gebhart/patrepeval huggingface dataset:
Recent progress of high performance polymer OLED and OPV materials for organic printed electronics (2014)

The development of organic printed electronics has been expanding to a variety of applications and is expected to bring innovations to our future life. Along with this trend, high performance organic materials with cost-efficient fabrication processes and specific features such as thin, light weight, bendable, and low power consumption are required. A variety of organic materials have been investigated in the development of this field. The basic guidelines for material design and the recent progress of polymer-based organic light-emitting diodes (OLEDs) and organic photovoltaic cells (OPVs) are reported.
ω-3 Polyunsaturated fatty acids prevent pressure overload-induced ventricular dilation and decrease in mitochondrial enzymes despite no change in adiponectin (2010)

These findings suggest ω-3 PUFA attenuates cardiac pathology in response to pressure overload independent of an elevation in adiponectin.
P0990RENINAAV DOSE-DEPENDENTLY EXACERBATE ALBUMINURIA AND GLOMERULOSCLEROSIS, AND REDUCE GFR IN FEMALE UNINEPHRECTOMIZED DB/DB MICE (2020)

Abstract Background and Aims Diabetic nephropathy (DN) is a long-term complication that occurs in ∼40% of diabetes patients and is a leading cause of end-stage renal disease. Despite recent emergence of SGLT2 inhibitors and GLP-1 receptor agonists for nephroprotection in diabetes patients, drug discovery has been halted by the lack of reliable rodent models exhibiting features of human DN. In a newly established mouse model of progressive DN, we investigate the effects of hypertension on kidney injury. Method Female db/db mice were uninephrectomized (UNx) at 8 weeks of age and injected i.v. with a Renin adeno-associated virus (AAV) construct at different doses to induce hypertension, while a LacZAAV construct was used as negative control. db/+ mice served as healthy controls. Hypertension was measured by tail cuff and glomerular filtration rate (GFR) transcutaneous recoding of FITC-sinistrin after i.v. bolus injection at 22 weeks of age. Urine ACR measured in spot urine samples collected before termination 24 weeks of age. Terminal kidney samples were collected for 3D image analyses, histopathological evaluation, and next generation sequencing for gene expression analyses. Results GFR measurements indicated hyperfiltration in all AAV-injected UNx db/db mice compared to db/+ mice, while ReninAAV tended to dose-dependently decrease GFR compared to LacZAAV in UNx db/db mice. Urine ACR was worsened by ReninAAV-induced hypertension compared to LacZAAV controls. Automized AI-based glomerulosclerosis scoring showed ReninAAV dose-dependent increases in glomerulosclerosis compared to LacZAAV controls. 3D kidney imaging demonstrated increased glomerular volume in LacZAAV UNx db/db mice compared to db/+ mice with no further effect in ReninAAV groups. RNA sequencing revealed upregulated gene expression markers of fibrogenesis (incl. Col1a1, Col3, Col4, Fn1, Lamc2 and Vim) and tubular injury markers (Ngal and Kim-1), as well as downregulation of proximal tubular markers (Megalin and Aqp1) in ReninAAV UNx db/db mice compare to LacZAAV controls. Conclusion ReninAAV-induced hypertension in female UNx db/db mice accelerates kidney injury in uninephrectomized db/db mice and aggravates GFR, albuminuria and glomerulosclerosis in parallel with increased expression of genes associated with tubular injury renal fibrosis. Together, these data confirm that ReninAAV UNx db/db mice is a reliable model of DN with features of late stage human disease.
Theory of Borazine-Derived Nanothreads: Enumeration, Reaction Pathways, and Piezoelectricity (2022)

