gebhart/patrepeval huggingface dataset:
Meningococcal Conjugate and Protein-Based Vaccines (2016)

A quadrivalent diphtheria toxoid-conjugated meningococcal ACYW CV (MenactraTM, Sanofi Pasteur) was licensed for use in 11-to 55-year-olds in January 2005 in the United States and in 2-to 10-year-olds in May 2006 in Canada. Data concerning one other A, C, Y, and W135 protein-PS CV (conjugated to CRM197) has also been reported (23,24).
Next-Generation Optical Fronthaul in the iCirrus Project (2018)

We discuss next-generation fronthaul solutions for 5G and legacy radio access networks. Architectures, findings and experimental results from recent lab and field trial activities are reported.
Importance of the Reducing Agent in Direct Reductive Heck Reactions (2017)

Abstract The role of the reductant in the palladium N‐heterocyclic carbene (NHC) catalyzed reductive Heck reaction and its effect on the mechanism of the reaction is reported. For the first time in this type of transformation, the palladium‐NHC‐catalyzed reductive Heck reaction was shown to proceed in the presence of LiOMe and i PrOH even at 10 °C to give the products very efficiently in excellent yields and with exceptional chemoselectivities. This study shows that the reaction proceeds through two distinct mechanisms that depend on the nature of the reducing agent. In the presence of a protic solvent or acidic medium the reaction undergoes protonation to yield the reduced product, whereas in the absence of proton source, it proceeds through the insertion of the reductant followed by reductive elimination. The kinetic data reveal that the oxidative addition is the rate‐determining step in the reaction. The reaction profiles show first‐order kinetics in aryl iodide and Pd and zero‐order kinetics in LiOMe, benzylideneacetone, and the excess amount of NHC ligand. In addition, the reaction progress kinetic analysis shows that neither catalyst decomposition nor product inhibition occurs during the reaction. DFT calculations of the key steps confirm that the oxidative addition step is the rate‐determining step in the reaction. Deuterium‐labeling experiments indicate that the product is formed by the protonation of the Pd−C alkyl bond of the intermediate formed after enone insertion into the Pd−C Ar bond. Application of chiral NHC ligands in the asymmetric reductive Heck reaction only results in poor enantioselectivities (enantiomeric excess up to 20 %) and is also substrate specific. DFT calculations suggest that the migration of the aryl group to the alkene of the substrate is the enantioselectivity‐determining step of the reaction. It is further shown that if the steric bulk at the enone is small (a methyl group), the two transition state barriers from [Pd II (L 2 )(ArI)(enone)] species C re and C si , which have the re and si face of the enone substrate coordinated to Pd, are very similar, in line with the experimental results. With a slightly larger group (an isopropyl substituent) a significant difference in energy barriers is calculated (2.6 kcal mol −1 ), and in the experiment this product is formed with a modest enantiomeric excess (up to 20 %).
Technical Considerations on Scanning and Image Analysis for Amyloid PET in Dementia (2017)

Brain imaging techniques, such as computed tomography (CT), magnetic resonance imaging (MRI), single photon emission computed tomography (SPECT), and positron emission tomography (PET), can provide essential and objective information for the early and differential diagnosis of dementia. Amyloid PET is especially useful to evaluate the amyloid-β pathological process as a biomarker of Alzheimer's disease. This article reviews critical points about technical considerations on the scanning and image analysis methods for amyloid PET. Each amyloid PET agent has its own proper administration instructions and recommended uptake time, scan duration, and the method of image display and interpretation. In addition, we have introduced general scanning information, including subject positioning, reconstruction parameters, and quantitative and statistical image analysis. We believe that this article could make amyloid PET a more reliable tool in clinical study and practice.
Ethics and IVF (1988)

While IVF has generated a great deal of publicity and comment, such concern over advances in science and medicine is nothing new. Three famous figures who had to contend with opposition to their work, on religious grounds, as has been the case with IVF, are Galileo, Darwin and Freud.
ENteric Immunity SImulator: A Tool for In Silico Study of Gastroenteric Infections (2012)

