gebhart/patrepeval huggingface dataset:
Synthesis and Assembly of Dipolar Heterostructured Tetrapods: Colloidal Polymers with “Giant tert‐butyl” Groups (2015)

Abstract We report on the first synthesis of a heterostructured semiconductor tetrapod from CdSe@CdS that carries a single dipolar nanoparticle tip from a core–shell colloid of Au@Co. A four‐step colloidal total synthesis was developed, where the key step in the synthesis was the selective deposition of a single AuNP tip onto a CdSe@CdS tetrapod under UV‐irradiation. Synthetic accessibility to this dipolar heterostructured tetrapod enabled the use of these as colloidal monomers to form colloidal polymers that carry the semiconductor tetrapod as a side chain group attached to the CoNP colloidal polymer main chain. The current report details a number of novel discoveries on the selective synthesis of an asymmetric heterostructured tetrapod that is capable of 1D dipolar assembly into colloidal polymers that carry tetrapods as side chain groups that mimic “giant tert ‐butyl groups”.
819 White Matter Activation Pathways in STN and GPi DBS for Parkinson’s Disease (2022)

INTRODUCTION: The subthalamic nucleus (STN) and globus pallidus interna (GPi) are common deep brain stimulation (DBS) targets for Parkinson’s disease (PD). DBS is thought to function by modulating downstream circuits, yet targeting is based on anatomy rather than structural connectivity. While tractography using normative connectomes has been used to study the impact of the hyperdirect pathway, cortical connectivity patterns only account for 20% of the variance in DBS response. Less is known about subcortical and cerebellar connectivity, and patient-specific tractography in DBS for PD. METHODS: Preoperative T1-weighted and diffusion-weighted MRI, postoperative CT, and clinical data were acquired for 49 patients (24 STN, 25 GPi) who underwent DBS for PD. After initial programming, the Lead DBS toolbox was used to model VAT based on the individual subject electrode and stimulation parameters. Whole-brain probabilistic tractography was performed from VAT using FSL (FMRIB's Software Library) to estimate activation pathways. Average activation pathways were generated for each target by weighting each subject’s pathways by unilateral MDS-UPDRS-III response to stimulation at initial programming. Comparison tractography was performed using 85-subject PD normative connectome. RESULTS: Analysis of weighted activation pathways reveals that STN-DBS strongly activates pathways to the caudate nucleus and bilateral cerebellum. In contrast, GPi-DBS activates pathways to the putamen and the ansa lenticularis. Furthermore, normative connectome tractography shows that the subcortical and cerebellar structural connectivity is not as well appreciated. Lastly,cortical pathways show that GPi DBS has increased premotor connectivity while STN DBS has robust motor connectivity, and confining the seeds to the STN and GPi does not diminish cortical connectivity. CONCLUSIONS: Activation pathways from STN and GPi therapeutic contacts have unique subcortical and cerebellar connectivity. White matter connections within the basal ganglia and cerebellum, including ansa lenticularis and regions associated with the DRTT, are connected to the therapeutic contacts, and this connectivity is not as well appreciated using normative connectome data. Activation pathways via the internal capsule alone cannot explain cortical connectivity. Further research to test the utility of defined connections using patient-specific tractography may help better predict DBS response or prospectively inform targeting.
So-Cheong-Ryong-Tang induces apoptosis through activation of the intrinsic and extrinsic apoptosis pathways, and inhibition of the PI3K/Akt signaling pathway in non-small-cell lung cancer A549 cells (2015)

These findings suggest that SCRT may play its anti-cancer actions partly through a suppression of the PI3K/Akt signal pathway in A549 cells, and further in vivo studies on the potential of SCRT for prevention and therapy of NSCLCs are warranted.
Predictors of Activity Limitation and Dependence on Walking Aids After Primary Total Hip Arthroplasty (2010)

Higher BMI, depression, older age, and female sex predict activity limitation and complete dependence on walking aids 2 and 5 years after primary THA.
Endophilin A1 induces different membrane shapes using a conformational switch that is regulated by phosphorylation (2014)

