gebhart/patrepeval huggingface dataset:
Employment of Iron-Binding Protein from <i>Haemophilus influenzae</i> in Functional Nanopipettes for Iron Monitoring (2018)

Because of the serious neurologic consequences of iron deficiency and iron excess in the brain, interest in the iron status of the central nervous system has increased significantly in the past decade. While iron plays an important role in many physiological processes, its accumulation may lead to diseases such as Huntington's, Parkinson's, and Alzheimer's. Therefore, it is important to develop methodologies that can monitor the presence of iron in a selective and sensitive manner. In this paper, we first showed the synthesis and characterization of the iron-binding protein (FBP) from Haemophilus influenzae, specific for ferrous ions. Subsequently, we employed this protein in our nanopipette platform and utilized it in functionalized nanoprobes to monitor the presence of ferrous ions. A suite of characterization techniques: absorbance spectroscopy, dynamic light scattering, and small-angle X-ray scattering were used for FBP. The functionalized Fe-nanoprobe calibrated in ferrous chloride enabled detection from 0.05 to 10 μM, and the specificity of the modified iron probe was evaluated by using various metal ion solutions.
Biomarkers for cervical cancer screening: the role of p16<sup>INK4a</sup>to highlight transforming HPV infections (2012)

Biomarkers indicating the initiation of neoplastic transformation processes in human papillomavirus (HPV)-infected epithelial cells are moving into the focus of cancer prevention research, particularly for anogenital cancer, including cancer of the uterine cervix. Based on the in-depth understanding of the molecular events leading to neoplastic transformation of HPV-infected human cells, the cyclin-dependent kinase inhibitor p16(INK4a) turned out to be substantially overexpressed in virtually all HPV-transformed cells. This finding opened novel avenues in diagnostic histopathology to substantially improve the diagnostic accuracy of cervical cancer and its precursor lesions. Furthermore, it provides a novel technical platform to substantially improve the accuracy of cytology-based cancer early-detection programs. Here, we review the molecular background and the current evidence for the clinical utility of the p16(INK4a) biomarker for HPV-related cancers, and cervical cancer prevention in particular.
Cooperative Downlink Max-Min Energy-Efficient Precoding for Multicell MIMO Networks (2016)

Energy efficiency (EE) optimization of wireless systems has attracted increasing attention recently due to its beneficial impacts on the environment and operational savings. Max-min user energy-efficient precoding for multicell multiple-input–multiple-output (MIMO) cooperative networks is investigated. The optimization problem is a nonconvex fractional programming problem, and optimal solutions are hard to find. Two different local optimization methods, namely, block coordinate descent and sequential convex approximation, are proposed to transform the original problem into a series of convex subproblems. In the former method, the relationship between the user rate and the minimum mean square error (MMSE) is utilized, and optimization of the transmitter matrix is formulated as a semidefinite program; the latter method is based on the convex approximation of the nonconvex rate function. The fractional subproblem is transformed into a parameterized subtractive form by exploiting the generalized fractional programming theorem in both methods. Two iterative-fairness-based energy-efficient algorithms are proposed with proved local convergence. Numerical results illustrate that the proposed max-min EE algorithms can improve EE with a performance loss in terms of the sum rate at a high signal-to-noise ratio (SNR) and achieve EE fairness among base stations with different transmit power levels.
Identification of distinct gene expression profiles in the synovium of patients with systemic lupus erythematosus (2007)

Arthritis in SLE has a very distinct molecular signature as compared with that in OA and RA, characterized by up-regulation of IFI genes and down-regulation of genes involved in ECM homeostasis.
ChemInform Abstract: Synthesis of Cyclooctenones Using Intramolecular Hydroacylation. (2001)

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.
&lt;i&gt;rev-1&lt;/i&gt; does not aggravate G-quadruplex deletions in &lt;i&gt;dog-1&lt;/i&gt; deficient animals. (2020)

