Miracle-dz/UniFAR-FTUs huggingface dataset:
[Determination of antibiotic chemicals using microbiological tests: evaluation of the limits of sensitivity].

Sensitivity of Bacillus subtilis BGA and Bacillus stearothermophilus var. calidolactis disc assays to 53 chemio-antibiotics was tested. Test-microorganisms were sown in two different mediums: PM Indicator Agar, Difco U.S.A. , and Standard II Nutrient Agar, Merck Germany, modified according to Nouws. The mediums were used with or without addition of Trimethoprim (at a concentration of 0.12 or 0.024 mcg/ml of medium for B. subtilis and for B. stearothermophilus respectively). B. stearothermophilus did not grow in Standard II. However, the B. subtilis assay gave the best results with Standard II, apart for aminoglycosides. The B. stearothermophilus disc assay was the most sensitive to penicillins (Minimum Inhibiting Concentration in mcg/ml, MIC, between 0.001 and 0.004), cephalosporins (MIC between 0.003 and 0.09, apart from Ceftazidime, 0.3) and aminoglycosides (MIC between 0.03 and 0.6). The B.subtilis disc assay showed better sensitivity to quinolines (MIC between 0.05 and 4) and to some tetracyclines (oxytetracycline and chlortetracycline, MIC 0.03). Trimethoprim, where added, determined a higher sensitivity to sulfonamides (MIC between 0.025 and 0.25).
IKKβ in Myeloid Cells Controls the Host Response to Lethal and Sublethal Francisella tularensis LVS Infection

Background The NF-κB activating kinases, IKKα and IKKβ, are key regulators of inflammation and immunity in response to infection by a variety of pathogens. Both IKKα and IKKβ have been reported to modulate either pro- or anti- inflammatory programs, which may be specific to the infectious organism or the target tissue. Here, we analyzed the requirements for the IKKs in myeloid cells in vivo in response to Francisella tularensis Live Vaccine Strain (Ft. LVS) infection. Methods and Principal Findings In contrast to prior reports in which conditional deletion of IKKβ in the myeloid lineage promoted survival and conferred resistance to an in vivo group B streptococcus infection, we show that mice with a comparable conditional deletion (IKKβ cKO) succumb more rapidly to lethal Ft. LVS infection and are unable to control bacterial growth at sublethal doses. Flow cytometry analysis of hepatic non-parenchymal cells from infected mice reveals that IKKβ inhibits M1 classical macrophage activation two days post infection, which has the collateral effect of suppressing IFN-γ+ CD8+ T cells. Despite this early enhanced inflammation, IKKβ cKO mice are unable to control infection; and this coincides with a shift toward M2a polarized macrophages. In comparison, we find that myeloid IKKα is dispensable for survival and bacterial control. However, both IKKα and IKKβ have effects on hepatic granuloma development. IKKα cKO mice develop fewer, but well-contained granulomas that accumulate excess necrotic cells after 9 days of infection; while IKKβ cKO mice develop numerous micro-granulomas that are less well contained. Conclusions Taken together our findings reveal that unlike IKKα, IKKβ has multiple, contrasting roles in this bacterial infection model by acting in an anti-inflammatory capacity at early times towards sublethal Ft. LVS infection; but in spite of this, macrophage IKKβ is also a critical effector for host survival and efficient pathogen clearance.
Genetic Diversity of Viable, Injured, and Dead Fecal Bacteria Assessed by Fluorescence-Activated Cell Sorting and 16S rRNA Gene Analysis

ABSTRACT A novel approach combining a flow cytometric in situ viability assay with 16S rRNA gene analysis was used to study the relationship between diversity and activity of the fecal microbiota. Simultaneous staining with propidium iodide (PI) and SYTO BC provided clear discrimination between intact cells (49%), injured or damaged cells (19%), and dead cells (32%). The three subpopulations were sorted and characterized by denaturing gradient gel electrophoresis (DGGE) of 16S rRNA gene amplicons obtained from the total and bifidobacterial communities. This analysis revealed that not only the total community but also the distinct subpopulations are characteristic for each individual. Cloning and sequencing of the dominant bands of the DGGE patterns showed that most of clones retrieved from the live, injured, and dead fractions belonged to Clostridium coccoides, Clostridium leptum, and Bacteroides. We found that some of the butyrate-producing related bacteria, such as Eubacterium rectale and Eubacterium hallii, were obviously viable at the time of sampling. However, amplicons affiliated with Bacteroides and Ruminococcus obeum- and Eubacterium biforme-like bacteria, as well as Butyrivibrio crossotus, were obtained especially from the dead population. Furthermore, some bacterial clones were recovered from all sorted fractions, and this was especially noticeable for the Clostridium leptum cluster. The bifidobacterial phylotypes identified in total samples and sorted fractions were assigned to Bifidobacterium adolescentis, Bifidobacterium longum, Bifidobacterium infantis, Bifidobacterium pseudocatenulatum, and Bifidobacterium bifidum. Phylogenetic analysis of the live, dead, and injured cells revealed a remarkable physiological heterogeneity within these bacterial populations; B. longum and B. infantis were retrieved from all sorted fractions, while B. adolescentis was recovered mostly from the sorted dead fraction.
Physical Fitness in Young Adults Born Preterm

