gebhart/patrepeval huggingface dataset:
A Bayesian model of acquisition and clearance of bacterial colonization (2018)

Bacterial populations that colonize a host play important roles in host health, including serving as a reservoir that transmits to other hosts and from which invasive strains emerge, thus emphasizing the importance of understanding rates of acquisition and clearance of colonizing populations. Studies of colonization dynamics have been based on assessment of whether serial samples represent a single population or distinct colonization events. A common solution to estimate acquisition and clearance rates is to use a fixed genetic distance threshold. However, this approach is often inadequate to account for the diversity of the underlying within-host evolving population, the time intervals between consecutive measurements, and the uncertainty in the estimated acquisition and clearance rates. Here, we summarize recently submitted work \cite{jarvenpaa2018named} and present a Bayesian model that provides probabilities of whether two strains should be considered the same, allowing to determine bacterial clearance and acquisition from genomes sampled over time. We explicitly model the within-host variation using population genetic simulation, and the inference is done by combining information from multiple data sources by using a combination of Approximate Bayesian Computation (ABC) and Markov Chain Monte Carlo (MCMC). We use the method to analyse a collection of methicillin resistant Staphylococcus aureus (MRSA) isolates.
Synthesis and biological activity of 8a-phenyldecahydroquinolines as probes of PCP's binding conformation. A new PCP-like compound with increased in vivo potency (1992)

The synthesis and chemical resolution of cis- and trans-fused 8a-phenyldecahydroquinolines 3 and 4 are described together with the affinity of the four optically pure compounds for the PCP recognition site of the NMDA receptor complex. These compounds were also evaluated for their antagonistic effects on cGMP levels in male Swiss Webster mice, and (-)-4 was found to exhibit in vivo potency comparable to that of MK-801. The results of the binding studies are interpreted in terms of a preferred orientation of PCP's N-H bond in binding to its NMDA receptor-associated recognition site.
Molecular remission is an independent predictor of clinical outcome in patients with mantle cell lymphoma after combined immunochemotherapy: a European MCL intergroup study (2009)

The prognostic impact of minimal residual disease (MRD) was analyzed in 259 patients with mantle cell lymphoma (MCL) treated within 2 randomized trials of the European MCL Network (MCL Younger and MCL Elderly trial). After rituximab-based induction treatment, 106 of 190 evaluable patients (56%) achieved a molecular remission (MR) based on blood and/or bone marrow (BM) analysis. MR resulted in a significantly improved response duration (RD; 87% vs 61% patients in remission at 2 years, P = .004) and emerged to be an independent prognostic factor for RD (hazard ratio = 0.4, 95% confidence interval, 0.1-0.9, P = .028). MR was highly predictive for prolonged RD independent of clinical response (complete response [CR], complete response unconfirmed [CRu], partial response [PR]; RD at 2 years: 94% in BM MRD-negative CR/CRu and 100% in BM MRD-negative PR, compared with 71% in BM MRD-positive CR/CRu and 51% in BM MRD-positive PR, P = .002). Sustained MR during the postinduction period was predictive for outcome in MCL Younger after autologous stem cell transplantation (ASCT; RD at 2 years 100% vs 65%, P = .001) and during maintenance in MCL Elderly (RD at 2 years: 76% vs 36%, P = .015). ASCT increased the proportion of patients in MR from 55% before high-dose therapy to 72% thereafter. Sequential MRD monitoring is a powerful predictor for treatment outcome in MCL. These trials are registered at www.clinicaltrials.gov as #NCT00209222 and #NCT00209209.
Correlation of F0F1-ATPase Inhibition and Antiproliferative Activity of Apoptolidin Analogues (2006)

