Miracle-dz/UniFAR-FTUs huggingface dataset:
Antimicrobial drug resistance and molecular characterization of Salmonella isolated from domestic animals, humans, and meat products.

OBJECTIVES 1) To characterize and determine genotypic relatedness of Salmonella serovars commonly isolated from domestic animals and humans in North Dakota, and 2) to assess their role in transferring antimicrobial resistance (AMR) to humans. MATERIALS AND METHODS A total of 434 Salmonella isolates obtained from 1) feces of apparently healthy feedlot, range, and dairy cattle in North Dakota; 2) clinical samples from sick or dead animals submitted to North Dakota State University-Veterinary Diagnostic Laboratory (2000-2005); 3) previous meat product surveillance studies in North Dakota; and 4) 179 samples from human patients in North Dakota (2000-2005) by the North Dakota Department of Health were studied. The isolates were initially serotyped and later genotyped by pulsed-field gel electrophoresis (PFGE) to investigate their relatedness. The National Antimicrobial Resistance Monitoring Systems panel was used to compare AMR profiles of animal and human isolates to assess a possible role of domestic animals in transfer of AMR to humans. RESULTS Salmonella Typhimurium was the predominant serotype in both humans (13.4%) and domestic animals (34.3%), followed by Newport in animals (2.6%) and human (3.9%). Salmonella Arizona (0.7%), Salmonella Give (0.9%), and Salmonella Muenster (3.5%) were isolated from sick or dead animals. PFGE results confirmed occurrence of similar Salmonella genotypes in both domestic animals and humans. AMR profiles showed that most animal strains were multidrug resistant. A single human isolate had PFGE and multidrug resistance profiles similar to a major cattle genotype, suggesting a possible AMR transmission from cattle to humans. CONCLUSION AND APPLICATION: Similar Salmonella genotypes were infecting domestic animals and humans in North Dakota. The AMR levels were higher in domestic animal isolates than in humans, implying that the occurrence of AMR in animal isolates may not translate directly into AMR in human isolates in North Dakota. This is helpful in determining future policies regarding antimicrobial drug use in domestic animals and humans.
Biological Gradient Between Long-Term Arsenic Exposure and Carotid Atherosclerosis

Background—Long-term exposure to ingested arsenic has been documented to induce peripheral vascular disease, ischemic heart disease, and cerebral infarction in a dose-response relationship. This study further examined the biological gradient between ingested inorganic arsenic and carotid atherosclerosis. Methods and Results—We studied 199 male and 264 female adult residents from the southwestern area of endemic arseniasis in Taiwan. The extent of carotid atherosclerosis was assessed by duplex ultrasonography. Diabetes mellitus was determined by oral glucose tolerance test, hypertension by mercury sphygmomanometers, and serum lipid profiles by autoanalyzers. Information regarding the consumption of high-arsenic artesian well water, cigarette smoking, and alcohol consumption was obtained through standardized questionnaire interviews. Logistic regression analysis was used to estimate the odds ratio and its 95% CI of carotid atherosclerosis for various risk factors. Three indices of long-term exposure to ingested arsenic, including the duration of consuming artesian well water, the average arsenic concentration in consumed artesian well water, and cumulative arsenic exposure, were all significantly associated with prevalence of carotid atherosclerosis in a dose-response relationship. The biological gradient remained significant after adjustment for age, sex, hypertension, diabetes mellitus, cigarette smoking, alcohol consumption, waist-to-hip ratio, and serum levels of total cholesterol and LDL cholesterol. The multivariate-adjusted odds ratio was 3.1 (95% CI 1.3 to 7.4) for those who had a cumulative arsenic exposure of ≥20 mg/L-years compared with those without exposure to arsenic from drinking artesian well water. Conclusions—Carotid atherosclerosis is associated with ingested inorganic arsenic, showing a significant biological gradient.
Comparison between noninvasive measurement of central venous pressure using near infrared spectroscopy with an invasive central venous pressure monitoring in cardiac surgical Intensive Care Unit