BACKGROUND: Young adults born preterm have higher levels of cardiometabolic risk factors than their term-born peers. Muscular and cardiorespiratory fitness have important cardiometabolic and other health benefits. We assessed muscular, cardiorespiratory, and self-rated fitness in preterm-born young adults. METHODS: We studied unimpaired participants of the ESTER (Ennenaikainen syntymä ja aikuisiän terveys [Preterm Birth and Early-Life Programming of Adult Health and Disease]) birth cohort study at age 23.3 (SD: 1.2) years: 139 born early preterm (EPT; <34 weeks), 247 late preterm (LPT; 34–36 weeks), and 352 at term (control group). We measured muscular fitness with the number of modified push-ups performed in 40 seconds and maximal handgrip strength of the dominant hand, cardiovascular fitness with heart rate at the end of a 4-minute step test, and self-rated fitness. Data were analyzed with linear regression. RESULTS: Young adults born EPT (−0.8; 95% confidence interval: −1.5 to −0.1; adjusted for gender, age, and source cohort) and LPT (−0.8; −1.4 to −0.3) performed fewer modified push-upsthan controls. Handgrip strength was 23.8 (0.9–46.8) N lower in EPT participants. Cardiorespiratory fitness, measured by submaximal step test, was similar. On a self-rated fitness scale (1–5), the EPT adults reported0.2 (0.0–0.4) lower scores than controls. After adjustment for early-life confounders, the results remained. They attenuated after further adjustment for mediating factors. CONCLUSIONS: Young adults born EPT and LPT had lower muscular fitness than controls, which may predispose them to cardiometabolic and other chronic diseases. Adults born EPT also perceived themselves as less fit than controls.
Mycoremediation of Endosulfan and Its Metabolites in Aqueous Medium and Soil by Botryosphaeria laricina JAS6 and Aspergillus tamarii JAS9

Microbial degradation offers an efficient and ecofriendly approach to remove toxicants from the contaminated environments. Botryosphaeria laricina JAS6 and Aspergillus tamarii JAS9 were capable of degrading endosulfan and their metabolites which were isolated through enrichment technique. Both the strains were able to withstand an exposure of 1300 mg/L and showed luxuriant growth at 1000 mg/L of endosulfan. The change in pH in the culture broth was from 6.8 to 3.4 and 3.8 during growth kinetic studies of JAS6 and JAS9 strains, respectively upon biological degradation of endosulfan. The degradation of endosulfan by JAS6 and JAS9 strains were examined by HPLC. The biodegradation rate constant (k) and the initial concentration were reduced by 50% (DT50) which was determined by first and pseudo first order kinetic models. In the present investigation it has been revealed that Botryosphaeria laricina JAS6 and Aspergillus tamarii JAS9 possessing endosulfan degrading capability are being reported for the first time. These findings confirm the degradation of endosulfan by JAS6 and JAS9 strains which were accompanied by significant reduction in the toxicity and could be used as remedial measure in contaminated environments.
Clinical Trial Design and Endpoints for Stage IV Melanoma in the Modern Era

Abstract Immunotherapies and targeted therapies for the treatment of metastatic or advanced melanoma produce unique patterns of antitumor response. Conventional outcome measures, such as median progression-free and overall survival, may not be ideally suited to identify all patients who derive a benefit from such therapies. Therefore, the introduction of additional endpoint measures, such as milestone comparisons, may be necessary to characterize the potential benefit of such treatment approaches. Immune checkpoint inhibitors induce durable responses in a portion of patients that may continue after treatment cessation. Measuring the associated treatment-free interval, treatment-free survival, and associated patient-reported outcomes could provide important information when implemented in prospective clinical trials. In this article, we discuss the limitations of current endpoint measures and the potential advantage of using novel endpoints and how these might be used in designing clinical trials to address critical unanswered questions for patients with metastatic melanoma.
Disruption of endoplasmic reticulum structure and integrity in lipotoxic cell death Published, JLR Papers in Press, September 7, 2006.

