Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and Characterization of Salmonellae in Commercial Ground Beef in the United States

ABSTRACT Commercially produced ground beef samples (n = 4,136) were collected from seven regions of the United States over a 24-month period (July 2005 to June 2007) and analyzed for the presence of Salmonella enterica by using methods that concurrently provided total prevalence and enumerable levels. The overall prevalence of Salmonella strains was 4.2%. Enumeration showed that 94.2% were present at levels below 2 CFU/g. Regional monthly prevalences of Salmonella strains varied from 1.8% to 6.5% but were not statistically different (P > 0.05). All Salmonella isolates were serotyped and their antibiotic susceptibilities determined and analyzed by pulsed-field gel electrophoresis (PFGE). The most common serotypes identified were Salmonella enterica serotypes Montevideo, Anatum, Muenster, and Mbandaka, with these accounting for one-half of the isolates obtained. The prevalence of multidrug-resistant (MDR) Salmonella was determined to be 0.6%. The most common MDR serotypes were Salmonella enterica serotypes Dublin, Reading, and Typhimurium. MDR strains had resistance to between 2 and 10 antibiotics. There were no regional differences in prevalence of MDR Salmonella. PFGE analysis revealed that indistinguishable XbaI and AvrII restriction digest patterns (RDPs) could be observed in isolates of the same serotype found in different regions and months of sampling. The RDPs of 19 Salmonella strains were compared to RDPs in the PulseNet USA database. Thirteen were indistinguishable from existing patterns, and the number of records for each ranged from 1 to 478. These data show that Salmonella prevalence in commercial ground beef is low and suggest that attempts to identify sources contributing to Salmonella in ground beef by serotype, antibiogram, and PFGE cannot be made without additional documented evidence.
Adaptation to natural facial categories

We assembled two independent data sets (ferns and angiosperms) and used the lycophyte Huperzia as the outgroup (not shown in Fig. 1) for both. For ferns, we sampled the chloroplast rbcL and rps4 genes for 45 taxa: 41 leptosporangiate ferns from all major lineages (focusing within the polypods), one horsetail, two seed plants, and the outgroup. For angiosperms, we sampled the chloroplast rbcL, atpB and nuclear small-subunit ribosomal DNA genes for 95 taxa (mostly a subset from data set in ref. 14): 84 angiosperms, eight gymnosperms, one leptosporangiate fern, one horsetail, and the outgroup. Most DNA sequence data were already available in GenBank; 19 new fern sequences were generated as part of this study following the DNA extraction, amplification and sequencing protocols in ref. 18, and are deposited in GenBank. For fern voucher information and GenBank accession numbers see Supplementary Information. Phylogenetic analyses using a bayesian approach were conducted separately for ferns and angiosperms with MrBayes version 3.0b4 (ref. 29). Each gene in each data set was assigned its own model of evolution (GTR þ I þ G for each gene, determined using a hierarchical likelihood ratio test approach) and analyses were conducted using four chains, run for a total of 10,000,000 generations, with trees sampled from the cold chain every 1,000 generations. The resulting 10,000 trees were plotted against their likelihoods to determine the point where the likelihoods converged on a maximum value, and all 500 trees (500,000 generations) before this convergence were discarded as the 'burn-in' phase. For each data set (ferns and angiosperms), we computed a majority-rule consensus of the remaining 9,500 trees. We used this phylogenetic hypothesis (with average branch lengths), as well as 1,000 trees randomly sampled from among the 9,500 trees, in the subsequent analyses. Divergence time estimates were obtained through penalized likelihood analyses (truncated Newton algorithm) of the fern and angiosperm consensus phylogenies in r8s version 1.60 (ref. 30). For each data set, fossil age constraints were applied as indicated in Table 1 (for details see Supplementary Information) and the appropriate smoothing value was determined using cross-validation. For angiosperms, fossil age constraints 22 (Table 1) were applied in two ways, differing only in the application of the fossil age of the angiosperm crown group (node b10 in Fig. 1b). The first approach was strict (age fixed at 132 Myr; ref. 22) and the second relaxed (minimum age constraint of 132 Myr applied). To …
Marker Constituents of the Natural Antioxidant Eucalyptus Leaf Extract for the Evaluation of Food Additives

