Miracle-dz/UniFAR-FTUs huggingface dataset:
Bias estimation for invariant systems on Lie groups with homogeneous outputs

In this paper, we provide a general method of state estimation for a class of invariant systems on connected matrix Lie groups where the group velocity measurement is corrupted by an unknown constant bias. The output measurements are given by a collection of actions of a single Lie group on several homogeneous output spaces, a model that applies to a wide range of practical scenarios. The proposed observer consists of a group estimator part, providing an estimate of a bounded state evolving on the Lie group, and a bias estimator part, providing an estimate of the bias in the associated Lie algebra. We employ the gradient of a suitable invariant cost function on the Lie group as an innovation term in the group estimator. We design the bias estimator such that it guarantees uniform local exponential stability of the estimation error dynamics around the zero error state. We propose a systematic methodology for the design of suitable cost functions on Lie groups by lifting invariant cost functions from the homogeneous output spaces. We show that the resulting observer is implementable based on available sensor measurements if the homogeneous output spaces are reductive. As an example, we derive an observer for rigid body attitude using vector and gyro measurements with unknown constant gyro bias.
A Brownian dynamics model for the chromatin fiber

MOTIVATION We describe a Brownian dynamics model for the folding of the chromatin fiber based on the model of Woodcock et al. (Proc Natl Acad Sci USA, 90, 9021-9025, 1993). The model takes into account the elastic properties of the DNA as well as the electrostatic interaction and nucleosomal excluded-volume interaction. The solvent is described as a viscous medium, the electrostatic interactions by a screened Coulomb potential. RESULTS The hydrodynamic properties and their dependence on the solvent's ionic strength are accurately reproduced by the model for nucleosome di- and tetramers. Ionic strength-dependent changes in mobility can be attributed to partial screening of the electrostatic repulsion between different segments of linker DNA. Formation of fiber-like structures occurs on time scales of several hundred microseconds for a linear configuration of 25 nucleosomes. The model was implemented by creating user-defined data types. Use of this so-called object-oriented paradigm allowed for a high degree of component reuse in simulation, analysis and visualization contexts. AVAILABILITY The described software is available on request from the authors. Additional information can be found on the WWW at http:/(/)www.dkfz-heidelberg.de/Macromol/ehrlich /chromatin.htm/.
Nitric oxide synthase inhibition reduces the O2 cost of force development in rat hindlimb muscles pump perfused at matched convective O2 delivery

Nitric oxide (NO) is a physiological mediator of skeletal muscle function. Specifically, NO affects cellular respiration and muscle contractility; however, the reduced blood flow and convective O2 delivery that result from impaired vasodilatation when NO synthase (NOS) is inhibited in vivo have obscured past interpretations of the effects of NO. Therefore, we studied the effect of NOS inhibition in an in situ pump‐perfused rat hindlimb to test the hypothesis that NOS inhibition would improve contractile and aerobic metabolic performance. Pump perfusion permitted matching of convective O2 delivery (516 ± 16 μmol O2 min−1 (100 g)−1; mean ±s.e. m. ) between groups, allowing us to investigate the effects of NOS inhibition independent of this variable. Three groups were studied. The perfusate of one group was treated with both adenosine (0.01 mm) and the NOS inhibitor, Nω‐nitro‐l‐arginine methyl ester (l‐NAME; 1 mm). Adenosine is a vasodilator that can act through both NO‐dependent and ‐independent pathways; the NO‐independent vasodilatory action of adenosine allowed us to match the perfusion rate and convective O2 delivery in this l‐NAME group to those of the other groups. In the second group the perfusate was treated with adenosine only (Ado). In the third group the perfusate received no treatment and served as a control (Con). Oxygen consumption ( ) was on average 26 and 14% lower during the contraction bout in l‐NAME and Ado, respectively, versus Con. In Ado, lactate efflux was similar to Con and force was reduced in proportion to versus Con, whereas l‐NAME was associated with a 32% lower lactate efflux and similar force to Con. Therefore, the lower :force development ratio in the l‐NAME group demonstrates that the O2 cost of force development is reduced by NOS inhibition independent of convective O2 delivery.
The Advection-Diffusion Problem for Stratospheric Flow. Part I: Concentration Probability Distribution Function

