gebhart/patrepeval huggingface dataset:
Incidence and characteristics of cancer-associated thrombosis in a racially diverse population: A population-based study. (2019)

e13088 Background: Venous thromboembolism (VTE) is a common complication in cancer patients, but contemporary data on the incidence and characteristics of cancer-associated VTE in different racial populations is limited. We sought to measure the incidence rate and characteristics of cancer-associated VTE in a racially diverse population. Methods: We performed a prospective, population–based cohort study of VTE in Oklahoma County, OK during April 1, 2012–March 31, 2014. Surveillance staff regularly visited all tertiary care and relevant outpatient facilities in the county and reviewed the text from all imaging results of chest computed tomography or magnetic resonance imaging, lung perfusion scans, and ultrasound of the extremities to identify cases of VTE. Data on patient characteristics were collected from the electronic medical record. VTE was considered cancer-associated if the patient had a history of cancer other than basal or squamous cell skin cancer. Cancer was defined as “active” if metastatic or diagnosed within 6 months prior to VTE. Associations and incidence were calculated using the chi-square test and Poisson regression, respectively. Results: Of 3,255 patients with ≥1 VTE event (deep-vein thrombosis and/or pulmonary embolism), 732 (23%) had a history of cancer, of whom 309 had active cancer. The types of cancer varied widely. The age-adjusted incidence of cancer-associated VTE was 648 per 100,000 adult population (age ≥ 18). Incidence increased with each decade of age. The racial/ethnic-specific incidence rates were as follows (each per 100,000): Whites non-hispanic (607), Blacks non-Hispanic (557), Native Americans (128), Asian/Pacific Islanders (113) and Hispanics (70). Risk factors for VTE among the 732 with cancer-associated VTE included previous VTE (19%), hospitalization (37%), surgery (33%), and central venous catheter (22%). Of those with a history of cancer ≥ 6 months previously, 32% had no other identifiable VTE risk factor. Conclusions: Cancer-associated VTE comprised about 20-25% of the total population burden of VTE. The incidence varied substantially by race/ethnicity. An appreciable proportion of those with a history of cancer ≥ 6 months previously subsequently developed VTE in the absence of other risk factors.
Informing geometric deep learning with electronic interactions to accelerate quantum chemistry (2022)

Predicting electronic energies, densities, and related chemical properties can facilitate the discovery of novel catalysts, medicines, and battery materials. However, existing machine learning techniques are challenged by the scarcity of training data when exploring unknown chemical spaces. We overcome this barrier by systematically incorporating knowledge of molecular electronic structure into deep learning. By developing a physics-inspired equivariant neural network, we introduce a method to learn molecular representations based on the electronic interactions among atomic orbitals. Our method, OrbNet-Equi, leverages efficient tight-binding simulations and learned mappings to recover high-fidelity physical quantities. OrbNet-Equi accurately models a wide spectrum of target properties while being several orders of magnitude faster than density functional theory. Despite only using training samples collected from readily available small-molecule libraries, OrbNet-Equi outperforms traditional semiempirical and machine learning-based methods on comprehensive downstream benchmarks that encompass diverse main-group chemical processes. Our method also describes interactions in challenging charge-transfer complexes and open-shell systems. We anticipate that the strategy presented here will help to expand opportunities for studies in chemistry and materials science, where the acquisition of experimental or reference training data is costly.
Panchromatic Ru(ii) sensitizers bearing single thiocyanate for high efficiency dye sensitized solar cells (2014)

We report on a new series of Ru(<sc>ii</sc>) sensitizers <bold>PRT-21–PRT-24</bold> suitable for high performance dye sensitized solar cells (DSCs).
Construction of EMSC-Islet Co-Localizing Composites for Xenogeneic Porcine Islet Transplantation (2018)