&lt;p&gt;Nested PCR was performed on genomic G4 site qua1466 (expected size: 1000bp). 5 adult worms per well lysed in 15 ul lysis buffer. 1ul lysis per well was used as a template for a nested PCR. No additional genomic instability was observed in &lt;i&gt;dog-1&lt;/i&gt; deficient animals after loss of REV-1. M denotes DNA marker. Wells were scored as positive when one or more bands appeared &lt;1000bp. Empty wells were not included in the quantification.&lt;/p&gt; &lt;p&gt;(PDF)&lt;/p&gt;
Coherent coupling between surface plasmons and excitons in semiconductor nanocrystals (2009)

We present an experimental demonstration of strong coupling between a surface plasmon propagating on a planar silver substrate, and the lowest excited state of CdSe nanocrystals. Variable-angle spectroscopic ellipsometry measurements demonstrated the formation of plasmon-exciton mixed states, characterized by a Rabi splitting of $\sim$ 82 meV at room temperature. Such a coherent interaction has the potential for the development of plasmonic non-linear devices, and furthermore, this system is akin to those studied in cavity quantum electrodynamics, thus offering the possibility to study the regime of strong light-matter coupling in semiconductor nanocrystals at easily accessible experimental conditions.
Reverse trajectory analysis of the hydrogen negative ion beam in a prototype accelerator for ITER (2022)

Abstract Reverse calculation of negative ion trajectory based on the measured beam emittance has been performed for the first time in multi-stage accelerator in order to reconstruct negative ion profile near meniscus, which has been a long-term issue for negative ion sources. According to reverse calculation, negative ions are mainly extracted from the periphery of extraction area, and the particles extracted from the aperture edge is lost on acceleration grids. By taking into account the lost component with reconstructed negative ion profile, the negative ion trajectory became consistent with observed beam traces on the acceleration grids. This result can be applied directly to the design of ITER accelerator as well as the other Cs-seeded negative ion sources.
MEMS optical position sensor for sun tracking (2015)

We demonstrate a sun tracking sensor fabricated in the MultiMEMS SensoNor process. The sensor uses a quadrant photodetector to determine the position of a projected shadow. Differential measurement of pairs of photodiodes allows simultaneous dual-axis readings. The sensing structure was manufactured in the commercial MultiMEMS process, so it can be easily reproduced in large quantities. The device was tested from -45° to +45° to verify performance. Results show a linear correlation between a mapped output and angle of incident light with an R <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> value of 0.995. The small size, robust structure, and minimal post-processing make it well-suited for sun tracking applications.
Hand-Held Plasma Isolation Device for Point-of-Care Testing (2010)

The ability to analyze a whole blood sample retrieved from a patient is a critical tool used for diagnosing many diseases and conditions. Real-time blood analyzers are already widely used in point-of-care diagnoses and treatment. Being able to analyze plasma that has been isolated from its whole blood source is another important diagnostic tool that has not yet been applied to point-of-care applications. Advancing plasma separation techniques to the extent that they can be integrated into a point-of-care device could expedite certain diagnostic decisions and treatments, increase the number and quality of diagnostic tests that can be administered point-of-care, and ultimately improve patient outcomes. The hand-held plasma isolation device (HHPID) utilizes a unique array of parallel fiber glass filters within a specialized housing to produce a plasma sample from a small quantity of whole blood. This can be done at a patient's bedside without a power supply. This would negate the need to send blood samples away to a laboratory to be centrifuged; a change that could save precious hours or minutes in critical care situations. Initial testing has suggested that the quality and composition of outputted plasma from the HHPID are comparable to plasma retrieved by centrifuging. The HHPID could serve as a companion device for current real-time blood analyzers, which can be enhanced to accept either a whole blood or a plasma sample depending on the blood parameter of interest.
Supplementary Figure Legends 1-8 from Inflammatory Processes Triggered by &lt;i&gt;Helicobacter pylori&lt;/i&gt; Infection Cause Aberrant DNA Methylation in Gastric Epithelial Cells (2023)

