Miracle-dz/UniFAR-FTUs huggingface dataset:
The medium-/long-chain fatty acyl-CoA dehydrogenase (fadF) gene of Salmonella typhimurium is a phase 1 starvation-stress response (SSR) locus.

Salmonella enterica serovar Typhimurium (S. typhimurium) is an enteric pathogen that causes significant morbidity in humans and other mammals. During their life cycle, salmonellae must survive frequent exposures to a variety of environmental stresses, e.g. carbon-source (C) starvation. The starvation-stress response (SSR) of S. typhimurium encompasses the genetic and physiological realignments that occur when an essential nutrient becomes limiting for bacterial growth. The function of the SSR is to produce a cell capable of surviving long-term starvation. This paper reports that three C-starvation-inducible lac fusions from an S. typhimurium C-starvation-inducible lac fusion library are all within a gene identified as fadF, which encodes an acyl-CoA dehydrogenase (ACDH) specific for medium-/long-chain fatty acids. This identification is supported by several findings: (a) significant homology at the amino acid sequence level with the ACDH enzymes from other bacteria and eukaryotes, (b) undetectable beta-oxidation levels in fadF insertion mutants, (c) inability of fad insertion mutants to grow on oleate or decanoate as a sole C-source, and (d) inducibility of fadF::lac fusions by the long-chain fatty acid oleate. In addition, the results indicate that the C-starvation-induction of fadF is under negative control by the FadR global regulator and positive control by the cAMP:cAMP receptor protein complex and ppGpp. It is also shown that the fadF locus is important for C-starvation-survival in S. typhimurium. Furthermore, the results demonstrate that fadF is induced within cultured Madin-Darby canine kidney (MDCK) epithelial cells, suggesting that signals for its induction (C-starvation and/or long-chain fatty acids) may be present in the intracellular environment encountered by S. typhimurium. However, fadF insertion mutations did not have an overt effect on mouse virulence.
Mutation rates in the dystrophin gene: A hotspot of mutation at a CpG dinucleotide

An analysis of mutations was performed in 141 Duchenne muscular dystrophy (DMD) patients previously found to be negative for large deletions by standard multiplex PCR assays. Comprehensive mutation scanning of all coding exons, adjacent intronic splice regions, and promoter sequences was performed by DOVAM‐S, a robotically enhanced, high throughput method that detects essentially all point mutations. Samples negative for point mutations were further analyzed for duplications by multiplex amplifiable probe hybridization (MAPH). Presumptive causative mutations were detected in 90% of the patients (70% protein truncating point mutations, 13% duplications, and 7% deletions not detected by the standard multiplex screening method). A total of 40 of the mutations are putatively novel. Most duplications involve multiple exons with an average and median size of about 160 and 153 kb, respectively. This is the first analysis of the absolute and relative rates of point mutations in the dystrophin gene. Relative to microdeletions (0.68 × 10–9 per bp per generation), transitions at CpG dinucleotides are enhanced 150‐fold while complex indels, the least common mutation type, are less frequent than microdeletions by a factor of five. The frequency of microdeletions and microinsertions at mononucleotide repeats increases exponentially with length. When compared to the well‐studied human factor IX gene (F9), the results are similar, with two exceptions: a hotspot of mutation in the dystrophin gene (c.8713C>T/p.R2905X) at a CpG dinucleotide and an altered size distribution of microdeletions. The hotspot reflects a difference in the underlying pattern of mutation, while the altered size distribution of microdeletions reflects certain abundant sequence motifs within the dystrophin coding sequence (relative to factor IX). Hum Mutat 25:177–188, 2005. © 2005 Wiley‐Liss, Inc.
Social-economic costs and quality of life of Alzheimer disease in the Canary Islands, Spain