The mixing of a passive tracer by realistic time-dependent stratospheric flow (European Centre for MediumRange Weather Forecasts winds) on an isentropic surface (420 K) is studied. Simulations of the advection‐ diffusion problem for an initially large-scale tracer field are carried out in the limit of weak diffusivity. Owing to chaotic advection, tracer variance is cascaded to small scales, where it can be dissipated despite the weak diffusivity. The tracer fluctuations are characterized in terms of their probability distribution function (PDF). The PDFs are characterized by a Gaussian core and ‘‘fat tails,’’ which fall more slowly than a Gaussian, and indicate anomalously high probability of extreme concentration fluctuations. Given the nonlinearity of many chemical reactions of interest, the anomalous prevalence of extreme fluctuations could have a profound effect on reactive tracers. Zonal variations of tracer are homogenized globally leading to a unimodal PDF. Initially meridional variations are strongly influenced by the presence of mixing barriers. Meridional gradients homogenize only within mixing zones of limited latitudinal extent, bounded by permeable mixing barriers. The PDF becomes multimodal, with distinct populations of air caused by blending of the concentration values within each mixing zone. The Tropics is a zone of weak mixing, and serves as an important repository of stratospheric tracers, which are episodically ejected into surf zones in the form of filaments bearing extreme concentration values. The shapes of the PDFs are discussed in terms of theoretical methods developed in the context of highly idealized mixing models. It is shown that such methods retain their utility when applied to realistic stratospheric mixing. The role of the probability distribution of finite-time Lyapunov exponents for the underlying trajectory problem is highlighted. The use of conditional averages of diffusion and dissipation is also illustrated. PDFs yielded by the idealized advection‐diffusion problem are found to resemble those appearing in a GCM simulation of N2O. The theoretical arguments and numerical results imply that under the assumption that the diffusivity is set so that the dissipation scale is comparable to model resolution, the concentration PDF eventually reaches a universal shape independent of model resolution after an initial transient stage. However, the width of the distribution, or equivalently the variance of the tracer fluctuation, increases algebraically as model resolution is refined.
Investigating the Climatology of Mesospheric and Thermospheric Gravity Waves at High Northern Latitudes

Investigating the Climatology of Mesospheric and Thermospheric Gravity Waves at High Northern Latitudes by Michael Ray Negale, Doctor of Philosophy Utah State University, 2018 Major Professor: Michael J. Taylor, Ph.D. Department: Physics The primary objective of this research is to investigate the characteristics and propagation of short-period (<1 hr) gravity waves (GWs) in the upper mesosphere (87 km) and thermosphere (100–300 km) at high northern latitudes, where high-quality measurements are few, but have shown strong wave activity and variability in their propagation directions. Knowledge of the spatial and temporal characteristics, and especially propagation directions, is vital to better understand both the dominant and recurrent sources of GWs and the momentum they transport into the upper atmosphere and ionosphere. New data from three proven instruments (an all-sky airglow imager (ASI), an Advanced Mesospheric Temperature Mapper (AMTM), and an incoherent scatter radar (ISR)) strategically located at two well-separated (>160◦ longitude) sites, have been used to identify and characterize over 1,200 discrete wave events. Concurrent imaging and radar measurements were made over a three-year period (2010–2013) from the Poker Flat Research Range (PFRR) Alaska (65◦ N, 147◦ W), while additional AMTM measurements were used from northern Norway (69◦ N, 16◦ E) during the winter of 2011–2012. Together these data have enabled a novel comparative study of the longitudinal variability in wave characteristics in the upper mesosphere and the first investigation of GW climatologies at two adjacent regions, in the upper mesosphere and thermosphere. Importantly, the capability of the Poker Flat ISR to observe waves during both the summer and winter seasons has provided essential new knowledge on the full seasonal thermospheric wave climatology. Chance observations of two SSW events
Requirement for Candida albicans Sun41 in Biofilm Formation and Virulence

