gebhart/patrepeval huggingface dataset:
Electronic structure of defects in amorphous arsenic (1979)

The cluster-Bethe-lattice method, self-consistent pseudopotentials, and tight-binding Hamiltonians are used to study the electronic structure of various possible defects in amorphous As. The electronic densities of states of isolated twofold coordinated As atoms, fourfold coordinated As atoms, "intimate valence alternation pairs," and vacancies are calculated. The origin, character, and localization of the resulting gap states are discussed. It is found that isolated fourfold coordinated As atoms give rise to states in the gap that are nondegenerate, fairly localized, and predominantly $p$-like in character. Moreover, our investigation indicates that the character and localization of the gap states arising from the "valence alternation pair" are consistent with the properties of optically induced paramagnetic states observed in amorphous As, while the electronic gap states of the vacancy defect may be consistent with the recently observed thermally generated paramagnetic states in this material.
THE VALUE OF RETINAL IMAGING WITH INFRARED SCANNING LASER OPHTHALMOSCOPY IN PATIENTS WITH STARGARDT DISEASE (2013)

Although SW-AF identifies regions of RPE atrophy, infrared-SLO also identifies the involvement of the choroid that has important implications for the potential improvement in visual function from treatment. Thus, infrared-SLO imaging offers an additional advantage beyond that obtained with SW-AF.
Laboratory-Based Correlative Soft X-ray and Fluorescence Microscopy in an Integrated Setup (2023)

Correlative microscopy is a powerful technique that combines the advantages of multiple imaging modalities to achieve a comprehensive understanding of investigated samples. For example, fluorescence microscopy provides unique functional contrast by imaging only specifically labeled components, especially in biological samples. However, the achievable structural information on the sample in its full complexity is limited. Here, the intrinsic label-free carbon contrast of water window soft X-ray microscopy can complement fluorescence images in a correlative approach ultimately combining nanoscale structural resolution with functional contrast. However, soft X-ray microscopes are complex and elaborate, and typically require a large-scale synchrotron radiation source due to the demanding photon flux requirements. Yet, with modern high-power lasers it has become possible to generate sufficient photon flux from laser-produced plasmas, thus enabling laboratory-based setups. Here, we present a compact table-top soft X-ray microscope with an integrated epifluorescence modality for 'in-situ' correlative imaging. Samples remain in place when switching between modalities, ensuring identical measurement conditions and avoiding sample alteration or destruction. We demonstrate our new method by multimodal images of several exemplary samples ranging from nanoparticles to various multicolor labeled cell types. A structural resolution of down to 50 nm was reached.
Rapid uptake by cultured tumor cells and intracellular behavior of 4'-O-tetrahydropyranyladriamycin. (1983)

Intracellular levels of 4'-O-tetrahydropyranyladriamycin (THP) and adriamycin (ADM) were measured by a fluorospectroscopic method, and the former was shown to be taken up by L5178Y cells much faster than ADM; the uptake velocity of THP at 1 microgram/ml was calculated to be about 170 times faster than that of ADM. High performance liquid chromatography of cell extracts indicated that THP exists mainly in nuclei intact without hydrolysis. The effect of THP in inhibiting [3H]thymidine incorporation into DNA also indicated that THP taken up by cells rapidly went to nuclei and inhibited DNA synthesis. Fifty percent inhibition concentrations of THP or ADM on [3H]-thymidine incorporation during a 60-minute period, 15 minutes after the addition, were 0.1 microgram/ml and 4.2 micrograms/ml, respectively. Similar results were obtained when L1210 cells were used in place of the L5178Y cells.
Supramolecular Structures of Zinc (II) (8-Quinolinolato) Chelates (2004)