Nanothreads are one-dimensional macromolecules formed by pressure-induced polymerization along stacks of multiply unsaturated (or highly strained) molecules such as benzene (or cubane). Borazine is isoelectronic to benzene yet with substantial bond polarity, thus motivating a theoretical examination of borazine-derived nanothreads with degrees of saturation of 2, 4, and 6 (defined as the number of four-coordinated boron and nitrogen atoms per borazine formula unit). The energy increases upon going from molecular borazine to degree-2 borazine-derived threads and then decreases for degree-4 and degree-6 nanothreads as more σ bonds are formed. With the constraint of no more than two borazine formula units within the repeat unit of the framework's bonding topology, there are only 13 fully saturated (i.e., degree-6) borazine-derived nanothreads that avoid energetically costly homopolar bonds (as compared to more than 50 such candidates for benzene-derived threads). Only two of these are more stable than borazine. Hypothetical pathways from molecular borazine to these two degree-6 borazine-derived nanothreads are discussed. This relative paucity of outcomes may assist in kinetic control of reaction products. Beyond the high mechanical strength also predicted for carbon-based threads, properties such as piezoelectricity and flexoelectricity may be accessible to the polar lattice of borazine-derived nanothreads, with intriguing prospects for expression in these extremely thin yet rigid objects.
Walking in Facebook: A Case Study of Unbiased Sampling of OSNs (2010)

With more than 250 million active users, Facebook (FB) is currently one of the most important online social networks. Our goal in this paper is to obtain a representative (unbiased) sample of Facebook users by crawling its social graph. In this quest, we consider and implement several candidate techniques. Two approaches that are found to perform well are the Metropolis-Hasting random walk (MHRW) and a re-weighted random walk (RWRW). Both have pros and cons, which we demonstrate through a comparison to each other as well as to the "ground-truth" (UNI - obtained through true uniform sampling of FB userIDs). In contrast, the traditional Breadth-First-Search (BFS) and Random Walk (RW) perform quite poorly, producing substantially biased results. In addition to offline performance assessment, we introduce online formal convergence diagnostics to assess sample quality during the data collection process. We show how these can be used to effectively determine when a random walk sample is of adequate size and quality for subsequent use (i.e., when it is safe to cease sampling). Using these methods, we collect the first, to the best of our knowledge, unbiased sample of Facebook. Finally, we use one of our representative datasets, collected through MHRW, to characterize several key properties of Facebook.
Inflammatory Effects of Highly Pathogenic H5N1 Influenza Virus Infection in the CNS of Mice (2012)

The A/VN/1203/04 strain of the H5N1 influenza virus is capable of infecting the CNS of mice and inducing a number of neurodegenerative pathologies. Here, we examined the effects of H5N1 on several pathological aspects affected in parkinsonism, including loss of the phenotype of dopaminergic neurons located in the substantia nigra pars compacta (SNpc), expression of monoamines and indolamines in brain, alterations in SNpc microglia number and morphology, and expression of cytokines, chemokines, and growth factors. We find that H5N1 induces a transient loss of the dopaminergic phenotype in SNpc and now report that this loss recovers by 90 d after infection. A similar pattern of loss and recovery was seen in monoamine levels of the basal ganglia. The inflammatory response in lung and different regions of the brain known to be targets of the H5N1 virus (brainstem, substantia nigra, striatum, and cortex) were examined at 3, 10, 21, 60, and 90 d after infection. In each of these brain regions, we found a significant increase in the number of activated microglia that lasted at least 90 d. We also quantified expression of IL-1α, IL-1β, IL-2, IL-6, IL-9, IL-10, IL-12(p70), IL-13, TNF-α, IFN-γ, granulocyte-macrophage colony-stimulating factor, granulocyte colony-stimulating factor, macrophage colony-stimulating factor, eotaxin, interferon-inducible protein 10, cytokine-induced neutrophil chemoattractant, monocyte chemotactic protein-1, macrophage inflammatory protein (MIP) 1α, MIP-1β, and VEGF, and found that the pattern and levels of expression are dependent on both brain region and time after infection. We conclude that H5N1 infection in mice induces a long-lasting inflammatory response in brain and may play a contributing factor in the development of pathologies in neurodegenerative disorders.
A 0.1-$\mu{\hbox {m}}$ 1.8-V 256-Mb Phase-Change Random Access Memory (PRAM) With 66-MHz Synchronous Burst-Read Operation (2007)