Clinical symptoms of microbial infection of the gastrointestinal (GI) tract are often exacerbated by inflammation induced pathology. Identifying novel avenues for treating and preventing such pathologies is necessary and complicated by the complexity of interacting immune pathways in the gut, where effector and inflammatory immune cells are regulated by anti-inflammatory or regulatory cells. Here we present new advances in the development of the ENteric Immunity SImulator (ENISI), a simulator of GI immune mechanisms in response to resident commensal bacteria as well as invading pathogens and the effect on the development of intestinal lesions. ENISI is a tool for identifying potential treatment strategies that reduce inflammation-induced damage and, at the same time, ensure pathogen removal by allowing one to test plausibility of in vitro observed behavior as explanations for observations in vivo, propose behaviors not yet tested in vitro that could explain these tissue-level observations, and conduct low-cost, preliminary experiments of proposed interventions/treatments. An example of such application is shown in which we simulate dysentery resulting from Brachyispira hyodysenteriae infection and identify aspects of the host immune pathways that lead to continued inflammation-induced tissue damage even after pathogen elimination.
Abundance of solar wind magnesium isotopes determined with WIND/MASS (1996)

We present first results of the abundance ratios of Mg isotopes in the solar wind using the high resolution mass spectrometer on the WIND spacecraft. The isotopic composition of Mg in the solar wind is consistent with terrestrial values. Our preliminary result is 24Mg:25Mg:26Mg=(0.792±0.006):(0.095±0.005):(0.113±0.005).
A Novel Visualization Technique for Electric Power Grid Analytics (2008)

The application of information visualization holds tremendous promise for the electric power industry, but its potential has so far not been sufficiently exploited by the visualization community. Prior work on visualizing electric power systems has been limited to depicting raw or processed information on top of a geographic layout. Little effort has been devoted to visualizing the physics of the power grids, which ultimately determines the condition and stability of the electricity infrastructure. Based on this assessment, we developed a novel visualization system prototype, GreenGrid, to explore the planning and monitoring of the North American Electricity Infrastructure. The paper discusses the rationale underlying the GreenGrid design, describes its implementation and performance details, and assesses its strengths and weaknesses against the current geographic-based power grid visualization. We also present a case study using GreenGrid to analyze the information collected moments before the last major electric blackout in the Western United States and Canada, and a usability study to evaluate the practical significance of our design in simulated real-life situations. Our result indicates that many of the disturbance characteristics can be readily identified with the proper form of visualization.
Phonon transmission across interfaces and the Kapitza resistance (1979)

The transmission of phonons across an interface between a classical solid and liquid helium is calculated. Several simple models of the helium system are considered. Calculations for a solid with a clean and perfect surface give a transmission coefficient for low-energy phonons. ($\ensuremath{\epsilon}&lt;20$ K), which is very small (typically \ensuremath{\le}0.1), and which decreases with decreasing energy. At energies above 30 K the transmission is predicted to have a larger value which is slowly varying with energy, and to be inversely proportional to the acoustical impedance of the solid. Possible mechanisms which increase the transmission for damaged or dirty surfaces are briefly discussed.
Protein Translocation at the Envelope and Thylakoid Membranes of Chloroplasts (1996)

Endosymbiotic evolution has resulted in the transfer of genes encoding the vast majority of the protein components of plastids to the nuclear genome. In response to this displacement of genetic material, plastids have evolved a system to post-translationally import nuclear encoded preproteins from their site of synthesis on cytoplasmic ribosomes. The protein import process can be viewed as a cascade of protein targeting events that are governed by a hierarchy of topogenic sequences. The targeting sequences are sequentially decoded resulting in the localization of the polypeptide to the appropriate organellar subcompartment (for review see Refs.
Adoptive cellular immunotherapy with APN401, autologous cbl-b silenced peripheral blood mononuclear cells: Data from a phase I study in patients with solid tumors. (2018)

