gebhart/patrepeval huggingface dataset:
Transcriptomics-based subphenotyping of the human placenta enabled by weighted correlation network analysis in early-onset preeclampsia with and without fetal growth restriction (2023)

Background: Placental disorders contribute to pregnancy complications, including preeclampsia (PE) and fetal growth restriction (FGR), but debate regarding their specific pathobiology persists. Our objective was to apply transcriptomics with weighted gene correlation network analysis (WGCNA) to further clarify the placental dysfunction in these conditions. Methods: We performed RNA sequencing with WGNCA using human placental samples (n=30), separated into villous tissue and decidua basalis, and clinically grouped as follows: (1) early-onset PE (EOPE)+FGR (n=7); (2) normotensive, nonanomalous preterm FGR (n=5); (2) EOPE without FGR (n=8); (4) spontaneous idiopathic preterm birth (PTB, n=5) matched for gestational age (GA); and (5) uncomplicated term births (TB, n=5). Our data was compared with RNA-seq datasets from public databases (GSE114691, GSE148241, and PRJEB30656; n=130 samples). Results: We identified 14 correlated gene modules in our specimens, of which most were significantly correlated with birthweight and maternal blood pressure. Of the 3 network modules consistently predictive of EOPE±FGR across datasets, we prioritized a co-expression gene group enriched for hypoxia-response and metabolic pathways for further investigation. Cluster analysis based on transcripts from this module and the glycolysis/gluconeogenesis metabolic pathway consistently distinguished a subset of EOPE±FGR samples with an expression signature suggesting modified tissue bioenergetics. We demonstrated that the expression ratios of LDHA/LDHB and PDK1/GOT1 could be used as surrogate indices for the larger panels of genes in identifying this subgroup. Conclusions: We provide novel evidence for a molecular subphenotype consistent with a glycolytic metabolic shift that occurs more frequently but not universally in placental specimens of EOPE±FGR
Downregulation of Renal MRPs Transporters in Acute Lymphoblastic Leukemia Mediated by the IL-6/STAT3/PXR Signaling Pathway (2021)

Inflammation-mediated changes in pharmacokinetics are thought to be executed through pathways IL-6-activated pathways, which can facilitate a better understanding of the potential for the use of IL-6 to predict the severity of adverse outcomes and the major implications on potential ALL treatments.
Operation and control of direct reforming fuel cell power plant (2002)

Computer simulation is used to analyze the operation and efficiency of a carbonate fuel cell power plant under load perturbations. The plant model is based on a 2 MW system design used in the Santa Clara Demonstration Project and includes: internal reforming carbonate fuel cell stack, cathode gas preparation system, heat recovery unit and fuel processing system. Model development for various processes is based on thermochemical principles and conservation of mass and energy. Overall plant efficiency is determined by net fuel consumption based on calculated gas compositions and auxiliary power consumption. During load maneuvering, several key operational constraints must be maintained. Among these are: allowable stack temperature deviation, baseline fuel utilization, steam/carbon ratio, and pressure difference between anode and cathode. Actual plant control schemes are used in the simulation and are evaluated for performance under load changes. The results of these simulations will be used as a benchmark and development tool for advanced intelligent controllers for autonomous and efficient operation of fuel cell systems.
Combined computational design of a zinc‐binding site and a protein–protein interaction: One open zinc coordination site was not a robust hotspot for de novo ubiquitin binding (2013)

We computationally designed a de novo protein-protein interaction between wild-type ubiquitin and a redesigned scaffold. Our strategy was to incorporate zinc at the designed interface to promote affinity and orientation specificity. A large set of monomeric scaffold surfaces were computationally engineered with three-residue zinc coordination sites, and the ubiquitin residue H68 was docked to the open coordination site to complete a tetrahedral zinc site. This single coordination bond was intended as a hotspot and polar interaction for ubiquitin binding, and surrounding residues on the scaffold were optimized primarily as hydrophobic residues using a rotamer-based sequence design protocol in Rosetta. From thousands of independent design simulations, four sequences were selected for experimental characterization. The best performing design, called Spelter, binds tightly to zinc (Kd < 10 nM) and binds ubiquitin with a Kd of 20 µM in the presence of zinc and 68 µM in the absence of zinc. Mutagenesis studies and nuclear magnetic resonance chemical shift perturbation experiments indicate that Spelter interacts with H68 and the target surface on ubiquitin; however, H68 does not form a hotspot as intended. Instead, mutation of H68 to alanine results in tighter binding. Although a 3/1 zinc coordination arrangement at an interface cannot be ruled out as a means to improve affinity, our study led us to conclude that 2/2 coordination arrangements or multiple-zinc designs are more likely to promote high-affinity protein interactions.
Learning to Build Natural Audio Production Interfaces (2019)

