gebhart/patrepeval huggingface dataset:
Diffusion Properties and 3D Architecture of Human Lower Leg Muscles Assessed with Ultra-High-Field-Strength Diffusion-Tensor MR Imaging and Tractography: Reproducibility and Sensitivity to Sex Difference and Intramuscular Variability (2018)

Purpose To demonstrate the reproducibility of the diffusion properties and three-dimensional structural organization measurements of the lower leg muscles by using diffusion-tensor imaging (DTI) assessed with ultra-high-field-strength (7.0-T) magnetic resonance (MR) imaging and tractography of skeletal muscle fibers. On the basis of robust statistical mapping analyses, this study also aimed at determining the sensitivity of the measurements to sex difference and intramuscular variability. Materials and Methods All examinations were performed with ethical review board approval; written informed consent was obtained from all volunteers. Reproducibility of diffusion tensor indexes assessment including eigenvalues, mean diffusivity, and fractional anisotropy (FA) as well as muscle volume and architecture (ie, fiber length and pennation angle) were characterized in lower leg muscles (n = 8). Intramuscular variability and sex differences were characterized in young healthy men and women (n = 10 in each group). Student t test, statistical parametric mapping, correlation coefficients (Spearman rho and Pearson product-moment) and coefficient of variation (CV) were used for statistical data analysis. Results High reproducibility of measurements (mean CV ± standard deviation, 4.6% ± 3.8) was determined in diffusion properties and architectural parameters. Significant sex differences were detected in FA (4.2% in women for the entire lower leg; P = .001) and muscle volume (21.7% in men for the entire lower leg; P = .008), whereas architecture parameters were almost identical across sex. Additional differences were found independently of sex in diffusion properties and architecture along several muscles of the lower leg. Conclusion The high-spatial-resolution DTI assessed with 7.0-T MR imaging allows a reproducible assessment of structural organization of superficial and deep muscles, giving indirect information on muscle function. ©RSNA, 2018 Online supplemental material is available for this article.
Thermoeconomic Considerations in the Optimum Allocation of Heat Transfer Inventory for Refrigeration and Heat Pump Systems (2002)

Abstract Thermoeconomics is defined as attaching monetary values to heat exchanger conductances of a given plant. In this study, optimum allocation of heat transfer inventory for heat exchangers in a refrigeration system with specified power input or cooling capacity, and for a heat pump with specified heating capacity is investigated. The ratio of hot- to cold-end conductance unit cost ratio, G, was considered in the analysis as an additional parameter of considerable importance to the designer. A closed-form expression is given in terms of unit cost of conductances of both the heat exchangers. The results show a strong dependence of the total cost on the absolute temperature ratios as well as the hot- to the cold-end conductance cost ratio. It is demonstrated in the illustrative example that for G=0.1, the conductance of the hot-end heat exchanger is about three times the cold-end heat exchanger.
Structure and luminescence properties of an amorphous hydrogenated carbon (1996)

Abstract A low hydrogen content form of amorphous hydrogenated carbon (a-C: H) was deposited from a magnetically confined plasma, for a range of self bias voltages. The structure was characterized in terms of its density, sp3 bonding fraction, H content, and H bonding. The Tauc optical gap was found to vary from 2 to 3 eV as the negative bias voltage decreased. The density of paramagnetic centres ranged from below 1018cm∼3 to above 1020cm″3. The films are strongly photoluminescent (PL) at room temperature. Their PL properties were measured and correlated with the optical gap and defect density. The PL and the PL efficiency was found to increase strongly with optical gap.
Piceatannol-Induced G1 Arrest of the Cell Cycle is Associated with Inhibition of Prostaglandin E2Production in Human Gastric Cancer AGS Cells (2012)