We investigate the oligomeric purity and stability of zinc (8-quinolinolato) (Znq2) and its methylated derivatives (nMeq2Zn, n = 2, 4, 5) through a combination of theoretical modeling of oligomerization energetics leading to supramolecular structures and experimental size-exclusion chromatography studies. Gas- and solution-phase (CHCl3) formation energies for dimeric, trimeric, and tetrameric species are reported. Favorable gas-phase thermodynamics were calculated and found to favor tetrameric structures for all Znq2 chelates (∼−50 kcal/mol for monomer dimerization to ∼−35 kcal/mol for dimer dimerization), with the exception of 2Meq2Zn, which gave lower formation energies by 30−45% due to steric hindrance. Solvation model computations indicate that these energies are reduced by ∼10−25% with the introduction of a dielectric medium. Computed structural parameters for the basic Zn−O core structure formed via bridging of phenolato oxygens do not change significantly as oligomer growth progresses. Size-exclusion chromatography experiments of crystalline and amorphous films (vapor deposited) dissolved in CHCl3 or CHCl3/DMSO mixtures showed that the dominant species for Znq2, 4Meq2Zn, and 5Meq2Zn is tetrameric, but partial disassociation to monomers can occur in the presence of nucleophilic solvent. The sterically hindered 2Meq2Zn was monomeric in all solvent systems. Implications for organic light-emitting devices using these materials are discussed.
Collaborative Drug Design of Plasmodium Kinase Inhibitors (2013)

Herein is reported the authors' experiences in establishing the Scientists Against Malaria (SAM) initiative, and the strategies employed, collaboration approach and supporting infrastructure are discussed. The collaboration initially progressed kinase inhibitor design and testing against a Plasmodium falciparum kinase as an antimalarial drug target. Swiss-based Douglas Connect coordinated the SAM consortium and test case as a part of SYNERGY, an ECFP7 research project on knowledge-oriented collaboration, and developed the specifications for carrying out the collaborative drug discovery project, including experimental and computational approaches. A collaboration pool with a focus on neglected diseases research was formed from members of the existing DC communities of practice (InnovationWell and eCheminfo CoPs). It was decided to form SAM as a Virtual Organization (VO) with the goal of designing novel drug candidates against malaria. The VO, which involved nine globally distributed partner organizations, was launched in Spring 2010, from which time the work activity reported herein was operational and ongoing for a subsequent nine months. The project involved the combination of computational and laboratory investigations producing large volumes of complex data and metadata, whose interpretation for analysis and decision-making involved many challenging and nonlinear activities. This type of work activity usually requires the substantial resources and infrastructure of a pharmaceutical company. During the pilot, the VO progressed a new “green-field” drug design project from a project start through target selection and modeling, computational modeling and design of ligands, biological materials and assay preparation, through to the completion of initial experimental screening testing in the laboratory, with a budget that was small for such a large-scale endeavor. During this process, a complex support infrastructure involving SYNERGY services was designed and tested and which put many important components in place for operating such a complex VO. The system achieved was a prototype which requires further development for further VO activity in this area. As the scale of the VO activity increases, and as a stage of multiple VOs in the future is entered, the challenge of managing events, complexity and resources will become even more complex. It is believed that a proof-of-concept has been established here for collaborative practices, culture and infrastructure in the context of drug discovery. The many challenges and lessons learned from this initial VO experience will facilitate future endeavors in this collaborative initiative, and provide a framework to guide other drug discovery collaborations.
Programming Colloidal Crystal Habit with Anisotropic Nanoparticle Building Blocks and DNA Bonds* (2020)

Colloidal crystallization can be programmed using building blocks consisting of a nanoparticle core and DNA bonds to form materials with controlled crystal symmetry, lattice parameters, stoichiometry, and dimensionality. Despite this diversity of colloidal 634crystal structures, only spherical nanoparticles crystallized with BCC symmetry experimentally yield single crystals with well-defined crystal habits. Here, we use low-symmetry anisotropic nanoparticles to overcome this limitation and to access single crystals with different equilibrium Wulff shapes: a cubic habit from cube-shaped nanoparticles, a rhombic dodecahedron habit from octahedron-shaped nanoparticles, and an octahedron habit from rhombic dodecahedron-shaped nanoparticles. The observation that one can control the microscopic shape of single crystals based upon control of particle building block and crystal symmetry has important fundamental and technological implications for this novel class of colloidal matter.
Large Unidirectional Magnetoresistance in a Magnetic Topological Insulator (2016)

