gebhart/patrepeval huggingface dataset:
Modeling the transmembrane domain of bacterial chemoreceptors (2002)

Bacterial chemoreceptors signal across the membrane by conformational changes that traverse a four-helix transmembrane domain. High-resolution structures are available for the chemoreceptor periplasmic domain and part of the cytoplasmic domain but not for the transmembrane domain. Thus, we constructed molecular models of the transmembrane domains of chemoreceptors Trg and Tar, using coordinates of an unrelated four-helix coiled coil as a template and the X-ray structure of a chemoreceptor periplasmic domain to establish register and positioning. We tested the models using the extensive data for cross-linking propensities between cysteines introduced into adjacent transmembrane helices, and we found that many aspects of the models corresponded with experimental observations. The one striking disparity, the register of transmembrane helix 2 (TM2) relative to its partner transmembrane helix 1, could be corrected by sliding TM2 along its long axis toward the periplasm. The correction implied that axial sliding of TM2, the signaling movement indicated by a large body of data, was of greater magnitude than previously thought. The refined models were used to assess effects of inter-helical disulfides on the two ligand-induced conformational changes observed in alternative crystal structures of periplasmic domains: axial sliding within a subunit and subunit rotation. Analyses using a measure of disulfide potential energy provided strong support for the helical sliding model of transmembrane signaling but indicated that subunit rotation could be involved in other ligand-induced effects. Those analyses plus modeled distances between diagnostic cysteine pairs indicated a magnitude for TM2 sliding in transmembrane signaling of several angstroms.
Probing Electronic Communication in Stable Benzene-Bridged Verdazyl Diradicals (2007)

Two benzene-bridged N,N'-bis(isopropyl)6-oxoverdazyl diradicals 7a (1,4-benzene-bridged) and 7b (1,3-benzene-bridged) were prepared and studied by an array of physicochemical techniques aimed at elucidating the intramolecular electronic and magnetic coupling between verdazyl chromophores. The very high stability of these diradicals permits comprehensive investigations of their properties for the first time. The UV-vis spectra suggest negligible direct conjugative overlap involving the radical SOMOs, although significant differences in higher energy absorptions suggest that radical orbitals other than the SOMO are likely communicating via the central p-phenylene bridge in 7a. The electrochemical features of the two diradicals are nearly identical; in each derivative, both radicals are oxidized essentially independently while the reductions occur in a stepwise manner with differences of approximately 100 mV between the two reductions. EPR and magnetic susceptibility collectively indicate that the para-bridged diradical is weakly antiferromagnetically coupled while the meta analogue is weakly ferromagnetically coupled, in accord with the topology of the substitution pattern on the central benzene ring.
Deficiency of TET3 leads to a genome-wide DNA hypermethylation episignature in human whole blood (2021)

TET3 encodes an essential dioxygenase involved in epigenetic regulation through DNA demethylation. TET3 deficiency, or Beck-Fahrner syndrome (BEFAHRS; MIM: 618798), is a recently described neurodevelopmental disorder of the DNA demethylation machinery with a nonspecific phenotype resembling other chromatin-modifying disorders, but inconsistent variant types and inheritance patterns pose diagnostic challenges. Given TET3's direct role in regulating 5-methylcytosine and recent identification of syndrome-specific DNA methylation profiles, we analyzed genome-wide DNA methylation in whole blood of TET3-deficient individuals and identified an episignature that distinguishes affected and unaffected individuals and those with mono-allelic and bi-allelic pathogenic variants. Validation and testing of the episignature correctly categorized known TET3 variants and determined pathogenicity of variants of uncertain significance. Clinical utility was demonstrated when the episignature alone identified an affected individual from over 1000 undiagnosed cases and was confirmed upon distinguishing TET3-deficient individuals from those with 46 other disorders. The TET3-deficient signature - and the signature resulting from activating mutations in DNMT1 which normally opposes TET3 - are characterized by hypermethylation, which for BEFAHRS involves CpG sites that may be biologically relevant. This work expands the role of epi-phenotyping in molecular diagnosis and reveals genome-wide DNA methylation profiling as a quantitative, functional readout for characterization of this new biochemical category of disease.
The Development of Nonalcoholic Fatty Liver Disease and Metabolic Syndromes in Diet-Induced Rodent Models (2023)