ABSTRACT The cell wall of Candida albicans lies at the crossroads of pathogenicity and therapeutics. It contributes to pathogenicity through adherence and invasion; it is the target of both chemical and immunological antifungal strategies. We have initiated a dissection of cell wall function through targeted insertional mutagenesis of cell wall-related genes. Among 25 such genes, we were unable to generate homozygous mutations in 4, and they may be essential for viability. We created homozygous mutations in the remaining 21 genes. Insertion mutations in SUN41, Orf19.5412, Orf19.1277, MSB2, Orf19.3869, and WSC1 caused hypersensitivity to the cell wall inhibitor caspofungin, while two different ecm33 insertions caused mild caspofungin resistance. Insertion mutations in SUN41 and Orf19.5412 caused biofilm defects. Through analysis of homozygous sun41Δ/sun41Δ deletion mutants and sun41Δ/sun41Δ+pSUN41-complemented strains, we verified that Sun41 is required for biofilm formation and normal caspofungin tolerance. The sun41Δ/sun41Δ mutant had altered expression of four cell wall damage response genes, thus suggesting that it suffers a cell wall structural defect. Sun41 is required for inducing disease, because the mutant was severely attenuated in mouse models of disseminated and oropharyngeal candidiasis. Although the mutant produced aberrant hyphae, it had no defect in damaging endothelial or epithelial cells, unlike many other hypha-defective mutants. We suggest that the sun41Δ/sun41Δ cell wall defect is the primary cause of its attenuated virulence. As a small fungal surface protein with predicted glucosidase activity, Sun41 represents a promising therapeutic target.
Impact of Interferon Lambda 4 Genotype on Interferon‐Stimulated Gene Expression During Direct‐Acting Antiviral Therapy for Hepatitis C

New directly acting antivirals (DAAs) provide very high cure rates in most patients infected by hepatitis C virus (HCV). However, some patient groups have been relatively harder to treat, including those with cirrhosis or infected with HCV genotype 3. In the recent BOSON trial, genotype 3, patients with cirrhosis receiving a 16‐week course of sofosbuvir and ribavirin had a sustained virological response (SVR) rate of around 50%. In patients with cirrhosis, interferon lambda 4 (IFNL4) CC genotype was significantly associated with SVR. This genotype was also associated with a lower interferon‐stimulated gene (ISG) signature in peripheral blood and in liver at baseline. Unexpectedly, patients with the CC genotype showed a dynamic increase in ISG expression between weeks 4 and 16 of DAA therapy, whereas the reverse was true for non‐CC patients. Conclusion: These data provide an important dynamic link between host genotype and phenotype in HCV therapy also potentially relevant to naturally acquired infection. (Hepatology 2018; 00:000‐000).
The G protein–coupled receptor P2RY8 and follicular dendritic cells promote germinal center confinement of B cells, whereas S1PR3 can contribute to their dissemination

The orphan Gα13-coupled receptor P2RY8 promotes clustering of B cells at the follicle center in an FDC-dependent manner. Egress of Gα13 or Arhgef1 mutant GC B cells into circulation depends on the function of the promigratory receptor S1pr3.
Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum

ABSTRACT The Deinococcus-Thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16S rRNA trees. No unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. In this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the Deinococcus-Thermus phylum but are not found in any other group of bacteria. The identified signatures include a 7-amino-acid (aa) insert in threonyl-tRNA synthetase, 1- and 3-aa inserts in the RNA polymerase β′ subunit, a 5-aa deletion in signal recognition particle (Ffh/SR54), a 2-aa insert in major sigma factor 70 (σ70), a 2-aa insert in seryl-tRNA synthetase (SerRS), a 1-aa insert in ribosomal protein L1, and a 2-aa insert in UvrA homologs. By using PCR primers for conserved regions, fragments of these genes were amplified from a number of Deinococcus-Thermus species, and all such fragments (except SerRS in Deinococcus proteolyticus) were found to contain the indicated signatures. The presence of these signatures in various species from all three known genera within this phylum, viz., Deinococcus, Thermus, and Meiothermus, provide evidence that they are likely distinctive characteristics of the entire phylum which were introduced in a common ancestor of this group. The signature in SerRS, which is absent in D. proteolyticus, was likely introduced after the branching of this species. Phylogenetic studies as well as the nature of the inserts in some of these proteins (viz., σ70 and SerRS) also support a sister group relationship between the Thermus and the Meiothermus genera. The identified signatures provide strong evidence for the monophyletic nature of the Deinococcus-Thermus phylum. These molecular markers should prove very useful in the identification of new species related to this group.
Human colonic biota studied by ribosomal DNA sequence analysis