A 256-Mb phase-change random access memory has been developed, featuring 66-MHz synchronous burst-read operation. Using a charge pump system, write performance was characterized at a low supply voltage of 1.8 V. Measured initial read access time and burst-read access time are 62 and 10 ns, respectively. The write throughput was 0.5 MB/s with internal times2 write and can be increased to ~2.67 MB/s with times16 write. Endurance and retention characteristics are measured to be 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">7</sup> cycles and ten years at 99 degC
A long-term mechanistic computational model of physiological factors driving the onset of type 2 diabetes in an individual (2018)

A computational model of the physiological mechanisms driving an individual's health towards onset of type 2 diabetes (T2D) is described, calibrated and validated using data from the Diabetes Prevention Program (DPP). The objective of this model is to quantify the factors that can be used for prevention of T2D. The model is energy and mass balanced and continuously simulates trajectories of variables including body weight components, fasting plasma glucose, insulin, and glycosylated hemoglobin among others on the time-scale of years. Modeled mechanisms include dynamic representations of intracellular insulin resistance, pancreatic beta-cell insulin production, oxidation of macronutrients, ketogenesis, effects of inflammation and reactive oxygen species, and conversion between stored and activated metabolic species, with body-weight connected to mass and energy balance. The model was calibrated to 331 placebo and 315 lifestyle-intervention DPP subjects, and one year forecasts of all individuals were generated. Predicted population mean errors were less than or of the same magnitude as clinical measurement error; mean forecast errors for weight and HbA1c were ~5%, supporting predictive capabilities of the model. Validation of lifestyle-intervention prediction is demonstrated by synthetically imposing diet and physical activity changes on DPP placebo subjects. Using subject level parameters, comparisons were made between exogenous and endogenous characteristics of subjects who progressed toward T2D (HbA1c > 6.5) over the course of the DPP study to those who did not. The comparison revealed significant differences in diets and pancreatic sensitivity to hyperglycemia but not in propensity to develop insulin resistance. A computational experiment was performed to explore relative contributions of exogenous versus endogenous factors between these groups. Translational uses to applications in public health and personalized healthcare are discussed.
Why Single-Beam Optical Tweezers Trap Gold Nanowires in Three Dimensions (2013)

Understanding whether noble-metal nanostructures can be trapped optically and under what conditions will enable a range of applications that exploit their plasmonic properties. However, there are several nontrivial issues that first need to be resolved. A major one is that metal particles experience strong radiation pressure in optical beams, while stable optical trapping requires an attractive force greater than this radiation pressure. Therefore, it has generally been considered impossible to obtain sufficiently strong gradient forces using single-beam optical tweezers to trap relatively large metal nanostructures in three dimensions. Here we demonstrate that a single, tightly focused laser beam with a wavelength of 800 nm can achieve three-dimensional optical trapping of individual gold (Au) nanowires with lengths over 2 μm. Nanowires can be trapped by the beam at one of their ends, in which case they undergo significant angular fluctuations due to Brownian motion of the untrapped end. They can also be trapped close to their midpoints, in which case they are oriented approximately perpendicular to the light polarization direction. The behavior is markedly different from that of Ag nanowires with similar length and diameter, which cannot be trapped in three dimensions by a single focused Gaussian beam. Our results, including electrodynamics simulations that help to explain our experimental findings, suggest that the conventional wisdom, which holds that larger metal particles cannot be trapped, needs to be replaced with an understanding based on the details of plasmon resonances in the particles.
Trends, Distribution, and Impact of Pediatric Messages in a Large Health System From 2019 to 2021 (2023)

This cohort study assesses changes in the volume of medical advice messages between 2019 and 2021, variation among pediatricians, and the association of volume with time spent working on the electronic health record outside clinical hours.
Sodium Phenylbutyrate Rescues Thyroid Hormone Transport in Brain Endothelial-Like Cells (2022)