In order to establish the marker constituents of the natural antioxidant food-additive Eucalyptus leaf extract, the UV-absorbing constituents of two eucalyptus leaf extracts registered as food additives (eucalyptus A and B) were investigated. Several major peaks on the reversed-phase HPLC chromatogram of eucalyptus A were characterized as gallic acid, ellagic acid, 3-O-β-D-glucuronides of quercetin and kaempferol, and a hydrolyzable tannin dimer, oenothein B, by direct comparison with authentic specimens isolated from Eucalyptus globulus leaves. A new gallotannin was found in the E. globulus leaf extract, and its structure was found to be 1,2,3,6-tetra-O-galloyl-β-D-galactose. Two major peaks on the HPLC chromatogram of eucalyptus B were identified as gallic acid and ellagic acid, indicative of degradation products from hydrolyzable tannins in the leaves. Considering the evaluation of antioxidant activity by radical scavenging ability, a standardization of eucalyptus leaf extract, including the antioxidative polyphenol, oenothein B, is proposed.
Modeling and extraction of interconnect capacitances for multilayer VLSI circuits

We report an accurate and practical method of estimating interconnect capacitances for a given circuit layout. The method allows extraction of the complete circuit level capacitances at each node in the circuit. The layout geometry is reduced into base elements that consist of different vertical profiles at each node in the layout. Accurate analytical models are developed for calculating capacitances of multilayer structures using a 2D capacitance simulator TDTL. These models are then transformed into 3D geometry. The resulting model capacitance values are found to be within 10% of both the measured data and 3D simulations of structures that are prevalent in typical VLSI chips. The models and their coefficients for different vertical profiles are stored in the capacitance extraction tool CUP, which is coupled to the layout extractor HILEX. As each base element has a unique vertical profile, the corresponding capacitance can easily be calculated for each node that is then written out to a circuit netlist. The comparisons of the models with the measured data, as well as 3D simulations results, are also discussed.
Bracketing effects in categorized survey questions and the measurement of economic quantities

In households surveys, quantities of interest are frequently elicited using categorized (range-card) formats rather than open-ended questions. One advantage of this format is that is typically reduces item non-response. Unfortunately, results from research in social psychology suggest that the choice of bracket values in range-card questions is likely to influence responses. As yet, there is not much known about the effects of bracketing bias on the measurement of economic quantities and regression analysis. This paper reports evidence on existence and size of bracketing bias based on data from controlled survey experiments. I also discuss strategies for avoiding bracketing bias in household surveys.
Heparin-Induced Thrombocytopenia: A Serious Complication of Heparin Therapy for Acute Stroke

Background: Despite the lack of supporting evidence, unfractionated heparin (UFH) is frequently given to acute ischemic stroke patients. This study was designed to determine the incidence of heparin-induced thrombocytopenia (HIT) during acute stroke and to elucidate the clinical features of stroke patients with HIT. Methods: Of 1,078 consecutive patients with acute ischemic stroke, 392 were given intravenous UFH. Ten of these developed prominent thrombocytopenia without any other underlying etiology; they were suspected of having HIT. These 10 patients were studied retrospectively. The clinical diagnosis of HIT was made according to two published scoring systems. Antiplatelet factor 4/heparin antibodies in the plasma were detected by the enzyme-linked immunosorbent assay (ELISA) and were confirmed by the 14C-serotonin release assay. Results: Eight patients met the criteria for clinical HIT according to both scoring systems. Of these, serological tests were positive in 2 patients only on ELISA and in 2 patients on both assays. The amount of UFH given was greater in the 4 patients with positive serological findings than in the others (p = 0.043). Three patients developed further thromboembolic events, including 1 patient who developed possible cancer-associated thrombosis. Two patients were dead and the remaining 6 patients were dependent at the time of hospital discharge. The clinical severity and outcome of these patients were relatively unfavorable compared to other acute patients. Conclusions: The prevalence of HIT was 0.5% based on both the clinical scoring systems and serological assays. Monitoring for HIT should be included in the medical management of stroke to avoid further complications.
Gap size dependence of the dielectric strength in nano vacuum gaps

We study the dielectric strength of vacuum gaps of under 100 nm. We find their dielectric strengths to have a power law dependence on the gap size. We apply this power law to find that the dielectric strength of a vacuum gap of 10 nm between two tungsten electrodes is 6.5 V/nm. The dielectric strength can be used to compute the maximum energy density, charge density, and power density. For tungsten, the maximum volumetric energy density is 190 MJ/m3. Nano vacuum gaps can discharge in 10 nanoseconds, giving a maximum gravitometric power density of 1012 W/kg. While the external discharge time is a few nanoseconds, the self-discharge time can be hours or days. The specific capacitance of a vacuum gap of size d is C = ε0/ d2. If d = 10nm then C = 8.85×104 F/m3.
Production, Manufacturing and Logistics Retail promotions with negative brand image effects: Is cooperation possible?