We report current-direction dependent or unidirectional magnetoresistance (UMR) in magnetic/nonmagnetic topological insulator (TI) heterostructures, Cr$_x$(Bi$_{1-y}$Sb$_y$)$_{2-x}$Te$_3$/(Bi$_{1-y}$Sb$_y$)$_2$Te$_3$, that is several orders of magnitude larger than in other reported systems. From the magnetic field and temperature dependence, the UMR is identified to originate from the asymmetric scattering of electrons by magnons. In particular, the large magnitude of UMR is an outcome of spin-momentum locking and a small Fermi wavenumber at the surface of TI. In fact, the UMR is maximized around the Dirac point with the minimal Fermi wavenumber.
Exploring the limits of hybrid TiO 2 /conjugated polymer photovoltaic cells (2005)

In hybrid polymer photovoltaics, conjugated polymers are combined with wide bandgap metal oxide semiconductors like TiO<sub>2</sub> or ZnO. Reported maximum power conversion efficiencies (PCE) at AM1.5G conditions for a hybrid polymer bulkheterojunction device are up to 1.6 %. In this paper we report on the current-voltage characteristics of bi-layer devices consisting of TiO<sub>2</sub> and a conjugated polymer. Several polymers with different optical bandgap were studied. The maximum External Quantum Efficiency (EQE) of the devices is comparable, but the PCE differs considerably (0.2-0.5%). The differences can for a large part be explained by the differences in optical bandgap of the polymers. It is shown that a low band gap is beneficial for the short circuit current, but does not automatically result in a high PCE as relative shifts of the highest occupied molecular orbital (HOMO) energy levels of the polymers reduce the open circuit voltage (V<sub>oc</sub>). The calculations show that a PCE up to ~ 19 % can be achieved using the maximum possible V<sub>oc</sub> and a fill factor of 80%. Judicious engineering of material combinations is required to achieve such a power output, and it expresses the need for a continuing search on potentially low cost, efficient metal oxide/polymer BHJ structures.
<title>Ultrasonic Tissue Characterization Using Spectrum Analysis</title> (1976)

Ultrasonic pulse-echo systems have proven a clinically effective means of obtaining detailed cross-sectional images of soft-tissue structures. These B-scan images are now employed in a diverse range of medical specialties including obstetrics, gynecology, cardiology, and ophthalmology. Initially, the diagnostic utility of ultrasonic imaging was restricted because of severe constraints imposed on image dynamic range by equipment components, including the CRT display itself. Because of these limitations, diagnosis was made on the basis of rather coarse morphological features such as the geometry of tissue interfaces. While echo amplitudes were known to be diagnostically significant they could only be assessed indirectly. The most common approach consisted of generating a series of images at a variety of sensitivity levels. &quot;Strong&quot; echoes persisted at low sensitivity settings while &quot;weak&quot; echoes were displayed only at high sensitivity settings.
Discordance between serum cardiac biomarker and immunoglobulin‐free light‐chain response in patients with immunoglobulin light‐chain amyloidosis treated with immune modulatory drugs (2010)

We evaluated the capability of soluble cardiac biomarkers to predict tolerability and outcomes of IMiD-containing treatments among 106 patients treated on clinical trials. Baseline elevations in troponin T (TnT) and N-terminal brain naturietic protein (NT-proBNP) predicted for an inability to tolerate IMiD-based regimens. The best predictors for early attrition during cycle 1 were TnT ≥ 0.07 μg/L and NT-proBNP ≥ 11,939 ng/L. NT-proBNP-response underperformed TnT-response as a predictor for overall survival (OS), but both predicted for early protocol attrition. Despite hematologic response, IMiD-treated patients were at higher risk for NT-proBNP rises and early drug discontinuation than a control population but not for early death. These observations prompt two questions: (1) does IMiD-based therapy lead to increased fluid retention and/or cardiac toxicity and (2) is an NT-proBNP-driven cardiac response system valid in IMiD-treated amyloidosis patients? Recognition of potential drug-induced cardiac toxicity is important so that increased cardiac surveillance and drug dose-adjustment or discontinuation may be implemented.
Body sway reflects joint emotional expression in music ensemble performance (2019)