Supplementary Figure Legends 1-8 from Inflammatory Processes Triggered by &lt;i&gt;Helicobacter pylori&lt;/i&gt; Infection Cause Aberrant DNA Methylation in Gastric Epithelial Cells
Myocardial Infarct Expansion and Matrix Metalloproteinase Inhibition (2003)

Background— A potential mechanism for left ventricular (LV) remodeling after myocardial infarction (MI) is activation of the matrix metalloproteinases (MMPs). This study examined the effects of MMP inhibition (MMPi) on regional LV geometry and MMP levels after MI. Methods and Results— In pigs instrumented with radiopaque markers to measure regional myocardial geometry, MI was created by ligating the obtuse marginals of the circumflex artery. In the first study, pigs were randomized to MMPi (n=7; PD166793, 20 mg · kg −1 · d −1 ) or MI only (n=7) at 5 days after MI, and measurements were performed at 2 weeks. Regional MI areas were equivalent at randomization and were increased in the MI-only group at 2 weeks after MI compared with the MMPi group. In the second study, pigs randomized to MMPi (n=9) or MI only (n=8) were serially followed up for 8 weeks. At 8 weeks after MI, LV end-diastolic dimension was lower with MMPi than in the MI-only group (4.7±0.1 versus 5.1±0.1 cm, P &lt;0.05). Regional MI area was reduced with MMPi at 8 weeks after MI (1.3±0.1 versus 1.7±0.1 cm 2 , P &lt;0.05). MMPi reduced ex vivo MMP proteolytic activity. In the MI region, membrane-type MMP levels were normalized and levels of the endogenous tissue inhibitor of MMPs (TIMP-1) were increased compared with normal levels with MMPi. These effects were not observed in the MI-only group. Conclusions— MMPi attenuated the degree of post-MI LV dilation and expansion of the infarct during the late phase of MI healing. In addition, exogenous MMPi caused region-specific modulation of certain MMP and TIMP species.
Analysis of the Behavior of Contact / Near-Contact Sliders with Asperity Contact and Meniscus Force (2002)

We numerically investigated contact characteristics of a contact pad with rough disk surface and possibility of a contact/near-contact slider, using a single-DOF slider and random wavy surface model with random roughness. From the contact analysis, it was found that contact stiffness and other characteristics are determined by asperity contact until the contact pad penetrates into the upper standard deviation of asperity peak height and that the contact stiffness tends to approach a constant value as the pad penetrates into average asperity height because the macroscopic deformation becomes predominant. Using the above contact characteristics, we simulated the behavior of a single-DOF slider and showed design conditions of disk waviness which can satisfy the tracking ability and wear durability in terms of wear volume and wear depth. Finally, we investigated the effect of meniscus force on the contact characteristics and the slider vibration.
<i>AJP-Cell Physiology</i> begins landmark reviews in cell physiology: an editorial from the senior editors of <i>AJP-Cell Physiology</i> (2017)

[No abstract]
A Unified Proteochemometric Model for Prediction of Inhibition of Cytochrome P450 Isoforms (2013)

A unified proteochemometric (PCM) model for the prediction of the ability of drug-like chemicals to inhibit five major drug metabolizing CYP isoforms (i.e. CYP1A2, CYP2C9, CYP2C19, CYP2D6 and CYP3A4) was created and made publicly available under the Bioclipse Decision Support open source system at www.cyp450model.org. In regards to the proteochemometric modeling we represented the chemical compounds by molecular signature descriptors and the CYP-isoforms by alignment-independent description of composition and transition of amino acid properties of their protein primary sequences. The entire training dataset contained 63 391 interactions and the best PCM model was obtained using signature descriptors of height 1, 2 and 3 and inducing the model with a support vector machine. The model showed excellent predictive ability with internal AUC = 0.923 and an external AUC = 0.940, as evaluated on a large external dataset. The advantage of PCM models is their extensibility making it possible to extend our model for new CYP isoforms and polymorphic CYP forms. A key benefit of PCM is that all proteins are confined in one single model, which makes it generally more stable and predictive as compared with single target models. The inclusion of the model in Bioclipse Decision Support makes it possible to make virtual instantaneous predictions (∼100 ms per prediction) while interactively drawing or modifying chemical structures in the Bioclipse chemical structure editor.
Self-starting of passively-mode-locked lasers with fast saturable absorbers (1993)

