gebhart/patrepeval huggingface dataset:
Autoregressive graph Volterra models and applications (2023)

Abstract Graph-based learning and estimation are fundamental problems in various applications involving power, social, and brain networks, to name a few. While learning pair-wise interactions in network data is a well-studied problem, discovering higher-order interactions among subsets of nodes is still not yet fully explored. To this end, encompassing and leveraging (non)linear structural equation models as well as vector autoregressions, this paper proposes autoregressive graph Volterra models (AGVMs) that can capture not only the connectivity between nodes but also higher-order interactions presented in the networked data. The proposed overarching model inherits the identifiability and expressibility of the Volterra series. Furthermore, two tailored algorithms based on the proposed AGVM are put forth for topology identification and link prediction in distribution grids and social networks, respectively. Real-data experiments on different real-world collaboration networks highlight the impact of higher-order interactions in our approach, yielding discernible differences relative to existing methods.
Formation of Polycyanoacrylate−Silica Nanocomposites by Chemical Vapor Deposition of Cyanoacrylates on Aerogels (2008)

Here, we report the first CVD reinforcement of silica aerogels using cyanoacrylates to create a silica-polycyanoacrylate nanocomposite. Deposition is fast and homogeneous through monolithic aerogels. The nanocomposite results in a 32× improvement over native silica aerogels while not diminishing the aerogels attractive physical properties.
Transductive Adaptation of Black Box Predictions (2016)

Access to data is critical to any machine learning component aimed at training an accurate predictive model. In reality, data is often a subject of technical and legal constraints. Data may contain sensitive topics and data owners are often reluctant to share them. Instead of access to data, they make available decision making procedures to enable predictions on new data. Under the black box classifier constraint, we build an effective domain adaptation technique which adapts classifier predictions in a transductive setting. We run experiments on text categorization datasets and show that significant gains can be achieved, especially in the unsupervised case where no labels are available in the target domain.
A novel triple-tracer approach to assess postprandial protein turnover (2018)

Insulin and nutrients have profound effects on proteome homeostasis. Currently no reliable methods are available to measure postprandial protein turnover. A triple-tracer method was developed using phenylalanine stable isotope tracers to estimate appearance rates of ingested (R<sub>a meal</sub>) and endogenous phenylalanine and the rate of phenylalanine disposal (R<sub>d</sub>). This was compared with the "traditional" dual-tracer method, using one (1-CM)- and two (2-CM)-compartment models. For both methods, [<sup>13</sup>C<sub>6</sub>]phenylalanine was given orally, and [<sup>15</sup>N]phenylalanine was constantly infused; the triple-tracer method added [<sup>2</sup>H<sub>5</sub>]phenylalanine, infused at rates to mimic meal [<sup>13</sup>C<sub>6</sub>]phenylalanine appearance. Additionally, incorporation of meal-derived phenylalanine into specific proteins was measured after purification by two-dimensional electrophoresis. The triple-tracer approach reduced modeling errors, allowing improved reconstruction of R<sub>a meal</sub> with a tracer-to-tracee ratio that was more constant and better estimated R<sub>d</sub>. The 2-CM better described phenylalanine kinetics and R<sub>d</sub> than 1-CM. Thus, the triple-tracer approach using 2-CM is superior for measuring non-steady-state postprandial protein turnover. This novel approach also allows measurement of postprandial synthesis rates of specific plasma proteins. We offer a valid non-steady-state model to measure postprandial protein turnover and synthesis of plasma proteins that can safely be applied in adults, children, and pregnant women.
Enhancement of phase sensitivity by exploring slow light in photonic crystals (2002)

We demonstrate how dramatic increases in the induced phase shifts caused by small changes in the index of refraction can be achieved by using very slow group velocities of light, which are readily achievable in photonic crystal systems. Combined with the fact that small group velocity greatly decreases the power requirements needed to operate a device, enhanced phase sensitivity may be used to decrease the size and power requirements of many devices, including switches, routers, all-optical logical gates, wavelength converters, etc. We demonstrate how these advantages can be used to design switches smaller than 20*200 square microns in size, using readily available materials, and at modest levels of power. With this approach, one could have "4O such devices on a surface 2*2 square cm, making it an important step towards large-scale all-optical integration.
Solar Variability Reduction Using Off-Maximum Power Point Tracking and Battery Storage (2017)