3055 Background: Casitas-B-lineage lymphoma protein – b (cbl-b), an E3 ubiquitin ligase is an important intracellular checkpoint limiting activation of lymphocytes and NK cells. Silencing of cbl-b enhances T cell and NK cell antitumor activity in mouse tumor models and in-vitro in human immune cells. APN401, an autologous cellular therapy consisting of ex-vivo cbl-b-silenced PBMCs, was evaluated in patients with solid tumors. Methods: Patients with metastatic solid tumors not eligible for standard therapies were included. Patients with autoimmune disease or requirement for immunosuppressive drugs were excluded. PBMCs were obtained by leukapheresis and were transfected with cbl-b- siRNA ex vivo by electroporation, and 5, 10 or 50 x 105 /PBMCs/kg were infused once shortly thereafter over 30 min. Results: 16 patients were treated with APN401. As a consequence of cbl-b silencing, all patient PBMC preparations produced enhanced amounts of cytokines IL-2 and IFN-g upon TCR stimulation in vitro. Moreover, evaluation of patient PBMCs responses to common tumor antigens were stronger over the course of the follow-up period. Four patients (2 pancreas 1colon cancer, 1 renal cancer) had stable disease as best tumor response during the study. The strongest response to tumor antigens was observed in the patient with the best objective clinical response (metastatic colon cancer; disease stabilization > 1 year). Infusions were well tolerated. Dose-limiting toxicities were not observed. Mild chills were the most commonly observed related adverse event, followed by mild anemia and fatigue. There was no immediate hypersensitivity or evidence for autoimmune adverse effects. Conclusions: Cbl-b-silenced PBMCs (APN401) from cancer patients respond to TCR stimulation and activation with tumor antigens. Strongest cell activation was seen in the patient with the best objective clinical response. 50 x 105 / kg APN401 was safe and well tolerated. Multiple infusions of APN401 are currently clinically tested. Clinical trial information: NCT03087591.
Communication With Disturbance Constraints (2014)

Motivated by the broadcast view of the interference channel, the new problem of communication with disturbance constraints is formulated. The rate-disturbance region is established for the single constraint case and the optimal encoding scheme turns out to be the same as the Han-Kobayashi scheme for the two user-pair interference channel. This result is extended to the Gaussian vector (multiple-input and multiple-output) case. For the case of communication with two disturbance constraints, inner and outer bounds on the rate-disturbance region for a deterministic model are established. The inner bound is achieved by an encoding scheme that involves rate splitting, Marton coding, and superposition coding, and is shown to be optimal in several nontrivial cases. This encoding scheme can be readily applied to discrete memoryless interference channels and motivates a natural extension of the Han-Kobayashi scheme to more than two user pairs.
Abstract IA-018: Molecular landmarks of tumor hypoxia across cancer types (2021)

Abstract Many primary tumor sub-regions have low levels of molecular oxygen, termed hypoxia. Hypoxic tumors are at elevated risk for local failure and distant metastasis, but the molecular hallmarks of tumor hypoxia remain poorly defined. To fill this gap, we quantified hypoxia in 8,006 tumors across 19 tumor types. In ten tumor types, hypoxia was associated with elevated genomic instability. In all 19 tumor types, hypoxic tumors exhibited characteristic driver mutation signatures. We observed widespread hypoxia-associated dysregulation of miRNAs across cancers and functionally validated miR-133a-3p as a hypoxia-modulated miRNA. In localized prostate cancer, hypoxia was associated with elevated rates of chromothripsis, allelic loss of PTEN and shorter telomeres. These associations are particularly enriched in polyclonal tumors, representing a constellation of features resembling tumor nimbosus – an aggressive cellular phenotype. Overall, this work establishes that tumor hypoxia may drive aggressive molecular features across cancers and shape the clinical trajectory of individual tumors. Citation Format: Vinayak Bhandari, Christianne Hoey, Lydia Liu, Emilie Lalonde, Jessica Ray, Julie Livingstone, Robert Lesurf, Yu-Jia Shiah, Tina Vujcic, Xiaoyong Huang, Shadrielle M.G. Espiritu, Lawrence E. Heisler, Fouad Yousif, Vincent Huang, Takafumi N. Yamaguchi, Cindy Q. Yao, Veronica Y. Sabelnykova, Michael Fraser, Melvin L.K. Chua, Theodorus van der Kwast, Stanley K. Liu, Paul C. Boutros, Robert G. Bristow. Molecular landmarks of tumor hypoxia across cancer types [abstract]. In: Proceedings of the AACR Virtual Special Conference on Radiation Science and Medicine; 2021 Mar 2-3. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(8_Suppl):Abstract nr IA-018.
Novel Paired Normal Prostate and Prostate Cancer Model Cell Systems Derived from African American Patients (2022)