Improving audio production tools provides a great opportunity for meaningful enhancement of creative activities due to the disconnect between existing tools and the conceptual frameworks within which many people work. In our work, we focus on bridging the gap between the intentions of both amateur and professional musicians and the audio manipulation tools available through software. Rather than force nonintuitive interactions, or remove control altogether, we reframe the controls to work within the interaction paradigms identified by research done on how audio engineers and musicians communicate auditory concepts to each other: evaluative feedback, natural language, vocal imitation, and exploration. In this article, we provide an overview of our research on building audio production tools, such as mixers and equalizers, to support these kinds of interactions. We describe the learning algorithms, design approaches, and software that support these interaction paradigms in the context of music and audio production. We also discuss the strengths and weaknesses of the interaction approach we describe in comparison with existing control paradigms.
A simple model for the falling cat problem (2018)

We introduce a specific four-particle, four degree-of-freedom model and calculate the rotation that can be achieved by purely internal torques and forces, keeping the total angular momentum zero. We argue that the model qualitatively explains much of the ability of a cat to land on its feet even though released from rest upside down.
Effects of Alkaline Treatment on the Characteristics of Chemical Pulps for Papermaking (2011)

The effects of alkaline treatment on the WRV, crystalline structure and sheet structure of softwood and hardwood bleached kraft pulp were investigated. Sodium hydroxide and sodium carbonate were used as chemicals for alkaline treatment and two levels of alkali dosage (5%, 10%) were applied respectively. Alkali treated and untreated pulp were refined to three levels (550, 450 and 350 mL CSF). WRV of the alkali treated pulps depended on the alkaline type and concentration. It was found that the crystalline structures of softwood and hardwood pulp were not changed by refining. Sodium carbonate and lower concentration of sodium hydroxide treatment did not caused any modification of cellulose crystalline structure, while higher concentration of sodium hydroxide treatment caused the partial modification of cellulose crystalline structure. Alkaline treatment of hardwood bleached kraft pulp led to the shrinkage of fiber diameter and bulky structure of sheet. Alkaline treatment of softwood bleached kraft pulp did not cause the significant change in fiber shrinkage and bulk of sheet.
A proposal for an owl rules language (2004)

Although the OWLWeb Ontology Language adds considerable expressive power to the Semantic Web it does have expressive limitations, particularly with respect to what can be said about properties. Wepresent ORL (OWL Rules Language), a Horn clause rules extension to OWL that overcomes many of these limitations. ORL extends OWL in a syntactically and semantically coherent manner: the basic syntax for ORL rules is an extension of the abstract syntax for OWL DL and OWLLite; ORL rules are given formal meaning via an extension of the OWLDL model-theoretic semantics; ORL rules are given an XML syntax basedon the OWL XML presentation syntax; and a mapping from ORL rules to RDF graphs is given based on the OWL RDF/XML exchange syntax. Wediscuss the expressive power of ORL, showing that the ontology consistency problem is undecidable, provide several examples of ORLusage, and discuss how reasoning support for ORL might be provided.
Direct SAR mapping by thermoacoustic imaging: A feasibility study (2016)

A novel thermoacoustic method for in vivo mapping of local SAR patterns in MRI has been proposed and verified in simulation and in a phantom experiment. Magn Reson Med 78:1599-1606, 2017. © 2016 International Society for Magnetic Resonance in Medicine.
High Temperature Characterization of a Radial Magnetic Bearing for Turbomachinery (2003)

