gebhart/patrepeval huggingface dataset:
Frustration in Super‐Ionic Conductors Unraveled by the Density of Atomistic States (2023)

The frustration in super-ionic conductors enables their exceptionally high ionic conductivities, which are desired for many technological applications including batteries and fuel cells. A key challenge in the study of frustration is the difficulties in analyzing a large number of disordered atomistic configurations. Using lithium super-ionic conductors as model systems, we propose and demonstrate the density of atomistic states (DOAS) analytics to quantitatively characterize the onset and degree of disordering, reveal the energetics of local disorder, and elucidate how the frustration enhances diffusion through the broadening and overlapping of the energy levels of atomistic states. Furthermore, material design strategies aided by the DOAS are devised and demonstrated for new super-ionic conductors. The DOAS is generally applicable analytics for unraveling fundamental mechanisms in complex atomistic systems and guiding material design.
NOVEL 3D LITHOGRAPHICALLY-PREPARED SOLID-PHASE SURFACES MADE FROM SU-8 FOR NEXT GENERATION SEQUENCING (2011)

A solid-phase PCR strategy on a novel 3-D substrate consisting of 2 ??m SU-8 pillars that are &amp;gt;5 ??m in height have been lithographically patterned onto quartz substrates and is reported. The surface chemistry of SU-8 allows the printing of PCR primers only onto the SU-8 pillars but not on the quartz substrate, which creates highly ordered arrays of clusters making imaging of the clonally-amplified DNA using high density CCDs more efficient. The 3D architecture employed herein also provides significantly improved signal-to-noise ratios for the next phase of the assay (e.g. sequencing-by-synthesis (SbS)) in next generation sequencing (NGS) instruments.
Variability of Pre-Dialysis Serum Sodium, a Risk Factor of Survival in Hemodialysis Patients: Results from the Global MONDO Initiative (2018)

Background Variability of laboratory parameters and serum sodium (SNa) observed to associated with adverse physical conditions in chronic hemodialysis (HD) patients (pts) [Nakazato Y et al]. SNa, the main determinant of plasma osmolality, play a key role in fluid shifts between the extra-&amp; intracellular compartments. Variability SNa, denoted as the measured-to-measured variation, affects the stability of cell volume. Methods All adult incident pts with more than 5 SNas during the first year on HD were included, outcomes were recorded over a 2 yrs period. Average baseline SNa as well as variabilities were computed by standard deviation (SD) of the residual, SD, relative range (the difference between the largest and smallest), average real variability (ARV). Cox proportional models with bivariate spline functions were applied to study the joint effects of SD of residual, SD, ARV and relative range of SNa, respectively. Cox proportional models with multiple adjustments were also used to further evaluate the adverse effect of SNa variability. Results Out of 30,174 pts (EU:15,660, Asia:8,749,US:2,691,UK:2,282, South America:791) were included, 7,021 (23.3%) died. Hyponatremia (SNa&lt;=135) was the most prominent predictor of increase mortality. For pts with SNa&gt;135, we didn't observe an association between SD residual and mortality. Increased risk of death with higher SD and ARV appeared to be present at all levels of SNa. A more pronounced effect of relative range was observed compared to SD and ARV. More significant effect was observed with the maximal SNa happened before the minimal SNa [Figure 1]. Cox proportional model with adjustments also yield the same results. Conclusion Given the positive association between mortality and higher SNa range,S, ARV regardless of the SNa level, these measures constitute novel prognostic indicators in HD therapy.
Multi-Agent Distributed Lifelong Learning for Collective Knowledge Acquisition (2018)

Lifelong machine learning methods acquire knowledge over a series of consecutive tasks, continually building upon their experience. Current lifelong learning algorithms rely upon a single learning agent that has centralized access to all data. In this paper, we extend the idea of lifelong learning from a single agent to a network of multiple agents that collectively learn a series of tasks. Each agent faces some (potentially unique) set of tasks; the key idea is that knowledge learned from these tasks may benefit other agents trying to learn different (but related) tasks. Our Collective Lifelong Learning Algorithm (CoLLA) provides an efficient way for a network of agents to share their learned knowledge in a distributed and decentralized manner, while eliminating the need to share locally observed data. We provide theoretical guarantees for robust performance of the algorithm and empirically demonstrate that CoLLA outperforms existing approaches for distributed multi-task learning on a variety of datasets.
Degradation of NO-nitrided SiC MOS interfaces by excimer ultraviolet light irradiation (2022)