Membrane remodeling is controlled by proteins that can promote the formation of highly curved spherical or cylindrical membranes. How a protein induces these different types of membrane curvature and how cells regulate this process is still unclear. Endophilin A1 is a protein involved in generating endocytotic necks and vesicles during synaptic endocytosis and can transform large vesicles into lipid tubes or small and highly curved vesicles in vitro. By using EM and electron paramagnetic resonance of endophilin A1, we find that tubes are formed by a close interaction with endophilin A1's BIN/amphiphysin/Rvs (BAR) domain and deep insertion of its amphipathic helices. In contrast, vesicles are predominantly stabilized by the shallow insertion of the amphipathic helical wedges with the BAR domain removed from the membrane. By showing that the mechanism of membrane curvature induction is different for vesiculation and tubulation, these data also explain why previous studies arrived at different conclusions with respect to the importance of scaffolding and wedging in the membrane curvature generation of BAR proteins. The Parkinson disease-associated kinase LRRK2 phosphorylates S75 of endophilin A1, a position located in the acyl chain region on tubes and the aqueous environment on vesicles. We find that the phosphomimetic mutation S75D favors vesicle formation by inhibiting this conformational switch, acting to regulate endophilin A1-mediated curvature. As endophilin A1 is part of a protein superfamily, we expect these mechanisms and their regulation by posttranslational modifications to be a general means for controlling different types of membrane curvature in a wide range of processes in vivo.
Gasification of metal-containing coals and carbons via their reaction with carbon dioxide (2018)

The effect of the nature of the metals (Cu, Ni, and Fe) deposited on carbon materials (coals) and the methods of preparation (conventional and microwave heating) of the most active Fe/C samples on their efficiency in the reaction of CO2-assisted conversion of coal into carbon monoxide is estimated.
Paralogous Regulators ArsR1 and ArsR2 of Pseudomonas putida KT2440 as a Basis for Arsenic Biosensor Development (2016)

Arsenic is at the top of the priority list of hazardous compounds issued by the U.S. Agency for Toxic Substances and Disease. The reason for the stunning arsenic resistance of many microorganisms is the existence of paralogous arsenic resistance operons. Pseudomonas putida KT2440 is a model organism for such bacteria, and their duplicated ars operons and in particular their ArsR transcription regulators have been studied in depth by in vivo approaches. Here we present an analysis of both purified ArsR paralogues by different biophysical techniques, and data obtained provide valuable insight into their structure and function. Particularly insightful was the comparison of ArsR effector profiles determined by in vitro and in vivo experimentation. We also report the use of both paralogues to construct robust and highly sensitive arsenic biosensors. Our finding that the deletion of both arsenic efflux pumps significantly increases biosensor sensitivity is of general relevance in the biosensor field.
Mg Anode Corrosion in Aqueous Electrolytes and Implications for Mg-Air Batteries (2016)

Aqueous Mg-air primary batteries possess many favorable attributes for energy storage because Mg is affordable, abundant, and lightweight. However, parasitic corrosion of Mg in aqueous electrolytes generates H2 and surprisingly increases with increasing current density during battery discharge (Mg oxidation), limiting the faradaic efficiency of aqueous Mg batteries. In this study, differential electrochemical mass spectrometry and H2 pressure rise measurements were used to characterize Mg corrosion in Mg-air batteries employing aqueous electrolytes with salts (NaCl, NaNO3, NaPO4, and a NaCl/NaPO4 mixture) that provide various degrees of Mg passivation. H2 evolution rates were highest in NaCl electrolytes and lowest in NaNO3 electrolytes. However, NaNO3 salts reduced the H2-evolving corrosion rate at the expense of introducing a nitrate to nitrite corrosion reaction into the battery. The combined Mg corrosion rate in the nitrate-based electrolyte was still lowest among those electrolytes studied. The nitrate to nitrite corrosion reaction also lowered the magnitude of the Mg anodic potential and therefore decreased the overall Mg-O2 battery voltage compared to the NaCl electrolyte. Nevertheless, Mg-O2 batteries utilizing a NaNO3 electrolyte allowed for 60% larger discharge capacity and 50% higher Mg oxidation faradaic efficiency compared to a NaCl electrolyte.
Autoantibody landscape of advanced prostate cancer (2020)

