gebhart/patrepeval huggingface dataset:
Scattering by an Array of Cylinders of Small Surface Impedance (1966)

Plane waves are considered to impinge at normal incidence half-space containing a random array of cylinders whose axes are parallel to the wavefronts and to each other. The relevant multiple-scattering theory has been given by Twersky [N. Y. Univ. Rept. EM-59 (1953)]. The average attenuation per unit distance within the array is calculated for various sizes of scatterers, radius 0.1–10 cm, and surface impedances R/ρc=0, −2&lt;X/ρc&lt;2. It is found that attenuation is directly proportional to cylinder radius. In a relief map of attenuation versus X/ρc and ka (k being the wavenumber), the attenuation becomes infinite at the origin but is otherwise zero when ka=0. When X/ρc is a stiffness reactance, the function is a series of ridges radiating from the vicinity of the origin—these ridges are sharp and high close to the origin, becoming broader and lower further away; each ridge is curved, being convex to the ka axis. For any given value of X/ρc, the greatest attenuation is found at frequencies near to the value given by ka=X/ρc. When X/ρc is a mass reactance, no interesting features arise and the surface is a gently sloping plateau.
Near threshold effects in positron-<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math>scattering (1993)

Structure has been observed in the total ionization cross section of ${\mathrm{O}}_{2}$ above 8 eV positron impact energy. A comparison with available data on the excitation to the Schumann-Runge continuum indicates that coupling effects between the positronium formation, excitation, and direct ionization channels may be responsible.
Radiometry imaging system with digital signal processing (1995)

The problem of high resolution radiometry imaging is considered. An iterative method of radiometry image processing is presented in the paper. The problem of image reconstruction is considered as the inverse ill-posed problem. The method proposed makes use of the iterative technique and regularization procedure to improve image quality. Nonlinearity of the method is provided by a nonnegative constrain and a space limitation on the probable image extent that makes possible to accomplish band-limited extrapolation and enhance the resolution.
Four Cases of Hemolytic Uremic Syndrome (HUS) Associated with Serotype O165 Verotoxin Producing Escherichia coli (VTEC) Identified by LPS-solid Phase Enzyme-Linked Immunosorbent Assay (ELISA) (1995)

Enzyme-linked immunosorbent assay using LPS derived from newly recognized serotype O165 verotoxin producing Escherichia coli (VTEC) could identify 4 cases of hemolytic uremic syndrome (HUS) associated with O165 VTEC. All 4 cases showed a typical clinical course seen in VTEC-associated HUS. We screened 33 cases of HUS whose pathogen was not identified by culture of serodiagnosis. The O165 serotype was not thought to be important not only as a VTEC but also as an enteropathogenic E. coli. However, the prevalence, 4 cases, was as high as of O111 serotype, which is the second major serotype of VTEC in Japan. We have to be careful for this serotype when we look for the pathogen of the patients with hemorrhagic colitis or with HUS.
The ancestral IncP replication system consisted of contiguous oriV and trfA segments as deduced from a comparison of the nucleotide sequences of diverse IncP plasmids (1993)

In most plasmids which have been studied to date the functions required for plasmid replication are clustered in a 2-3 kb region. However, in all known naturally occurring plasmids of the Escherichia coli incompatibility group P the essential replication functions, oriV, the vegetative replication origin and trfA, which encodes proteins essential to activate oriV, are separated by blocks of DNA consisting of either known genes conferring resistance to antimicrobial agents and/or putative transposable elements. Nucleotide sequence comparisons reported here reveal that these blocks of DNA have inserted at different points into a backbone of DNA common to IncP plasmids. The results indicate that in the common ancestor of present IncP plasmids oriV and trfA must have been contiguous, whilst a rho-independent transcriptional terminator, now lost in IncP alpha plasmids, may have prevented trfA operon transcription from interfering with the activity of oriV.
Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences (2020)

Pathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet, there is no current consensus on how to measure genomic variation. To test the effect of the variant-identification approach on transmission inferences for <i>Mycobacterium tuberculosis,</i> we conducted an experiment in which five genomic epidemiology groups applied variant-identification pipelines to the same outbreak sequence data. We compared the variants identified by each group in addition to transmission and phylogenetic inferences made with each variant set. To measure the performance of commonly used variant-identification tools, we simulated an outbreak. We compared the performance of three mapping algorithms, five variant callers and two variant filters in recovering true outbreak variants. Finally, we investigated the effect of applying increasingly stringent filters on transmission inferences and phylogenies. We found that variant-calling approaches used by different groups do not recover consistent sets of variants, which can lead to conflicting transmission inferences. Further, performance in recovering true variation varied widely across approaches. While no single variant-identification approach outperforms others in both recovering true genome-wide and outbreak-level variation, variant-identification algorithms calibrated upon real sequence data or that incorporate local reassembly outperform others in recovering true pairwise differences between isolates. The choice of variant filters contributed to extensive differences across pipelines, and applying increasingly stringent filters rapidly eroded the accuracy of transmission inferences and quality of phylogenies reconstructed from outbreak variation. Commonly used approaches to identify <i>M. tuberculosis</i> genomic variation have variable performance, particularly when predicting potential transmission links from pairwise genetic distances. Phylogenetic reconstruction may be improved by less stringent variant filtering. Approaches that improve variant identification in repetitive, hypervariable regions, such as long-read assemblies, may improve transmission inference.
Molecular and phenotypic description of Pneumocystis wakefieldiae sp. nov., a new species in rats. (2012)

Organisms in the genus Pneumocystis are fungi that reside in the lungs of mammals that can cause a lethal pneumonia once the hosts lose immune function. The genus Pneumocystis contains many members, but only two species have been described formally to date, P. carinii, the type species found in rats, and P. jirovecii, resident in human beings. Rats have been shown to harbor another organism in addition to P. carinii, Pneumocystis wakefieldiae sp. nov., formerly known as Pneumocystis carinii f. sp. ratti, which is described here. Although often found together and morphologically similar, P. carinii and P. wakefieldiae are phenotypically and genetically divergent. We used the phylogenetic species recognition approach to distinguish these organisms as two distinct species and estimated the evolutionary time of their separation. Nucleotide sequence comparisons of seven homologous genes showed 4-7% divergence between the P. wakefieldiae and P. carinii sequences, which was in contrast to the 0-0.8% divergence observed within P. carinii species. Even greater divergence (30%) occurred in sequences located between genes. The MSG (major surface glycoprotein) gene families of P. carinii and P. wakefieldiae are 35% divergent from one another and differ with respect to sequence elements associated with regulation of their transcription. Differences in reactivity of monoclonal antibodies and polyclonal antisera reflected these genetically distinct surface antigens. Karyotypic analysis of P. wakefieldiae produced a single profile that was distinct from all 12 profiles known for P. carinii. Eight homologous genes were localized to chromosomes of different sizes in the two species. The cumulative genotypic and phenotypic data support a species distinction between these two organisms.
Improving the performance of SOMFA by use of standard multivariate methods (2005)

Self-Organizing Molecular Field Analysis (SOMFA) comes with a built-in regression methodology, the Self-Organizing Regression (SOR), instead of relying on external methods such as PLS. In this article we present a proof of the equivalence between SOR and SIMPLS with one principal component. Thus, the modest performance of SOMFA on complex datasets can be primarily attributed to the low performance of the SOMFA regression methodology. A multi-component extension of the original SOR methodology (MCSOR) is introduced, and the performances of SOR, MCSOR and SIMPLS are compared using several datasets. The results indicate that in general the performance of SOMFA models is greatly improved if SOR is replaced with a more sophisticated regression method. The results obtained for the Cramer (CBG) dataset further underline the fact that it is a very poor benchmark dataset and should not be used to evaluate the performance of QSAR techniques.
Endovascular Management of Malperfusion in Acute Type B Aortic Dissections (2011)