[structure: see text] Apoptolidin (1) exhibits potent and highly selective apoptosis inducing activity against sensitive cancer cell lines and is hypothesized to act by inhibition of mitochondrial F(0)F(1)-ATP synthase. A series of apoptolidin derivatives, including a new intermolecular Diels-Alder adduct, were analyzed for antiproliferative activity in E1A-transformed rat fibroblasts. Potent F(0)F(1)-ATPase inhibition was not a sufficient determinant of antiproliferative activity for several analogues, suggesting the existence of a secondary biological target or more complex mode of action for apoptolidin.
A Motion Vector Prediction Method For Multi-view Video Coding (2008)

This paper proposes a motion vector (MV) prediction algorithm for increasing the gain of multiview video coding (MVC). In the conventional MVC algorithms, the main feature that brings coding gain is the interview MV estimation and compensation in anchor frames. Although all the other frames (non-anchor frames) also consider both temporal and interview MVs, the interview MVs are usually outnumbered by the temporal MVs. Note that the H.264 schemes encode the MVs in DPCM style and thus the accuracy of MV prediction from neighboring ones is important. When an interview MV is being considered, the conventional method predicts it by neighboring MVs regardless of their being temporal or interview directions, which results in inaccurate prediction and thus rare use of interview MVs. Hence we propose a new MV prediction and encoding scheme especially for the interview MVs. The proposed method first estimates the interview MVs that are not sent to the decoder, from the temporal reference frames. The interview MVs are well estimated in most cases because the depth information does not change rapidly. By using the estimated interview MVs instead of temporal MVs, current interview MV being encoded is more accurately predicted and thus the chance of their use is increased. This results in the increase of coding gain about 0.2dB on average and 0.33dB at maximum.
Improved Defibrillation Threshold With a New Epicardial Carbon Electrode Compared With a Standard Epicardial Titanium Patch (1995)

Compared with a titanium patch, the new braided epicardial electrode significantly decreases the defibrillation energy requirements. This effect can be maximized by using an endocardial carbon-platinum-iridium prototype as cathode and a short duration biphasic waveform.
Photolysis of ((3-(Trimethylsilyl)propoxy)phenyl)phenyliodonium Salts in the Presence of 1-Naphthol and 1-Methoxynaphthalene (2000)

Direct photolysis of ((3-trimethylsilylpropoxy)phenyl)phenyliodonium salts with different counteranions (Cl(-), SbF(6)(-), and B(C(6)F(5))(4)(-)) in methanol leads to products by both heterolytic and homolytic processes. In the presence of 1-naphthol and 1-methoxynaphthalene, products formed by a heterolytic reaction disappear, suggesting an electron-transfer process occurs between excited 1-naphthol/1-methoxynaphthalene and the iodonium salts. In the case of 1-methoxynaphthalene, three phenylated methoxynaphthalene isomers are produced. These are produced as radical coupling products from the phenyl radical and 1-methoxynaphthalene radical cation.
Thermal therapies and photodynamic therapy for early esophageal neoplasia (2015)

Barrett's esophagus (BE) is a premalignant lesion that may further develop into dysplasia and lead to adenocarcinoma of the esophagus. Once only performed in referral centers, endoscopic resection (ER) of focal early tumors is now performed in many centers, while referral centers now have programs that include endoscopic mucosal resection, endoscopic submucosal dissection in selected cases and ablation of residual Barrett's, to prevent the development of metachronous lesions after focal ablation. In the nineties some of the thermal ablation techniques used in the setting of BE and early esophageal adenocarcinoma have seen their utility changing or have not yet gained acceptance. These techniques include: photodynamic therapy (PDT), argon plasma coagulation (APC) and cryotherapy (CT). This chapter summarizes the knowledge acquired with these techniques and tries to define the potential residual niches of application as well as possible further progresses which could be made in thermal ablation.
Immunopeptidomics-based design of mRNA vaccine formulations against Listeria monocytogenes (2022)