In this work a solar power tracking algorithm is implemented by filtering the incoming array's real-time maximum power point (MPP) to track the plant's average power output. It is shown that when variability reduction requirements are imposed, MPP is no longer the best operating strategy for maximum energy delivery. The resulting off-MPP algorithm follows a reduced set point in time intervals with high irradiance variability and avoids injecting into the grid the large power swings typical in photovoltaic (PV) arrays. The tracking algorithm is shown to couple well with energy storage systems (ESSs), such as batteries, resulting in reduced storage capacity requirements and power delivery necessary to offset solar variability. We show PV ramp rate violations are decreased significantly using the tracking algorithm and a minimally sized ESS.
Full Length Vpu from HIV-1: Combining Molecular Dynamics Simulations with NMR Spectroscopy (2006)

Based on structures made available by solution NMR, molecular models of the protein Vpu from HIV-1 were built and refined by 6 ns MD simulations in a fully hydrated lipid bilayer. Vpu is an 81 amino acid type I integral membrane protein encoded by the human immunodeficiency virus type-1 (HIV-1) and closely related simian immunodeficiency viruses (SIVs). Its role is to amplify viral release. Upon phosphorylation, the cytoplasmic domain adopts a more compact shape with helices 2 and 3 becoming almost parallel to each other. A loss of helicity for several residues belonging to the helices adjacent to both ends of the loop region containing serines 53 and 57 is observed. A fourth helix, present in one of the NMR-based structures of the cytoplasmic domain and located near the C-terminus, is lost upon phosphorylation.
Evolution of the blood–brain barrier in newly forming multiple sclerosis lesions (2011)

The rapid change of enhancement dynamics from centrifugal to centripetal reflects the outward growth of MS lesions around their central vein and suggests that factors mediating lesion growth and tissue repair derive from different locations at different times. We propose a model of new lesion growth that unites our imaging observations with existing pathology data.
A Novel Engineered Small Protein for Positron Emission Tomography Imaging of Human Programmed Death Ligand-1: Validation in Mouse Models and Human Cancer Tissues (2018)

The <sup>64</sup>Cu-FN3<sub>hPD-L1</sub> radiotracer represents a novel, small, and high-affinity binder for imaging hPD-L1 in tumors. Our data support further exploration and clinical translation of this binder for noninvasive identification of cancer patients who may respond to immune checkpoint blockade therapies.
Field Inhomogeneity Correction Based on Gridding Reconstruction for Magnetic Resonance Imaging (2007)

Spatial variations of the main field give rise to artifacts in magnetic resonance images if disregarded in reconstruction. With non-Cartesian k-space sampling, they often lead to unacceptable blurring. Data from such acquisitions are usually reconstructed with gridding methods and optionally restored with various correction methods. Both types of methods essentially face the same basic problem of adequately approximating an exponential function to enable an efficient processing with fast Fourier transforms. Nevertheless, they have commonly addressed it differently so far. In the present work, a unified approach is pursued. The principle behind gridding methods is first generalized to nonequispaced sampling in both domains and then applied to field inhomogeneity correction. Three new algorithms, which are compatible with a direct conjugate phase and an iterative algebraic reconstruction, are derived in this way from a straightforward embedding of the data into a higher dimensional space. Their evaluation in simulations and phantom experiments with spiral k-space sampling shows that one of them promises to provide a favorable compromise between fidelity and complexity compared with existing algorithms. Moreover, it allows a simple choice of key parameters involved in approximating an exponential function and a balance between the accuracy of reconstruction and correction.
The SEKOIA Trial: A Structural and Symptomatic Efficacy (2012)