Self-starting of passively modelocked lasers with fast saturable absorbers is examined.
Land-Use Choices: Balancing Human Needs and Ecosystem Function (2004)

Conversion of land to grow crops, raise animals, obtain timber, and build cities is one of the foundations of human civilization. While land use provides these essential ecosystem goods, it alters a range of other ecosystem functions, such as the provisioning of freshwater, regulation of climate and biogeochemical cycles, and maintenance of soil fertility. It also alters habitat for biological diversity. Balancing the inherent trade-offs between satisfying immediate human needs and maintaining other ecosystem functions requires quantitative knowledge about ecosystem responses to land use. These responses vary according to the type of land-use change and the ecological setting, and have local, short-term as well as global, long-term effects. Land-use decisions ultimately weigh the need to satisfy human demands and the unintended ecosystem responses based on societal values, but ecological knowledge can provide a basis for assessing the trade-offs.
Regulation of Erythropoietin Receptor Activity in Endothelial Cells by Different Erythropoietin (EPO) Derivatives: An in Vitro Study (2013)

In endothelial cells, erythropoietin receptors (EPORs) mediate the protective, proliferative and angiogenic effects of EPO and its analogues, which act as EPOR agonists. Because hormonal receptors undergo functional changes upon chronic exposure to agonists and because erythropoiesis-stimulating agents (ESAs) are used for the long-term treatment of anemia, it is critical to determine the mechanism by which EPOR responsiveness is regulated at the vascular level after prolonged exposure to ESAs. Here, we investigated EPOR desensitization/resensitization in human umbilical vein endothelial cells (HUVECs) upon exposure to three ESAs with different pharmacokinetic profiles, epoetin alpha (EPOα), darbepoetin alpha (DarbEPO) and continuous EPOR activator (CERA). These agonists all induced activation of the transcription factor STAT-5, which is a component of the intracellular pathway associated with EPORs. STAT-5 activation occurred with either monophasic or biphasic kinetics for EPOα/DarbEPO and CERA, respectively. ESAs, likely through activation of the STAT-5 pathway, induced endothelial cell proliferation and stimulated angiogenesis in vitro, demonstrating a functional role for epoetins on endothelial cells. All epoetins induced EPOR desensitization with more rapid kinetics for CERA compared to EPOα and DarbEPO. However, the recovery of receptor responsiveness was strictly dependent on the type of epoetin, the agonist concentration and the time of exposure to the agonist. EPOR resensitization occurred with more rapid kinetics after exposure to low epoetin concentrations for a short period of desensitization. When the highest concentration of agonists was tested, the recovery of receptor responsiveness was more rapid with CERA compared to EPOα and was completely absent with DarbEPO. Our results demonstrate that these three ESAs regulate EPOR resensitization by very different mechanisms and that both the type of molecule and the length of EPOR stimulation are factors that are critical for the control of EPOR functioning in endothelial cells. The differences observed in receptor resensitization after stimulation with the structurally different ESAs are most likely due different control mechanisms of receptor turnover at the intracellular level.
ORIGINAL ARTICLE: The Combination of the Gastrointestinal Integrin (α4β7) and Selectin Ligand Enhances T‐Cell Migration to the Reproductive Tract During Infection with <i>Chlamydia trachomatis</i> (2009)

A unique population of memory T lymphocytes expressing both α4β7 and CLA gain access to reproductive tract tissues during a sexually transmitted infection with C. trachomatis and should be considered in development of vaccines against sexually transmitted infections.
<i>SYNFORM</i> ISSUE 2008/09 (2008)