Endovascular coverage of the proximal entry tear in acute type B dissections complicated by end-organ malperfusion resulted in correction of malperfusion in the majority of patients. It is a reasonable first line of treatment, but its superiority must be assessed in comparison with other techniques, such as fenestration.
A MODULAR MOMENTUM-EXCHANGE/ELECTRODYNAMIC-REBOOST TETHER SYSTEM ARCHITECTURE (2003)

The Momentum-Exchange/Electrodynamic-Reboost (MXER) Tether Boost Facility concept has the potential to achieve significant reductions in launch costs for a number of space missions. In this document, we investigate the design of the MXER Tether Boost Facility and develop a highly modular architecture that will enable the system to be designed, built, launched, operated, and maintained at low cost. Using this modular approach, we develop a concept design for a MXER Tether Boost Facility optimized for boosting 2,000 kg payloads from a 250 km drop-off orbit to geostationary transfer orbits. To enable it to boost multiple payloads, the system incorporates a propellantless electrodynamic tether reboost system that enables it to restore the orbital energy transferred to each payload within a period of 45 days. Based upon this concept design, we have developed a mass estimate preliminary configuration design, and found that this modular MXER Tether Boost Facility will have a mass and stowed volume that will enable it to be launched by a SeaLaunch Zenit-2 rocket. Once the system has been deployed on-orbit, its modular design enables its capacity to be expanded in a bootstrap manner.
Introduction (2007)

Network models are used to describe power grids, cellular telecommunications systems, large-scale manufacturing processes, computer systems, and even systems of elevators in large office buildings. Although the applications are diverse, there are many common goals:
Minisatellite Markers Reveals Frequent Genetic Exchanges among House Mouse Subspecies (2007)

National audience
Structural Analysis of Au-Pd Core-Shell Nanoparticles (2007)

Extract Extended abstract of a paper presented at Microscopy and Microanalysis 2007 in Ft. Lauderdale, Florida, USA, August 5 – August 9, 2007
Large current enhancement in n-MOSFETs with strained Si on insulator (2007)

As scaling of the critical transistor dimensions below 65 nm has been slowed down, the implementation of novel materials, especially high mobility channel materials is most attractive to boost the transistor performance. Applying strain to silicon has become a successful route. The electron mobility can be enhanced by biaxial strain introduced into Si by epitaxial growth of Si on a strain relaxed SiGe layer or by so called process induced methods applied directly on transistor level. The combination of strained Si and SOI is particularly promising due to the combination of the enhanced mobilities and the inherent advantages of SOI. First long channel n-MOSFETs with gate lengths of 5 to 50 mum and a 6.6 nm thick SiO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gate dielectric were fabricated. For comparison, devices on unstrained SOI were made. The transfer characteristics of a fully depleted sSOI-MOSFET with a gate length of 5 mum and a gate width of 20 mum indicating an inverse sub-threshold slope of 75mV/dec.
Perturbation of single hematopoietic stem cell fates in artificial niches (2008)

Hematopoietic stem cells (HSCs) are capable of extensive self-renewal in vivo and are successfully employed clinically to treat hematopoietic malignancies, yet are in limited supply as in culture this self-renewal capacity is lost. Using an approach at the interface of stem cell biology and bioengineering, here we describe a novel platform of hydrogel microwell arrays for assessing the effects of either secreted or tethered proteins characteristic of the in vivo microenvironment, or niche, on HSC fate in vitro. Time-lapse microscopic analyses of single cells were crucial to overcoming inevitable heterogeneity of FACS-enriched HSCs. A reduction in proliferation kinetics or an increase in asynchronous division of single HSCs in microwells in response to specific proteins (Wnt3a and N-Cadherin) correlated well with subsequent serial long-term blood reconstitution in mice in vivo. Single cells that divided once in the presence of a given protein were capable of in vivo reconstitution, providing evidence of self-renewal divisions of HSCs in vitro. These results validate the hydrogel microwell platform as a broadly applicable paradigm for dissecting the regulatory role of specific signals within a complex stem cell niche.
MDMA-assisted psychotherapy for treatment of anxiety and other psychological distress related to life-threatening illnesses: a randomized pilot study (2020)