Introduction: Central venous pressure (CVP) measurement is essential in the management of certain clinical situations, including cardiac failure, volume overload and sepsis. CVP measurement requires catheterization of the central vein which is invasive and may lead to complications. The aim of this study was to evaluate the accuracy of measurement of CVP using a new noninvasive method based on near infrared spectroscopy (NIRS) in a group of cardiac surgical Intensive Care Unit (ICU) patients. Methodology: Thirty patients in cardiac surgical ICU were enrolled in the study who had an in situ central venous catheter (CVC). Sixty measurements were recorded in 1 h for each patient. A total of 1800 values were compared between noninvasive CVP (CVPn) obtained from Mespere VENUS 2000 CVP system and invasive CVP (CVPi) obtained from CVC. Results: Strong positive correlation was found between CVPi and CVPn (R = 0.9272, P < 0.0001). Linear regression equation - CVPi = 0.5404 + 0.8875 × CVPn (r2 = 0.86, P < 0.001), Bland-Altman bias plots showed mean difference ± standard deviation and limits of agreement: −0.31 ± 1.36 and − 2.99 to + 2.37 (CVPi-CVPn). Conclusion: Noninvasive assessment of the CVP based on NIRS yields readings consistently close to those measured invasively. CVPn may be a clinically useful substitute for CVPi measurements with an advantage of being simple and continuous. It is a promising tool for early management of acute state wherein knowledge of CVP is helpful.
Phylogenies and Community Ecology

▪ Abstract As better phylogenetic hypotheses become available for many groups of organisms, studies in community ecology can be informed by knowledge of the evolutionary relationships among coexisting species. We note three primary approaches to integrating phylogenetic information into studies of community organization: 1. examining the phylogenetic structure of community assemblages, 2. exploring the phylogenetic basis of community niche structure, and 3. adding a community context to studies of trait evolution and biogeography. We recognize a common pattern of phylogenetic conservatism in ecological character and highlight the challenges of using phylogenies of partial lineages. We also review phylogenetic approaches to three emergent properties of communities: species diversity, relative abundance distributions, and range sizes. Methodological advances in phylogenetic supertree construction, character reconstruction, null models for community assembly and character evolution, and metrics of community .
Disaster Recovery Site Evaluations and Selections for Information Systems of Academic Big Data

The most dramatic factor shaping the future of higher education is Big Data and analytics. In the Big Data era, the explosive growth of massive data manipulations imposes a heavy burden on computation, storage, and communication in data centers. Increasing uncertainties in information system availability have become a daily serious problem. An appropriate evaluation and selection of the right information system disaster recovery (DR) site can ensure business continuity and investment optimization. Therefore, this research aims to establish an analytic framework for evaluating, selecting DR sites for academic Big Data. The proposed analytic framework is consisting of the Decision-Making Trial and Evaluation Laboratory (DEMATEL), DEMATEL-based network process (DNP) and VIsekriterijumsko KOmpromisno Rangiranje (VIKOR) methods. An empirical study based on a real Big Data DR application of an Asian high-performance computer center’s evaluation and selection of DR sites for academic Big Data will be used to illustrate the feasibility of the proposed framework. The analytic results can serve as a foundation for information technology (IT) administrators’ strategies to reduce the performance gaps of a DR site for Big Data manipulations in general, and academic Big Data manipulations in special.
Does the Mismatch Match the Penumbra?: Magnetic Resonance Imaging and Positron Emission Tomography in Early Ischemic Stroke

Background and Purpose— In ischemic stroke, diffusion-weighted (DW) and perfusion-weighted (PW) magnet resonance imaging (MRI) is used to define the mismatch as the therapeutic target. With positron emission tomography (PET), we characterized the metabolic patterns of tissue compartments identified by MRI and compared the volumes of mismatch to those of PET-defined penumbra. Methods— In 6 acute (median, 5.2 hours) and 7 chronic (median, 10 days) stroke patients in whom a mismatch was defined by PW/DW MRI, PET was performed (median, 120-minute delay). Cerebral blood flow (CBF), oxygen metabolism (CMRO2), and oxygen extraction fraction (OEF) was determined in the areas of DWI lesion, mismatch, and oligemia. Then, the mismatch volume was compared with the volume of penumbra. Results— DWI lesions showed impaired tissue integrity (low CMRO2 and low OEF). Mismatch areas were viable (normal CMRO2) but showed largely varying OEF. Oligemic areas had metabolic patterns comparable to normal tissue. A mismatch volume was found in all 13 patients. However, only 8 of 13 had a corresponding penumbra volume that covered only a part of the mismatch. Conclusion— Our comparative PET/MRI study confirmed the current pathophysiological hypothesis for the DWI lesion and for the oligemic areas. However, the mismatch area did not reliably detect elevated OEF and overestimated the penumbra defined by PET.
Profiling user experience in digital games with the flow model