Cell dysfunction and death induced by lipid accumulation in nonadipose tissues, or lipotoxicity, may contribute to the pathogenesis of obesity and type 2 diabetes. However, the mechanisms leading to lipotoxic cell death are poorly understood. We recently reported that, in Chinese hamster ovary (CHO) cells and in H9c2 cardiomyoblasts, lipid overload induced by incubation with 500 μM palmitate leads to intracellular accumulation of reactive oxygen species, which subsequently induce endoplasmic reticulum (ER) stress and cell death. Here, we show that palmitate also impairs ER function through a more direct mechanism. Palmitate was rapidly incorporated into saturated phospholipid and triglyceride species in microsomal membranes of CHO cells. The resulting membrane remodeling was associated with dramatic dilatation of the ER and redistribution of protein-folding chaperones to the cytosol within 5 h, indicating compromised ER membrane integrity. Increasing β-oxidation, through the activation of AMP-activated protein kinase, decreased palmitate incorporation into microsomes, decreased the escape of chaperones to the cytosol, and decreased subsequent caspase activation and cell death. Thus, palmitate rapidly increases the saturated lipid content of the ER, leading to compromised ER morphology and integrity, suggesting that impairment of the structure and function of this organelle is involved in the cellular response to fatty acid overload.
Location-Specific Epigenetic Regulation of the Metallothionein 3 Gene in Esophageal Adenocarcinomas

Background Metallothionein 3 (MT3) maintains intracellular metal homeostasis and protects against reactive oxygen species (ROS)-induced DNA damage. In this study, we investigated the epigenetic alterations and gene expression of the MT3 gene in esophageal adenocarcinomas (EACs). Methods and Results Using quantitative bisulfite pyrosequencing, we detected unique DNA methylation profiles in the MT3 promoter region. The CpG nucleotides from −372 to −306 from the transcription start site (TSS) were highly methylated in tumor (n = 64) and normal samples (n = 51), whereas CpG nucleotides closest to the TSS (−4 and +3) remained unmethylated in all normal and most tumor samples. Conversely, CpG nucleotides in two regions (from −139 to −49 and +296 to +344) were significantly hypermethylated in EACs as compared to normal samples [FDR<0.001, −log10(FDR)>3.0]. The DNA methylation levels from −127 to −8 CpG sites showed the strongest correlation with MT3 gene expression (r = −0.4, P<0.0001). Moreover, the DNA hypermethylation from −127 to −8 CpG sites significantly correlated with advanced tumor stages and lymph node metastasis (P = 0.005 and P = 0.0313, respectively). The ChIP analysis demonstrated a more repressive histone modification (H3K9me2) and less active histone modifications (H3K4me2, H3K9ace) in OE33 cells than in FLO-1 cells; concordant with the presence of higher DNA methylation levels and silencing of MT3 expression in OE33 as compared to FLO-1 cells. Treatment of OE33 cells with 5-Aza-deoxycitidine restored MT3 expression with demethylation of its promoter region and reversal of the histone modifications towards active histone marks. Conclusion In summary, EACs are characterized by frequent epigenetic silencing of MT3. The choice of specific regions in the CpG island is a critical step in determining the functional role and prognostic value of DNA methylation in cancer cells.
Breakthrough Technologies A High-Throughput , Field-Based Phenotyping Technology for Tall Biomass Crops 1