Listeria monocytogenes is a foodborne intracellular bacterial pathogen leading to human listeriosis. Despite a high mortality rate and increasing antibiotic resistance no clinically approved vaccine against Listeria is available. Attenuated Listeria strains offer protection and are tested as antitumor vaccine vectors, but would benefit from a better knowledge on immunodominant vector antigens. To identify novel antigens, we screen for Listeria peptides presented on the surface of infected human cell lines by mass spectrometry-based immunopeptidomics. In between more than 15,000 human self-peptides, we detect 68 Listeria immunopeptides from 42 different bacterial proteins, including several known antigens. Peptides presented on different cell lines are often derived from the same bacterial surface proteins, classifying these antigens as potential vaccine candidates. Encoding these highly presented antigens in lipid nanoparticle mRNA vaccine formulations results in specific CD8<sup>+</sup> T-cell responses and induces protection in vaccination challenge experiments in mice. Our results can serve as a starting point for the development of a clinical mRNA vaccine against Listeria and aid to improve attenuated Listeria vaccines and vectors, demonstrating the power of immunopeptidomics for next-generation bacterial vaccine development.
Technology base studies of long-term MCFC performance (1995)

Cathode dissolution into the electrolyte matrix and endurance of current collector/separator plate materials are the main life-limiting factors of the state-of-the art MCFC. These components are also major contributors to the total system cost. Therefore, to reduce capital cost, it is necessary to minimize hardware corrosion and increase cell life. This study consists of experimental evaluation of corrosion processes with the objective to further practical; understanding of corrosion behavior of alloys and alloy components under cathodic gas conditions. Nickel, iron, cobalt and stainless steels 310 and 316L are analyzed. The experimental study consists of (1) Observation of open circuit potential (OCP) changes. Surface reactions occurring without net passage of current are proposed based on this measurement. (2) Applying cyclic voltammetry, which provides information about the possible electrode reactions at different stages of polarization. (3) Applying AC impedance to support the result of tasks 1 and 2 at different stages of oxidation, and data analysis by means of equivalent circuits. Open circuit conditions as well as positive and negative polarization are used in the impedance measurements. (4) Surface analysis of the electrodes by SEM-EDX and X-ray diffraction. To obtain more information from electrochemical measurements a novel approach has been applied in cell design. In this two-electrode approach, one electrode is fully immersed, and the other is wetted by carbonate melt via an alumina tube which has a thin film on it. While camera observation of these two different electrode conditions will identify the effect of carbonate wetting on the state of the surface, electrochemical measurements enable a quantitative comparison between complete submersion and wetting by a film of carbonate.
Achieving Budget-Balance with Vickrey-Based Payment Schemes in Combinatorial Exchanges (2001)

Generalized Vickrey mechanisms have received wide attention in the combinatorial auction design literature because they are efficient and strategy-proof. However, it is well known that it is impossible for an exchange, with multiple buyers and sellers and voluntary participation, to be efficient and budget-balanced, even relaxing dominant strategy requirements. Except for special cases, a market-maker in an efficient exchange must make more payments than it collects. Taking a constructive approach, we clear exchanges to maximize reported surplus, and explore the efficiency effects of different budget-balanced payment rules. The payment rules are formulated to minimize the distance to Vickrey payments, under different metrics. Different rules lead to different levels of truth-revelation, and therefore efficiency. Experimental and theoretical analysis suggest a simple Threshold scheme, which gives surplus to agents with payments further than a certain threshold value from their Vickrey payments, has good properties. The scheme exploits agent uncertainty about bids from other agents to reduce manipulation opportunities.
Scheduling Algorithms For Hierarchical Data Control Flow Graphs (1992)

Abstract New algorithms for the allocation, assignment and scheduling of a hierarchical data control flow graph (DCFG) with imposed timing constraints are presented. the hierarchical allocation environment performs a probabilistic search through the design space and converges towards a final solution by iteratively calling and interchanging resource utilisation information with the assignment and scheduling subroutines. The allocation, assignment and scheduling problem is posed in a such a way that the specific costs of all hardware elements are taken into account and simultaneously addressed. the proposed algorithms have novel constructive and rejectionless iterative improvement probabilistic components. The effectiveness of the algorithms is demonstrated with the aid of extensive experimental results. In addition to the standard benchmarks, we have studied a broad class of test examples of a very diverse nature, thus covering the global design space. We also discuss how min‐bound estimations are used to more easily and realistically assess the quality of the allocation, assignment and scheduling algorithms.
InclusiveFaceNet: Improving Face Attribute Detection with Race and Gender Diversity (2017)