Open loop, experimental force and power measurements of a radial, redundant-axis, magnetic bearing at temperatures to 1000°F (538°C) and rotor speeds to 15,000 RPM along with theoretical temperature and force models are presented in this paper. The experimentally measured force produced by a single C-core circuit using 22 A was 600 lb. (2.67 kN) at room temperature and 380 lb. (1.69 kN) at 538°C. These values were compared with force predictions based on a 1D magnetic circuit analysis and a thermal analysis of gap growth as a function of temperature. The analysis showed that the reduction of force at high temperature is mostly due to an increase in radial gap due to test conditions, rather that to reduced core permeability. Tests under rotating conditions showed that rotor speed has a negligible effect on the bearing’s static force capacity. One C-core required approximately 340 W of power to generate 190 lb. (845 N) of magnetic force at 538°C, however the magnetic air gap was much larger than at room temperature. The data presented is after bearing operation for eleven total hours at 538°C and six thermal cycles.
UPTAKE AND METABOLISM OF GLUTAMATE IN ASTROCYTES CULTURED FROM DISSOCIATED MOUSE BRAIN HEMISPHERES (1977)

Abstract— Uptake kinetics of l ‐glutamate in cultured, normal glia cells obtained from the brain hemispheres of newborn mice were measured together with the activities of the glutamate metabolizing enzymes, glutamic‐oxaloacetate‐transaminase, glutamate dehydrogenase and glutamine synthetase. During 3 weeks of culturing, the activities of the enzymes rose from low neonatal values toward the levels in the adult brain (206, 12.3 and 25.9 nmol. min −1 . mg −1 cell protein for the three enzymes, respectively). The uptake kinetics indicated an unsaturable component together with an uptake following Michaelis‐Menten kinetics with a K m of 220 μ m and a V max of 7.9 nmol. min −1 . mg −1 cell protein. The saturable glutamate uptake was inhibited by d ‐glutamate, l ‐aspartate and α‐aminoadipate whereas l ‐glutamine, GABA and glutarate had no effect. The uptake which was Ca 2+ ‐independent had a K m for sodium of 18m m and it was stimulated by an increase in the external potassium concentration from 5 to 10 and 25 m m. The results suggest that glia cells are important for the uptake of glutamate from synaptic clefts and for the subsequent metabolism of glutamate.
DEPs Induce Local IgE Class Switching Independent of Their Ability to Stimulate iBALT (2022)

Background. Diesel exhaust particles (DEPs) have a great impact on general increase of atopic diseases worldwide. However, it is still unknown whether DEPs induce systemic B-cell IgE class switching in secondary lymphoid organs or locally in lungs, in inducible bronchial-associated lymphoid tissue (iBALT). The aim of this work was to identify the exact site of DEPs mediated B-cell IgE class switching and pro-allergic antibodies production. Methods. We immunized BALB/c mice with different OVA doses (0.3 and 30 &amp;micro;g) intranasally in the presence and absence of two types of DEPs, SRM1650B and SRM2786. We used low (30 &amp;micro;g) and high (150 &amp;micro;g) DEPs doses in our study. Results. Only high DEP dose induced IgE production regardless of particle type. Local IgE class switching was stimulated upon treatment with both types of particles with both low and high antigen doses. Despite the similar ability of two standard DEP samples to stimulate IgE production, their ability to induce iBALT formation and growing, was markedly different upon co-administration together with low antigen doses. Conclusion. DEPs induced local IgE class switching takes place in pre-existing iBALTs, independently of de novo iBALT formation, at least in the case of SRM1650B co-administrated with low antigen doses.
Unstable degenerative spondylolisthesis of the cervical spine (1995)

Unstable degenerative spondylolisthesis of the cervical spine is very rare. Slip usually occurs at the C3 on C4 or C4 on C5 levels, immediately above a stiff lower cervical spine. There are two clinical patterns: that with neurological involvement causing cervicobrachial pain or myelopathy and that with neck pain alone. The diagnosis can be made by flexion/extension radiography. All of our eight patients had localised fusion, three anterior and five posterior, and all had satisfactory results one to seven years after operation.
Analysis of Fluorinated Polyimides Flown on the Materials International Space Station Experiment (2015)

This Technical Memorandum documents the results from the Materials on International Space Station Experiment (MISSE) series involving fluorinated polyimide films analyzed at NASA Marshall Space Flight Center. These films may be used in thermal control, sunshield, solar sail, solar concentrator, and other lightweight polymer film applications. Results include postflight structural integrity, visual observations, determination of atomic oxygen erosion yield, and optical property changes as compared to preflight values.
CircRNAs as a Novel Class of Potential Diagnostic Biomarkers inBipolar Disorders (2023)