Objectives: To examine the economic burden (direct and indirect costs) of Alzheimer disease (AD) and to analyze the impact on health-related quality of life (HRQOL) for patients with AD and caregivers in 2001 in the Canary Islands, Spain. Methods: Two hundred thirty-seven patients (61% of those contacted) were recruited from the Alzheimer’s Disease Association in the Canary Islands. Demographic, health resources utilization, informal care, indirect costs, and quality of life data were collected from primary caregivers of patients as proxy respondents. HRQOL was measured for patients and caregivers with the generic questionnaire EQ-5D. Results: The average annual cost per patient with AD was 28,198 (US $36,144). The most important categories of costs were for informal care and drugs. Costs increased with cognitive impairment with an average annual cost of 14,956 (US $19,171) for mild, 25,562 (US $32,765) for moderate, and 41,669 (US $53,411) for severe patients. The total cost of patients with AD in Canary Islands was 259 (US $332) million. The HRQOL with the EQ-5D social tariff was 0.29 for patients and 0.67 for caregivers. The EQ-5D VAS (thermometer) score was 42 for patients and 62 for caregivers. Conclusions: Direct health care costs of AD represented 2.4% of the total public health care expenditure in the Canary Islands. Across all severity levels, we estimated a total annual cost of 10 (US $13) billion for AD patients older than 65 years in Spain. The degree of severity of the patients with AD substantially influenced the quality of life of the patients but not that of the caregivers.
Ecological divergence of closely related Diplostomum (Trematoda) parasites

Parasite life-cycles present intriguing model systems to study divergence in resource use and ecology between parasite taxa. In ecologically similar taxa, consistent selective forces may lead to convergence of life-history traits, but resource overlap and similarity of life-cycles may also promote divergence between the taxa in (1) use of host species or (2) specific niche within a host. We studied the life-history characteristics of 2 sympatric species of Diplostomum parasites, D. spathaceum and D. gasterostei, concentrating particularly on differences in intermediate host use and characteristics of the infective stages between the species. This group of trematodes is a notoriously difficult challenge for morphological taxonomy and therefore any information on the ecology of these species can also be helpful in resolving their taxonomy. We observed that these species indeed had diverged as they used mainly different snail and fish species as intermediate hosts and in controlled experiments infected different regions of the eye (lens and vitreous body) of a novel fish host. Interestingly, cercarial characteristics (activity and life-span) were similar between the species and the species were difficult to separate at the cercarial stage unless one observes their swimming behaviour. The release of cercaria from the snail hosts was higher in D. spathaceum, but when cercarial numbers were proportioned to the volume of the snail host, the production was higher in D. gasterostei suggesting differences in the rate of snail host exploitation between the parasite species. These results corroborate the prediction that closely related parasite taxa which are competing for the same resources should have diverged in their life-history characteristics and host use.
Pseudo-Polar Fourier Transform-Based Compressed Sensing MRI

The use of radial k-space trajectories has drawn strong interest from researchers for their potential in developing fast imaging methods in magnetic resonance imaging (MRI). Compared with conventional Cartesian trajectories, radial sampling collects more data from the central k-space region and the radially sampled data are more incoherent. These properties are very suitable for compressed sensing (CS)-based fast imaging. When reconstructing under-sampled radial data with CS, regridding and inverse-regridding are needed to transfer data between the image and frequency domains. In each CS iteration, two-dimensional interpolations are implemented twice in the regridding and inverse-regridding, introducing errors and undermining reconstruction quality. To overcome these problems, a radial-like pseudo-polar (PP) trajectory is proposed for the CS MRI applications. The PP trajectory preserves all the essential features of radial trajectory and allows an image reconstruction with PP fast Fourier transform (PPFFT) instead of interpolations. This paper attempts to investigate the performance of PP trajectory-based CS-MRI. In CS-based image reconstruction, the transformation of PP-sampled k-space data into the image domain is realized through PPFFT, which is based on the standard one-dimensional FFT and the fractional Fourier transform. To evaluate the effectiveness of the proposed methods, both numerical and experimental data are used to compare the new methods with conventional approaches. The proposed method provided high-quality reconstruction of the MR images with over 2-dB gain in peak signal-to-noise ratio while keeping structural similarity over 0.88 in different situations. Compared with the conventional radial sampling-based CS MRI methods, the proposed method achieves a more accurate reconstruction with respect to image detail/edge preservation and artifact suppression. The successful implementation of the PP subsampling-based CS scheme provides a practical and accurate CS-based rapid imaging method for clinical applications.
Toxicity Analysis of N- and C-Terminus-Deleted Vegetative Insecticidal Protein from Bacillus thuringiensis