포도, 대황, 사탕수수 등을 포함한 다양한 식물에서 발견되는 hydroxystilbene의 일종인 piceatannol은 암세포의 증식을 억제하고 apoptosis를 유발하는 것으로 알려져 있다. 본 연구에서는 AGS 인체위암세포를 대상으로 piceatannol에 의한 암세포 증식억제 과정에서 나타나는 또 다른 현상들을 조사하기 위하여 실시되었다. Piceatannol이 처리된 AGS 위암세포는 piceatannol의 처리 농도의 증가에 따라 생존율이 감소되었으며, 이는 세포주기 G1 arrest 유발과 연관이 있음을 MTT assay와 flow cytometry 분석을 통하여 확인하였다. Piceatannol에 의한 AGS 세포의 G1 arrest는 Cdks 및 cyclins의 발현 변화 및 Cdk 저해제인 p21의 발현을 전사 및 번역 수준에서 증가시켰으며, pRB 단백질의 인산화 감소 및 E2F1의 발현 억제와 연관성이 있었다. 아울러 piceatannol은 COX-2의 mRNA 및 단백질의 발현을 억제하였으나 COX-1의 발현에는 영향을 미치지 않았으며, piceatannol에 의한 COX-2의 발현억제는 PGE2의 생성 저하와 관련이 있었다. 본 연구의 결과는 piceatannol에 의한 세포주기 G1 arrest 유발이 COX-2의 선택적 발현 차단과 연관이 있음을 보여 주는 것이다.
Metal Triflate-Promoted Allylic Substitution Reactions of Cinnamyl Alcohol in the Presence of Orthoesters and Acetals (2019)

The product distribution of ethers formed from the reaction of cinnamyl alcohol with orthoesters in the presence of indium (III) triflate (InOTf)<sub>3</sub> is dependent on both the reaction temperature and catalyst loading. Carrying out the reaction at room temperature under low loadings of the catalyst leads to a facile reaction generating the unexpected secondary allyl ether as the major product. In contrast, carrying out the reaction under higher catalyst loadings at elevated temperatures provides the expected primary linear ether in high yield and with excellent selectivity. The etherification reaction is also effective in the presence of acetals and ketals in place of orthoesters and allows for the development of the procedure to encompass a telescoped etherification protocol in which the acetal is generated in situ.
Abstract LB-352: B-CLL phenotype in Eµ-miR-29 transgenic mice (2010)

Abstract B-cell chronic lymphocytic leukemia (B-CLL) is the most common leukemia in the western world. Human B-CLL occurs in two forms: aggressive (showing high ZAP-70 expression and unmutated IgH VH) and indolent (showing low ZAP-70 expression and mutated IgH VH). We found that miR-29a is upregulated in indolent human B-CLL compared to aggressive B-CLL and normal CD19+ B-cells. To study the role of miR-29 in B-CLL, we generated Eµ-miR-29 transgenic mice overexpressing miR-29 in mouse B-cells. Flow cytometric analysis revealed a markedly expanded CD5+ population in the spleen of these mice starting at 2 months of age. Over 80% of miR-29 transgenic mice exhibited an expanded population of CD5+ B-cells, a characteristic of the B-CLL phenotype. An average of 56% of the B-cell population in these transgenics were CD5 positive. At the age of 2 years these mice showed significantly enlarged spleens and an increase in CD5+ B-cell population of up to 100% of B-cells. Over 8% (3/36) of Eµ-miR-29 transgenic mice developed frank leukemia and prematurely died from the disease at the age of 24-26 months. The expanded CD5+ B-cell population was found to be proliferative, with an increased number of cells in the S-phase of the cell cycle, compared to wild type CD19+ B-cells. These results suggest that deregulation of miR-29 can cause, or at least significantly contribute to the pathogenesis of indolent B-CLL. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr LB-352.
Interaction of berenil with the EcoRI dodecamer d(CGCGAATTCGCG)2 in solution studied by NMR (1991)