Bipolar disorder (BD) is a severe mood disorder with uncertain causes and debilitating signs and symptoms. Gene expression is crucial to the pathophysiology of BD and could be influenced by genetic or epigenetic factors, by either direct modification of mRNA templates or by regulation of post-transcriptional translation. Recent evidence has shown that several critical processes in psychiatric diseases, such as neuronal activity or plasticity, synaptic transmission, and neuronal depolarization, have all been linked to circular RNAs (circRNAs). The circRNA profile of neuronal cells, which may be easily ascertained by a liquid biopsy, may shed light on the molecular pathophysiology of psychiatric disorders, including BD. This approach could aid in future development in diagnosis and treatment. In this review, we provide an in-depth understanding of the roles of circRNAs in the pathophysiology of BD and offer new insight into their potential as emerging diagnostic tools and therapeutic targets.
High Performance Long-Wave Infrared (LWIR) HgCdTe on Silicon (2005)

Abstract : It is critical in the field of infrared imaging to reduce focal plane array costs and simultaneously improve their performance. The use of long wavelength infrared HgCdTe grown on Si substrates will reduce array costs, increase their mechanical strength and permit the fabrication of larger area arrays than possible with present-day technology based on bulk CdZnTe substrates.
Imaging of pulmonary mass lesions with whole-body positron emission tomography and fluorodeoxyglucose (1993)

This is the first report of whole-body PET FDG imaging in patients with thoracic lesions. PET FDG imaging accurately detected metabolically active tumor (both intrathoracic and extrathoracic) in patients with bronchogenic carcinoma, pulmonary metastatic disease, and Hodgkin lymphoma. Because lung cancer is characteristically a multisystem disease, this whole-body PET FDG technique has significant implications for treatment planning.
Risk of Ischemic Stroke in Patients With Coronavirus Disease 2019 (COVID-19) vs Patients With Influenza (2020)

In this retrospective cohort study from 2 New York City academic hospitals, approximately 1.6% of adults with COVID-19 who visited the emergency department or were hospitalized experienced ischemic stroke, a higher rate of stroke compared with a cohort of patients with influenza. Additional studies are needed to confirm these findings and to investigate possible thrombotic mechanisms associated with COVID-19.
Anti-MY9-blocked-ricin: an immunotoxin for selective targeting of acute myeloid leukemia cells (1991)

The use of immunotoxins (IT) to selectively destroy acute myeloid leukemia (AML) cells in vivo or in vitro is complicated by both the antigenic similarity of AML cells to normal progenitor cells and the difficulty of producing a sufficiently toxic conjugate. The monoclonal antibody (MoAb) anti-MY9 is potentially ideal for selective recognition of AML cells because it reacts with an antigen (CD33) found on clonogenic AML cells from greater than 80% of cases and does not react with normal pluripotent stem cells. In this study, we describe an immunotoxin that is selectively active against CD33+ AML cells: Anti-MY9-blocked-Ricin (Anti-MY9-bR), comprised of anti-MY9 conjugated to a modified whole ricin that has its nonspecific binding eliminated by chemical blockage of the galactose binding domains of the B-chain. A limiting dilution assay was used to measure elimination of HL-60 leukemic cells from a 20-fold excess of normal bone marrow cells. Depletion of CD33+ HL-60 cells was found to be dependent on the concentration of Anti-MY9-bR and on the duration of incubation with IT at 37 degrees C. More than 4 logs of these leukemic cells were specifically depleted following short exposure to high concentrations (10(-8) mol/L) of Anti-MY9-bR. Incubation with much lower concentrations of Anti-MY9-bR (10(-10) mol/L), as compatible with in vivo administration, resulted in 2 logs of depletion of HL-60 cells, but 48 to 72 hours of continuous exposure were required. Anti-MY9-bR was also shown to be toxic to primary AML cells, with depletion of greater than 2 logs of clonogenic cells following incubation with Anti-MY9-bR 10(-8) mol/L at 37 degrees C for 5 hours. Activity of Anti-MY9-bR could be blocked by unconjugated Anti-MY9 but not by galactose. As expected, Anti-MY9-bR was toxic to normal colony-forming unit granulocyte-monocyte (CFU-GM), which expresses CD33, in a concentration- and time-dependent manner, and also to burst-forming unit-erythroid and CFU-granulocyte, erythroid, monocyte, megakaryocyte, although to a lesser extent. When compared with anti-MY9 and complement (C'), Anti-MY9-bR could be used in conditions that provided more effective depletion of AML cells with substantially less depletion of normal CFU-GM. Therefore, Anti-MY9-bR may have clinical utility for in vitro purging of AML cells from autologous marrow when used at high IT concentrations for short incubation periods. Much lower concentrations of Anti-MY9-bR that can be maintained for longer periods may be useful for elimination of AML cells in vivo.
Radiative decay and dephasing in plasmonic band gap structures (2003)