We demonstrate an approach to face attribute detection that retains or improves attribute detection accuracy across gender and race subgroups by learning demographic information prior to learning the attribute detection task. The system, which we call InclusiveFaceNet, detects face attributes by transferring race and gender representations learned from a held-out dataset of public race and gender identities. Leveraging learned demographic representations while withholding demographic inference from the downstream face attribute detection task preserves potential users' demographic privacy while resulting in some of the best reported numbers to date on attribute detection in the Faces of the World and CelebA datasets.
Solid state13C andin situ1H NMR study on the effect of melamine on the thermal degradation of a flexible polyurethane foam (2000)

The aim of this investigation is to ascertain whether the mode of action of melamine in flexible polyurethane (PU) involves condensed phase chemistry in terms of promoting char formation. A combination of in situ 1H NMR analysis, solid state 13C NMR characterization of chars prepared ex situ, and normal TGA and DSC has been employed. Solid state 13C NMR indicates that there is no major discernible difference in the structure of the dichloromethane-insoluble chars prepared with and without melamine, the remaining polyol only accounting for 20–25 % of the total carbon at 350 °C, but still being quite mobile. However, in situ 1H NMR provides definitive evidence that melamine acts in the condensed phase in terms of promoting the formation of rigid char which forms in more significant quantity by 450 °C. No increase in the residue yields is observed by TGA upon melamine addition, probably due to a combination of the small sample size and open sample holder in relation to the in situ 1H NMR analysis which also involves fairly slow heating. © 2000 Society of Chemical Industry
Fast Imaging Technique to Study Drop Impact Dynamics of Non-Newtonian Fluids (2014)

In the field of fluid mechanics, many dynamical processes not only occur over a very short time interval but also require high spatial resolution for detailed observation, scenarios that make it challenging to observe with conventional imaging systems. One of these is the drop impact of liquids, which usually happens within one tenth of millisecond. To tackle this challenge, a fast imaging technique is introduced that combines a high-speed camera (capable of up to one million frames per second) with a macro lens with long working distance to bring the spatial resolution of the image down to 10 µm/pixel. The imaging technique enables precise measurement of relevant fluid dynamic quantities, such as the flow field, the spreading distance and the splashing speed, from analysis of the recorded video. To demonstrate the capabilities of this visualization system, the impact dynamics when droplets of non-Newtonian fluids impinge on a flat hard surface are characterized. Two situations are considered: for oxidized liquid metal droplets we focus on the spreading behavior, and for densely packed suspensions we determine the onset of splashing. More generally, the combination of high temporal and spatial imaging resolution introduced here offers advantages for studying fast dynamics across a wide range of microscale phenomena.
Version traveler: fast and memory-efficient version switching in graph processing systems (2016)

Multi-version graph processing, where each version corresponds to a snapshot of an evolving graph, is a common scenario in large-scale graph processing. Straightforward application of existing graph processing systems often yields suboptimal performance due to high version-switching cost. We present Version Traveler (VT), a graph processing system featuring fast and memory-efficient version switching. VT achieves fast version switching by (i) representing differences among versions as deltas and (ii) constructing the next version by integrating the in-memory graph representation of the current version with the delta(s) relating the two versions. Furthermore, VT maintains high computation performance and memory compactness. Our evaluation using multi-version processing workloads with realistic datasets shows that VT outperforms PowerGraph-- running 23x faster with a 15% memory overhead. VT is also superior to four multi-version processing systems, achieving up to 90% improvement when jointly considering processing time and resource consumption.
Service Program Mobility: A new Paradigm for Mobile Operators' Service Delivery (2012)