<b><i>Background:</i></b> Monocarboxylate transporter 8 (MCT8) deficiency is a rare genetic disease leading to a severe developmental delay due to a lack of thyroid hormones (THs) during critical stages of human brain development. Some MCT8-deficient patients are not as severely affected as others. Previously, we hypothesized that these patients' mutations do not affect the functionality but destabilize the MCT8 protein, leading to a diminished number of functional MCT8 molecules at the cell surface. <b><i>Methods:</i></b> We have already demonstrated that the chemical chaperone sodium phenylbutyrate (NaPB) rescues the function of these mutants by stabilizing their protein expression in an overexpressing cell system. Here, we expanded our previous work and used iPSC (induced pluripotent stem cell)-derived brain microvascular endothelial-like cells (iBMECs) as a physiologically relevant cell model of human origin to test for NaPB responsiveness. The effects on mutant MCT8 expression and function were tested by Western blotting and radioactive uptake assays. <b><i>Results:</i></b> We found that NaPB rescues decreased mutant MCT8 expression and restores transport function in iBMECs carrying patient's mutation MCT8-P321L. Further, we identified MCT10 as an alternative TH transporter in iBMECs that contributes to triiodothyronine uptake, the biological active TH. Our results indicate an upregulation of MCT10 after NaPB treatment. In addition, we detected an increase in thyroxine (T4) uptake after NaPB treatment that was not mediated by rescued MCT8 but an unidentified T4 transporter. <b><i>Conclusions:</i></b> We demonstrate that NaPB is suitable to stabilize a pathogenic missense mutation in a human-derived cell model. Further, it activates TH transport independent of MCT8. Both options fuel future studies to investigate repurposing the Food and Drug Administration-approved drug NaPB in selected cases of MCT8 deficiency.
Multivariate Residualization in Medical Imaging Analysis (2023)

Nuisance variables in medical imaging research are common, complicating association and prediction studies based on image data. Medical image data are typically high dimensional, often consisting of many highly correlated features. As a result, computationally efficient and robust methods to address nuisance variables are difficult to implement. By-region univariate residualization is commonly used to remove the influence of nuisance variables, as are various extensions. However, these methods neglect multivariate properties and may fail to fully remove influence related to the joint distribution of these regions. Some methods, such as functional regression and others, do consider multivariate properties when controlling for nuisance variables. However, the utility of these methods is limited for data with many image regions due to computational and model complexity. We develop a multivariate residualization method to estimate the association between the image and nuisance variable using a machine learning algorithm and then compute the orthogonal projection of each subject's image data onto this space. We illustrate this method's performance in a set of simulation studies and apply it to data from the Alzheimer's Disease Neuroimaging Initiative (ADNI).
Oil fields, hedge funds, and drugs (2009)

Statistical analysis is a fundamental method in analysis, design, and optimization of large systems with uncertainties. It is being applied in drug development, analyzing financial markets, search for new oil fields, and many more areas. As the silicon process technology scales to its limits, uncertainty plays an increasing role and has made its way into tools such as yield analysis, statistical time analysis, etc. In this educational panel, we will start with a short tutorial on Monte Carlo methods including their use in EDA. Three experts from distinct application fields will then follow and discuss their experience in using Monte Carlo methods for solving large-scale problems in their domain. It may come as a surprise to some attendees of DAC to learn how much commonality there is between methods used in EDA and other field that seem far-fetched.
<title>Progress on 300-mm wafer lithography equipment and processes</title> (2001)

SEMICONDUCTOR300 was the first pilot-production facility for 300mm wafers in the world. The company, a joint venture between Motorola, Inc. and Infineon Technologies started in early 1998 to test and compare process, metrology and probe equipment, develop robust processes, and manufacture products using a 300mm wafer tool set. The lithography tools included I-line steppers, an I-line scanner, a DUV stepper, and DUV scanners. All of these exposure tools were running in-line with various photoresist coat and develop tracks. The lithography tools were used to build both 64M and 256M DRAM devices and aggressive test vehicles. The process capability of the initial 0.25 micrometers reference process was done and compared to the 200mm data set of the sister factory. Automation issues for lithography tools were addressed and the cost metrics were calculated. SC300 demonstrated that a manufacturable 300mm lithography tool set and process for various ground rule devices was possible with the required performance in image transfer, CD control, and overlay. Further testing on 0.18micrometers and 0.15micrometers ground rule features indicated a sufficient process window for potential manufacturing. Additionally, it was demonstrated that non-concentric subfield stepping was feasible.
Left Ventricular Assist Device Implantation in Patients with Preoperative Severe Mitral Regurgitation (2021)