Abstract The impact of excimer ultraviolet (UV) light irradiation on SiO 2 /SiC(0001) and (112̄0) interfaces was examined to get insight into the effect of NO nitridation. While NO nitridation appears to be effective in passivating the electron traps at the SiO 2 /SiC interfaces, we found that the nitridation induces additional traps that are not active until UV light is irradiated. The traps include those causing hysteresis and frequency dispersion in the C – V characteristics and those affecting the long-term reliability of MOS devices. A non-nitrided SiO 2 /SiC interface was less sensitive to UV light, indicating the instability of the nitrided SiC MOS structure.
Synthetic scaffolds for 3D cell cultures and organoids: applications in regenerative medicine (2021)

Three-dimensional (3D) cell cultures offer an unparalleled platform to recreate spatial arrangements of cells <i>in vitro</i>. 3D cell culture systems have gained increasing interest due to their evident advantages in providing more physiologically relevant information and more predictive data compared to their two-dimensional (2D) counterpart. Design and well-established fabrication of organoids (a particular type of 3D cell culture system) are nowadays considered a pivotal achievement for their ability to replicate <i>in vitro</i> cytoarchitecture and the functionalities of an organ. In this condition, pluripotent stem cells self-organize into 3D structures mimicking the <i>in vivo</i> microenvironments, architectures and multi-lineage differentiation. Scaffolds are key supporting elements in these 3D constructs, and Matrigel is the most commonly used matrix despite its relevant translation limitations including animal-derived sources, non-defined composition, batch-to-batch variability and poorly tailorable properties. Alternatively, 3D synthetic scaffolds, including self-assembling peptides, show promising biocompatibility and biomimetic properties, and can be tailored on specific target tissue/cells. In this review, we discuss the recent advances on 3D cell culture systems and organoids, promising tools for tissue engineering and regenerative medicine applications. For this purpose, we will describe the current state-of-the-art on 3D cell culture systems and organoids based on currently available synthetic-based biomaterials (including tailored self-assembling peptides) either tested in <i>in vivo</i> animal models or developed <i>in vitro</i> with potential application in the field of tissue engineering, with the aim to inspire researchers to take on such promising platforms for clinical applications in the near future.
Immunohistochemistry in the diagnosis of malignant pleural mesothelioma: Trends in Australia and a literature review (2012)

Reflecting the acceptance of diagnostic panels and increased availability of antibodies, an increase in the use of IHC stains for MPM diagnosis has occurred over the past two decades although uncertainty persists as to the optimal panel composition.
High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men (2020)

Elucidating virus-host interactions responsible for HIV-1 transmission is important for advancing HIV-1 prevention strategies. To this end, single genome amplification (SGA) and sequencing of HIV-1 within the context of a model of random virus evolution has made possible for the first time an unambiguous identification of transmitted/founder viruses and a precise estimation of their numbers. Here, we applied this approach to HIV-1 env analyses in a cohort of acutely infected men who have sex with men (MSM) and found that a high proportion (10 of 28; 36%) had been productively infected by more than one virus. In subjects with multivariant transmission, the minimum number of transmitted viruses ranged from 2 to 10 with viral recombination leading to rapid and extensive genetic shuffling among virus lineages. A combined analysis of these results, together with recently published findings based on identical SGA methods in largely heterosexual (HSX) cohorts, revealed a significantly higher frequency of multivariant transmission in MSM than in HSX [19 of 50 subjects (38%) versus 34 of 175 subjects (19%); Fisher's exact p = 0.008]. To further evaluate the SGA strategy for identifying transmitted/founder viruses, we analyzed 239 overlapping 5′ and 3′ half genome or env-only sequences from plasma viral RNA (vRNA) and blood mononuclear cell DNA in an MSM subject who had a particularly well-documented virus exposure history 3–6 days before symptom onset and 14–17 days before peak plasma viremia (47,600,000 vRNA molecules/ml). All 239 sequences coalesced to a single transmitted/founder virus genome in a time frame consistent with the clinical history, and a molecular clone of this genome encoded replication competent virus in accord with model predictions. Higher multiplicity of HIV-1 infection in MSM compared with HSX is consistent with the demonstrably higher epidemiological risk of virus acquisition in MSM and could indicate a greater challenge for HIV-1 vaccines than previously recognized.
Sensor array for toxic gas detection (2023)