Abstract Although the importance of T-cell immune responses is well appreciated in cancer, autoantibody responses are less well-characterized. Nevertheless, autoantibody responses are of great interest, as they may be concordant with T-cell responses to cancer antigens or predictive of response to cancer immunotherapies. We performed serum epitope repertoire analysis (SERA) on a total of 1,229 serum samples obtained from a cohort of 72 men with metastatic castration-resistant prostate cancer (mCRPC) and 1,157 healthy control patients to characterize the autoantibody landscape of mCRPC. Using whole-genome sequencing results from paired solid-tumor metastasis biopsies and germline specimens, we identified tumor-specific epitopes in 29 mutant and 11 non-mutant proteins. Autoantibody enrichments for the top candidate autoantigen (NY-ESO-1) were validated using ELISA performed on the prostate cancer cohort and an independent cohort of 106 patients with melanoma. Our study recovers antigens of known importance and identifies novel tumor-specific epitopes of translational interest in advanced prostate cancer. Statement of significance Autoantibodies have been shown to inform treatment response and candidate drug targets in various cancers. We present the first large-scale profiling of autoantibodies in advanced prostate cancer, utilizing a new next-generation sequencing-based approach to antibody profiling to reveal novel cancer-specific antigens and epitopes. Disclosure of Potential Conflicts of Interest JJA reports receiving consulting income from Janssen Biotech and Merck and honoraria from Astellas for speaker’s fees. MR reports receiving commercial research support from Novartis, Johnson &amp; Johnson, Merck, Astellas, and Medivation, and is a consultant/advisory board member for Constellation Pharmaceuticals, Amgen, Ambrx, Johnson &amp; Johnson, and Bayer. A.R. has received honoraria from consulting with Amgen, Bristol-Myers Squibb, Chugai, Dynavax, Genentech, Merck, Nektar, Novartis, Roche and Sanofi, is or has been a member of the scientific advisory board and holds stock in Advaxis, Arcus Biosciences, Bioncotech Therapeutics, Compugen, CytomX, Five Prime, RAPT, ImaginAb, Isoplexis, Kite-Gilead, Lutris Pharma, Merus, PACT Pharma, Rgenix and Tango Therapeutics. FYF serves on the advisory board for Dendreon, EMD Serono, Janssen Oncology, Ferring, Sanofi, Blue Earth Diagnostics, Celgene, consults for Bayer, Medivation/Astellas, Genetech, and Nutcracker Therapeutics, has honoraria from Clovis Oncology, and is a founder and has an ownership stake in PFS Genomics. SGZ and FYF have patent applications with Decipher Biosciences. SGZ and FYF have a patent application licensed to PFS Genomics. SGZ and FYF have patent applications with Celgene. WAH, RW, KK, PSD, and JCS have ownership of stocks or shares at Serimmune, paid employment at Serimmune, board membership at Serimmune, and patent applications on behalf of Serimmune.
Clinical validation of Whole Genome Sequencing for cancer diagnostics (2020)

Abstract Whole genome sequencing (WGS) using fresh frozen tissue and matched blood samples from cancer patients is becoming in reach as the most complete genetic tumor test. With a trend towards the availability of small biopsies and the need to screen an increasing number of (complex) biomarkers, the use of a single all-inclusive test is preferred over multiple consecutive assays. To meet high-quality diagnostics standards, we optimized and clinically validated WGS sample and data processing procedures resulting in a technical success rate of 95.6% for fresh-frozen samples with sufficient (≥20%) tumor content. Independent validation of identified biomarkers against commonly used diagnostic assays showed a high sensitivity (recall) (98.5%) and precision (positive predictive value) (97.8%) for detection of somatic SNV and indels (across 22 genes), and high concordance for detection of gene amplification (97.0%, EGRF and MET ) as well as somatic complete loss (100%, CDKN2A /p16). Gene fusion analysis showed a concordance of 91.3% between DNA-based WGS and an orthogonal RNA-based gene fusion assay. Microsatellite (in)stability assessment showed a sensitivity of 100% with a precision of 94%, and virus detection (HPV) an accuracy of 100% compared to standard testing. In conclusion, whole genome sequencing has a &gt;95% sensitivity and precision compared to routinely used DNA techniques in diagnostics and all relevant mutation types can be detected reliably in a single assay.
Decreased expression and promoter methylation of the menin tumor suppressor in pancreatic ductal adenocarcinoma (2009)

