Miracle-dz/UniFAR-FTUs huggingface dataset:
Distributions of Salmonella Subtypes Differ between Two U.S. Produce-Growing Regions

ABSTRACT Salmonella accounts for approximately 50% of produce-associated outbreaks in the United States, several of which have been traced back to contamination in the produce production environment. To quantify Salmonella diversity and aid in identification of Salmonella contamination sources, we characterized Salmonella isolates from two geographically diverse produce-growing regions in the United States. Initially, we characterized the Salmonella serotype and subtype diversity associated with 1,677 samples collected from 33 produce farms in New York State (NYS). Among these 1,677 samples, 74 were Salmonella positive, yielding 80 unique isolates (from 147 total isolates), which represented 14 serovars and 23 different pulsed-field gel electrophoresis (PFGE) types. To explore regional Salmonella diversity associated with production environments, we collected a smaller set of samples (n = 65) from South Florida (SFL) production environments and compared the Salmonella diversity associated with these samples with the diversity found among NYS production environments. Among these 65 samples, 23 were Salmonella positive, yielding 32 unique isolates (from 81 total isolates), which represented 11 serovars and 17 different PFGE types. The most common serovars isolated in NYS were Salmonella enterica serovars Newport, Cerro, and Thompson, while common serovars isolated in SFL were Salmonella serovars Saphra and Newport and S. enterica subsp. diarizonae serovar 50:r:z. High PFGE type diversity (Simpson's diversity index, 0.90 ± 0.02) was observed among Salmonella isolates across both regions; only three PFGE types were shared between the two regions. The probability of three or fewer shared PFGE types was <0.000001; therefore, Salmonella isolates were considerably different between the two sampled regions. These findings suggest the potential for PFGE-based source tracking of Salmonella in production environments.
Integrated silicon nitride microdisk lasers based on quantum dots

On-chip waveguide-coupled silicon nitride microdisk lasers are demonstrated using a 55 nm CdSe/CdS quantum dots film as gain material. The devices were fabricated with a hybrid integration technique able to embed quantum dots in SiN cavities. Lasing is achieved under optical pumping with a record low threshold of 26.8 μJ·cm-2 in a 7 μm-diameter disk.
Augur - A Tool for the Analysis of Graph Transformation Systems

We describe the tool Augur for the verification of systems with dynamically evolving structure specified by graph transformation. After giving a short introduction to graph transformation systems (GTSs), we describe the verification techniques used by the tool, namely the approximation of GTSs by Petri nets. Instead of verifying properties directly in the original system, they can be checked on the approximating Petri net. We explain the workings of the different modules of the Augur tool using two small case studies where we model reconfigurable networks and mobile processes. Appeared in The Formal Specification Column
Coefficients of Finite Difference Operator for Rectangular Cell NS-FDTD Method

The nonstandard finite difference time domain (NS-FDTD) method is a dispersion error reduction technique for the FDTD method. High accuracy is achieved by the optimal selection of the coefficients used for the finite difference (FD) operators in the NS-FDTD method. However, the previously published method of obtaining the coefficients for rectangular cells, using a full numerical technique, takes an enormous amount of computing time. To solve this difficulty, we propose a semi-analytical method to obtain the optimal coefficients with a far higher computational efficiency. It is shown, by numerical tests, that the optimal coefficients need six significant digits for accurate NS-FDTD solutions. Consequently our new method can reduce the computing time to obtain the optimal coefficients from an estimated 42 × 104 minutes by the previous method to about 7 seconds for three dimensional rectangular cells.
Predicting Outcomes on the Liver Transplant Waiting List in the United States: Accounting for Large Regional Variation in Organ Availability and Priority Allocation Points

Background The probability of liver transplant and death on the waiting list in the United States varies greatly by donation service area (DSA) due to geographic differences in availability of organs and allocation of priority points, making it difficult for providers to predict likely outcomes after listing. We aimed to develop an online calculator to report outcomes by region and patient characteristics. Methods Using the Scientific Registry of Transplant Recipients database, we included all prevalent US adults aged 18 years or older waitlisted for liver transplant, examined on 24 days at least 30 days apart over a 2-year period. Outcomes were determined at intervals of 30 to 365 days. Outcomes are reported by transplant program, DSA, region, and the nation for comparison, and can be shown by allocation or by laboratory model for end-stage liver disease (MELD) score (6-14, 15-24, 25-29, 30-34, 35-40), age, and blood type. Results Outcomes varied greatly by DSA; for candidates with allocation MELD 25-29, the 25th and 75th percentiles of liver transplant probability were 30% and 67%, respectively, at 90 days. Corresponding percentiles for death or becoming too sick to undergo transplant were 5% and 9%. Outcomes also varied greatly for candidates with and without MELD exception points. Conclusions The waitlist outcome calculator highlights ongoing disparities in access to liver transplant and may assist providers in understanding and counseling their patients about likely outcomes on the waiting list.
Determination of fumonisins B1 and B2 in cornflakes by high performance liquid chromatography and immunoaffinity clean-up