Joint action is essential in daily life, as humans often must coordinate with others to accomplish shared goals. Previous studies have mainly focused on sensorimotor aspects of joint action, with measurements reflecting event-to-event precision of interpersonal sensorimotor coordination (e.g., tapping). However, while emotional factors are often closely tied to joint actions, they are rarely studied, as event-to-event measurements are insufficient to capture higher-order aspects of joint action such as emotional expression. To quantify joint emotional expression, we used motion capture to simultaneously measure the body sway of each musician in a trio (piano, violin, cello) during performances. Excerpts were performed with or without emotional expression. Granger causality was used to analyze body sway movement time series amongst musicians, which reflects information flow. Results showed that the total Granger-coupling of body sway in the ensemble was higher when performing pieces with emotional expression than without. Granger-coupling further correlated with the emotional intensity as rated by both the ensemble members themselves and by musician judges, based on the audio recordings alone. Together, our findings suggest that Granger-coupling of co-actors' body sways reflects joint emotional expression in a music ensemble, and thus provide a novel approach to studying joint emotional expression.
Abstract 9320: Biological Sex as a Modifier of the Natural History of Dilated Cardiomyopathy (2021)

Introduction: Dilated cardiomyopathy (DCM) has a ~20% 5-year mortality rate. Understanding the impact of biological sex offers scope to improve outcomes. Objective: Investigate potential sex specific differences in the outcome of DCM. Methods: Prospective longitudinal observational cohort study of 604 patients (n=206 women, 398 men) with DCM confirmed by cardiac MRI. The median follow up for cardiovascular death, major heart failure and arrhythmic events was 3.9 years. Results: At baseline women had higher left ventricular ejection fraction (LVEF), smaller left ventricular volumes, less myocardial fibrosis and lower serum troponin concentrations (all p&lt;0.05, Table 1), with no difference in age at study enrolment or medication. Despite this favourable profile, within 2 years women had more primary outcome events than men (Figure) with Kaplan Meier estimates of 10.7% vs 5.1%; adjusted* hazard ratio 3.47, 95% CI 1.81 to 6.65, [*age, LVEF, troponin, LMNA , left atrial volume and myocardial fibrosis]. Between 2-5 years, men and women had similar outcomes (adjusted* HR 0.55; 0.17,1.78). An LVEF &lt;35% in men (HR 3.21, 1.67 to 6.18, C-statistic 0.647) but &lt;40% in women (HR 2.37, 1.05 to 5.36, C statistic 0.602) had the greatest discrimination for predicting outcome. Conclusions: Female sex is an adverse modifier of the early natural history of DCM. There is evidence for sex specific risk stratification thresholds. Sex should be considered a determining variable in DCM care.
Stepped Propane Adsorption in Pure-Silica ITW Zeolite (2018)

Gas adsorption over zeolites is at the basis of important applications of this class of microporous crystalline solids, notably as separation media and catalysts, but it may also be complex and not straightforward to understand. Here we report that for temperature below 323 K propane adsorption on the small-pore pure-silica zeolite ITW exhibits a clear step (pseudosaturation). This is absent in the case of propene and the other small linear alkanes. An intermediate plateau, clearly observed in the 293 K isotherm, always occurs when one molecule of propane is loaded in every other cage, i.e., at half-saturation. The simulation results show a swelling of the ITW structure upon propane adsorption. The strong dependence of available pore volume on the adsorbate loading level implies that adsorption cannot occur on the void structure while saturation can only be reached on highly loaded structures. To account for this unprecedented adsorption phenomenon, we propose the term "guest-modulated effect".
A HfO2‐Based Complementary Switching Crossbar Adder (2015)