We consider a channel of distribution with a single manufacturer M and a retailer R. M advertises in national media to build up the image for one of his brands. R promotes locally the brand to increase sales revenue, but these efforts are harmful to the brand image. We address the question whether the two firms can agree to participate in a cooperative promotion program where M pays part of the costs incurred by R when promoting the brand. The model is a differential game with an infinite time horizon. Two Nash equilibria serve as benchmarks for assessing the feasibility of the cooperative program: one in which R is myopic and one in which R is far-sighted. Our results show that a cooperative program is implementable if the level of initial brand image is ‘‘small’’, or if the level of initial brand image is ‘‘intermediate’’ and promotion is not too damaging to the brand image. In the remaining cases a game without promotional support is played and R should behave myopically in such cases. 2002 Elsevier Science B.V. All rights reserved.
Growth Hormone Enhances Amino Acid Uptake by the Human Small Intestine

ObjectiveThe effects of growth hormone (GH) on the luminal transport of amino acids and glucose by the human small intestine were investigated. Summary Background DataThe anabolic effect of growth hormone administration is associated with nitrogen retention and an increase muscle strength, but the impact of growth hormone on nutrient uptake from the gut lumen has not been examined. MethodsTwelve healthy patients received a daily subcutaneous dose of low-dose GH (0.1 mg/kg), high-dose GH (0.2 mg/kg), or no treatment (controls) for 3 days before surgery. At operation, ileum (8 patients) or jejunum (4 patients) was resected, and brush border membrane vesicles (BBMVs) were prepared by differential centrifugation. Vesicle purity was confirmed by a 16-fold enrichment of marker enzymes. The carrier-mediated transport of glutamine (System B), leucine (System L), alanine (System B), arginine (System y+), MeAIB (methyl α-aminoisobutyric acid [System A]), and glucose (Na+-dependent glucose transporter) by BBMVs was measured by a rapid mixing/filtration technique. ResultsTreatment with low-dose GH resulted in a statistically insignificant increase in amino acid transport rates in jejunal and ileal BBMVs. High-dose GH resulted in a generalized 20%- to 70%- stimulation of amino acid transport, whereas glucose transport was not affected. The effects of GH were similar in ileum and jejunum. Kinetic analysis of the transport of glutamine (the most abundant amino acid in the body and the principal gut fuel) and the essential amino acid leucine revealed that the increase in transport was caused by a 50% increase in carrier Vmax, consistent with an increase in the number of functional carriers in the brush border membrane. Pooled analysis of transport velocities demonstrated that total rates of amino acid uptake from the gut lumen were increased significantly by 35% in GH-treated patients. ConclusionsThe ability of GH to enhance amino acid uptake from the gut lumen provides energy and precursors for protein synthesis in the gut mucosa, as well as additional substrate for anabolism in other organs.
Effect of Insect Larval Midgut Proteases on the Activity of Bacillus thuringiensis Cry Toxins

ABSTRACT To test the possibility that proteolytic cleavage by midgut juice enzymes could enhance or inhibit the activity of Bacillus thuringiensis insecticidal toxins, once activated, the effects of different toxins on the membrane potential of the epithelial cells of isolated Manduca sexta midguts in the presence and absence of midgut juice were measured. While midgut juice had little effect on the activity of Cry1Aa, Cry1Ac, Cry1Ca, Cry1Ea, and R233A, a mutant of Cry1Aa from which one of the four salt bridges linking domains I and II of the toxin was eliminated, it greatly increased the activity of Cry1Ab. In addition, when tested in the presence of a cocktail of protease inhibitors or when boiled, midgut juice retained almost completely its capacity to enhance Cry1Ab activity, suggesting that proteases were not responsible for the stimulation. On the other hand, in the absence of midgut juice, the cocktail of protease inhibitors also enhanced the activity of Cry1Ab, suggesting that proteolytic cleavage by membrane proteases could render the toxin less effective. The lower toxicity of R233A, despite a similar in vitro pore-forming ability, compared with Cry1Aa, cannot be accounted for by an increased susceptibility to midgut proteases. Although these assays were performed under conditions approaching those found in the larval midgut, the depolarizing activities of the toxins correlated only partially with their toxicities.
Circadian serum melatonin profiles in patients suffering from chronic renal failure.