The determination of fumonisins in cornflakes is a challenging matter as the actually available methods for the analysis of corn do not perform well when applied to this more complex matrix. After testing several factors that may affect the analytical performance, an accurate method for the determination of fumonisin B1 (FB1) and B2 (FB2) in cornflakes has been developed. The method uses immunoaffinity chromatography for clean-up and high performance liquid chromatography (HPLC) for quantification of the toxins. Samples were extracted twice with acetonitrile-methanol-water (25:25:50) and the combined extracts were diluted with phosphate buffered saline (PBS) and applied to a FumoniTest™ immunoaffinity column. After washing with PBS, fumonisins were eluted from the column with methanol and reacted with o-phthaldialdehyde/2-mercaptoethanol to form fluorescent derivatives. Fumonisin derivatives were analysed by reversed phase HPLC with fluorometric detection using methanol-0.1 M phosphate buffer (77:23; pH adjusted at 3.35) as mobile phase. The average recoveries for FB1 and FB2 spiked in the ranges of 0.33–2.80 μg/g and 0.17–1.40 μg/g were 102.6% and 95.1%, respectively, with average relative standard deviations of 9% and 8%. The limit of quantiWcation for FB1 and FB2 was 0.005 μg/g based on a signal-to-noise ratio of 6:1 by using a sensitive Xuorescence detector. The method was used to analyse 18 cornflakes and cornflake cereals samples for FB1 and FB2 contamination. All but one sample were found to be contaminated, with maximum FB1 and FB2 concentrations of 1.092 μg/g and 0.235 μg/g, respectively. Mean FB1 and FB2 concentrations were 0.157 μg/g and 0.036 μg/g, respectively.
Competition and Innovation: Does the Distance to the Technology Frontier Matter?

This paper provides new evidence on the relationship between innovation, competitionnand distance to the technology frontier, using enterprise surveys from 40 developing and transition countries. Different from previous empirical studies, the distance to frontier is measured by a firm's technology level relative to its main competitor. This self-reported comparison allows to capture a crucial determinant of a firm's business strategy and its response to competition. The findings from the empirical analysis are as follows. Firstly, firms with more advanced technology compared to their main competitors have more product innovations. Secondly, there is evidence that innovation and competition are more positively correlated at low levels of competition than at high levels. With some measures of competition,nthe correlation is highest at intermediate levels of competition, which suggestsnan inverted-U relationship. Thirdly, in certain specifications, competition is most positively correlated with product innovation when a firm is more advanced than its main competitor. In other cases, this correlation is strongest for firms that are at the same technology level as their competitors. However, the differences in the correlations between more and less advanced firms are not always significant.
Comparing the Quality of Accruals for Alternative Summary Performance Measures in the Real Estate Investment Trust (REIT) Industry

This study examines Funds from Operations (FFO), a non-GAAP summary performance measure used extensively by the Real Estate Investment Trust (REIT) industry, by comparing the quality of accruals in FFO and in net income. Accrual quality is empirically evaluated from regressions relating accruals to past, present, future cash flows and changes in revenue, with larger residuals implying lower accrual quality. Results show that the accruals component of FFO is of higher quality than the accruals component of net income. The study then considers how the individual accrual items excluded from FFO, but included in net income contribute to the accrual quality differences of the two measures. I show that all these accrual items (including depreciation and some non-recurring accruals) are of low quality and are insignificant in predicting future cash flows. Since accounting depreciation is supposed to help match revenue with expenses, it is surprising to find that depreciation accruals are of low quality for the REIT industry. Further analysis on depreciation shows that the low quality of depreciation accruals for REIT firms is due to estimation errors and managerial manipulation and, to some extent, extreme changes in market inflation.
Secrecy Performance Optimization for Wireless Powered Communication Networks With an Energy Harvesting Jammer

In this paper, we consider a wireless powered communication network with an energy harvesting (EH) jammer where eavesdroppers try to wiretap the communication between users and a hybrid access-point (H-AP). In our system, the H-AP first transmits an energy signal to recharge the batteries of the EH users and the EH jammer in the energy transfer (ET) phase. Then, in the subsequent information transfer (IT) phase, each user sends information to the H-AP in a time division multiple access manner, while the jammer generates jamming signals to interfere the eavesdroppers. We adopt two different secrecy performance measurements according to the level of channel state information (CSI) of the eavesdroppers. First, with a single user, we maximize the secrecy rate by optimizing the time allocation between the ET and the IT phase when perfect CSI of the eavesdroppers is available at all nodes. In contrast, when the instantaneous CSI of the eavesdroppers is not available at legitimate nodes, we analyze and minimize the secrecy outage probability. We also extend the single user analysis to a more general multi-user situation with an additional consideration of the transmit power allocation at the jammer. Finally, we evaluate the performance of our proposed solutions through simulations and demonstrate that a performance gain compared to conventional schemes becomes more pronounced with the increased number of eavesdroppers and users.
Calf Muscle Venous Thrombosis