Background Pancreatic islet transplantation is an ultimate solution for treating patients with type 1 diabetes. The pig is an ideal donor of islets for replacing scarce human islets. Besides immunological hurdles, non-immunological factors including fragmentation and delayed engraftment of porcine islets need to be solved for successful porcine islet xenotransplantation. In this study, we suggest a simple but effective modality, a cell/islet co-localizing composite, to overcome these challenges. Methods Murine mesenchymal stem cells (MSCs) were prepared from bone marrow, and endothelial-like mesenchymal stem cells (EMSCs) were differentiated from MSCs with optimized culture conditions. Differing amounts of MSCs and EMCs were co-cultured with isolated porcine islet cells (1000 IEQs) to generate MSC- and EMSC-islet co-localizing composites. The composites were assessed for their magnitude of fragmentation, mass preservation, and in vitro angiogenesis potential. Results MSCs and EMCs evenly coated the surface of porcine islets (>85%) through optimized culture conditions. Both MSCs and EMSCs significantly reduced the fragmentation of porcine islets and increased the islet masses, designated as IEQs. In fibrin in vitro angiogenesis analysis, constructed EMSC-islet composites showed higher angiogenic potentials than naked islets, human endothelial cell-islet composites, and MSC-islet composites. Conclusions This novel delivery method of EMSC-porcine islet co-localizing composites may have beneficial effects on the engraftment of transplanted islets by prevention of fragmentation and enhancement of revascularization. This work was supported by a grant from the Korea Healthcare Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry for Health and Welfare, Republic of Korea (Grant No. HI13C0954).
DNA methyltransferase inhibitor 5-azacytidine in high dose promotes ultrastructural maturation of cardiomyocyte (2020)

These data suggest that treatment with 5-Aza in high dose could promote differentiation of ADSCs into cardiomyocyte-like cells. These differentiated cells could be used for regeneration of damaged cardiomyocytes with the 3D scaffold for delivery of the cells.
Metamodel-Driven Interfaces for Engineering Design: Impact of Delay and Problem Size on User Performance (2005)

In this paper, we present results from a follow-up study to our previous research involving the use of a metamodel-driven, graphical design interface for sizing the plan view layout of an aircraft wing to minimize cost subject to three constraints. This study extends our work by examining the impact of (i) varying problem size, i.e., the number of design variables (2, 4, or 6) that the user can manipulate, and (ii) a longer response delay (1.5 seconds) on user performance. Design effectiveness is measured by calculating the percent error between a submitted design and the known optimum, and design efficiency is measured by recording the completion time for solving the wing design problem. Fortyeight users participated in the study. Response delay and problem size both had a significant effect on design effectiveness: the 1.5 second delay increased average error by 150% compared to the no delay case, and the average error more than doubled each time the problem size increased. Problem size also had a significant effect on design efficiency: the average completion times for the 4 and 6 variable problems were more than double the completion time for the 2 variable problem. Average completion time also increased as the response delay increased, but this effect was not significant at the 5% level. Although the interaction between delay and problem size was not significant, the impact of the response delay on design efficiency and design effectiveness did decrease as problem size increased. Correlations between user performance and responses to preand post-test questionnaires are also discussed along with the implications of our findings for the development of metamodel-driven, graphical design interfaces.
Catalytic Oxi-Crackinng as a Route to Olefins-Efficient Mo-Li/MgO catalysts for hexane conversion (2009)

Introduction Oxidative catalytic cracking of naphtha range hydrocarbons is conceptually a promising alternative to steam cracking for the production of light olefins. Efforts in the last years to develop efficient catalysts have not shown promise; the rates and olefin selectivities achieved are insufficient for commercialization. Recent work in our laboratories shows sol-gel synthesized Li/MgO catalyst as promising catalysts for the oxidative conversion of propane to propylene [1]. In this paper we investigate oxicracking of hexane over modified Li/MgO catalysts and look at the possibility (i) to enhance hydrogen abstraction, which is the rate limiting step in oxidative conversion and (ii) to maximize propylene selectivities (as against ethylene from steam cracking)
Biochemical Discovery, Intracellular Evaluation, and Crystallographic Characterization of Synthetic and Natural Product Adenosine 3′,5′-Cyclic Monophosphate-Dependent Protein Kinase A (PKA) Inhibitors (2023)