A portable instrument for use in the field in detecting and identifying a hazardous component in air or other gas including an array of small sensors which upon exposure to the gas from a pattern of electrical responses, a source of standard response patterns characteristic of various components, and microprocessor means for comparing the sensor-formed response pattern with one or more standard patterns to thereby identify the component on a display. The number of responses may be increased beyond the number of sensors by changing the operating voltage, temperature or other condition associated with one or more sensors to provide a plurality of responses from each of one or more of the sensors. In one embodiment, the instrument is capable of identifying anyone of over 50-100 hazardous components.
Managing tuberculosis and adverse reactions to treatment (2010)

The floxacrine derivative S 82 5455, 7-chloro-1-( 4N - methylpiperazino -1N-imino)-10-hydroxy-1, 2, 3, 4-tetrahydro-3-(4-trifluoromethylphenyl)-9(10 H)- acridone , shows a high activity against blood induced infection of a drug-sensitive line of Plasmodium berghei in mice and rats. The dosis curativa minima/ dosis tolerata maxima values against the drug-sensitive P. berghei strain ascertained in the '28-day test' in mice, were 1.56 (X 5)/400 (X 1) mg/kg after the oral route 3.12(X 5)/400(X 1) mg/kg after the subcutaneous (sc) route. Morphological changes in erythrocytic stages of P. berghei following a single oral/sc dose of 25 and 50 mg/kg respectively in rats were at first swollen lacunes of the endoplasmic reticulum and extremely enlarged mitochondrion (6 h after treatment), then an apparent vacuolisation of the cytoplasm and pyknosis of the nucleus, as well as distinctly enlarged perinuclear space and later marked fissuring of the cytoplasm. After 23 h most of the parasites were destroyed by disruption of their pellicle. The majority of the degenerate parasites were situated outside of the apparently ruptured host cell. The remnants of damaged parasites and host cells disappeared completely from smears 96 h after treatment at all oral and sc doses used.
Migration of Skin Dendritic Cells in Response to Ionizing Radiation Exposure (2009)

We describe an imaging assay that monitors the migration of two unique subsets of immune dendritic cells (DC), interstitial dendritic cells (iDC) and Langerhans cells (LC), found in the dermal and epidermal layers of skin, respectively. Using this assay, we study responses of these cells to ionizing radiation. Results obtained using whole-mount histology and fluorescence microscopy suggest that ionizing radiation triggered the migration of both major histocompatibility complex (MHC) class II(+) iDC and Langerin(+) LC in a dose- and time-dependent manner. Migration appeared to be limited by local administration of recombinant IL-12, a potent immunostimulatory cytokine known to induce DNA repair. Those findings were extended to an in vivo model by injecting fluorescently conjugated anti-MHC class II antibodies intradermally into the ears of live, anesthetized mice and visualizing the DC population in the same ear before and after radiation exposure using confocal microscopy.
Molecular imaging of tissue with high-contrast multispectral photosensitizing polarimetric imaging techniques (2009)

Backscattered laser beam contributions from biological fluids doped with optically active molecules were measured utilizing single-detection autobalanced polarimetric detection principles. The outcome of this study indicates that both the Detective Quantum Efficiency (DQE) and the Degree of Linear polarization (DOLP) of backscattered optical signals increase with increasing the concentrations of molecular optically active dopants. This translates to enhanced signal-to-noise ratio and contrast.
ROS induction as a strategy to target persister cancer cells with low metabolic activity in NRAS mutated melanoma (2022)