ABSTRACT A vegetative insecticidal protein (VIP)-encoding gene from a local isolate of Bacillus thuringiensis has been cloned, sequenced, and expressed in Escherichia coli. The expressed protein shows insecticidal activity against several lepidopteran pests but is ineffective against Agrotis ipsilon. Comparison of the amino acid sequence with those of reported VIPs revealed a few differences. Analysis of insecticidal activity with N- and C-terminus deletion mutants suggests a differential mode of action of VIP against different pests.
Restricted localization of L1 and N‐CAM at sites of contact between Schwann cells and neurites in culture

Schwann cell‐axon contacts in developing and regenerating peripheral nerve in situ contain high levels of the recognition molecules L1 and N‐CAM, while the molecules are not detectable at the ab‐axonal cell surface of Schwann cells. To investigate whether Schwann cells, axons, or both contribute to the localization of the molecules at Schwann cell‐axon contacts, a heterologous cell culture system consisting of Schwann cells from mice and neurons from chicken was investigated by immunoelectron microscopy using species‐specific L1 and N‐CAM antibodies. We showed that Schwann cells expressed both molecules only at sites of contact between Schwann cells and neurites and other Schwann cells. Schwann cells not in contact with other cells expressed both molecules on their entire cell surface. In contrast, neurites expressed G4, an L1‐related molecule in chicken, on their entire cell surface independently of whether they were in contact with other cells or not. Thus, cultured Schwann cells localize L1 and N‐CAM selectively at cell contact sites and may thereby stabilize their attachment to the neighboring cellular partners. © 1994 Wiley‐Liss, Inc.
Systemic Risk Measurement: Bucketing G-SIBs Between Literature and Supervisory View

The general consensus on the need to enhance the resilience of the financial system has led to the imposition of higher capital requirements for certain institutions, supposedly based on their contribution to systemic risk. Global Systemically Important Banks (G-SIBs) are divided into buckets based on their required additional capital buffers ranging from 1% to 3.5%. We measure the marginal contribution to systemic risk of 26 G-SIBs using the Distressed Insurance Premium methodology proposed by Huang et al. (2009) and examine ranking consistency with that using the SRISK of Acharya et al. (2012). We then compare bucketing using the two academic approaches and supervisory buckets. Because it leads to capital surcharges, bucketing should be consistent, irrespective of methodology. Instead, discrepancies in the allocation between buckets emerge and this suggests the complementary use of other methodologies.
The effect of simvastatin on the proteome of detergent‐resistant membrane domains: Decreases of specific proteins previously related to cytoskeleton regulation, calcium homeostasis and cell fate

Cell death induced by over‐activation of glutamate receptors occurs in different neuropathologies. Cholesterol depletors protect from neurotoxic over‐activation of glutamate receptors, and we have recently reported that this neuroprotection is associated with a reduction of the N‐methyl‐D‐aspartate subtype of glutamate receptors in detergent‐resistant membrane domains (DRM). In the present study we used comparative proteomics to further identify which proteins, besides the N‐methyl‐D‐aspartate receptor, change its percentage of association to DRM after treatment of neurons with simvastatin. We detected 338 spots in neuronal DRM subjected to 2‐DE; eleven of these spots changed its intensity after treatment with simvastatin. All 11 differential spots showed reduced intensity in simvastatin‐treated samples and were identified as adipocyte plasma membrane associated protein, enolase, calretinin, coronin 1a, f‐actin capping protein α1, f‐actin capping protein α2, heat shock cognate protein 71, malate dehydrogenase, n‐myc downregulated gene 1, prohibitin 2, Rab GDP dissociation inhibitor, translationally controlled tumor protein and voltage dependent anion selective channel protein 1. The proteins tested colocalized with the lipid raft marker caveolin‐1. Interestingly, the proteins we have identified in the present study had been previously reported to play a role in cell fate and, thus, they might represent novel targets for neuroprotection.
Antizyme Targets Cyclin D1 for Degradation