The recent demonstration that adenosine 3',5'-cyclic monophosphate (cAMP)-dependent protein kinase A (PKA) plays an oncogenic role in a number of important cancers has led to a renaissance in drug development interest targeting this kinase. We therefore have established a suite of biochemical, cell-based, and structural biology assays for identifying and evaluating new pharmacophores for PKA inhibition. This discovery process started with a 384-well high-throughput screen of more than 200,000 substances, including fractionated natural product extracts. Identified active compounds were further prioritized in biochemical, biophysical, and cell-based assays. Priority lead compounds were assessed in detail to fully characterize several previously unrecognized PKA pharmacophores including the generation of new X-ray crystallography structures demonstrating unique interactions between PKA and bound inhibitor molecules.
Simple expressions for the maximum omnidirectional bandgap of bilayer photonic crystals (2011)

We propose three dimensionless approximate expressions to predict the thickness filling factor, gap center, and gap width of the maximum omnidirectional gap (MODG) for various refractive indices in one-dimensional photonic crystals. These expressions are simple and do not include trigonometric or inverse trigonometric functions. It is easy to obtain the MODG from given refractive indices but also to estimate the refractive indices from the MODG based on the results.
Multiple Choice Test Questions for Propagation of Errors: Scientific Computing Introduction (2003)

Take a test on Propagation of Errors: Scientific Computing Introduction. The test is based on six levels of Bloom's Taxonomy
Impact of Antimalarial Treatment and Chemoprevention on the Drug Sensitivity of Malaria Parasites Isolated from Ugandan Children (2015)

Changing treatment practices may be selecting for changes in the drug sensitivity of malaria parasites. We characterized ex vivo drug sensitivity and parasite polymorphisms associated with sensitivity in 459 Plasmodium falciparum samples obtained from subjects enrolled in two clinical trials in Tororo, Uganda, from 2010 to 2013. Sensitivities to chloroquine and monodesethylamodiaquine varied widely; sensitivities to quinine, dihydroartemisinin, lumefantrine, and piperaquine were generally good. Associations between ex vivo drug sensitivity and parasite polymorphisms included decreased chloroquine and monodesethylamodiaquine sensitivity and increased lumefantrine and piperaquine sensitivity with pfcrt 76T, as well as increased lumefantrine sensitivity with pfmdr1 86Y, Y184, and 1246Y. Over time, ex vivo sensitivity decreased for lumefantrine and piperaquine and increased for chloroquine, the prevalences of pfcrt K76 and pfmdr1 N86 and D1246 increased, and the prevalences of pfdhfr and pfdhps polymorphisms associated with antifolate resistance were unchanged. In recurrent infections, recent prior treatment with artemether-lumefantrine was associated with decreased ex vivo lumefantrine sensitivity and increased prevalence of pfcrt K76 and pfmdr1 N86, 184F, and D1246. In children assigned chemoprevention with monthly dihydroartemisinin-piperaquine with documented circulating piperaquine, breakthrough infections had increased the prevalence of pfmdr1 86Y and 1246Y compared to untreated controls. The noted impacts of therapy and chemoprevention on parasite polymorphisms remained significant in multivariate analysis correcting for calendar time. Overall, changes in parasite sensitivity were consistent with altered selective pressures due to changing treatment practices in Uganda. These changes may threaten the antimalarial treatment and preventive efficacies of artemether-lumefantrine and dihydroartemisinin-piperaquine, respectively.
Probing Co-Assembly of Supramolecular Photocatalysts and Polyelectrolytes Using Isothermal Titration Calorimetry (2017)

The creation of renewable fuels to replace dwindling fossil energy resources is one of the greatest challenges facing the scientific community. Generating H<sub>2</sub> fuel from water is a carbon-neutral strategy that demonstrates great promise. Photocatalysts of the molecular architecture [{(TL)<sub>2</sub>Ru(BL)}<sub>2</sub>RhX<sub>2</sub>]<sup>5+</sup> (BL = bridging ligand, TL = terminal ligand, X = halide) catalyze the formation of H<sub>2</sub> in deoxygenated organic solvents but are limited by poor performance in air-saturated aqueous solutions. Addition of the water-soluble polyelectrolyte poly(sodium 4-styrenesulfonate) (PSS) was recently shown as being a promising new strategy to increase efficiency and stability of H<sub>2</sub> evolving photocatalysts in air-saturated aqueous solutions. Herein we investigate intermolecular interactions between Ru,Rh,Ru photocatalysts and water-soluble polyelectrolytes using isothermal titration calorimetry (ITC). ITC studies provide insight into the thermodynamic forces that drive assembly of PSS-photocatalyst aggregates and give new evidence for the intermolecular forces that lead to increased photocatalytic efficiency.
On the Roles of the Nuclear Non-Coding RNA-Dependent Membrane-Less Organelles in the Cellular Stress Response (2023)