Abstract Metabolic reprogramming is an emerging hallmark of resistance to cancer therapy but may generate vulnerabilities that can be targeted with small molecules. Multi-omics analysis revealed that NRAS-mutated melanoma cells with a mesenchymal transcriptional profile adopt a quiescent metabolic program to resist cellular stress response induced by MEK-inhibitor resistance. However, as a result of elevated baseline ROS levels, these cells become highly sensitive to ROS induction. In vivo xenograft experiments and single-cell RNA sequencing demonstrated that intra-tumor heterogeneity requires the combination of a ROS-inducer and a MEK-inhibitor to target both tumor growth and metastasis. By ex vivo pharmacoscopy of 62 human metastatic melanomas, we found that MEK-inhibitor resistant tumors significantly benefitted from the combination therapy. Finally, we profiled 486 cancer cell lines and revealed that oxidative stress responses and translational suppression are biomarkers of ROS-inducer sensitivity, independent of cancer indication. These findings link transcriptional plasticity to a metabolic phenotype that can be inhibited by ROS-inducers in melanoma and other cancers. Statement of Significance Targeted-therapy resistance in cancer arises from genetic selection and both transcriptional and metabolic adaptation. We show that metabolic reprogramming sensitizes resistant cells to ROS-induction in combination with pathway inhibitors. Predictive biomarkers of metabolic sensitivity to ROS-inducing agents were identified in many cancer entities, highlighting the generalizability of this treatment approach. Graphical summary
Fluorescence-Based Rapid Detection of Microbiological Contaminants in Water Samples (2012)

Microbiological contamination of process waters is a current issue for pharmaceutical industries. Traditional methods require several days to obtain results; therefore, rapid microbiological methods are widely requested to shorten time-to-result. Milliflex Quantum was developed for the rapid detection and enumeration of microorganisms in filterable samples. It combines membrane filtration to universal fluorescent staining of viable microorganisms. This new alternative method was validated using European and United States Pharmacopeia definitions, with sterile water and/or sterile water artificially contaminated with microorganisms. The Milliflex Quantum method was demonstrated to be reliable, robust, specific, accurate, and linear over the whole range of assays following these guidelines. The Milliflex Quantum system was challenged to detect natural contaminants in different types of pharmaceutical purified process waters. Milliflex Quantum was demonstrated to detect accurately contaminants 3- to 7-fold faster than traditional membrane filtration method. The staining procedure is nondestructive allowing downstream identification following a positive result. The Milliflex Quantum offers a fast, sensitive, and robust alternative to the compendial membrane filtration method.
Characterization of a Ca2+-stimulated Mg2+-dependent adenosine triphosphatase in Friend murine erythroleukemia cell plasma membranes. (1984)

Since agents which affect Ca2+ fluxes have been shown to affect the commitment to terminal differentiation of murine erythroleukemia cells treated with an inducer of differentiation (Bridges, K., Levenson, R., Housman, D., and Cantley, L. (1981) J. Cell Biol. 90, 542-544), we investigated the presence of Ca2+-transport systems in plasma membranes isolated from these cells. Plasma membranes from murine erythroleukemia cells exhibited a high affinity (Ca2+-Mg2+)-ATPase activity with a Vmax of 29 +/- 4 nmol/mg/min and an apparent K0.5 for free Ca2+ of 0.13 microM. This activity was strongly inhibited in a dose-dependent fashion by low concentrations of trifluoperazine, compound 48/80, lanthanum, and vanadate with I50 of 29 microM, 1.75 micrograms/ml, 1.5 microM, and 0.4 microM, respectively. The inhibitory effect of compound 48/80 was specifically reversed by exogenously added calmodulin. Phosphorylation of plasma membranes with [gamma-32P] ATP followed by sodium dodecyl sulfate electrophoretic analysis at low pH revealed a Ca2+-dependent phosphoprotein with an apparent molecular mass of 138,000 daltons which co-migrated with the Ca2+-dependent phosphoprotein from human erythrocytes and was separable from sarcoplasmic reticulum (Ca2+-Mg2+)-ATPase. The 32P incorporated into the phosphoprotein could be chased with unlabeled ATP and the protein-phosphate bond was unstable at alkaline pH suggesting an acylphosphate ATPase intermediate like that previously characterized in other (Ca2+-Mg2+)-ATPases.
Survey of radiopharmaceutical dosing strategies for bone and PET scans (2013)