Loss of menin, a tumor suppressor coded by the MEN1 gene, is a key factor in the pathogenesis of multiple endocrine neoplasia type I and in a percentage of sporadic endocrine tumors of the pancreas and parathyroid glands. This study investigated expression of the menin protein in the normal exocrine pancreas and in pancreatic ductal adenocarcinoma (PDAC), the most common pancreatic tumor. Immunofluorescence (IF) analyses showed that menin is expressed at high levels in normal acinar and duct cells. Examination of 24 clinical samples of PDAC revealed a pronounced decrease in menin expression in all tumors examined. To identify alterations underlying this defect, we searched for disruption and epigenetic silencing of the MEN1 gene. Analysis of nine laser-microdissected tumors revealed loss of heterozygosity of intragenic (one tumor) or adjacent (three tumors) MEN1 microsatellite markers. Methylation of CpG sites in the MEN1 promoter was documented in five of 24 tumors. IF analyses also revealed low to undetectable menin expression in the PDAC cell lines MiaPaCa-2 and Panc-1. Ectopic expression of menin in these cells resulted in a marked alteration of the cell cycle, with an increase in the G1/S+G2 ratio. These findings represent the first evidence that the MEN1 gene is a target of mutation and methylation in PDAC and that menin influences the cell cycle profile of duct cells.
Measurements of Higgs boson properties in the diphoton decay channel with 36  fb−1 of pp collision data at s=13  TeV with the ATLAS detector (2018)

Properties of the Higgs boson are measured in the two-photon final state using 36.1 fb -1 of protonproton collision data recorded at ffiffi ffi s p 13 TeV by the ATLAS experiment at the Large Hadron Collider.
A Regional Slocum Glider Network in the Mid-Atlantic Bight Leverages Broad Community Engagement (2010)

Abstract Autonomous underwater gliders have proven to be a cost-effective technology for measuring the 3-D ocean and now represent a critical component during the design and implementation of the Mid-Atlantic Regional Ocean Observing System (MARCOOS), a Region of the U.S. Integrated Ocean Observing System. The gliders have been conducting regional surveys of the Mid-Atlantic (MA) Bight, and during the 3 years of MARCOOS, the glider fleet has conducted 22 missions spanning 10,867 km and collecting 62,824 vertical profiles of data. In addition to collecting regional data, the gliders have facilitated collaboration for partners outside of MARCOOS. The existence of the MA glider observatory provided a unique test bed for cyber-infrastructure tools being developed as part of the National Science Foundation’s Ocean Observatory Initiative. This effort allowed the Ocean Observatory Initiative software to integrate the MARCOOS assets and provided a successful demonstration of an ocean sensor net. The hands-on experience of the MA glider technicians supported training and provided assistance of collaborators within the Caribbean Regional Association, also a region of the U.S. Integrated Ocean Observing System, to assess the efficacy of gliders to resolve internal waves. Finally, the glider fleet has enabled sensor development and testing in a cost-effective manner. Generally, new sensors were tested within the MARCOOS domain before they were deployed in more extreme locations throughout the world’s oceans. On the basis of this experience, the goal of the MARCOOS glider team will be to expand the MA network in coming years. The potential of how an expanded network of gliders might serve national needs was illustrated during the 2010 Macondo Gulf of Mexico oil spill, where gliders from many institutions collected subsurface mesoscale data to support regional models and oil response planning. The experience gained over the last 5 years suggests that it is time to develop a national glider network.
LATERAL COLLATERAL LIGAMENT REPAIR OF THE ELBOW USING TRANSOSSEOUS SUTURES RESTORES JOINT KINEMATICS AND STABILITY (2009)

This in-vitro study evaluated the influence of ligament tensioning and the effectiveness of lateral collateral ligament (LCL) repair using transosseous sutures on the initial kinematics and stability of the elbow. Six fresh upper-extremities were mounted in a motion simulator with tracking system, which enabled both passive and simulated active elbow flexion. The intact elbow was tested then the LCL was sectioned from its humeral origin and repaired with a transosseous suture technique. Locking sutures were placed in the LCL and passed through a humeral bone tunnel entering at the centre of curvature of the capitellum with exit holes in the lateral epicondyle. An actuator pulled on the sutures to achieve 20, 40 and 60 N of LCL repair tension and the sutures were then secured. The dependent variable of this study was the motion pathways of the ulna relative to the humerus. The data were analyzed using a two-way, repeated-measures ANOVA with relevant post-hoc paired t-tests. With the arm oriented in the horizontal position under varus gravity loading, the repairs tracked in greater valgus than the intact LCL regardless of the repair tension. The larger the initial repair tension, the more the elbows tracked in valgus. Initial tension of 60 N was statistically different than the intact LCL with the forearm in pronation (p=0.04). Both the 40 and 60 N initial tensions were statistically different than the intact LCL with the forearm in supination (p Repair of the LCL using transosseous sutures effectively restores the varus stability of the elbow. The initial tension of LCL repairs affects the kinematics of the elbow, with a tendency to over-tighten the ligament and pull the elbow into valgus. These data suggest that acute repair of the LCL should be performed using a transosseous suture technique, and that a tension of 20N or perhaps less is sufficient to restore stability.
Project RAMA: Reconstructing Asteroids Into Mechanical Automata (2017)