Recent advances in omics technologies have not been accompanied by equally efficient, cost-effective, and accurate phenotyping methods required to dissect the genetic architecture of complex traits. Even though high-throughput phenotyping platforms have been developed for controlled environments, field-based aerial and ground technologies have only been designed and deployed for short-stature crops. Therefore, we developed and tested Phenobot 1.0, an auto-steered and self-propelled fieldbased high-throughput phenotyping platform for tall dense canopy crops, such as sorghum (Sorghum bicolor). Phenobot 1.0 was equipped with laterally positioned and vertically stacked stereo RGB cameras. Images collected from 307 diverse sorghum lines were reconstructed in 3D for feature extraction. User interfaces were developed, and multiple algorithms were evaluated for their accuracy in estimating plant height and stem diameter. Tested feature extraction methods included the following: (1) Userinteractive Individual Plant Height Extraction (UsIn-PHe) based on dense stereo three-dimensional reconstruction; (2) Automatic Hedge-based Plant Height Extraction (Auto-PHe) based on dense stereo 3D reconstruction; (3) User-interactive Dense Stereo Matching Stem Diameter Extraction; and (4) User-interactive Image Patch Stereo Matching Stem Diameter Extraction (IPaS-Di). Comparative genome-wide association analysis and ground-truth validation demonstrated that both UsIn-PHe and Auto-PHe were accurate methods to estimate plant height, while Auto-PHe had the additional advantage of being a completely automated process. For stem diameter, IPaS-Di generated the most accurate estimates of this biomass-related architectural trait. In summary, our technology was proven robust to obtain ground-based high-throughput plant architecture parameters of sorghum, a tall and densely planted crop species.
CNS or bone marrow involvement as risk factors for poor survival in post-transplantation lymphoproliferative disorders in children after solid organ transplantation.

PURPOSE To identify prognostic factors of survival in pediatric post-transplantation lymphoproliferative disorder (PTLD) after solid organ transplantation. PATIENTS AND METHODS A multicenter, retrospective case analysis of 55 pediatric solid organ graft recipients (kidney, liver, heart/lung) developing PTLD were reported to the German Pediatric-PTLD registry. Patient charts were analyzed for tumor characteristics (histology, immunophenotypes, cytogenetics, Epstein-Barr virus [EBV] detection), stage, treatment, and outcome. Probability of overall and event-free survival was analyzed in defined subgroups using univariate and Cox regression analyses. RESULTS PTLD was diagnosed at a median time of 29 months after organ transplantation, with a significantly shorter lag time in liver (0.83 years) versus heart or renal graft recipients (3.33 and 3.10 years, respectively; P = .001). The 5-year overall and event-free survival was 68% and 59%, respectively, with 59% of patients surviving 10 years. Stage IV disease with bone marrow and/or CNS involvement was associated independently with poor survival (P = .0005). No differences in outcome were observed between early- and late-onset PTLD, monomorphic or polymorphic PTLD, and EBV-positive or EBV-negative PTLD, respectively. Patients with Burkitt or Burkitt-like PTLD and c-myc translocations had short survival (< 1 year). CONCLUSION Stage IV disease is an independent risk factor for poor survival in pediatric PTLD patients. Prospective multicenter trials are needed to delineate additional risk factors and to assess treatment approaches for pediatric PTLD.
A multiwavelength study of the Seyfert 1 galaxy MCG-6-30-15

We present a multiwaveband spectroscopic study of the nearby Seyfert 1 galaxy MCG-6-30-15. New optical spectra from the Anglo-Australian Telescope are presented which clearly show the effects of dust extinction/reddening on both the emission line spectrum and the non-stellar AGN continuum. The reddening is constrained to be in the range E(B-V)=0.61-1.09. Spectroscopy in the X-ray band, with both ROSAT and ASCA, reveal absorption by the warm absorber but little or no neutral absorption expected to accompany the dust responsible for the optical reddening. The dusty warm absorber solution to this discrepancy is discussed and photoionization models of such warm absorbers are constructed. The optical spectrum also displays the relatively strong `coronal' lines of [FeX]6375, [FeXI]7892 and [FeXIV]5303. We show that these lines may plausibly originate from the outer regions of the warm absorber, although better calculations of the collision strengths for these transitions are required in order to conclusively address this issue. We also present new ultraviolet data from the International Ultraviolet Explorer and suggest that much of the observed UV flux is scattered into our line of sight (with a scattering fraction of 1-5 per cent). We conclude with a discussion of the global energetics of this system.
Visualization of Allostery in P-Selectin Lectin Domain Using MD Simulations