Overproduction of the ornithine decarboxylase (ODC) regulatory protein ODC-antizyme has been shown to correlate with cell growth inhibition in a variety of different cell types. Although the exact mechanism of this growth inhibition is not known, it has been attributed to the effect of antizyme on polyamine metabolism. Antizyme binds directly to ODC, targeting ODC for ubiquitin-independent degradation by the 26 S proteasome. We now show that antizyme induction also leads to degradation of the cell cycle regulatory protein cyclin D1. We demonstrate that antizyme is capable of specific, noncovalent association with cyclin D1 and that this interaction accelerates cyclin D1 degradation in vitro in the presence of only antizyme, cyclin D1, purified 26 S proteasomes, and ATP. In vivo, antizyme up-regulation induced either by the polyamine spermine or by antizyme overexpression causes reduction of intracellular cyclin D1 levels. The antizyme-mediated pathway for cyclin D1 degradation is independent of the previously characterized phosphorylation- and ubiquitination-dependent pathway, because antizyme up-regulation induces the degradation of a cyclin D1 mutant (T286A) that abrogates its ubiquitination. We propose that antizyme-mediated degradation of cyclin D1 by the proteasome may provide an explanation for the repression of cell growth following antizyme up-regulation.
Life expectancy at birth and life disparity: an assessment of sex differentials in mortality in India

This study aims to examine the sex differentials in life expectancy at birth and life disparity, and to estimate the age-specific contribution of the differences for India and its major states. Life dispari-ty measures the variation in the distribution of deaths, and life expectancy at birth measures the average length of life. Complete life tables generated from death rates and abridged life tables of the Sample Reg-istration System in India from 1970–1975 to 2006–2010 were used to fulfill the research goals. Stepwise replacement algorithm was used for the decomposition of sex differences in life expectancy at birth and in life disparity. The results indicate that the increase in life expectancy at birth and decline in life disparity was higher for females. The sex differential was more prominent in urban areas than in rural areas. A ma-jority of the states in India experienced changes in the direction and magnitude of sex differentials in life expectancy at birth and life disparity from 1970–1975 to 2006–2010. The sex differentials in life expec-tancy at birth and life disparity in 1970–1975 were primarily attributed to child mortality, whereas the sex differentials in recent decades were attributed to adult mortality.
Salivary flow rate, buffer capacity, and urea concentration in adolescents with type 1 diabetes mellitus

Abstract Background: The objective of the study was to analyze salivary flow rate, urea concentration, and buffer capacity in adolescents with type 1 diabetes mellitus (type 1 DM) in two different stages. Methods: This study was performed on adolescents (14–19 years), allocated between two groups: type 1 DM group comprised 32 adolescents with type 1 DM, and non-type 1 DM group comprised 32 nondiabetics. The adolescents in type 1 DM group were evaluated at a baseline (T0) and after 15 months (T1), and those in non-type 1 DM group were only evaluated at T0. Diabetic status was determined by glycosylated hemoglobin (GHb) and capillary glucose tests. Measurement of salivary flow was performed by means of stimulated saliva (SSFR) collection. The buffer capacity (BC) was determined, and analysis of urea salivary concentration was performed using the colorimetric method. Results: At T0, there were significant differences between diabetics and nondiabetics for SSFR and BC (p<0.05). In diabetics, SSFR was 0.790 mL/min in T0 and 0.881 mL/min in T1 (p>0.05). BC at T0 was 4.8, and at T1, it was 3.9 (p=0.000). Urea concentration mean value had a significant decrease at T1 (28.13) compared with T0 (34.88) (p=0.013). There was a negative correlation between SSFR and urea salivary concentration at both T0 (r=−0.426, p≤0.05) and T1 (r=−0.601, p≤0.01). Conclusions: In adolescents with type 1 DM, hyposalivation at T0 was associated with an increase in urea salivary concentration. At T1, hyposalivation was associated with a reduction in BC, and an increase in salivary urea.
Location of Mental Foramen Based on Soft- and Hard-Tissue Landmarks in a Chinese Population