OBJECTIVES In spite of broad interest, intensive studies on function of melatonin have not yielded much information about relationships between this hormone and kidneys in health, and particularity, in disease. Very little is known about the circadian plasma melatonin concentrations in patients with chronic renal failure (CRF). There are only a few studies dealing with melatonin concentrations in renal diseases, mainly performed in hemodialyzed patients with end-stage renal disease (ESRD). Moreover, the most melatonin assays were performed during the daytime, and the results are conflicting. Therefore, the aim of the present study was to determine the circadian melatonin profiles in patients with different stages of CRF. MATERIAL AND METHODS Twenty four patients (13 males and 11 females) with CRF aged 35 to 58 years (mean+/-SEM: 47.0+/-1.6 years) were included in the study. Patients were divided into two groups: group 1 -- patients with compensated CRF (serum creatinine: 2.0-5.0 mg/dL), group 2 -- patients with ESRD (serum creatinine: > 8,0 mg/dL). The control group consisted of 20 healthy volunteers (10 males and 10 females) aged 35 to 55 years (mean+/-SEM: 46.0+/-1.5 years) checked not to have renal failure [serum creatinine: 0.8-1.4 mg/dL], and matched according to sex and age. Blood samples were collected at 08:00, 12:00, 16:00, 20:00, 24:00, 02:00, 04:00, and 08:00 h. Melatonin concentration was measured by enzyme immunoassay. RESULTS In both groups of patients with chronic renal failure, i.e. in patients with compensated disease and in patients with end-stage renal disease melatonin nocturnal concentrations were significantly lower then those in healthy volunteers. Moreover, in patients with compensated renal failure also day-time melatonin concentrations were significantly depressed. Area under curve was significantly lower in both groups of patients in comparison with the control group. CONCLUSIONS The mechanism of depressed melatonin concentrations in CRF observed in our study remains unclear. However, it seems possible that decline in melatonin levels is due to impairment in adrenergic function that occurs in CRF. Because the studies on the melatonin secretion in CRF bring about conflicting results, the relationship between renal diseases and melatonin secretion needs further investigations.
Dynamic Ligand Modulation of EPO Receptor Pools, and Dysregulation by Polycythemia-Associated EPOR Alleles

Erythropoietin (EPO) and its cell surface receptor (EPOR) are essential for erythropoiesis; can modulate non-erythroid target tissues; and have been reported to affect the progression of certain cancers. Basic studies of EPOR expression and trafficking, however, have been hindered by low-level EPOR occurrence, and the limited specificity of anti-EPOR antibodies. Consequently, these aspects of EPOR biology are not well defined, nor are actions of polycythemia- associated mutated EPOR alleles. Using novel rabbit monoclonal antibodies to intracellular, PY- activated and extracellular EPOR domains, the following properties of the endogenous hEPOR in erythroid progenitors first are unambiguously defined. 1) High- Mr EPOR forms become obviously expressed only when EPO is limited. 2) EPOR-68K plus -70K species sequentially accumulate, and EPOR-70K comprises an apparent cell surface EPOR population. 3) Brefeldin A, N-glycanase and associated analyses point to EPOR-68K as a core-glycosylated intracellular EPOR pool (of modest size). 4) In contrast to recent reports, EPOR inward trafficking is shown (in UT7epo cells, and primary proerythroblasts) to be sharply ligand-dependent. Beyond this, when C-terminal truncated hEPOR-T mutant alleles as harbored by polycythemia patients are co-expressed with the wild-type EPOR in EPO-dependent erythroid progenitors, several specific events become altered. First, EPOR-T alleles are persistently activated upon EPO- challenge, yet are also subject to apparent turn-over (to low-Mr EPOR products). Furthermore, during exponential cell growth EPOR-T species become both over-represented, and hyper-activated. Interestingly, EPOR-T expression also results in an EPO dose-dependent loss of endogenous wild-type EPOR's (and, therefore, a squelching of EPOR C-terminal- mediated negative feedback effects). New knowledge concerning regulated EPOR expression and trafficking therefore is provided, together with new insight into mechanisms via which mutated EPOR-T polycythemia alleles dysregulate the erythron. Notably, specific new tools also are characterized for studies of EPOR expression, activation, action and metabolism.
Constitutive and basal secretion from the endocrine cell line, AtT-20