The season of conferences is moving into top gear, and the agenda of SYNFORM is becoming quite crowded.Indeed, in the forthcoming issues we will report on several top events of the year 2008, such as the 236th ACS Conference that was recently held in Philadelphia (in the next issue of SYNFORM), and the looming 2nd EuCheMS Chemistry Congress in Turin.Although there are no conference reports in this issue, we cover some of the most exciting achievements in the area of organic synthesis, published in the current literature.Two out of four come from Japan, and specifically from the lab of Dr. Yukishige Ito, who revealed a stereoselective entry to β-L-rhamnopyranosides, and from the group of Professor Naoto Chatani and Dr. Mamoru Tobisu, who discovered how to use anisole derivatives as substrates for the Suzuki-Miyaura cross-coupling.Europe is represented by the group of Dr. Jieping Zhu (France), who developed an elegant and effective total synthesis of the alkaloid (-)-quinocarcin.Since the issue would not be complete without America, the fourth SYNSTORY article is focused on another innovative cross-coupling reaction, recently reported by the group of Professor Jin-Quan Yu (USA).
Immobilization of glucose oxidase in thin polypyrrole films: Influence of polymerization conditions and film thickness on the activity and stability of the immobilized enzyme (1993)

Using monomers that polymerize to form electrically conducting polymers, one can control the thickness of the polymer film and the amount of enzyme that can be immobilized in the films. First, an investigation of the major variables that influence the immobilization of glucose oxidase by entrapment in polypyrrole films, prepared by electropolymerization from aqueous solutions containing the enzyme and monomer, was carried out. Then the optimized conditions were used to assess the effects of film thickness on the activity and stability of immobilized enzyme. For the films ranged in thickness from 0.1 microm to 1.6 microm, the resulting apparent activity and stability of the immobilized enzyme were found to be a strong function of the polymer film thickness. Above a thickness of 1.0 microm, the apparent activity of the immobilized enzyme increases linearly with increasing film thickness. The nonlinearity observed for films of thickness less than 1.0 microm can be attributed to the changes observed in the morphology of the resulting polypyrrole films. Furthermore, it was noted that when the glucose oxidase/polypyrrole films are stored in phosphate buffer, at 4 degrees C, the observed rate of loss in apparent activity of the immobilized enzyme is highest for the first few days, also being higher for the thinner films. However, after the loosely entrapped enzyme is leached from the polymer film, the rate of loss in activity is very low indicating that the well-entrapped enzyme, as well as the polypyrrole films, exhibit good stability. Finally, the reproducibility of the immobilization technique is excellent.
Childhood Onset of Stiff-Man Syndrome (2013)

Childhood-onset SMS is a rare but underrecognized and treatable disorder. Serological and electrophysiological testing aid diagnosis.
Routing for Video Communications over Wireless Ad Hoc Networks (2008)

Multihop wireless networks (e.g., ad hoc networks) are characterized by
infrastructure independence and user mobility, making them an excellent match for applications that demand great simplicity and flexibility
in deployment and operations. However, the resulting fragile multihop
wireless paths and dynamic topology pose significant technical challenges
for enabling multimedia services in such networks. This chapter studies the problem of cross-layer multipath routing for multiple description
(MD) video in multihop wireless networks. In particular, we provide practical solutions to the following key questions: (i) How to formulate a
multimedia-centric routing problem that minimizes video distortion by
choosing optimal paths? (ii) What are the performance limits? (iii) How
to design an efficient solution procedure? (iv) How to implement the proposed algorithms in a distributed environment? We show that cross-layer
design is imperative and effective to meeting the stringent quality of service
(QoS) requirements of multimedia applications in highly dynamic multihop
wireless networks.
Evaluation of cochlear implants as an auditory prosthesis (1977)

Thirteen persons who had single-channel electrodes implanted in scala vestibuli were subjected to a large battery of psychoacoustic tests. The battery included measures of sound-field thresholds; intensity, frequency, and temporal discrimination; masking; pattern recognition; word recognition; and lipreading. The results of these tests can be organized around the concept of listening through a single auditory channel. [This work was conducted under contract from NINCDS (NO1-NS-5-2331) to the Eye and Ear Hospital of Pittsburgh.]