The conformation of the EcoRI dodecamer d(CGCGAATTCGCG)2 has been examined in solution by 1H and 31P NMR. Spin-spin coupling constants and nuclear Overhauser (NOE) enhancement spectroscopy show that all deoxyriboses lie in the south domain, with a small admixture of the north conformation (0-20%). The time dependence of the nuclear Overhauser enhancements also reveals a relatively uniform conformation at the glycosidic bonds (average angle, chi = -114 degrees). The average helical twist is 36.5 degrees (9.8 base pairs per turn). Tilt angles are small (in the range 0 to -10 degrees), and roll angles are poorly determined. Unlike single-crystal X-ray studies of the same sequence, there is no evidence for asymmetry in the structure. Both the NOE intensities and 31P relaxation data imply conformational anomalies at the C3-G4/C9-G10 and the A5-A6/T7-T8 steps. Berenil binds in 1:1 stoichiometry to the dodecamer with high affinity (Kd = 1 microM at 298 K) and causes substantial changes in chemical shifts of the sugar protons of nucleotides Ado 5-Cyt 9 and of the H2 resonances of the two Ado residues. No significant asymmetry appears to be induced in the DNA conformation on binding, and there is no evidence for intercalation, although the binding site is not centrosymmetric. NOEs are observed between the aromatic protons of berenil and the H1' of both Thy 7 and Thy 8, as well as to Ado 5 and Ado 6 H2. These results firmly establish that berenil binds via the minor groove and closely approaches the nucleotides Ado 6, Thy 7, and Thy 8. On the basis of quantitative NOE spectroscopy and measurements of spin-spin coupling constants, changes in the conformations of the nucleotides are found to be small. Using the observed NOEs between the ligand and the DNA together with the derived glycosidic torsion angles, we have built models that satisfy all of the available solution data. The berenil molecule binds at the 5'-AAT (identical to 5'-ATT on the complementary strand) site such that (i) favorable hydrogen bonds are formed between the charged amidinium groups and the N3 atoms of Ado 6 and Ado 18 and (ii) the ligand is closely isohelical with the floor of the minor groove.
Genetic landscape of extreme responders with anaplastic oligodendroglioma: NRG Oncology/RTOG 9402. (2016)

2054 Background: The randomized multicenter RTOG 9402 trial showed a significant survival benefit in patients with 1p/19q co-deleted anaplastic oligodendrogliomas (AO) who received both radiation (RT) and chemotherapy (PCV regimen) versus RT alone. Interestingly, substantial separation of the survival curves was only seen after 7.3 years. We aimed to determine whether there are specific genetic alterations that can distinguish co-deleted AO patients who benefit from the addition of PCV from those who do not. Methods: Whole exome sequencing on matched tumor and normal DNA was performed on all available short-term (STS) and long-term survivors (LTS) who received RT+PCV. The hTERTand risk allele (G) of rs55705857 status of both cohorts of patients were also analyzed. Results: Seven STS (5 with survival of < 7.3y, 2 with later progression) and 8 LTS (7 with survival of ≥ 7.3y without progression) had sufficient material for whole exome sequencing. Several specimens could not be included due to limited quantities or degradation of the material. Among the specimens studied, there was no significant difference between the groups regarding age, performance status and extent of resection. The average number of somatic mutations for STS vs. LTS was 4 vs. 7. Most common mutations identified were IDH1 (in 57% STS and in 88% LTS), CIC (29% and 75%, respectively) and FUBP1 (71% and 50%, respectively). The hTERT promoter was mutated in 71% STS and in all LTS. Risk allele (G) of rs55705857 was identified in all patients (GA in 43% and 25%, respectively). Intriguingly, mutations of ESX1were found only in the LTS (38%) and not the STS group. Conclusions: Our results did not identify a distinct genetic signature that correlates with improved benefit from chemotherapy with PCV in patients with newly diagnosed 1p/19q co-deleted AO; however, differences in alterations of ESX1 warrant further investigation.
Breast Cancer Detection by Optomechanical Imaging (2012)

A new functional imaging system, which combines precise mechanical articulation and dynamic optical tomography for the detection breast cancer, is presented. Results obtained indicate that a wealth of new contrast features is accessible.
Internal Morphologies of Cycled Li-Metal Electrodes Investigated by Nano-Scale Resolution X-ray Computed Tomography (2017)

While some commercially available primary batteries have lithium metal anodes, there has yet to be a commercially viable secondary battery with this type of electrode. Research prototypes of these cells typically exhibit a limited cycle life before dendrites form and cause internal cell shorting, an occurrence that is more pronounced during high-rate cycling. To better understand the effects of high-rate cycling that can lead to cell failure, we use ex situ nanoscale-resolution X-ray computed tomography (nano-CT) with the aid of Zernike phase contrast to image the internal morphologies of lithium metal electrodes on copper wire current collectors that have been cycled at low and high current densities. The Li that is deposited on a Cu wire and then stripped and deposited at low current density appears uniform in morphology. Those cycled at high current density undergo short voltage transients to >3 V during Li-stripping from the electrode, during which electrolyte oxidation and Cu dissolution from the current collector may occur. The effect of temperature is also explored with separate cycling experiments performed at 5 and 33 °C. The resulting morphologies are nonuniform films filled with voids that are semispherical in shape with diameters ranging from hundreds of nanometers to tens of micrometers, where the void size distributions are temperature-dependent. Low-temperature cycling elicits a high proportion of submicrometer voids, while the higher-temperature sample morphology is dominated by voids larger than 2 μm. In evaluating these morphologies, we consider the importance of nonidealities during extreme charging, such as electrolyte decomposition. We conclude that nano-CT is an effective tool for resolving features and aggressive cycling-induced anomalies in Li films in the range of 100 nm to 100 μm.
Bad Words: Finding Faults in Spirit's Syslogs (2008)