Dietary macronutrients are essential for metabolic regulation and insulin function. The present study examined the effects of different high-fat diets (HFDs) and high-carbohydrate diets (HCDs) on the development of non-alcoholic fatty liver disease and metabolic syndrome indices in healthy adult male Wistar albino rats. Forty-two rats were distributed into six groups (<i>n</i> = 7), which were fed the following for 22 weeks: (1) a control diet; (2) a high-carbohydrate, low-fat diet (HCD-LFD); (3) high-saturated-fat, low-carbohydrate diet (HSF-LCD); (4) a high-monounsaturated-fat diet (HMUSF); (5) a high medium-chain fat diet (HMCF); and a (6) a high-carbohydrate, high-fiber diet (HCHF). In comparison to the control, the body weight increased in all the groups. The HSF-LCD group showed the highest levels of cholesterol, triglyceride, low-density lipoprotein, hepatic enzyme, insulin resistance, and Homeostatic Model Assessment for Insulin Resistance. A liver histology analysis of the HSF-LCD group showed macrovesicular hepatic steatosis associated with large hepatic vacuolation. Additionally, it showed marked periportal fibrosis, especially around the blood vessels and blood capillaries. The lowest levels of fasting glycemia, insulin, and HOMA-IR were observed in the HCHF group. In conclusion, these findings show that dietary saturated fat and cholesterol are principal components in the development and progression of non-alcoholic fatty liver disease in rats, while fiber showed the greatest improvement in glycemic control.
A TWO‐DIMENSIONAL ZHU—ZIENKIEWICZ METHOD FOR GRADIENT RECOVERY FROM FINITE‐ELEMENT SOLUTIONS (1993)

The gradient recovery method proposed by Zhu and Zienkiewicz for one‐dimensional problems is generalized to two dimensions, using quadrilateral elements. Its performance is compared with that of conventional local smoothing techniques and of direct differentiation of the finite‐element solution, on finite‐element approximations to analytically known polynomial and transcendental functions on a quadrilateral second‐order finite‐element mesh. The new method appears to be reliable and more stable than local smoothing, and to provide better accuracy than direct differentiation, at low computational cost.
Improved determination of biplane imaging geometry and 3D coronary arterial tree from two views (2002)

The authors propose a new technique for estimation of 3D biplane imaging geometry based on two perspective projection angiograms acquired at arbitrary orientations. With the calculated imaging geometry, the 3D coronary arterial structures can then be reconstructed. Given 8 or more corresponding object points in both views, a linear algorithm is first applied to obtain an initial estimate of the imaging geometry in terms of a rotation matrix [R] and a unit translation vector t/spl I.oarr/. The solution provided by the linear algorithm is then used as an initial estimate for the second step, in which constrained nonlinear optimization with uncertain prior information of the imaging system is employed to complete an optimal estimate of the imaging geometry. The accuracy of this method was evaluated by using a computer-simulated coronary arterial tree.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
"African Voices" : Smithsonian Project Brings Africa Alive (2014)

Overview of the 'African Voices' Project and exhibition hall in the National Museum of Natural History; various galleries are described.
Measurement of post-fire hillslope erosion to evaluate and model rehabilitation treatment effectiveness and recovery (2005)

The increasing size and severity of wildfires in the western United States has caused a corresponding increase in post-fire emergency erosion control activities. Hillslope treatments, such as broadcast seeding, mulching and installed barriers, are applied to reduce runoff and erosion, as well as downslope sedimentation. However, there are few data to determine if these post-fire treatments are practical and effective. Direct measurement of hillslope erosion, particularly in the remote settings where wildfires occur, is time consuming and costly. Rainfall simulation, sediment fences and paired catchment studies have been adapted for measuring post-fire erosion in the mountainous forest regions of the western USA. The use of paired catchments to measure hillslope erosion and evaluate treatment effectiveness is illustrated by an ongoing experiment of six contour-felled log erosion barrier research sites. Deciding which type of treatments to use, as well as the locations and timing of application, requires treatment cost and effectiveness to be weighed against potential damage from unmitigated erosion. To assist in this process, a web-based Erosion Risk Management Tool has been developed that incorporates variability in rainfall, burn severity and soil properties, as well as treatment options to provide probabilistic erosion estimates for 4 years after a fire.
DNA-based Methods for Detection of Genetically Modified Events in Food and Supply Chain (2016)