Strontium ranelate, an antiosteoporotic drug developed for the treatment of postmenopausal osteoporosis, delayed radiographic progression of knee osteoarthritis and improved symptoms. This reports on The Efficacy and Safety of Two Doses of Strontium Ranelate Versus Placebo, Administered Orally for Three Years in the Treatment of Knee Osteoarthritis [SEKOIA] trial [Reginster JY et al. Ann Rheum Dis 2012].
Phase Retrieval with Application to Optical Imaging: A contemporary overview (2015)

The problem of phase retrieval, i.e., the recovery of a function given the magnitude of its Fourier transform, arises in various fields of science and engineering, including electron microscopy, crystallography, astronomy, and optical imaging. Exploring phase retrieval in optical settings, specifically when the light originates from a laser, is natural since optical detection devices [e.g., charge-coupled device (CCD) cameras, photosensitive films, and the human eye] cannot measure the phase of a light wave. This is because, generally, optical measurement devices that rely on converting photons to electrons (current) do not allow for direct recording of the phase: the electromagnetic field oscillates at rates of ~1015â€‰Hz, which no electronic measurement device can follow. Indeed, optical measurement/detection systems measure the photon flux, which is proportional to the magnitude squared of the field, not the phase. Consequently, measuring the phase of optical waves (electromagnetic fields oscillating at 1015â€‰Hz and higher) involves additional complexity, typically by requiring interference with another known field, in the process of holography.
421 Prognostic value of short-term heart rate variability changes in heart failure patients treated with cardiac resynchronization therapy (2005)

We aimed to report the prognostic value of short-term heart rate variability (HRV) changes induced by cardiac resynchronization therapy (CRT) in advanced heart failure (HI e) patients (pts). Methods: Stored data were retrieved of 113 Ht e pts (NYHA functional class III or IV, left ventricular ejection fraction <35%, QRS duration > 120 ms) receiving a CRT device capable of continous assessment of the HRV through calculation of SDANN, the standard deviation of the averages of intrinsic intervals in the 288 5-minutes segments of a day. Major cardiovascular events were death from any cause, urgent heart transplantation, implantation of left ventricular assist device, hospitalisation for cardiac reason and DC-shock for ventricular arrhythmia. Results: CRT induced an increase of SDANN at 3 months of follow-up (from 69 -4-23 ms to 93 -4-27 ms, p<0,001) which was consistent with improvement of functional capacity and reversed mal-adaptation remodeling. Percentage of change in HRV at 4 weeks from CRT initiation predicted maj or cardiovascular events. Indeed, 1-year event-free survival rate (Fig.
Many human peripheral VH5-expressing IgM+ B cells display a unique heavy-chain rearrangement (2007)

The immunoscope methodology has proven useful to analyze T-cell repertoires in mice and humans. We adapted it to the analysis of VH chains of human peripheral B cells by setting up a quantification of various VH and JH segments and the profiling of IgM-, IgG-, IgA- and IgE-expressing B cells. We then tested the hypothesis that the human B-cell and T-cell repertoires have a similar diversity of VH and V-beta rearrangements. We studied in more detail the VH5 family because it is not abundantly used, which facilitated the analysis. The data showed that the number of distinct VH5 rearrangements in all samples studied is close to the number of cells in the sample. This contrasts with T cells in which we previously showed that distinct V-beta rearrangements amount to a few percent of the number of T cells because each V-beta chain is on the average paired with approximately 25 alpha chains. Thus, in the VH5 family, the light chains add little quantitative diversity to that produced by the heavy chain alone. Whether this feature can be generalized to other VH chains is discussed.
Regional particle size dependent deposition of inhaled aerosols in rats and mice (2011)

The deposition patterns of aerosols between 0.5 and 5.0 µm showed an increase in both overall and peripheral deposition as the particle size decreased. The Onion Model allows a more complex analysis of regional deposition in preclinical models.
Use of a Sonogashira—Acetylide Coupling Strategy for the Synthesis of the Aromatic Spiroketal Skeleton of γ‐Rubromycin (VII). (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Comparison of MALDI-TOF MS With HPLC and Nucleic Acid Sequencing for the Identification of Mycobacterium Species in Cultures Using Solid Medium and Broth (2013)

