression. In addition, ECM-induced MMP-9 expression was blocked in macrophages in which EP4 was silenced by small interfering RNA. Thus, COX-2-dependent ECM-induced proteinase expression is effectively blocked by selective inhibition of EP4, a member of the PGE2 family of receptors.