At the beginning of the 21st century, it became obvious that radical changes had taken place in the concept of living matter and, in particular, in the concept of the organization of intracellular space. The accumulated data testify to the essential importance of phase transitions of biopolymers (first of all, intrinsically disordered proteins and RNA) in the spatiotemporal organization of the intracellular space. Of particular interest is the stress-induced reorganization of the intracellular space. Examples of organelles formed in response to stress are nuclear A-bodies and nuclear stress bodies. The formation of these organelles is based on liquid-liquid phase separation (LLPS) of intrinsically disordered proteins (IDPs) and non-coding RNA. Despite their overlapping composition and similar mechanism of formation, these organelles have different functional activities and physical properties. In this review, we will focus our attention on these membrane-less organelles (MLOs) and describe their functions, structure, and mechanism of formation.
Azidocarbonyl‐substituted cubanoureas (1993)

Abstract Despite the angular strain associated with the assembly of small rings, 1,2‐diisocyanatocubane reacts with trimethylsilyl azide under mild conditions to form a hexacyclic ring assembly that contains an imidazolidone ring fused to one edge of cubane. This compound was identified as an azidocarbonyl‐substituted cubanourea by means of X‐ray crystal structure analysis of the nitro‐derivative, the energetic compound N ‐azidocarbonyl‐ N 1 ‐nitrocubanourea.
Animal Detector System for Forest Monitoring using OpenCV and Raspberry-pi (2023)

Abstract: The presented prototype system offers a solution for tracking animals, assets, or people using only Global System for Mobile Communications (GSM) services. The development and application of living terrain by humans have led to harm to wild creatures, making it crucial to explore animal monitoring system technology. This project utilizes a GSM modem to send SMS notifications to the designated person, allowing for real-time tracking of the target. Such a system could have great significance in protecting and preserving wildlife in the face of rapid population and financial growth
Regulation of c‐fos expression in senescing Werner syndrome fibroblasts differs from that observed in senescing fibroblasts from normal donors (1995)

The Werner syndrome (WS) is a segmental progeroid syndrome caused by a recessive mutation (WRN) mapped to 8p12. The replicative life spans of somatic cells cultured from WS patients are substantially reduced compared to age-matched controls. Certain molecular concomitants of the replicative decline of normal fibroblast cultures have recently been defined, and it appears that multiple changes in gene expression accompany normal cell senescence. If the mechanisms by which WS cells exit the cell cycle were entirely comparable, the molecular markers of senescence should be identical in normal and WS cells. We find that this is not the case. The constitutive expression of statin, a nuclear protein associated with the nonproliferating state, was comparably expressed in normal and WS senescent cells. Likewise, the steady state levels of p53, a protein known to be involved in the G1 checkpoint of the cell cycle, were similar in early-passage fibroblasts from normal and WS subjects. The levels of p53 were not increased in senescent fibroblasts, whether derived from normal or WS subjects. By contrast, the inducibility of mRNA and protein expression of the c-fos protooncogene is preserved in late-passage WS cells. This is in contrast to what is observed in late-passage fibroblasts from normal subjects. Additional genotypes will have to be examined, however, to determine the specificity of this new aspect of the WS phenotype.
Radioprotective Effects of Melatonin on Radiation-Induced Cataract (2005)