Efficient detection strategies for genetically modified (GM) crops need to be in compliance with regulatory frameworks and address consumer concerns. The present review describes widely employed DNA-based technologies for GM detection. Polymerase chain reaction (PCR) and real-time PCR (qPCR) are the methods that can be used for qualitative and quantitative analysis of GM crops due to their specificity, sensitivity and robustness. With increase in number and complexity of genetic elements in newly developed GM events, strategies based on matrix approach, real-time PCR-based multi-target system, loop-mediated isothermal amplification, next generation sequencing, have emerged, which could facilitate cost-effective, rapid, on-site or high throughput GM detection.
Comments on “Amplitude Dispersion and Nonlinear Instability of Whistlers” (1971)

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Personalized Gene Expression Profile Information Predicts Severity of Systemic Sclerosis Despite Heterogeneity of Disease (2018)

Background Systemic sclerosis (scleroderma, SSc) is an autoimmune disease that shows considerable heterogeneity in progression rate and clinical presentation amongst patients. Along with vascular damage and aberrant autoantibody production, SSc causes fibrosis of skin and internal organs. SSc is classified into two clinical subgroups: diffuse and limited, based on amount of skin involvement. Fibrosis of vital organs, mainly lung and heart, causes morbidity and mortality as a result of SSc. The modified Rodnan skin score (mRSS) is currently used to measure severity and disease progression, but is limited by variable sensitivity across disease progression. Thus, the objective of our study was to improve understanding of SSc by developing a method to predict SSc severity based on unbiased, personalized information (gene expression profiles) and evaluate heterogeneity of fibroblast activity between patients. Methods We used gene expression data from skin biopsies from 93 donors (mRSS 0–43) to train and test performance of several candidate prediction models. We used the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to identify pathways associated with the genes that defined low and high severity SSc patient groups. We performed qRT‐PCR on fibroblasts derived from multiple SSc patients to examine heterogeneity between donors. Results We developed the first classification model to accurately predict SSc severity based on gene signature and the clinical measurement of mRSS. DAVID analysis identified several pathways that were enriched with genes from the high and low severity profiles and relevance of several of these pathways were supported by the current literature. Overall, patients with more severe SSc expressed higher levels of genes associated with JAK/STAT signaling and innate immunity. We are currently investigating these and other pathways for their role in disease. qRT‐PCR analysis of fibroblasts demonstrated a heterogeneous response to fibrotic and anti‐fibrotic factors, underscoring the need for a personalized medicine approach to this disease. Treatment with TGF‐beta elicited variable levels of expression of pro‐fibrotic genes including Fibronectin, Tenascin C, and Collagen I. Likewise, pro‐fibrotic chemokines had variable effects across fibroblast samples. Conclusions Our study represents the first time that an independently validated classification model has been used to predict SSc severity based on personalized, patient‐specific information. This model yields gene signatures of high and low severity groups and may inform treatment of this highly variable disease. Our methodology can be applied to other datasets to build prognostic models for SSc and other fibrotic diseases. Support or Funding Information This work was supported by grants from NIAMS (AR68317 CCY) and the University of Pittsburgh School of Nursing. This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .
Serological and immunochemical characteristics of Ge-negative red cells and anti-Ge (1988)

Gerbich-negative red cells lack Beta and gamma sialoglycoproteins (SGPs), which are now known to carry the Gerbich (Ge) antigens. Gerbich and Yus-type Ge-negative red cells possess distinct diffuse SGPs that migrate on sodium dodecyl sulphate polyacrylamide gel electrophoresis in a position between those normally occupied by Beta and gamma SGPs. Both these SGPs lack tie2 antigens and possess epitopes recognized by monoclonal anti-Beta These SGPs differ from each other in at least two ways. The SGP associated with the Gerbich type also lacks the Ge3 antigen and is resistant to trypsin treatment. The SGP associated with the Yus type possesses the antigenic determinant recognized by anti-Ge3 and is sensitive to trypsin digestion.
A mapping mechanism for objects persistence in multivalued database (2009)