Accurate fault detection is a key element of resilient computing. Syslogs provide key information regarding faults, and are found on nearly all computing systems. Discovering new fault types requires expert human effort, however, as no previous algorithm has been shown to localize faults in time and space with an operationally acceptable false positive rate. We present experiments on three weeks of syslogs from Sandia's 512-node "Spirit" Linux cluster, showing one algorithm that localizes 50% of faults with 75% precision, corresponding to an excellent false positive rate of 0.05%. The salient characteristics of this algorithm are (1) calculation of nodewise information entropy, and (2) encoding of word position. The key observation is that similar computers correctly executing similar work should produce similar logs.
Oracles in Software Networks (2015)

For Turing and the majority of computer scientists, an Oracle is a device that supplies a Turing machine with the values of some function (on the natural numbers or words in some alphabet) that is not recursively, e.g., Turing-machine, computable. Now technological innovations and social progress necessitate further changes to the concept of an Oracle.
Single effective neuron (1991)

We consider a network of N symmetrically interconnected neurons. Through the procedure of adiabatic elimination (separation of time scales), the dynamics of a single neuron is obtained, in closed form, from the system of coupled differential equations that describe the N-neuron problem. For the deterministic case, our approach yields an explicit form for the single-neuron ``self-coupling'' term ${\mathit{J}}_{11}$. The case of noisy neurons containing both Langevin and multiplicative noise (in the synaptic connections) is also considered.
Enhanced internalization of lipid nanocapsules in human glioblastoma cells: Influence of the concentration of surface-functionalizing NFL peptide (2017)

Glioblastoma multiforme (GBM) patients have median survival of 14 months after current treatments. Therefore, more efficacious therapies are necessary. Lipid nanocapsules (LNC) functionalized with NFL.TBS-40.63 peptide (NFL) showed enhanced internalization in mouse GBM cells. The aim of the study was to evaluate the effect of the surface-functionalizing FAM-NFL (fluoNFL) concentrations on LNC uptake in U87MG human GBM cells. A ferrocifen-type anticancer molecule (FcTriOH) was encapsulated in the nanocarriers and their in vitro efficacy on U87MG cells was evaluated. Finally, in vivo antitumor effect of the formulations were evaluated in ectopic U87MG tumor model in mice.
High-NA swing curve effects (2001)

The periodic variations of dose-to-clear, reflection and CD with resist thickness are well known phenomena commonly known as swing curves. Proper process control dictates that the resist thickness is chosen at a swing extreme, so as to reduce dose variation. Swing curves are commonly calculated for normal incidence waves. The recent trends toward high NA optics and use of off-axis illumination introduce oblique waves into the swing curve problem. Significant shifts in the magnitude and the phase of the different swing curves are now possible, and these shifts depend on exposure illumination configuration. This paper will discuss the impact of oblique waves on the swing curve. Experimental swing curves for both 248 and 193nm resist processes will be compared with expectations from simulations.
24-Hour Intraocular Pressure of Young Healthy Humans in Supine Position: Rhythm and Reproducibility (2012)

In a constant supine position, all subjects exhibited a nyctohemeral IOP rhythm present at an average rate of 80% of all sessions. With the currently available methods of tonometry, intrasubject reproducibility of rhythmic parameters and IOP values is limited. IOP values in the morning and IOP MESOR were the most reproducible parameters among the six visits.
Short-Acting T-Type Calcium Channel Antagonists Significantly Modify Sleep Architecture in Rodents (2010)