Because of the immersive user experience (UX), digital games are the most popular form of entertainment today. Game designers have found Csikszentmihalyi's flow model useful in order to optimize UX. Although the flow model is widely used in both the game design and research, it tends to narrow UX down to an optimal flow channel. Based on the analysis of self-report data of 2,436 gamers, we studied psychological dimensions of UX within all four channels of the original flow model, namely, flow, boredom, apathy, and anxiety. Our analysis suggests renaming boredom, apathy, and anxiety channels respectively as relaxation, impassiveness, and overwhelm, at least in the context of digital games. Our results also point out the relevance of a multidimensional UX evaluation in future projects, which aim at enhancing UX outside the flow channel or assessing outcomes related to digital games.
Two Models of Minimalist, Incremental Syntactic Analysis

Minimalist grammars (MGs) and multiple context-free grammars (MCFGs) are weakly equivalent in the sense that they define the same languages, a large mildly context-sensitive class that properly includes context-free languages. But in addition, for each MG, there is an MCFG which is strongly equivalent in the sense that it defines the same language with isomorphic derivations. However, the structure-building rules of MGs but not MCFGs are defined in a way that generalizes across categories. Consequently, MGs can be exponentially more succinct than their MCFG equivalents, and this difference shows in parsing models too. An incremental, top-down beam parser for MGs is defined here, sound and complete for all MGs, and hence also capable of parsing all MCFG languages. But since the parser represents its grammar transparently, the relative succinctness of MGs is again evident. Although the determinants of MG structure are narrowly and discretely defined, probabilistic influences from a much broader domain can influence even the earliest analytic steps, allowing frequency and context effects to come early and from almost anywhere, as expected in incremental models.
Focal delivery during direct infusion to brain: role of flow rate, catheter diameter, and tissue mechanics.

Direct interstitial infusion is a technique capable of delivering agents over both small and large dimensions of brain tissue. However, at a sufficiently high volumetric inflow rate, backflow along the catheter shaft may occur and compromise delivery. A scaling relationship for the finite backflow distance along this catheter in pure gray matter ( x m) has been determined from a mathematical model based on Stokes flow, Darcy flow in porous media, and elastic deformation of the brain tissue: x m = constant Q o3 R 4 r c4 G -3μ-1( Q o = volumetric inflow rate, R = tissue hydraulic resistance, r c = catheter radius, G = shear modulus, and μ = viscosity). This implies that backflow is minimized by the use of small diameter catheters and that a fixed (minimal) backflow distance may be maintained by offsetting an increase in flow rate with a similar decrease in catheter radius. Generally, backflow is avoided in rat gray matter with a 32-gauge catheter operating below 0.5 μl/min. An extension of the scaling relationship to include brain size in the resistance term leads to the finding that absolute backflow distance obtained with a given catheter and inflow rate is weakly affected by the depth of catheter tip placement and, thus, brain size. Finally, an extension of the model to describe catheter passage through a white matter layer before terminating in the gray has been shown to account for observed percentages of albumin in the corpus callosum after a 4-μl infusion of the compound to rat striatum over a range of volumetric inflow rates.
Active compliant motion : a survey

Whether they are asked to polish or assemble parts, clean the house or open doors, the future generation of robots will have to cope with contact tasks under uncertainty in a stable and safe manner. Obtaining a controlled contact motion under uncertainty is still a major challenge for the robotics community. At present most research groups focus on one of the subcomponents (i.e., modeling, planning, estimation or control) of the system, and no overall system is developed yet. This paper presents a literature survey of the state-of-the-art of the subcomponents and points to the need for effective integration of those components.
The Pattern of R2 Retrotransposon Activity in Natural Populations of Drosophila simulans Reflects the Dynamic Nature of the rDNA Locus