Calf muscle veins have been demonstrated to be one of the most frequent areas that develop deep venous thrombosis (DVT), both as an isolated finding and in combination with proximal DVT. Calf muscle venous thrombosis (CMVT) has been shown to be more frequently associated with localized calf tenderness, and when left untreated, a proportion tend to propagate proximally and may lead to pulmonary embolism. Imaging with duplex venous scanning is fairly sensitive in the diagnosis of CMVT. Treatment recommendations for CMVT are variable with some studies showing clear clinical benefit of anticoagulation therapy and others showing no benefit.
Respiration metabolism of Group B Streptococcus is activated by environmental haem and quinone and contributes to virulence

Group B Streptococcus (GBS) is a common constituent of the vaginal microflora, but its transmission to newborns can cause life‐threatening sepsis, pneumonia and meningitis. Energy metabolism of this opportunist pathogen has been deduced to be strictly fermentative. We discovered that GBS undergoes respiration metabolism if its environment supplies two essential respiratory components: quinone and haem. Respiration metabolism led to significant changes in growth characteristics, including a doubling of biomass and an altered metabolite profile under the tested conditions. The GBS respiratory chain is inactivated by: (i) withdrawing haem and/or quinone, (ii) treating cultures with a respiration inhibitor or (iii) inactivating the cydA gene product, a subunit of cytochrome bd quinol oxidase, in all cases resulting in exclusively fermentative growth. cydA inactivation reduced GBS growth in human blood and strongly attenuated virulence in a neonatal rat sepsis model, suggesting that the animal host may supply the components that activate GBS respiration. These results suggest a role of respiration metabolism in GBS dissemination. Our findings show that environmental factors can increase the flexibility of GBS metabolism by activating a newly identified respiration chain. The need for two environmental factors may explain why GBS respiration metabolism was not found in previous studies.
Is Genetic Testing in IBD Ready for Prime Time?

In spite of the complexities of the human genome and the heterogeneity of patients with inflammatory bowel disease, enormous progress has been made in the identification of genes associated with inflammatory bowel disease (for a good review see (1)). The identification of these genes has and will continue to provide important clues to the pathogenesis of IBD. As clinicians who care for patients with inflammatory bowel disease we have several goals for genetic testing. Those goals are to predict who will get the disease, predict the disease course, and predict response to therapy. Much excitement accompanied the identification of CARD15/NOD2 as a disease susceptibility gene in patients with Crohn's disease (2,3). Part of the excitement resides in the function of the CARD15/NOD2 gene as a pathogen recognition receptor. The CARD15/NOD2 proteins encoded by the CD-associated gene variants have a decreased ability to bind to the bacterial ligand, muramyl dipeptide, resulting in a reduced capacity to activate proinflammatory signals in the presence of intracellular bacteria (4). Given the evidence that Crohn's disease results from an aberrant host immune response in the presence of luminal bacteria, CARD15/NOD2 provides an important link between genes and the microflora.
Schwann cells originating from skin-derived precursors promote peripheral nerve regeneration in rats

Artificial guidance channels containing Schwann cells can promote the regeneration of injured peripheral nerve over long distances. However, primary Schwann cells are not suitable for autotransplantation. Under specific conditions, skin-derived progenitors can be induced to differentiate into Schwann cells. Therefore, adult rat dorsal skin (dermis)-derived progenitors were isolated and induced to differentiate with DMEM/F12 containing B27, neuregulin 1, and forskolin. Immunofluorescence staining and reverse transcription polymerase chain reaction (RT-PCR) confirmed that the resultant cells were indeed Schwann cells. Artificial guidance channels containing skin-derived progenitors, Schwann cells originating from skin-derived progenitors, or primary Schwann cells were used to bridge 5 mm sciatic nerve defects. Schwann cells originating from skin-derived progenitors significantly promoted sciatic nerve axonal regeneration. The significant recovery of injured rat sciatic nerve function after the transplantation of Schwann cells originating from skin-derived progenitors was confirmed by electromyogram. The therapeutic effect of Schwann cells originating from skin-derived progenitors was better than that of skin-derived progenitors. These findings indicate that Schwann cells originating from skin-derived precursors can promote peripheral nerve regeneration in rats.
Analysis and Design of a Novel Circularly Polarized Antipodal Linearly Tapered Slot Antenna