Agreement with nucleic acid sequencing for species present in Mycobacterium Library v1.0 was 97.6% (81/83) for isolates cultured on solid medium and 97.5% (79/81) for those cultured in broth.
ChemInform Abstract: An Efficient Stereoselective Synthesis of δ4,5‐Pipecolic Esters. (1993)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Abstract 1966: Comparison of Right Ventricular Strain and Strain Rate in Patients with Arrhythmogenic Right Ventricular Cardiomyopathy, Right Ventricular Outflow Tract Tachycardia, and Matched Controls (2007)

Background: Arrhythmogenic right ventricular cardiomyopathy (ARVC) is characterized by fibro-fatty replacement of RV myocardium leading to ventricular tachycardia and sudden death in otherwise healthy individuals. Diagnosis is challenging as there are no diagnostic tests with adequate accuracy. Current diagnosis of ARVC is made by the task force criteria. One of the main diagnostic dilemmas continues to be distinguishing ARVC from a relatively benign entity of right ventricular out flow tract tachycardia (RVOT VT). Assessment of myocardial strain and strain rate has been used to study patients with ischemic heart disease and has shown utility in identifying subtle myocardial dysfunction not detected by routine wall motion assessment. The goal of this study was to compare myocardial strain and strain rates in patients with ARVC, RVOT VT and matched controls. Methods: We prospectively enrolled 12 patients with ARVC (based on task force criteria), 10 with RVOT VT, and 22 age and gender matched controls. Echo studies (including tissue Doppler derived myocardial strain echocardiography) were performed with commercially available systems (GE, Vivid 7). Peak systolic RV myocardial strain and strain rate were measured at base, mid, and apical RV free wall and compared. Results: ARVC patients had significantly lower peak systolic RV strain compared to both RVOT VT patients and matched controls (Table ). There was also significantly lower peak systolic strain rate at the apical RV myocardium in patients with ARVC compared to both those with RVOT VT (p=0.02) and controls (p=0.01). Conclusions: Patients with ARVC have abnormally low RV systolic strain and strain rates when compared to matched controls as well as those with RVOT VT. This modality can be routinely used in assessing patients suspected of ARVC as it might assist in earlier diagnosis as well as help in distinguishing patients with ARVC from those with RVOT VT. P&lt;0.05 compared to controls, † P&lt;0.05 compared to RVOT VT group
Abstract 3531: Papillary thyroid carcinomas with and without lymph node metastasis show differences in tumor-infiltrating leukocytes (2012)

Abstract Papillary thyroid carcinoma is the most common endocrine malignancy with approximately 48,000 new cases expected in 2011. Additionally, the incidence has doubled over the last three decades. While 20-year survival rates are extremely high with usual therapy, 15% will have recurrence and 5-10% will die from their disease. If refractory to standard treatment, no sufficient adjuvant therapies are available. Cancer immunotherapy uses a patient's own immune system to recognize and eliminate malignant cells. The potential advantages of this approach over conventional treatments include the systemic trafficking of immune cells to treat primary and metastatic disease, inherent antigen-specificity of adaptive immunity to minimize collateral damage, and most importantly, the induction of immunological memory to prevent recurrent disease. The degree and type of immune response are poorly understood in thyroid cancer. In this study, papillary thyroid cancer samples, with normal tissue matched to the same specimen, from de-identified patients were obtained retrospectively from the Norris Cancer Center Tumor Bank and stained using immunohistochemistry with antibodies specific for CD8 and CD16. Sections were evaluated for tumor-infiltrating leukocyte location, intra-tumor versus invading margin, and percentage of CD8 or CD16 positive lymphocytes, respectively. The results were analyzed for correlation between immune infiltrate and clinical parameters. Nineteen cases of papillary thyroid cancer were studied. The mean patient age was 40 years (range 22-55). Seven of nineteen patients had lymph node metastasis. An organized lymphocytic infiltration was seen in seven samples and was significantly correlated with the presence with CD8+ and CD16+ cells, at the invading margin and tumor parenchyma, respectively. Age &amp;lt;40 years was significantly associated with this pattern of CD8+ and CD16+ cells compared to those older than 40. Lymph node metastasis was significantly association with an increased level of intra-tumoral CD8+ cell infiltration and there was a non-significant trend towards a positive association between nodal metastasis and intra-tumoral CD16+ cell infiltration. The present study demonstrates an increase in cell-mediated immune infiltration in samples that have nodal metastases versus those that do not, suggesting that immune therapy may be utilized in the future treatment of aggressive thyroid carcinoma to improve disease response. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 3531. doi:1538-7445.AM2012-3531
Disruption of Vertical Motility by Shear Triggers Formation of Thin Phytoplankton Layers (2009)