Rapid growth of future information technology depends on energy‐efficient computation and ultra‐high density data storage. Non‐volatile redox‐based resistive switching memory (ReRAM) devices offer logic‐in‐memory capabilities and can redefine the von Neumann computer architecture. Especially complementary resistive switches (CRSs) enable the integration of highly dense passive nano‐crossbar arrays in 4 F 2 structure ( F is the minimum feature size) without the need of selector devices. To reduce fabrication complexity further, single ReRAM device in complementary switching (CS) mode is a viable option. Here, the implementation of in‐memory‐adders using Pt|HfO 2 |Hf|Pt‐based CS devices, which are integrated into 1 × n passive crossbar arrays, is reported. First, the feasibility of all CRS‐logic functions with these CS devices is shown, which offer high‐endurance (10 9 cycles) under pulse conditions. Afterward, two multi‐bit crossbar adders, the Toggle‐Cell Adder and the Pre‐Calculation Adder, are experimentally demonstrated under pulse conditions realizing addition and subtraction operations. These results prove the functional efficiency of the crossbar adder approach, paving the path for highly advanced ReRAM‐based computing‐in‐memory architectures.
Visualizing the Journey of Fenofibrate through the Rat Gastrointestinal Tract by Matrix-Assisted Laser Desorption/Ionization–Mass Spectrometry Imaging (2021)

Mapping the spatial distribution of a drug throughout the gastrointestinal tract (GIT) after oral ingestion can provide novel insights into the interaction between the drug, the oral drug delivery system, and the GIT. Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) is a molecular imaging technique that can analyze molecules in the cryosections of tissues, determining their localization with a spatial resolution of 10-100 μm. The overall aim of this study was to use MALDI-MSI to visualize the distribution and spatial location of a model prodrug (fenofibrate) through the rat GIT. Furthermore, the distribution and spatial colocalization of taurocholate and phospholipids in the rat GIT in relation to fenofibrate were investigated. Rats were given a fenofibrate suspension of 10 mg/mL by oral gavage. Blood samples were drawn, and the rats were euthanized at three different time points. The GIT was collected and frozen, and MALDI-MSI was applied on cross sections of the stomach and intestine. Fenofibrate was detected by MALDI-MSI throughout the GIT, which also revealed that fenofibrate was hydrolyzed to the active drug fenofibric acid already in the stomach. Furthermore, the presence of lyso-phosphatidylcholine (lyso-PC) and taurocholate was confirmed in the lumen of the small intestine. MALDI-MSI was shown to be a useful qualitative tool for localizing parent prodrugs and active drugs, with a possibility for gaining insight into not only the location for activation but also the role of endogenous molecules in the process.
Supplementary Methods, Figures 1-7 from Development of a Multiplex Quantitative PCR Signature to Predict Progression in Non–Muscle-Invasive Bladder Cancer (2023)

Supplementary Methods, Figures 1-7 from Development of a Multiplex Quantitative PCR Signature to Predict Progression in Non–Muscle-Invasive Bladder Cancer
InSAR time series investigation of land subsidence due to groundwater overexploitation in Tehran, Iran (2008)

Land surface deformation associated with groundwater overexploitation is a serious challenge for plain aquifers of Iran, particularly in semiarid and arid region. In the Greater Tehran area, the capital of Iran with a population of 14 million people, ground-water discharge has exceeded natural recharge over the last decades, causing significant drawdown of groundwater level and land subsidence. In this study we use 46 Envisat ASAR data acquired in descending and ascending orbits between 2003 and 2007 to examine in detail the spatio-temporal pattern of land subsidence in Tehran.
Optical-Frequency Transfer over a Single-Span 1840 km Fiber Link (2013)

To compare the increasing number of optical frequency standards, highly stable optical signals have to be transferred over continental distances. We demonstrate optical-frequency transfer over a 1840-km underground optical fiber link using a single-span stabilization. The low inherent noise introduced by the fiber allows us to reach short term instabilities expressed as the modified Allan deviation of 2×10(-15) for a gate time τ of 1 s reaching 4×10(-19) in just 100 s. We find no systematic offset between the sent and transferred frequencies within the statistical uncertainty of about 3×10(-19). The spectral noise distribution of our fiber link at low Fourier frequencies leads to a τ(-2) slope in the modified Allan deviation, which is also derived theoretically.