Objects persistence has been popular recently since it has become a necessary practice to shuttle objects between in-memory and in-storage status. Most researchers focus on objects to relational data model mapping but few on objects to multivalued data model (O/M). Nevertheless, existing mapping mechanisms are either hard to be extended or difficult to be managed. This paper presents a mechanism for mapping from objects to multivalued databases. A detailed mapping solution is exhibited. Besides, an interactive mapping configuration facility has been developed to ease the configuration instead of manual scripts editing. Experiments show that around 92% of the time is saved to configure the domain classes mapping by using the configuration facility of the proposed persistence mechanism in contrast to manual editing used in other similar mapping mechanisms. Simulation results show that this mapping mechanism not only shortens the overall development period, but also comparatively easy to be managed and extended.
Large-scale experimental study of Internet performance using video traffic (2002)

In this paper, we analyze the results of a seven-month real-time streaming experiment, which was conducted between a number of unicast dialup clients, connecting to the Internet through access points in more than 600 major U.S. cities, and a backbone video server. During the experiment, the clients streamed low-bitrate MPEG-4 video sequences from the server over paths with more than 5,000 distinct Internet routers. We describe the methodology of the experiment, the architecture of our NACK-based streaming application, study end-to-end dynamics of 16 thousand ten-minute sessions (85 million packets), and analyze the behavior of the following network parameters: packet loss, round-trip delay, oneway delay jitter, packet reordering, and path asymmetry. We also study the impact of these parameters on the quality of real-time streaming.
37‐4: Micro LED Defect Analysis via Photoluminescent and Cathodoluminescent Imaging (2020)

Ultra‐high resolution micro LED displays are emerging as a viable technology for self‐emissive displays. One challenge for displays with millions of pixels is process control and defect analysis during LED fabrication and transfer. Here we investigate two non‐destructive test methods, photoluminescent and cathodoluminescent imaging, and compare them to electroluminescent images to verify LED fidelity and evaluate these methods as potential tools for defect analysis.
Targeting Iron-Dependent DNA Synthesis with Gallium and Transferrin-Gallium (1991)

While iron is essential for numerous intracellular processes, its critical role in DNA synthesis relates to the activity of the iron-containing M2 subunit of ribonucleotide reductase, the enzyme responsible for the synthesis of deoxyribonucleotides. Gallium, a metal which resembles iron with respect to transferrin (Tf) binding, cellular uptake by the Tf receptor and incorporation into ferritin, blocks the cellular uptake of iron and inhibits cell growth. Exposure of HL60 cells to Tf-gallium (Ga) results in decreased deoxyribonucleotide synthesis and a diminution in the electron spin resonance (ESR) spectroscopy signal of ribonucleotide reductase, findings consistent with inhibition of this enzyme. In the present study, Ga nitrate blocked the uptake of 59Fe by L1210 cells and inhibited their proliferation. The ribonucleotide reductase M2 subunit ESR signal in cell cytoplasmic extracts was markedly inhibited in Ga-treated cells; however, the signal was restored to normal within 10 min of exposure of these cytoplasmic extracts to ferrous ammonium sulfate. These results confirm that Ga inhibits DNA synthesis by specifically limiting the amount of intracellular iron needed for the activity of the M2 subunit of ribonucleotide reductase. Further studies utilizing HL60 cells made resistant to Ga showed that these cells were also more resistant to growth inhibition by an anti-Tf receptor monoclonal antibody and deferoxamine. Ga blocks cell growth through inhibition of iron-dependent DNA synthesis. Cells appear to overcome the effects of Ga through compensatory mechanisms involving cellular iron metabolism.
Myriberine A, a New Alkaloid with an Unprecedented Heteropentacyclic Skeleton from Myrioneuron faberi (2013)

Myriberine A (1) possessing an unprecedented carbon skeleton was isolated from Myrioneuron faberi. The structure and absolute configuration of 1 were elucidated by a combination of spectroscopic data, X-ray crystallographic, and computational methods. Myriberine A (1) demonstrated inhibition against the hepatitis C virus (HCV) life cycle in vitro.
Iterated multisource exchangeability models for individualized inference with an application to mobile sensor data (2020)