94 Objectives Increased concerns about radiation dose in the public and medical community have motivated efforts to develop diagnostic reference levels in nuclear medicine and an improved understanding of dosing strategies used in current practice. In this work, the Intersocietal Accreditation Commission (IAC) and the SNMMI Dose Optimization task force partnered to summarize dosing strategies across multiple institutions for Tc-99m MDP bone and FDG-PET scans. Methods Accreditation materials from IAC Nuclear/PET accredited facilities for bone and FDG-whole body PET studies were evaluated. The average administered activity for each facility was calculated from patient reports. Sites were categorized based on their type (hospital, private, mobile, etc.) and their reported dosing strategy (fixed, range or weight-based dosing). Results Analysis was performed for 225 and 95 facilities performing bone scans and FDG-PET scans, respectively. For bone imaging, 58% of the clinics reported using a range of doses compared to 42% that report using a fixed dose. The average MDP activity was 930 +/- 118 MBq[710 to 1,315 range] MBq (25.1 +/- 3.2 mCi). For FDG-PET, most sites (64%) use a range-based dosing strategy and the overall average activity was 508 +/- 117 [108-875] MBq (13.7 +/- 3.2 mCi). In general, there were no observable major differences in dosing between the types of facilities, except in the case of the mobile centers, which used on average 30% more dose for both bone and PET scanning. However, the numbers of mobile units were small: 1 and 3 for bone and FDG-PET scans, respectively. Conclusions This survey of a variety of facilities presents anticipated results: on average dosing is in keeping with SNMMI practice guidelines and there is a wide range of dosing strategies in the United States. These types of evaluations are crucial for establishing diagnostic reference levels and communicating the importance of selecting appropriate dosing strategies.
Molecular Dynamics Simulations Guide Chimeragenesis and Engineered Control of Chemoselectivity in Diketopiperazine Dimerases (2023)

In the biosynthesis of the tryptophan-linked dimeric diketopiperazines (DKPs), cytochromes P450 selectively couple DKP monomers to generate a variety of intricate and isomeric frameworks. To determine the molecular basis for selectivity of these biocatalysts we obtained a high-resolution crystal structure of selective Csp<sup>2</sup> -N bond forming dimerase, AspB. Overlay of the AspB structure onto C-C and C-N bond forming homolog NzeB revealed no significant structural variance to explain their divergent chemoselectivities. Molecular dynamics (MD) simulations identified a region of NzeB with increased conformational flexibility relative to AspB, and interchange of this region along with a single active site mutation led to a variant that catalyzes exclusive C-N bond formation. MD simulations also suggest that intermolecular C-C or C-N bond formation results from a change in mechanism, supported experimentally through use of a substrate mimic.
Development of a Low-Profile to F-Shape Transition Barrier Segment (2007)

The purpose of the research reported herein was to develop a transition barrier segment that can be used to connect the low-profile barrier (LPCB(1)-92) to the standard height, F-shape portable concrete barrier (CSB-04). The design of the new transition barrier segment is such that no new hardware is required to connect the transition barrier segment to the low-profile barrier and the F-shape barrier. Researchers used computer simulations to evaluate the proposed design and to examine the location of critical impact points that were used in specifying impact conditions for a full-scale evaluation of the new design. Results of two full-scale tests coupled with results from the computer simulations show that the new transition barrier segment is ready for immediate implementation.
Hall effect in a magnetic field parallel to interfaces of a III-V semiconductor quantum well (1998)

We have discovered that the spin-orbit coupling of electrons confined in a III-V semiconductor quantum well gives rise to an anomalous Hall current when both magnetic field and electric field are applied parallel to interfaces of the well. This Hall current is always perpendicular to the electric field, and depends strongly on the orientations of the electric and magnetic fields with respect to crystal axes. The Hall current is larger in samples with lower electron mobility. Our theory predicts that this effect can be observed in asymmetric quantum wells grown along the [011] direction, but not in [001]- and [111]-oriented quantum wells.
Stable Parametric Macromodeling Using a Recursive Implementation of the Vector Fitting Algorithm (2009)

A novel least-squares fitting technique is presented for the macromodeling of parameterized frequency responses. Such parametric macromodel can be used for the design, study, and optimization of microwave structures. A key benefit of the proposed method, is that the poles of the macromodel are guaranteed stable by construction. This can easily be enforced when using the presented macromodel representation.