Human colonic biota is a complex microbial ecosystem that serves as a host defense. Unlike most microbial ecosystems, its composition has been studied extensively by relatively efficient culture methods. We have compared an established culture-based method with direct amplification and partial sequencing of cloned 16S rRNA genes from a human fecal specimen. Nine cycles of PCR were also compared with 35 cycles. Colonies and cloned amplicons were classified by comparing their ribosomal DNA (rDNA; DNA coding for rRNA) sequences with rDNA sequences of known phylogeny. Quantitative culture recovered 58% of the microscopic count. The 48 colonies identified gave 21 rDNA sequences; it was estimated that 72% of the rDNA sequences from the total population of culturable cells would match these 21 sampled sequences (72% coverage). Fifty 9-cycle clones gave 27 sequences and 59% coverage of cloned rDNAs. Thirty-nine rDNAs cloned after 35 cycles of PCR gave 13 sequences for 74% coverage. Thus, the representation of the ecosystem after 35 cycles of PCR was distorted and lacked diversity. However, when the number of temperature cycles was minimized, biodiversity was preserved, and there was good agreement between culturing bacteria and sampling rDNA directly.
A Boundary-Element Analysis of TEM Cells in Three Dimensions

Transverse electromagnetic (TEM) transmission-line cells are modeled and analyzed in three dimensions based on a mixed discretization using both constant and linear boundary elements. In particular, the distributed characteristic impedance along the line is evaluated for symmetrical square TEM cells of the type built at the National Bureau of Standards (NBS) in order to confirm the validity of the present numerical technique. Comparison with experimental results is shown. This paper shows that our numerical approach should contribute to TEM cell design.
Soluble L-selectin is present in human plasma at high levels and retains functional activity

L-selectin expressed by granulocytes, lymphocytes, and monocytes is responsible for initial leukocyte attachment to inflamed endothelium and high endothelial venules of peripheral lymph nodes. After leukocyte activation in vitro, L-selectin is rapidly shed from the cell surface. In this study, shed L-selectin (sL-selectin) from both lymphocytes and neutrophils was demonstrated to be present in high levels in human plasma by Western blot analysis and using a quantitative ELISA. In serum from normal human blood donors, a mean sL-selectin level of 1.6 +/- 0.8 micrograms/ml (n = 63) was found by ELISA. In addition, semipurified sL-selectin from plasma inhibited L-selectin-specific attachment of lymphocytes to cytokine-activated endothelium in a dose- dependent manner. L-selectin-dependent leukocyte attachment was completely inhibited at sL-selectin concentrations of 8-15 micrograms/ml, while physiological concentrations of sL-selectin caused a small but consistent inhibition of lymphocyte attachment. sL-selectin in plasma also inhibited anti-L-selectin mAb (2-5 micrograms/ml) binding to the surface of leukocytes. Interestingly, one epitope present within the EGF-like domain of L-selectin was lost in sL- selectin, suggesting a conformational change in the structure of the receptor after shedding. The presence of serum sL-selectin with functional activity indicates a potential role for sL-selectin in the regulation of leukocyte attachment to endothelium.
An Empirical Analysis of Analysts' Target Prices: Short Term Informativeness and Long Term Dynamics

Using a large database of analysts' target prices issued over the period 1997-1999, we examine short-term market reactions to target price revisions and long-term comovement of target and stock prices. We find a significant market reaction to the information contained in analysts' target prices, both unconditionally and conditional on contemporaneously issued stock recommendation and earnings forecast revisions. Using a cointegration approach, we analyze the long-term behavior of market and target prices. We find that, on average, the one-year-ahead target price is 28 percent higher than the current market price. Copyright (c) 2003 by the American Finance Association.
Assessment of ADHD Documentation From Candidates Requesting Americans With Disabilities Act (ADA) Accommodations for the National Board of Osteopathic Medical Examiners COMLEX Exam