The success of modern medicine creates a growing population of those suffering from life-threatening illnesses (LTI) who often experience anxiety, depression, and existential distress. We present a novel approach; investigating MDMA-assisted psychotherapy for the treatment of anxiety in people with an LTI. Participants with anxiety from an LTI were randomized in a double-blind study to receive MDMA (125 mg, n = 13) or placebo (n = 5) in combination with two 8-h psychotherapy sessions. The primary outcome was change in State-Trait Anxiety Inventory (STAI) Trait scores from baseline to one month post the second experimental session. After unblinding, participants in the MDMA group had one open-label MDMA session and placebo participants crossed over to receive three open-label MDMA sessions. Additional follow-up assessments occurred six and twelve months after a participant's last experimental session. At the primary endpoint, the MDMA group had a greater mean (SD) reduction in STAI-Trait scores, - 23.5 (13.2), indicating less anxiety, compared to placebo group, - 8.8 (14.7); results did not reach a significant group difference (p = .056). Hedges' g between-group effect size was 1.03 (95% CI: - 5.25, 7.31). Overall, MDMA was well-tolerated in this sample. These preliminary findings can inform development of larger clinical trials to further examine MDMA-assisted psychotherapy as a novel approach to treat individuals with LTI-related anxiety.Trial Registration: clinicaltrials.gov Identifier: NCT02427568, first registered April 28, 2015.
Pathogenesis of edema formation in burn injuries (1992)

One of the obvious acute features of cutaneous thermal injury is the swelling of the involved tissue. This swelling is caused by a fluid shift from circulating plasma. Along with the evolution of intravenous fluid therapy in trauma and surgery, the implementation of such therapy to burn victims has improved survival. Edema generation aggravated by fluid therapy may, however, represent a source of increased morbidity. This paper presents a review of the literature on postburn edema generation, focusing mainly on fluid physiology. It is well documented that fluid is lost from the circulation into burned tissue because of a moderate increase in capillary permeability to fluid and macromolecules and a modest increase in hydrostatic pressure inside the perfusing microvessels. Recently it was discovered that a very negative interstitial pressure develops in thermally injured skin. This pressure constitutes a strong "suction" adding markedly to the edema generating effect of increased capillary permeability and pressure.
MPI Collectives on Modern Multicore Clusters: Performance Optimizations and Communication Characteristics (2008)

The advances in multicore technology and modern interconnects is rapidly accelerating the number of cores deployed in today's commodity clusters. A majority of parallel applications written in MPI employ collective operations in their communication kernels. Optimization of these operations on the multicore platforms is the key to obtaining good performance speed-ups. However, designing these operations on the modern multicores is a non-trivial task. Modern multicores such as Intel's Clovertown and AMD's Opteron feature various architectural attributes resulting in interesting ramifications. For example, Clovertown deploys shared 12 caches for a pair of cores whereas in Opteron, 12 caches are exclusive to a core. Understanding the impact of these architectures on communication performance is crucial to designing efficient collective algorithms. In this paper, we systematically evaluate these architectures and use these insights to develop efficient collective operations such as MPI_Bcast, MPI_Allgather, MPI_Allreduce and MPI_Alltoall. Further, we characterize the behavior of these collective algorithms on multicores especially when concurrent network and intra-node communications occur. We also evaluate the benefits of the proposed intra-node MPI_Allreduce over Opteron multicores and compare it with Intel Clovertown systems. The optimizations proposed in this paper reduce the latency of MPI-Bcast and MPI_Allgather by 1.9 and 4.0 times, respectively on 512 cores. For MPI_Allreduce, our optimizations improve the performance by as much as 33% on the multicores. Further, we observe up to three times improvement in performance for matrix multiplication benchmark on 512 cores.
Evaluation of serum hepcidin concentrations in cancer and leukemia patients (2008)