Allostery of P-selectin lectin (Lec) domain followed by an epithelial growth factor (EGF)-like domain is essential for its biological functionality, but the underlying pathways have not been well understood. Here the molecular dynamics simulations were performed on the crystallized structures to visualize the dynamic conformational change for state 1 (S1) or state 2 (S2) Lec domain with respective bent (B) or extended (E) EGF orientation. Simulations illustrated that both S1 and S2 conformations were unable to switch from one to another directly. Instead, a novel S1' conformation was observed from S1 when crystallized B-S1 or reconstructed “E-S1” structure was employed, which was superposed well with that of equilibrated S1 Lec domain alone. It was also indicated that the corresponding allosteric pathway from S1 to S1' conformation started with the separation between residues Q30 and K67 and terminated with the release of residue N87 from residue C109. These results provided an insight into understanding the structural transition and the structure-function relationship of P-selectin allostery.
Combustion of Argemone mexicana biodiesel blends in a constant-volume DICI engine

ABSTRACT Argemone mexicana methyl ester, prepared by a transesterification process, was tested for combustion analysis with variation of blends and loads at a fixed compression ratio of 17.5. Maximum cylinder pressure was obtained for a 40% blend due to longer combustion duration. The combustion parameter net heat release rate and cumulative heat release rate increase with engine load. The net heat release rate decreases and cumulative heat release rate increases with an increase in the percentage of biodiesel. The crank angle position corresponding to maximum pressure shifts away with an increase in the proportion of biodiesel. The maximum pressure rise rate is highest for diesel and its occurrence is advanced with loading and percentage of biodiesel. Combustion duration decreases with engine loading and increases with concentration.
Structural and Biochemical Characterization of SrcA, a Multi-Cargo Type III Secretion Chaperone in Salmonella Required for Pathogenic Association with a Host

Many Gram-negative bacteria colonize and exploit host niches using a protein apparatus called a type III secretion system (T3SS) that translocates bacterial effector proteins into host cells where their functions are essential for pathogenesis. A suite of T3SS-associated chaperone proteins bind cargo in the bacterial cytosol, establishing protein interaction networks needed for effector translocation into host cells. In Salmonella enterica serovar Typhimurium, a T3SS encoded in a large genomic island (SPI-2) is required for intracellular infection, but the chaperone complement required for effector translocation by this system is not known. Using a reverse genetics approach, we identified a multi-cargo secretion chaperone that is functionally integrated with the SPI-2-encoded T3SS and required for systemic infection in mice. Crystallographic analysis of SrcA at a resolution of 2.5 Å revealed a dimer similar to the CesT chaperone from enteropathogenic E. coli but lacking a 17-amino acid extension at the carboxyl terminus. Further biochemical and quantitative proteomics data revealed three protein interactions with SrcA, including two effector cargos (SseL and PipB2) and the type III-associated ATPase, SsaN, that increases the efficiency of effector translocation. Using competitive infections in mice we show that SrcA increases bacterial fitness during host infection, highlighting the in vivo importance of effector chaperones for the SPI-2 T3SS.
Impact of Atrial Fibrillation on Stroke‐Related Healthcare Costs

Background Limited data exist on the economic implications of stroke among patients with atrial fibrillation (AF). This study assesses the impact of AF on healthcare costs associated with ischemic stroke (IS), hemorrhagic stroke (HS), or transient ischemic attack (TIA). Methods and Results A retrospective analysis of MarketScan claims data (2005‐2011) for AF patients ≥18 years old with ≥1 inpatient claim for stroke, or ≥1 ED or inpatient claim for TIA as identified by ICD‐9‐CM codes who had ≥12 months continuous enrollment prior to initial stroke. Initial event‐ and stroke‐related costs 12 months post‐index were compared among patients with AF and without AF. Adjusted costs were estimated, controlling for demographics, comorbidities, anticoagulant use, and baseline resource use. Data from 23 807 AF patients and 136 649 patients without AF were analyzed. Unadjusted mean cost of the index event was $20 933 for IS, $59 054 for HS, $8616 for TIA hospitalization, and $3395 for TIA ED visit. After controlling for potential confounders, adjusted mean incremental costs (index plus 12‐month post‐index) for AF patients were higher than those for non‐AF patients by: $4726, $7824, and $1890 for index IS, HS, TIA (identified by hospitalization), respectively, and $1700 for TIA (identified by ED) (all P<0.01). In multivariate regression analysis, AF was associated with a 20% (IS), 13% (HS), and 18% (TIA) increase in total stroke‐related costs. Conclusion Stroke‐related care for IS, HS, and TIA is costly, especially among individuals with AF. Reducing the risk of AF‐related stroke is important from both clinical and economic standpoints.