One of the mechanisms proposed to explain lens opacification is the oxidation of crystallins, either by radiation or reactive oxygen species (ROS). It has been shown that melatonin has both an anti-peroxidative effect on several tissues and a scavenger effect on ROS. The purpose of this study was to determine the antioxidant role of melatonin (5 mg/kg/day) against radiation-induced cataract in the lens after total-cranium irradiation of rats with a single dose of 5 Gy. Sprague-Dawley rats were divided into four groups. Control group received neither melatonin nor irradiation. Irradiated rats (IR) and melatonin+irradiated rats (IR+Mel) groups were exposed to total cranium irradiation of 5 Gy in a single dose by using a cobalt-60 teletherapy unit. IR+Mel and melatonin (Mel) groups were administered 5 mg/kg melatonin daily by intraperitoneal injections during ten days. Chylack's cataract classification was used in this study. At the end of the 10th day, the rats were killed and their eyes were enucleated to measure the antioxidant enzymes i.e. the activity of superoxide dismutase (SOD) and glutathione peroxidase (GSH-Px), and lipid peroxidation level (malondialdehyde (MDA)). Irradiation significantly increased the MDA level, as an end product of lipid peroxidation, and also significantly decreased SOD and GSH-Px activity, emphasizing the generation of increased oxidative stress. Rats injected with melatonin only did not cause cataract formation. Melatonin supplementation with irradiation significantly increased the activity of SOD and GSH-Px enzymes and significantly decreased the MDA level. Total cranium irradiation of 5 Gy in a single dose enhanced cataract formation, and melatonin supplementation protected the lenses from radiation-induced cataract formation. Our results suggest that supplementing cancer patients with adjuvant therapy of melatonin may reduce patients suffering from toxic therapeutic regimens such as chemotherapy and/or radiotherapy and may provide an alleviation of the symptoms due to radiation-induced organ injuries.
Effects of Disorder on Carrier Transport inCu2SnS3 (2015)

Cu${}_{2}$SnS${}_{3}$ is a promising, earth-abundant photovoltaic material, but disorder in the positions of Cu and Sn cations in its crystal lattice complicate its electronic transport. The authors find that even after substantially increasing its cation ordering via annealing, minority-carrier transport is still dominated by disorder effects, as revealed by spectroscopy plus Monte Carlo simulations. These results identify important challenges to the implementation of Cu${}_{2}$SnS${}_{3}$ in solar cells, and carry implications for other semiconductors of this type, such as Cu${}_{2}$ZnSn(S,Se)${}_{4}$ (CZTS).
A New Phase-Locked Loop System for Three-Phase Applications (2012)

This paper presents a new three-phase phase-locked loop (PLL) system that primarily estimates the phase angles, frequency, and magnitudes of the a three-phase input signal and also provides a filtered version of the input. It is then extended to the estimation of sequence components, their magnitudes, and phase angles. As compared with the conventional three-phase PLL, this method does not suffer from errors that are caused by signal unbalance and dc offset. It also provides estimate for several other variables which are not included in the conventional three-phase PLL. As compared with the method of using three independent single-phase enhanced PLLs, the proposed method offers a simpler structure. Moreover, the estimated frequency is more accurate and smoother because it uses the information from all three phases to estimate a single value for frequency. The paper also presents a modification that makes the PLL parameters independent from the input signal amplitude. The same modification is applicable to existing methods such as conventional three-phase PLL. Simulation and experimental results are presented to confirm desirable performance of the proposed method.
Catheter Ablation in Persistent AF, the Evolution towards a More Pragmatic Strategy (2021)

Atrial fibrillation (AF) is the most common cardiac arrhythmia worldwide and represents a heterogeneous disorder with a complex pathological basis. While significant technological advances have taken place over the last decade in the field of catheter ablation of AF, response to ablation varies and long-term success rates in those with persistent AF remain modest. Mechanistic studies have highlighted potentially different sustaining factors for AF in the persistent AF population with substrate-driven focal and re-entrant sources in the body of the atria identified on invasive and non-invasive mapping studies. Translation to clinical practice, however, remains challenging and the application of such mapping techniques to clinical ablation has yet to demonstrate a significant benefit beyond pulmonary vein isolation (PVI) alone in the persistent AF cohort. Recent advances in catheter and ablation technology have centered on improving the durability of ablation lesions at index procedure and although encouraging results have been demonstrated with early studies, large-scale trials are awaited. Further meaningful improvement in clinical outcomes in the persistent AF population requires ongoing advancement in the understanding of AF mechanisms, coupled with continuing progress in catheter technology capable of delivering durable transmural lesions.