This paper presents and characterizes a novel antipodal linearly tapered slot antenna for generating the circularly polarized (CP) field. By introducing two symmetrical slots on the top and bottom layers of a rectangular WR-15 waveguide, we could obtain circular polarization with an axial ratio bandwidth of 34.1%. The waveguide was used to feed the proposed antenna with very wideband impedance matching. The antenna can achieve impedance bandwidth of 40% for S(1,1) <;-15 dB from 50 to 75 GHz. The simulation and measurement results show that the antenna can produce very good radiation patterns, with stable gain of 9.8 dBi ± 1.24 dBi, low back radiation, and narrow beamwidth over the operating frequency range. The working principle of this CP antenna is explained, using theoretical equations and explicit current distributions. The proposed antenna is easy to manufacture and is a compact candidate for high performance CP millimeter-wave antenna.
Firms' Information Environments and Board Independence

A feature of recent regulatory developments, such as CLERP 9 in Australia and Sarbannes Oxley in the United States, is that they prescribe uniform governance mechanisms for all firms, a 'one size fits all' approach. However, there is scant empirical evidence of whether this is efficient, and in the extant empirical literature there is only equivocal guidance on the more general question of how firm characteristics impact the selection of governance mechanisms. Addressing, at least in part this issue, this study evaluates the impact of the firms' information environment and the ability of accounting information to capture this on the demand for independent boards of directors as a governance mechanism. Price to book (P/B) and price to earnings (P/E) are used to evaluate the firms' information environment and the extent to which it is captured by accounting information. Evidence is provided of joint P/B, P/E firm classification capturing significant differences in board independence across firms. Importantly, supplementing P/B with P/E identifies significant differences in board independence within high and low P/B firms. Furthermore, evidence is provided of a strong, positive correlation between board size and board independence suggesting that independent directors are added to boards rather than used to supplant inside directors. This brings into question the appropriateness of regulation uniformly prescribing corporate governance mechanisms.
MINERAL LIMITATION OF ZOOPLANKTON: STOICHIOMETRIC CONSTRAINTS AND OPTIMAL FORAGING

Nutritional deficiencies are a very common phenomenon, and consumers generally face food that is not optimally suited for their needs. Especially herbivores are habitually confronted with food of inferior quality, usually a result of too-low nutrient concentrations in plant material. Waterfleas of the genus Daphnia are good model organisms to study the effect of inferior quality food, and how animals deal with this. We tested the effect of algae to which we had given different phosphorus contents on both life history and feeding parameters of Daphnia magna. Phosphorus content of the algae strongly af- fected both the growth rate and the feeding activity of the daphniids. Feeding activity increased with declining food quality (increase in C:P ratio of the algae), whereas growth rates were maximal at intermediate C:P levels. We conclude that the direct limitation of phosphorus is a very important factor determining food quality for zooplankters. Daphniids counterbalanced lower P content of their food by spending more C (energy) on acquiring this limiting resource. This implies that when Daphnia are given phosphorus-limited food both the addition of phosphorus and the addition of carbon (energy) should increase the growth rate of the animals (co-limitation). The influence of the phosphorus content of the food on the feeding activity of Daphnia offers a mechanistic explanation for the observed homeostasis in daphniids.
Plateau iris in Asian subjects with primary angle closure glaucoma.

OBJECTIVE To determine the prevalence of plateau iris in Asian eyes with primary angle closure glaucoma (PACG) using ultrasound biomicroscopy (UBM). METHODS In this cross-sectional observational study, subjects older than 40 years with PACG who had a patent laser peripheral iridotomy underwent UBM in 1 eye. Ultrasound biomicroscopy images were qualitatively analyzed using standardized criteria. Plateau iris in a quadrant was defined by anteriorly directed ciliary body, absent ciliary sulcus, steep iris root from its point of insertion followed by a downward angulation, flat iris plane, and irido-angle contact. At least 2 quadrants had to fulfill these UBM criteria for an eye to be classified as having plateau iris. RESULTS One hundred eleven subjects (70 from Singapore, 41 from Thailand) with PACG were recruited. The mean (SD) age was 65.6 (8.1) years, and 63.9% were female. Based on standardized UBM criteria, plateau iris was found in 36 of 111 eyes (32.4%; 95% confidence interval, 24.4%-41.6%). In these 36 eyes, quadrant-wise analysis showed 66.7% had plateau iris in 2 quadrants; 22.2%, in 3 quadrants; and 11.1%, in all quadrants. CONCLUSIONS About 30% of PACG eyes with a patent laser peripheral iridotomy were found to have plateau iris on UBM, highlighting the importance of non-pupil block mechanisms in Asian individuals.