Cells derived from prostatectomies of AA patients conferred a bimodal cellular phenotype, recapitulating clinical prostate cellular complexity in this model cell system. Comparisons of viability responses of tumor derived to normal epithelial cells offer the potential for screening therapeutic drugs. Therefore, these paired prostate epithelial cell cultures provide an <i>in vitro</i> model system suitable for studies of molecular mechanisms in health disparities.
The nature of multiphoton fluorescence from red blood cells (2016)

We report on the nature of multiphoton excited fluorescence observed from human erythrocytes (red blood cells RBC's) and their "ghosts" following 800nm sub-15 fs excitation. The detected optical signal is assigned as two-photon excited fluorescence from hemoglobin. Our findings are supported by wavelength-resolved fluorescence lifetime decay measurements using time-correlated single photon counting system from RBC's, their ghosts as well as <i>in vitro </i>samples of various fluorophores including riboflavin, NADH, NAD(P)H, hemoglobin. We find that low-energy and short-duration pulses allow two-photon imaging of RBC’s, but longer more intense pulses lead to their destruction.
In Utero Exposure To Endocrine Disrupting Chemicals, Micro-Rna Profiles, And Fetal Growth: A Pilot Study Protocol (2019)

<i>Background:</i> The developing fetus is particularly vulnerable to the effects of endocrine disrupting chemicals (EDCs). Molecular fingerprints of EDCs can be identified via microRNA (miRNA) expression profiles and may be etiologically implicated in the developmental origin of disease (DOHaD). <i>Methods/design:</i> This pilot study includes pregnant women at high risk (smoking at conception), and low risk (non-smoking at conception) for SGA birth (birthweight<10<sup>th</sup> percentile for gestational age). We have randomly selected 12 mothers (3 high-risk SGA birth, 3 low-risk SGA birth, 3 high-risk non-SGA birth, 3 low-risk non-SGA birth), with EDC measurements from gestational week 17. All offspring are female. We aim to test the stability of our samples (maternal serum, cord blood, placenta tissue), observe the differential expression of miRNA profiles over time (gestational weeks 17, 25, 33, 37, birth), and study the consistency between maternal EDC measures and miRNA expression profiles across our repeated measures. <i>Expected impact of the study for Public Health:</i> Results from this pilot study will inform the development of a larger cohort wide analysis, and will impact the current state of knowledge in the fields of public health, epigenetics, and the DOHaD.
Osteogenic protein-1 differentially regulates the mRNA expression of bone morphogenetic proteins and their receptors in primary cultures of osteoblasts (2000)

The mRNA expression patterns of several bone morphogenetic proteins (BMPs) and their receptors (BMPRs) in long-term primary cultures of fetal rat calvaria (FRC) cells were examined by Northern analysis. Their temporal orders of expression were correlated with those of several biochemical markers characteristic of osteoblastic cell differentiation. Distinct temporal patterns of expression of BMPs and BMPRs during osteoblastic cell differentiation were observed. BMP-2 and BMP-7 mRNA levels did not change significantly. BMP-4 mRNA expression increased and reached a peak prior to matrix formation. BMP-5 mRNA expression increased during the mineralization phase and BMP-6 mRNA expression increased throughout all phases of cell differentiation. Effects of BMP-7 (Osteogenic Protein-1; OP-1) on the expression patterns of several other members of the BMP family and the receptors were also studied. OP-1 downregulated the BMP-4, -5, and -6 mRNA levels by a maximal of 2-fold, 1.5-fold, and 6-fold, respectively. OP-1 did not change significantly the OP-1 and BMP-2 mRNA expression. Of the three type I BMPR examined, OP-1 upregulated ActR-I and BMPR-IA mRNA expression slightly but with statistical significance. OP-1 downregulated BMPR-IB mRNA expression slightly. OP-1 upregulated BMPR-II mRNA expression by a maximum of 2-fold. Our findings demonstrate that OP-1 differentially regulates the mRNA expression of several related members of the BMP family and their receptors in osteoblasts. The observations suggest that OP-1 action on osteoblastic cells involves a complex regulation of gene expression of related members of the BMP family and their receptors in a cell differentiation stage dependent manner.
The infrapatellar fat pad is a dynamic and mobile structure, which deforms during knee motion, and has proximal extensions which wrap around the patella (2018)