A novel phenyl acetamide series of short-acting T-type calcium channel antagonists has been identified and evaluated using in vitro and in vivo assays. Heterocycle substitutions of the 4-position of the phenyl acetamides afforded potent and selective antagonists that exhibited desired short plasma half-lives across preclinical species. Lead compound TTA-A8 emerged as a compound with excellent in vivo efficacy as indicated by its significant modulation of rat sleep architecture in an EEG telemetry model, favorable pharmacokinetic properties, and excellent preclinical safety. TTA-A8 recently progressed into human clinical trials, and in line with our predictions, preliminary studies (n = 12) with a 20 mg oral dose afforded a high C max of 1.82 ± 0.274 μM with an apparent terminal half-life of 3.0 ± 1.1 h.
Lateral Friction Behavior of a Thin, Tensioned Tape Wrapped Over a Grooved Roller: Experiments and Theory (2016)

Effects of friction forces on the lateral dynamics of a magnetic recording tape, wrapped around a grooved roller are investigated experimentally and theoretically. Tape is modeled as a viscoelastic, tensioned beam subjected to belt-wrap pressure and friction forces. Including the effects of stick and slip and velocity dependence of the friction force render the tape's equation of motion nonlinear. In the experiments, tape was wrapped under tension around a grooved roller in a customized tape path. The tape running speed along the axial direction was set to zero, thus only the lateral effects were studied. The grooved roller was attached to an actuator, which moved the roller across the tape. Tests were performed in slow and fast actuation modes. The slow mode was used to identify an effective static, or breakaway, friction coefficient. In the fast mode, the roller was actuated with a 50 Hz sinusoid. The same effective friction coefficient was deduced from the fast actuation mode tests. This test mode also revealed a periodic stick–slip phenomenon. The stick-to-slip and slip-to-stick transitions occurred when the tape vibration speed matched the roller actuation speed. Both experiments and theory show that upon slip, tape vibrates primarily at its natural frequency, and vibrations are attenuated relatively fast due to frictional and internal damping. This work also shows that an effective friction coefficient can be described that captures the complex interactions in lateral tape motion (LTM) over a grooved roller.
Deep Sets (2017)

We study the problem of designing models for machine learning tasks defined on \emph{sets}. In contrast to traditional approach of operating on fixed dimensional vectors, we consider objective functions defined on sets that are invariant to permutations. Such problems are widespread, ranging from estimation of population statistics \cite{poczos13aistats}, to anomaly detection in piezometer data of embankment dams \cite{Jung15Exploration}, to cosmology \cite{Ntampaka16Dynamical,Ravanbakhsh16ICML1}. Our main theorem characterizes the permutation invariant functions and provides a family of functions to which any permutation invariant objective function must belong. This family of functions has a special structure which enables us to design a deep network architecture that can operate on sets and which can be deployed on a variety of scenarios including both unsupervised and supervised learning tasks. We also derive the necessary and sufficient conditions for permutation equivariance in deep models. We demonstrate the applicability of our method on population statistic estimation, point cloud classification, set expansion, and outlier detection.
Systematics of araphid diatoms with asymmetric rimoportulae or densely packed virgae, with particular attention to Hyalosynedra (Ulnariaceae, Bacillariophyta) (2018)

Synedroid diatoms are morphologically characterized by a putative synapomorphic structure called an ocellulimbus, a terminal pore field whose surface is depressed relative to the rest of the valve surface. Among these diatoms is the genus Hyalosynedra Williams and Round. Characters associated with that genus are bilayered wall construction, densely packed virgae and an asymmetric rimoportula. However, these characters diagnose partially overlapping (incongruent) groups. The apical pore field itself, when present, is sometimes sunken deeply, sometimes weakly and sometimes not at all among these diatoms. Here we make additional morphological observations and add molecular sequence data (nuclear SSU rDNA, rbcL, psbC) to attempt to resolve these apparent conflicts. The molecular phylogeny does not resolve any morphological character without homoplasy, but conversely does resolve taxa which share an asymmetric rimoportula and/or densely packed virgae into a single clade we call the “hyalosynedroid” taxa. This clade contains our representatives of Thalassionematales which had been linked to Hyalosynedra by the bilayered wall structure and the possession by some species of an asymmetric rimoportula. We describe three new genera, and a total of 11 new species. Whereas four species of Hyalosynedra were previously described, we describe three new species of Hyalosynedra, describe the new genus Divergita with three species (one new, one transferred from Synedra and one from Hyalosynedra), and the new genus Stricosus with seven new species. A key to species of Hyalosynedra, Divergita and Stricosus is included.