The purpose of the present study was to determine the location of the mental foramen (MF) based on soft- and hard-tissue landmarks, to facilitate prediction of the location of this structure during facial and dental surgery. Forty-two hemispheres of 21 adult cadavers (16 men and 5 women; aged 30-75 years) were dissected to expose the MF. The locations of the MFs were evaluated with direct and photographic measurements. Most of the MFs presented a single foramen (95%), except for only 2 cases with double foramina (5%). The MFs localized 23.38 ± 2.00 mm inferior and 3.55 ± 1.70 mm medial to the cheilion in the front view while 23.59 ± 2.11 mm inferior and 7.19 ± 3.03 mm posterior to the cheilion in the lateral view. Based on the hard-tissue landmarks, we found that most of the MFs localized inferior the second premolar in most of the cases (73.8%), and the MFs localized 23.34 ± 2.39 mm below the cusp tip of the second premolar, 16.56 ± 2.53 mm below the inferior alveoli, and 15.56 ± 1.74 mm superior the bottom of the mandible. The position of the MF varied from 8.7 degrees medial to 15.5 degrees posterior in the vertical angle with the change of surgical body position from supine to lay-side position. Our results may provide a more detailed information to predict the location of the MFs.
Melanoma Differentiation–Associated Gene 5 Senses Hepatitis B Virus and Activates Innate Immune Signaling To Suppress Virus Replication

Retinoic acid–inducible gene-I (RIG-I) and melanoma differentiation–associated gene 5 (MDA5) belong to the RIG-I–like receptors family of pattern recognition receptors. Both RIG-I and MDA5 have been shown to recognize various viral RNAs, but whether they mediate hepatitis B virus (HBV) infection remains unclear. In this study, we demonstrated that the expression of MDA5, but not RIG-I, was increased in Huh7 cells transfected with the HBV replicative plasmid and in the livers of mice hydrodynamically injected with the HBV replicative plasmid. To further determine the effect of RIG-I–like receptors on HBV replication, we cotransfected the HBV replicative plasmid with RIG-I or MDA5 expression plasmid into Huh7 cells and found that MDA5, but not RIG-I at a similar protein level, significantly inhibited HBV replication. Knockdown of endogenous MDA5, but not RIG-I, in Huh7 cells transfected with the HBV replicative plasmid significantly increased HBV replication. Of particular interest, we found that MDA5, but not RIG-I, was able to associate with HBV-specific nucleic acids, suggesting that MDA5 may sense HBV. Finally, we performed in vivo experiments by hydrodynamic injection of the HBV replicative plasmid into wild-type, MDA5−/−, MDA5+/−, or RIG-I+/− mice, and found that MDA5−/− and MDA5+/− mice, but not RIG-I+/− mice, exhibited an increase of HBV replication as compared with wild-type mice. Collectively, our in vitro and in vivo studies both support a critical role for MDA5 in the innate immune response against HBV infection.
Antibacterial activity of different natural honeys from Transylvania, Romania

Honey is used in food industry and medicine due to its nutritive, therapeutic and dietetic qualities. The microbiological characteristics of 10 unpasteurized honey samples of known origin, collected from Transylvania beekeepers (Romania) were determined. The antibacterial activity of these types of honey against Escherichia coli, Staphylococcus aureus, Staphylococcus epidermidis, Salmonella enteritidis, Salmonella anatum, Salmonella choleraesuis, Bacillus cereus, Bacillus subtilis subsp. spizizenii and Listeria monocytogenes strains was studied. The most sensitive to the antibacterial activity were the two staphylococus strains (the largest diameter of inhibition zone was 18 mm) and B. subtilis strains (13.5 mm). The strains of B. cereus, E. coli, L. monocytogenes and Salmonella spp. were found to present resistance to some of the honey samples. Manna, sunflower and polyfloral honeys presented high antibacterial activity while acacia and linden honeys had a lower activity in terms of the number of sensible strains. Statistical analysis shows that the type of strains and the type of honey have influence on the diameter of inhibition.