We report spatial and spectral domain measurements of the dephasing of surface plasmon excitations in metal films with periodic nano-hole arrays. A Rayleigh-like scattering of surface plasmons by the periodic hole array is the microscopic origin of the dephasing.
GOSSIB vs. IP traceback rumors (2003)

To identify sources of distributed denial-of-service attacks, path traceback mechanisms have been proposed. Traceback mechanisms relying on probabilistic packet marking (PPM) have received most attention, as they are easy to implement and deploy incrementally. We introduce a new concept, namely Groups Of Strongly SImilar Birthdays (GOSSIB), that can be used by to obtain effects similar to a successful birthday attack on PPM schemes. The original and most widely known IP traceback mechanism, compressed edge fragment sampling (CEFS), was developed by Savage et al. (2000). We analyze the effects of an attacker using GOSSIB against CEFS and show that the attacker can seed misinformation much more efficiently than the network is able to contribute real traceback information. Thus, GOSSIB will render PPM effectively useless. It can be expected that GOSSIB has similar effects on other PPM traceback schemes and that standard modifications to the systems will not solve the problem.
An Assembly of Proteins and Lipid Domains Regulates Transport of Phosphatidylserine to Phosphatidylserine Decarboxylase 2 in Saccharomyces cerevisiae (2013)

Saccharomyces cerevisiae uses multiple biosynthetic pathways for the synthesis of phosphatidylethanolamine. One route involves the synthesis of phosphatidylserine (PtdSer) in the endoplasmic reticulum (ER), the transport of this lipid to endosomes, and decarboxylation by PtdSer decarboxylase 2 (Psd2p) to produce phosphatidylethanolamine. Several proteins and protein motifs are known to be required for PtdSer transport to occur, namely the Sec14p homolog PstB2p/Pdr17p; a PtdIns 4-kinase, Stt4p; and a C2 domain of Psd2p. The focus of this work is on defining the protein-protein and protein-lipid interactions of these components. PstB2p interacts with a protein encoded by the uncharacterized gene YPL272C, which we name Pbi1p (PstB2p-interacting 1). PstB2p, Psd2, and Pbi1p were shown to be lipid-binding proteins specific for phosphatidic acid. Pbi1p also interacts with the ER-localized Scs2p, a binding determinant for several peripheral ER proteins. A complex between Psd2p and PstB2p was also detected, and this interaction was facilitated by a cryptic C2 domain at the extreme N terminus of Psd2p (C2-1) as well the previously characterized C2 domain of Psd2p (C2-2). The predicted N-terminal helical region of PstB2p was necessary and sufficient for promoting the interaction with both Psd2p and Pbi1p. Taken together, these results support a model for PtdSer transport involving the docking of a PtdSer donor membrane with an acceptor via specific protein-protein and protein-lipid interactions. Specifically, our model predicts that this process involves an acceptor membrane complex containing the C2 domains of Psd2p, PstB2p, and Pbi1p that ligate to Scs2p and phosphatidic acid present in the donor membrane, forming a zone of apposition that facilitates PtdSer transfer.
Characteristics of Thin-Film p-ZnMgO/n-ITO Heterojunctions on Glass Substrates (2004)

Thin films of oriented, polycrystalline p-type were deposited on n-type indium-tin oxide (ITO)-coated glass substrates by pulsed laser deposition at 400°C to form transparent wide bandgap heterojunctions. The characteristics of Au, Ni, or Pt contacts subsequently deposited on these heterojunction layers were examined. In each case, rectifying behavior of the p-n junction was obtained. The junctions display a negative temperature coefficient for reverse breakdown voltage. This approach looks promising as a means of realizing low-cost-substrate transparent electronics. © 2004 The Electrochemical Society. All rights reserved.