Purpose: Every year increasing numbers of candidates request special accommodations for high-stakes medical licensing examinations, due to ADHD, on the basis of the Americans with Disabilities Act (ADA). This poses significant challenges for both the applicant and the medical boards and has significant financial, legal, and ethical implications. The purpose of this survey is to review all applications requesting ADA accommodations, on the basis of ADHD, submitted to the National Board of Osteopathic Medical Examiners (NBOME) COMLEX exam. Method: The authors review all 50 requests for special accommodations, on the basis of ADHD, submitted to the NBOME between 2005 and 2007. All requests are reviewed by the investigators independently and then cross-checked to determine interrater reliability. Results: Of all applicants, only 14% (7/50) provide sufficient documentation to support a diagnosis of ADHD. Interrater reliability is high. Conclusions: The majority of applicants who request special testing accommodations on the basis of ADHD do not provide adequate documentation to the medical boards to support the diagnosis.
In Vitro Pharmacodynamics of Polymyxin B and Tigecycline Alone and in Combination against Carbapenem-Resistant Acinetobacter baumannii

ABSTRACT Carbapenem-resistant Acinetobacter baumannii is increasing in prevalence. Polymyxin B and tigecycline are among the most active antibiotics used against this pathogen in vitro. Past in vitro studies, however, neglected the importance of simulating exposures observed in humans to determine their antibacterial effects. In this study, four carbapenem-resistant A. baumannii isolates were evaluated using an in vitro pharmacodynamic model. Free-drug exposures using 1 mg/kg of body weight of polymyxin B every 12 h (q12h), 100 and 200 mg tigecycline q12h, and the combination of these regimens were simulated. The microbiological responses to these treatments were measured by the change in log10 CFU/ml over 24 h and the area under the bacterial killing and regrowth curve (AUBC). Resistance was assessed by a population analysis profile (PAP) conducted after 24 h of treatment. Polymyxin B achieved a reduction on the order of −2.05 ± 0.68 log10 CFU/ml against these A. baumannii isolates, while all isolates grew to control levels with tigecycline monotherapy. Combination therapy with polymyxin B plus 200 mg tigecycline q12h achieved a greater reduction in bacterial density than did therapy with polymyxin B alone (−3.31 ± 0.71 versus −2.05 ± 0.68 log10 CFU/ml, P < 0.001) but not significantly different than combination therapy with 100 mg tigecycline q12h (−2.45 ± 1.00 log10 CFU/ml, P = 0.370). Likewise, combination therapy with polymyxin B plus 200 mg tigecycline q12h significantly reduced the AUBC compared to that with polymyxin B alone (62.8 ± 8.9 versus 79.4 ± 10.5 log10 CFU/ml, P < 0.05). No changes in the PAP from baseline were observed for either antibiotic alone. In this study, combination therapy with simulated exposures of polymyxin B and tigecycline at an aggressive dose of 200 mg q12h produced synergistic or additive effects on humans against these multidrug-resistant A. baumannii strains.
Outcome of Pancreas Transplantation in Recipients Older Than 50 Years: A Single-Centre Experience

Background. Pancreas transplantation (PT) remains the only treatment that can restore insulin independence among insulin-dependent diabetics. An ageing population in developed countries has led to an increasing number of older patients who may be suitable for PT. Some investigators argue that PT in recipients older than 50 years has an inferior outcome compared with the younger group. Methods. The object of this study was to compare the outcomes of 31 PT in patients aged 50 and above 105 PT in recipients below 50 years performed between June 2001 and December 2007. Results. The incidence of general posttransplant complications were similar in both; 60% in less than 50 vs. 58% in more than or equal to 50, P=0.539. So, as the incidence of other surgical complication in the more than or equal to 50 group compared with less than 50 (graft thrombosis 13% vs. 11.5%; bleeding 19% vs. 6.7%; abdominal abscess 23% vs. 19%; pancreatic leak 13% vs. 9.6%). There was no significant difference in the incidence of urinary tract infection and early rejection in either group. However, the incidence of respiratory tract infection was significantly higher in more than or equal to 50 (38.7% in ≥50 vs. 9.6% in <50, P=0.003). One-year patient survival was 88% in more than or equal to 50 vs. 92% in less than 50 group, P=0.399; and pancreas graft survival rate was similar (79% in the ≥50 and 74% in <50, P=0.399). Conclusion. This study demonstrates that it is feasible to safely transplant potentional PT recipients aged 50 and above. However, good medical assessment and careful patient selection is strongly recommended.