Proximal IFP extensions are a novel description. The IFP is a dynamic structure, displacing significantly during knee motion, which is, therefore, vulnerable to interference from trauma or repetitive overload. Given that this trauma is often surgical, it may be appropriate that surgeons learn to minimize injury to the fat pad at surgery.
Decreasing initial telomere length in humans intergenerationally understates age‐associated telomere shortening (2015)

Telomere length shortens with aging, and short telomeres have been linked to a wide variety of pathologies. Previous studies suggested a discrepancy in age-associated telomere shortening rate estimated by cross-sectional studies versus the rate measured in longitudinal studies, indicating a potential bias in cross-sectional estimates. Intergenerational changes in initial telomere length, such as that predicted by the previously described effect of a father's age at birth of his offspring (FAB), could explain the discrepancy in shortening rate measurements. We evaluated whether changes occur in initial telomere length over multiple generations in three large datasets and identified paternal birth year (PBY) as a variable that reconciles the difference between longitudinal and cross-sectional measurements. We also clarify the association between FAB and offspring telomere length, demonstrating that this effect is substantially larger than reported in the past. These results indicate the presence of a downward secular trend in telomere length at birth over generational time with potential public health implications.
Power sharing correction in angle droop controlled inverter interfaced microgrids (2015)

Power sharing between angle-droop controlled inverter-based sources largely depends on the line impedances and choice of droop coefficients. Simple power correction methods such as set-point correction and droop coefficient modification work satisfactorily for specific network topologies and require only limited amount of communication. However, their performance can be inadequate for microgrids with different topologies. In this work, we propose a topology-independent power sharing correction technique based on inter-node communications in order to eliminate the power sharing errors between inverters. We analyse stability and convergence of the proposed solution and present simulation results. Finally, we study the robustness of frequency-droop and angle-droop controlled systems with respect to unknown impedances and parameter uncertainties.
Pulmonary Veno-Occlusive Disease After Autologous Bone Marrow Transplant in a Child With Stage IV Neuroblastoma: Case Report and Literature Review (2003)

Pulmonary veno-occlusive disease (PVOD) is a rare, almost universally fatal complication of chemotherapy and bone marrow transplantation with few treatment options. A 19-month-old boy with stage 4 neuroblastoma with fatal PVOD following high-dose chemotherapy with autologous peripheral blood stem cell rescue is described here. A comprehensive literature review revealed 40 case reports of PVOD in oncology patients. Various therapeutic modalities were attempted, with four survivors. PVOD should be considered in patients with dyspnea and cardiomegaly. Less invasive diagnostic methods and more effective therapies are needed.
Actinopolysporins A–C and Tubercidin as a Pdcd4 Stabilizer from the Halophilic Actinomycete Actinopolyspora erythraea YIM 90600 (2011)

Our current natural product program utilizes new actinomycetes originating from unexplored and underexplored ecological niches, employing cytotoxicity against a selected panel of cancer cell lines as the preliminary screen to identify hit strains for natural product dereplication, followed by mechanism-based assays of the purified natural products to discover potential anticancer drug leads. Three new linear polyketides, actinopolysporins A (1), B (2), and C (3), along with the known antineoplastic antibiotic tubercidin (4), were isolated from the halophilic actinomycete Actinopolyspora erythraea YIM 90600, and the structures of the new compounds were elucidated on the basis of spectroscopic data interpretation. All four compounds were assayed for their ability to stabilize the tumor suppressor programmed cell death protein 4 (Pdcd4), which is known to antagonize critical events in oncogenic pathways. Only 4 significantly inhibited proteasomal degradation of a model Pdcd4-luciferase fusion protein, with an IC50 of 0.88±0.09 μM, unveiling a novel biological activity for this well-studied natural product.