The pattern and frequency of insertions that enable transposable elements to remain active in a population are poorly understood. The retrotransposable element R2 exclusively inserts into the 28S rRNA genes where it establishes long-term, stable relationships with its animal hosts. Previous studies with laboratory stocks of Drosophila simulans have suggested that control over R2 retrotransposition resides within the rDNA loci. In this report, we sampled 180 rDNA loci of animals collected from two natural populations of D. simulans. The two populations were found to have similar patterns of R2 activity. About half of the rDNA loci supported no or very low levels of R2 transcripts with no evidence of R2 retrotransposition. The remaining half of the rDNA loci had levels of R2 transcripts that varied in a continuous manner over almost a 100-fold range and did support new retrotransposition events. Structural analysis of the rDNA loci in 18 lines that spanned the range of R2 transcript levels in these populations revealed that R2 number and rDNA locus size varied 2-fold; however, R2 activity was not readily correlated with either of these parameters. Instead R2 activity was best correlated with the distribution of elements within the rDNA locus. Loci with no activity had larger contiguous blocks of rDNA units free of R2-insertions. These data suggest a model in which frequent recombination within the rDNA locus continually redistributes R2-inserted units resulting in changing levels of R2 activity within individual loci and persistent R2 activity within the population.
PARP expression in germ cell tumours

Background Poly(ADP-ribose)polymerase (PARP) inhibitors represent a new class of promising drugs in anticancer therapy. Aims To evaluate PARP expression in testicular germ cell tumours (GCTs) and to correlate expression patterns with clinicopathological variables. Methods In this translational study, tumour specimens from 124 patients with GCTs (114 patients with testicular primary tumours and 10 with extragonadal GCTs) were identified. PARP expression was detected by immunohistochemistry using monoclonal antibodies, scored by the multiplicative quickscore (QS) method and compared to PARP expression in normal testicular tissue. Results We observed higher expression of PARP in testicular tumours compared to normal testicular tissue (mean QS=10.04 vs 3.31, p<0.0000001). Mean QS±SD for each histological subtype was as follows: intratubular germ cell neoplasia unclassified (IGCNU)=18.00±0.00, embryonal carcinoma=9.62±5.64, seminoma=9.74±6.51, yolk sac tumour=7.8±7.20, teratoma=5.87±5.34, and choriocarcinoma=4.50±8.33. The PARP overexpression (QS>9) was most often detected in IGCNU (100% of specimen with PARP overexpression), seminona (52.6%), embryonal carcinoma (47.0%), yolk sac tumour (33.3%), teratoma (26.7%) and choriocarcinoma (25.0%), compared to 1.9% of normal testicular tissue specimens. There was no association between PARP expression and clinical variables. Conclusions In this pilot study, we showed for the first time, that PARP is overexpressed in testicular germ cell tumours compared to normal testis.
Cergutuzumab amunaleukin (CEA-IL2v), a CEA-targeted IL-2 variant-based immunocytokine for combination cancer immunotherapy: Overcoming limitations of aldesleukin and conventional IL-2-based immunocytokines

ABSTRACT We developed cergutuzumab amunaleukin (CEA-IL2v, RG7813), a novel monomeric CEA-targeted immunocytokine, that comprises a single IL-2 variant (IL2v) moiety with abolished CD25 binding, fused to the C-terminus of a high affinity, bivalent carcinoembryonic antigen (CEA)-specific antibody devoid of Fc-mediated effector functions. Its molecular design aims to (i) avoid preferential activation of regulatory T-cells vs. immune effector cells by removing CD25 binding; (ii) increase the therapeutic index of IL-2 therapy by (a) preferential retention at the tumor by having a lower dissociation rate from CEA-expressing cancer cells vs. IL-2R-expressing cells, (b) avoiding any FcγR-binding and Fc effector functions and (c) reduced binding to endothelial cells expressing CD25; and (iii) improve the pharmacokinetics, and thus convenience of administration, of IL-2. The crystal structure of the IL2v-IL-2Rβγ complex was determined and CEA-IL2v activity was assessed using human immune effector cells. Tumor targeting was investigated in tumor-bearing mice using 89Zr-labeled CEA-IL2v. Efficacy studies were performed in (a) syngeneic mouse models as monotherapy and combined with anti-PD-L1, and in (b) xenograft mouse models in combination with ADCC-mediating antibodies. CEA-IL2v binds to CEA with pM avidity but not to CD25, and consequently did not preferentially activate Tregs. In vivo, CEA-IL2v demonstrated superior pharmacokinetics and tumor targeting compared with a wild-type IL-2-based CEA immunocytokine (CEA-IL2wt). CEA-IL2v strongly expanded NK and CD8+ T cells, skewing the CD8+:CD4+ ratio toward CD8+ T cells both in the periphery and in the tumor, and mediated single agent efficacy in syngeneic MC38-CEA and PancO2-CEA models. Combination with trastuzumab, cetuximab and imgatuzumab, all of human IgG1 isotype, resulted in superior efficacy compared with the monotherapies alone. Combined with anti-PD-L1, CEA-IL2v mediated superior efficacy over the respective monotherapies, and over the combination with an untargeted control immunocytokine. These preclinical data support the ongoing clinical investigation of the cergutuzumab amunaleukin immunocytokine with abolished CD25 binding for the treatment of CEA-positive solid tumors in combination with PD-L1 checkpoint blockade and ADCC competent antibodies.
Vacuum Requirements for Heavy Ion Synchrotrons