Many interesting ideas have been conceived for building space-based infrastructure in cislunar space. From O'Neill's space colonies, to solar power satellite farms, and even prospecting retrieved near earth asteroids. In all the scenarios, one thing remained fixed - the need for space resources at the outpost. To satisfy this need, O'Neill suggested an electromagnetic railgun to deliver resources from the lunar surface, while NASA's Asteroid Redirect Mission called for a solar electric tug to deliver asteroid materials from interplanetary space. At Made In Space, we propose an entirely new concept. One which is scalable, cost effective, and ensures that the abundant material wealth of the inner solar system becomes readily available to humankind in a nearly automated fashion. We propose the RAMA architecture, which turns asteroids into self-contained spacecraft capable of moving themselves back to cislunar space. The RAMA architecture is just as capable of transporting conventional-sized asteroids on the 10-meter length scale as transporting asteroids 100 meters or larger, making it the most versatile asteroid retrieval architecture in terms of retrieved-mass capability. This report describes the results of the Phase I study funded by the NASA NIAC program for Made In Space to establish the concept feasibility of using space manufacturing to convert asteroids into autonomous, mechanical spacecraft. Project RAMA, Reconstituting Asteroids into Mechanical Automata, is designed to leverage the future advances of additive manufacturing (AM), in-situ resource utilization (ISRU) and in-situ manufacturing (ISM) to realize enormous efficiencies in repeated asteroid redirect missions. A team of engineers at Made In Space performed the study work with consultation from the asteroid mining industry, academia, and NASA. Previous studies for asteroid retrieval have been constrained to studying only asteroids that are both large enough to be discovered, and small enough to be captured and transported using Earth-launched propulsion technology. Project RAMA is not forced into this constraint. The mission concept studied involved transporting a much larger approximately 50-meter asteroid to cislunar space. Demonstration of transport of a 50-meter-class asteroid has several ground-breaking advantages. First, the returned material is of an industrial, rather than just scientific, quantity (greater than 10,000 tonnes versus approximately10s of tonnes). Second, the useless material in the asteroid is gathered and expended as part of the asteroid's propulsion system, allowing the returned asteroid to be considerably purer than a conventional asteroid retrieval mission. Third, the infrastructure used to convert and return the asteroid is reusable, and capable of continually returning asteroids to cislunar space.
Molecular imaging of hemoglobin using ground state recovery pump-probe optical coherence tomography (2007)

We have undertaken an effort to further develop ground state recovery Pump-Probe Optical Coherence Tomograpy (gsrPPOCT) to specifically target and measure 3-D images of hemoglobin concentration with the goals of mapping tissue vasculature, total hemoglobin, and hemoglobin oxygen saturation. As a first step toward those goals we have measured the gsrPPOCT signal from the hemoglobin in the filament arteries of a zebra danio fish. We have further processed the resulting signal to extract a qualitative map of the hemoglobin concentration. We have also demonstrated the potential to use ground state recovery times to differentiate between two chromophores which may prove to be an effective tool for differentiating between oxy and deoxy hemoglobin.
Plasma Co-Sputtering Methods for the One-Step Synthesis of Pt-C Nanowires Composites With Enhanced Electrocatalytic Properties (2013)

Abstract not Available.
Manganese-Enhanced MRI of the Brain in Healthy Volunteers (2019)

Manganese ions released from mangafodipir successfully enable noninvasive visualization of intra- and extracranial structures that lie outside the blood-brain barrier without adverse clinical effects, setting the stage for future neuroradiologic investigation in disease.