Thin layers of phytoplankton are important hotspots of ecological activity that are found in the coastal ocean, meters beneath the surface, and contain cell concentrations up to two orders of magnitude above ambient concentrations. Current interpretations of their formation favor abiotic processes, yet many phytoplankton species found in these layers are motile. We demonstrated that layers formed when the vertical migration of phytoplankton was disrupted by hydrodynamic shear. This mechanism, which we call gyrotactic trapping, can be responsible for the thin layers of phytoplankton commonly observed in the ocean. These results reveal that the coupling between active microorganism motility and ambient fluid motion can shape the macroscopic features of the marine ecological landscape.
Expectations for Manuscripts on Biomass Feedstocks and Processing in ACS Sustainable Chemistry & Engineering (2020)

status: Published
Biological properties of two models of calcitonin gene related peptide with idealized amphiphilic .alpha.-helices of different lengths (1988)

Previous studies on calcitonin gene related peptide (CGRP) have demonstrated that it has the characteristics of an amphiphilic peptide, and from an examination of the sequence, we have proposed that it contains an amphiphilic alpha-helix. We have synthesized two analogues of CGRP which have different lengths of idealized amphiphilic alpha-helical secondary structure. The first model, CGRM-1, has been substituted with residues generating an idealized amphiphilic alpha-helix in the region between residues 8 and 25, equivalent to approximately five turns of an alpha-helix. This peptide is not an agonist in any of our bioassays, but it does bind with low affinity to rCGRP receptors in crude liver membranes. Our second model, CGRM-2, has an idealized amphiphilic alpha-helix between residues 8 and 18, which is equivalent to approximately three turns of an alpha-helix. In an in vitro rat vas deferens assay, this peptide is an agonist with a potency one-fourth that of the native hormone. However, the potency of CGRM-2 in an adenylate cyclase assay is much lower, only 1/140th the potency of CGRP. Both model peptides display amphiphilic characteristics commensurate with their design. We conclude that there is an amphiphilic alpha-helix in rCGRP between residues 8 and 18 and that this helix terminates in the vicinity of residue 18.
Adaptive gappy proper orthogonal decomposition for particle image velocimetry data reconstruction (2012)

This work presents a novel method for replacing erroneous measurements in digital particle image velocimetry (DPIV) data using an adaptive reconstruction with gappy proper orthogonal decomposition (POD). Previous studies have shown that gappy POD can be used to replace erroneous data with high accuracy. Conventional gappy POD methods employ a spatially constant number of modes for reconstructing the missing information across the entire field. In contrast, the method presented herein proposes a locally adaptive criterion that allows for determination of the optimum number of POD modes required for the reconstruction of each replaced measurement. This reconstruction produces higher accuracy results using more POD modes than with previous POD methods. The new method was compared against commonly utilized techniques for DPIV vector replacement, namely Kriging, bootstrapping and basic interpolation, as well as previously presented POD reconstruction techniques. The results showed that the adaptive gappy POD reconstruction provides higher accuracy and robustness.