Experimental charge-changing cross sections for uranium ions incident on H2 and N2 at 1.4 MeV/u are presented and extrapolation to higher energies is discussed briefly. The beam losses caused by charge-changing collisions between heaviest ions and residual gas molecules in a synchrotron have been calculated for different injection energies and ionic charge states. For example, if a beam of U+10-ions is accelerated from 1.4 MeV/u to 100 MeV/u by an average electric field BR=112 V/m an average working pressure of about 1×10-11 mbar is necessary to limit beam losses to several percent.
Trends in antimicrobial susceptibility among isolates of Campylobacter species in Ireland and the emergence of resistance to ciprofloxacin

Measurements were made of the susceptibility to six commonly prescribed antibiotics, including erythromycin, tetracycline and ciprofloxacin, of 130 isolates of Campylobacter jejuni and 15 isolates of Campylobacter coli cultured from human and poultry sources during 2000. The results were compared with the results from a collection of strains isolated between 1996 and 1998. The levels of resistance to erythromycin remained low, 2 per cent and 4.4 per cent for the human and poultry isolates, respectively. Resistance to tetracycline had increased to 31 per cent and 24.4 per cent from 13.9 per cent and 18.8 per cent for the human and poultry isolates, respectively. However, the resistance to ciprofloxacin of the strains isolated during 2000 had increased to 30 per cent, whereas between 1996 and 1998 there had been no resistance to this agent among human isolates, and only 3-1 per cent resistance among poultry isolates. The molecular basis for this resistance has been shown to be the result of a single amino acid substitution, Thr-86-lle, in the gyrA subunit of DNA gyrase in C jejuni. A subset of 59 isolates was tested by molecular methods and all of the 25 phenotypically resistant isolates possessed this substitution. None of the human isolates had been treated with ciprofloxacin before their laboratory isolation.
UvA-DARE (Digital Academic Repository) LOFAR Low-band Antenna Observations of the 3C 295 and Boötes Fields: Source Counts and Ultra-steep Spectrum Sources

We present Low Frequency Array (LOFAR) Low Band observations of the Boötes and 3C 295 fields. Our images made at 34, 46, and 62 MHz reach noise levels of 12, 8, and 5 mJy beam−1, making them the deepest images ever obtained in this frequency range. In total, we detect between 300 and 400 sources in each of these images, covering an area of 17–52 deg2. From the observations, we derive Euclidean-normalized differential source counts. The 62 MHz source counts agree with previous GMRT 153 MHz and Very Large Array 74 MHz differential source counts, scaling with a spectral index of −0.7. We find that a spectral index scaling of −0.5 is required to match up the LOFAR 34 MHz source counts. This result is also in agreement with source counts from the 38 MHz 8C survey, indicating that the average spectral index of radio sources flattens toward lower frequencies. We also find evidence for spectral flattening using the individual flux measurements of sources between 34 and 1400 MHz and by calculating the spectral index averaged over the source population. To select ultra-steep spectrum (α < −1.1) radio sources that could be associated with massive high-redshift radio galaxies, we compute spectral indices between 62 MHz, 153 MHz, and 1.4 GHz for sources in the Boötes field. We cross-correlate these radio sources with optical and infrared catalogs and fit the spectral energy distribution to obtain photometric redshifts. We find that most of these ultra-steep spectrum sources are located in the 0.7 z 2.5 range.