The delivery of emerging, high performance mobile services is traditionally limited to the cellular operator home domain. Due to the centralized nature of service platforms, resource-demanding services suffer from long delays when a user is accessing them when roaming. With the globalization of our society, such data intensive services are enabled at the high cost required by provisioning high-speed inter-domain connections. Delivering those services from the local, visited domain (instead of the home domain), does not only overcome the aforementioned limitations, but also opens new possibilities for service delivery. An operator could expand its service delivery reach to a global coverage, enjoying all the benefits of such a move. We propose Service Program Mobility as a novel paradigm for global service provisioning. Our system architecture realizes dynamic service component migration across operator domains and platforms to offer the same experience to roaming users as they would have in the home network.
Polymer Solar Cells: Bithiophene Imide and Benzodithiophene Copolymers for Efficient Inverted Polymer Solar Cells (Adv. Mater. 17/2012) (2012)

R. P. H. Chang, A. Facchetti, T. J. Marks, and co-workers synthesize bithiophene imide and benzodithiophene donor–acceptor polymer semiconductors for application in organic photovoltaic cells. Stable inverted solar cells are fabricated and achieve high power-con-version efficiencies of up to 5.5%, with open circuit voltages greater than 0.9 V, as a result of the low-lying HOMO levels of the polymers. This work, presented on page 2242, demonstrates that bithiophene imide is a promising building block for high-performance polymer donor materials for solar cell applications.
Long-Range Effects on Calcium Binding and Conformational Change in the N-Domain of Calmodulin (2001)

Proteins within the EF-hand protein family exhibit different conformational responses to Ca(2+) binding. Calmodulin and other members of the EF-hand protein family undergo major changes in conformation upon binding Ca(2+). However, some EF-hand proteins, such as calbindin D9k (Clb), bind Ca(2+) without a significant change in conformation. Here, we investigate the effects of replacement of a leucine at position 39 of the N-terminal domain of calmodulin (N-Cam) with a phenylalanine derived from Clb. This variant is studied alone and in the context of other mutations that affect the conformational properties of N-Cam. Strikingly, the introduction of Phe39, which is distant from the calcium binding sites, leads to a significant enhancement of Ca(2+) binding affinity, even in the context of other mutations which trap the protein in the closed form. The results yield novel insights into the evolution of EF-hand proteins as calcium sensors versus calcium buffers.
Remote dose imaging from Cherenkov light using spatially resolved CT calibration in breast radiotherapy (2022)

This approach provides evidence that the planning CT scan can mitigate some of the tissue-specific attenuation in Cherenkov images, allowing them to be translated into near surface dose images.
Influence of Temperature and Sliding Speed on Friction and Wear of SiSiC and MgO-ZrO2 (2008)

The influence of temperature from 22 to 1000 C and the sliding velocity in the range from 0.03 up to 3 m/s under unlubricated conditions of self-mated SiSiC and MgO-ZrO/sub 2/ wear couples is described. The coefficient of friction of both materials is mostly greater than 0.3. With SiSiC as friction and wear material, it is possible to operate unlubricated up to 800 C without adhesion phenomena. 6 references.
Out-of-plane dispersion and homogenization in photonic crystal slabs (2005)

We report a measurement of out-of-plane dispersion in two-dimensional photonic crystal slabs. Using terahertz time-domain spectroscopy, we obtain the complex transmission coefficient over a broad spectrum, ranging from the long wavelength (homogeneous) limit up to beyond the first few guided resonances. Despite the absence of a band gap, the out-of-plane dispersion is significant and in addition exhibits a complicated spectral dependence. Calculations of the effective refractive index which assume translational invariance in the direction perpendicular to the slab are in only approximate agreement with the measured homogeneous effective index and dispersion. In contrast, numerical simulations which accurately account for the finite slab thickness give much more accurate predictions.
ChemInform Abstract: Enantioselective Synthesis of Taxol Side Chain via Regio‐ and Stereoselective Reaction of 4(R)‐Carbethoxy‐5(S)‐phenyl‐1,3,2‐ dioxathiolane‐2‐oxide. (1995)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.