20581 Background: Hepcidin controls iron homeostasis by regulating iron uptake and redistribution in response to systemic iron requirements: high circulating iron leads to hepcidin expression which in turn decreases circulating iron. Hepcidin can also be induced by inflammation, which may lead to inappropriately low circulating iron levels, as seen in functional iron deficiency, a proposed causative factor in the anemia of inflammation. This study aimed to establish the hepcidin concentrations and hence the potential role of functional iron deficiency in contributing to anemia in cancer and leukemia patient populations. Methods: Sera from the following populations were analyzed: chemotherapy-induced anemia (CIA, n=100), anemia of cancer (AoC, n=30), sepsis (n=25), myelodysplastic syndrome (MDS, n=8), healthy controls (n=60), iron deficiency anemia (IDA, n=12), acute myeloid leukemia (AML, n=13), acute lymphoblastic leukemia (ALL, n=4), chronic myeloid leukemia (CML, n=10), multiple myeloma (MM, n=8) and chronic lymphocytic leukemia (CLL, n=11). Serum hepcidin concentrations were assessed by a sensitive, quantitative HPLC-MS/MS method. Iron indices and CRP (as an inflammatory marker) were also measured. Results: Serum hepcidin was elevated in a subset of patients with CIA (84±86ng/ml), AoC (100±97ng/ml), sepsis (189±204ng/ml), MDS (238±159ng/ml) and leukemia (223±203ng/ml). Serum hepcidin was not elevated in healthy donors (7±19ng/ml) or patients with IDA (9±14ng/ml). Further analysis of leukemia patient sera revealed elevated serum hepcidin in all patients with AML (354±153ng/ml) and ALL (532±266ng/ml), a spectrum of hepcidin concentrations within CML (156±179ng/ml) and MM (162±112ng/ml) patient populations. Hepcidin concentrations were elevated in CLL patients (59±29ng/ml), albeit to a lesser degree than observed in the other subsets evaluated. In some patient populations, elevated CRP and hepcidin concentrations were both present. Conclusions: This study demonstrates that hepcidin concentrations are elevated in multiple cancer and leukemia patient populations raising the possibility that functional iron deficiency may play a role in the etiology of anemia in cancer patients. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Expert Testimony Other Remuneration Amgen, Inc. Amgen, Inc.
Designing On-Road Vehicle Test Programs for the Development of Effective Vehicle Emission Models - eScholarship (2005)

Mobile source emission models for years have depended on laboratory-based dynamometer data. Recently, however, portable emission measurement systems (PEMS) have become commercially available and in widespread use, and make on-road real-world measurements possible. As a result, the newest mobile source emission models (e.g., U.S. Environmental Protection Agency’s mobile vehicle emission simulator) are becoming increasingly dependent on PEMS data. Although on-road measurements are made under more realistic conditions than laboratory-based dynamometer test cycles, they introduce influencing variables that must be carefully measured for properly developed emission models. Further, test programs that simply measure in-use driving patterns of randomly selected vehicles will result in models that can effectively predict current-year emission inventories for typical driving conditions. However, when predicting more aggressive transportation operations than current typical operations (e.g., higher speeds, accelerations), the model predictions will be less certain. In this paper, various issues associated with on-road emission measurements and modeling are presented. Further, an example on-road emission data set and the reduction in estimation error through the addition of a short aggressive driving test to the in-use data are examined. On the basis of these results, recommendations are made on how to improve the on-road test programs for developing more robust emission models.
Gate metallization "Sinking" into the active channel in Ti/W/Au metallized power MESFET's (1986)

Commercial power MESFET's with Ti/W/Au gate metallization show a failure mode consisting of a decrease in I <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dss</inf> and V <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">p</inf> and an increase in R <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</inf> . The failure mechanism was investigated by electrical and structural analyses with SEM, microprobe, and Auger spectrometry, and turns out to be a thermally activated Au-GaAs interdiffusion leading to encroachment of the gate metal on the channel. This may be common to all Au-metallized MESFET's and can lead to burn-out of devices.