We examined cardiac features associated with residual mitral regurgitation (MR) following continuous-flow left ventricular assist device (cfLVAD) implant. From 2003 to 2017, 134 patients with severe MR underwent cfVLAD implant without mitral valve (MV) intervention. Echocardiographic (echo) assessment occurred pre-cfLVAD, early post-cfLVAD, and at last available echo. Ventricular and atrial volumes were calculated from established formulas and normalized to be predicted. Cluster analysis based on preoperative normalized left ventricular and atrial volumes, and MV height identified grades 1, 2, and 3 with progressively larger cardiac chamber sizes. Median early echo follow-up was 0.92 (0.55, 1.45) months and the last follow-up was 15.12 (5.28, 38.28) months. Mitral regurgitation improved early after cfLVAD by 2.10 ± 1.16 grades (p < 0.01). Mitral regurgitation severity at the last echocardiogram positively correlated with the preoperative left ventricular volume (p = 0.014, R = 0.212), left atrial volume (p = 0.007, R = 0.233), MV anteroposterior height (p = 0.032, R = 0.185), and MV mediolateral diameter (p = 0.043, R = 0.175). Morphologically, smaller grade 1 hearts were correlated with MR resolution at the late follow-up (p = 0.023). Late right ventricular failure (RVF) at the last clinical follow-up was less in grade 1 (4/48 [8.3%]) compared with grades 2 and 3 (26/86 [30.2%]), p = 0.004). Grade 1 cardiac dimensions correlates with improvement in severe MR and had less late RVF.
Rejuvenation by Partial Reprogramming of the Epigenome (2017)

Epigenetic variation with age is one of the most important hallmarks of aging. Resetting or repairing the epigenome of aging cells in intact animals may rejuvenate the cells and perhaps the entire organism. In fact, differentiated adult cells, which by definition have undergone some epigenetic changes, are capable of being rejuvenated and reprogrammed to create pluripotent stem cells and viable cloned animals. Apparently, such reprogramming is capable of completely resetting the epigenome. However, attempts to fully reprogram differentiated cells in adult animals have failed in part because reprogramming leads to the formation of teratomas. A preliminary method to partially reprogram adult cells in mature Hutchinson-Gilford Progeria Syndrome (HGPS) mice by transient induction of the Yamanaka factors OSKM (Oct4/Sox2/Klf4/c-Myc) appears to ameliorate aging-like phenotypes in HGPS mice, and promote youthful regenerative capability in middle-aged wild-type individuals exposed to beta cell and muscle cell-specific toxins. However, whatever epigenetic repair is induced by transient reprogramming does not endure and may be due to the induction of key homeostatic regulators instead. Some of the effect of transient reprogramming may result from increased proliferation and enhanced function of adult stem cells. Partial reprogramming may point the way to new antiaging and proregenerative therapeutics. Redifferentiation of cells into their preexisting phenotype with simultaneous epigenomic rejuvenation is an interesting variation that also should be pursued. However, discovery of methods to more precisely repair the epigenome is the most likely avenue to the development of powerful new antiaging agents.
De novo chromosome-length assembly of the mule deer ( Odocoileus hemionus ) genome (2021)

ABSTRACT The mule deer ( Odocoileus hemionus ) is an ungulate species that ranges from western Canada to central Mexico. Mule deer are an essential source of food for many predators, are relatively abundant, and commonly make broad migration movements. A clearer understanding of the mule deer genome can help facilitate knowledge of its population genetics, movements, and demographic history, aiding in conservation efforts. While mule deer are excellent candidates for population genomic studies because of their large population size, continuous distribution, and diversity of habitat, few genomic resources are currently available for this species. Here, we sequence and assemble the mule deer genome into a highly contiguous chromosome-length assembly for use in future research using long-read sequencing and Hi-C. We also provide a genome annotation and compare demographic histories of the mule deer and white-tail deer using PSMC. We expect this assembly to be a valuable resource in the continued study and conservation of mule deer.