A variant of the ACTH-secreting pituitary cell line, AtT-20, has been isolated that does not make ACTH, sulfated proteins characteristic of the regulated secretory pathway, or dense-core secretory granules but retains constitutive secretion. Unlike wild type AtT-20 cells, the variant cannot store or release on stimulation, free glycosaminoglycan (GAG) chains. In addition, the variant cells cannot store trypsinogen or proinsulin, proteins that are targeted to dense core secretory granules in wild type cells. The regulated pathway could not be restored by transfecting with DNA encoding trypsinogen, a soluble regulated secretory protein targeted to secretory granules. A comparison of secretion from variant and wild type cells allows a distinction to be made between constitutive secretion and basal secretion, the spontaneous release of regulated proteins that occurs in the absence of stimulation.
Climate and environment in southwest Sweden 15.5–11.3 cal. ka BP

Lake sedimentary records that allow documentation of the distinct climatic and environmental shifts during the early part of the Last Termination are scarce for northern Europe. This multi‐proxy study of the sediments of Atteköpsmosse, southwest Sweden, therefore fills an important gap and provides detailed information regarding past hydroclimatic conditions and local environmental responses to climatic shifts. Lake infilling started c. 15.5 cal. ka BP, but low aquatic productivity, cold summer lake water temperatures, unstable catchments, and scarce herb and shrub vegetation prevailed until c. 14.7–14.5 cal. ka BP. Inflow of warmer air masses and higher July air temperatures favoured a rise in aquatic productivity and lake water summer temperatures, and the establishment of a diverse herb, shrub and dwarf shrub vegetation, which also included tree birch c. 14.5 cal. ka BP. Freshening of the moisture source region c. 13.7–13.6 cal. ka BP does not seem to have had a large impact on the ancient lake and its catchment, as lake aquatic productivity increased further and lake water summer temperatures and minimum mean July air temperatures remained around 12–14 °C. In contrast, further freshening of the moisture source region c. 13 cal. ka BP triggered a decrease in lake productivity, drier conditions and lower lake water summer temperatures. Macroscopic finds of tree Betula and Pinus sylvestris at 13–12.8 cal. ka BP demonstrate the presence of these trees in the lake's catchment. The transition into the Holocene (11.6–11.5 cal. ka BP) is marked by a change in chironomid assemblages and by a rise in lake water summer temperatures and aquatic productivity. These changes were followed by the re‐establishment of a diverse aquatic and terrestrial vegetation, including tree birch and Pinus sylvestris at 11.4 cal. ka BP.
THE JCMT GOULD BELT SURVEY: EVIDENCE FOR DUST GRAIN EVOLUTION IN PERSEUS STAR-FORMING CLUMPS

The dust emissivity spectral index, β, is a critical parameter for deriving the mass and temperature of star-forming structures and, consequently, their gravitational stability. The β value is dependent on various dust grain properties, such as size, porosity, and surface composition, and is expected to vary as dust grains evolve. Here we present β, dust temperature, and optical depth maps of the star-forming clumps in the Perseus Molecular Cloud determined from fitting spectral energy distributions to combined Herschel and JCMT observations in the 160, 250, 350, 500, and 850 μm bands. Most of the derived β and dust temperature values fall within the ranges of 1.0–2.7 and 8–20 K, respectively. In Perseus, we find the β distribution differs significantly from clump to clump, indicative of grain growth. Furthermore, we also see significant localized β variations within individual clumps and find low-β regions correlate with local temperature peaks, hinting at the possible origins of low-β grains. Throughout Perseus, we also see indications of heating from B stars and embedded protostars, as well evidence of outflows shaping the local landscape.