Researchers are increasingly interested in using sensor technology to collect accurate activity information and make individualized inference about treatments, exposures, and policies. How to optimally combine population data with data from an individual remains an open question. Multisource exchangeability models (MEMs) are a Bayesian approach for increasing precision by combining potentially heterogeneous supplemental data sources into analysis of a primary source. MEMs are a potentially powerful tool for individualized inference but can integrate only a few sources; their model space grows exponentially, making them intractable for high-dimensional applications. We propose iterated MEMs (iMEMs), which identify a subset of the most exchangeable sources prior to fitting a MEM model. iMEM complexity scales linearly with the number of sources, and iMEMs greatly increase precision while maintaining desirable asymptotic and small sample properties. We apply iMEMs to individual-level behavior and emotion data from a smartphone app and show that they achieve individualized inference with up to 99% efficiency gain relative to standard analyses that do not borrow information.
Effect of aging on the microstructure evolution, thermal and mechanical properties of mica/epoxy composite (2003)

The mica/epoxy composite used in generator (rated 22 KV and 560 MVA) stator windings was exposed under air or hydrogen atmosphere at 180/spl deg/C for 1000 hours. The measurements of glass transition temperature and storage modulus were conducted using differential scanning calorimeter (DSC) and dynamic mechanical analyzer (DMA). The defect evolution was investigated by scanning electron microscope (SEM) in control and aged specimens. The SEM microstructural analysis showed that the degradation occurred fast aged specimens in air as the size of cavities increases at the mica/epoxy interface. The aged specimens in hydrogen showed retarded generation and growth of cavities. All specimen showed cavities and cracks at the mica/epoxy interface. Which could cause premature failure. The microstructural analysis indicates that reducing defect formation in operation would greatly extend the lifetime of mica/epoxy composite.
Insulin-Stimulated Akt Kinase Activity Is Reduced in Skeletal Muscle From NIDDM Subjects (1998)

The serine/threonine kinase Akt (PKB/Rac) has been implicated as playing a role in the insulin-signaling pathway to glucose transport. Little is known regarding the regulation of Akt kinase activity in insulin-sensitive tissues, such as skeletal muscle, or whether this regulation is altered in insulin-resistant states such as NIDDM. We examined the effect of insulin on Akt kinase activity in skeletal muscle from six NIDDM patients and six healthy subjects. Whole-body insulin sensitivity, assessed by the euglycemic-hyperinsulinemic clamp, was significantly lower in NIDDM subjects (P < 0.001), and this was accompanied by impaired in vitro insulin-stimulated glucose transport in skeletal muscle. In both groups, insulin induced a significant increase in Akt kinase activity, but the response to maximal insulin (60 nmol/l) was markedly reduced in skeletal muscle from NIDDM subjects (66% of control levels, P < 0.01). Impaired Akt kinase activity was not accompanied by decreased protein expression of Akt. Instead, a trend toward increased Akt expression was noted in skeletal muscle from NIDDM subjects (P < 0.1). These parallel defects in insulin-stimulated Akt kinase activity and glucose transport in diabetic skeletal muscle suggest that reduced Akt kinase activity may play a role in the development of insulin resistance in NIDDM.
Adjuvant endocrine therapy uptake, toxicity, quality of life, and prediction of early discontinuation (2023)

Tolerability and adherence to ET remains a challenge for patients who switch to a second ET. An early discontinuation model using patient-reported outcomes identifies patients likely to discontinue their adjuvant ET. Improved management of toxicities and novel more tolerable adjuvant ETs are needed for maintaining patients on treatment.
Iron‐Catalyzed Asymmetric Olefin cis‐Dihydroxylation with 97 % Enantiomeric Excess (2008)

Big cis-ster: The use of an (R,R)-bipyrrolidine backbone with two α-methylpyridine pendant arms affords a tetradentate N4 ligand that coordinates an iron center with cis-α topology (see picture; Fe purple, C gray, N blue, O red, S yellow, F green). This complex catalyzes the reaction between H2O2 and cis-2-heptene to afford a cis-diol product in very high enantioselectivity.