gebhart/patrepeval huggingface dataset:
Using a ResearchKit Smartphone App to Collect Rheumatoid Arthritis Symptoms From Real-World Participants: Feasibility Study (Preprint) (2017)

<sec> <title>BACKGROUND</title> Using smartphones to enroll, obtain consent, and gather self-reported data from patients has the potential to enhance our understanding of disease burden and quantify physiological impact in the real world. It may also be possible to harness integral smartphone sensors to facilitate remote collection of clinically relevant data. </sec> <sec> <title>OBJECTIVE</title> We conducted the Patient Rheumatoid Arthritis Data From the Real World (PARADE) observational study using a customized ResearchKit app with a bring-your-own-device approach. Our objective was to assess the feasibility of using an entirely digital approach (social media and smartphone app) to conduct a real-world observational study of patients with rheumatoid arthritis. </sec> <sec> <title>METHODS</title> We conducted this observational study using a customized ResearchKit app with a bring-your-own-device approach. To recruit patients, the PARADE app, designed to guide patients through a series of tasks, was publicized via social media platforms and made available for patients in the United States to download from the Apple App Store. We collected patient-reported data, such as medical history, rheumatoid arthritis-related medications (past and present), and a range of patient-reported outcome measures. We included in the assessment a joint-pain map and a novel objective assessment of wrist range of movement, measured by the smartphone-embedded gyroscope and accelerometer. </sec> <sec> <title>RESULTS</title> Within 1 month of recruitment via social media campaigns, 399 participants self-enrolled, self-consented, and provided complete demographic data. Joint pain was the most frequently reported rheumatoid arthritis symptom to bother study participants (344/393, 87.5%). Severe patient-reported wrist pain appeared to be inversely linked with the range of wrist movement measured objectively by the app. At study entry, 292 of 399 participants (73.2%) indicated a preference for participating in a mobile app–based study. The number of participants in the study declined to 45 of 399 (11.3%) at week 12. </sec> <sec> <title>CONCLUSIONS</title> Despite the declining number of participants over time, the combination of social media and smartphone app with sensor integration was a feasible and cost-effective approach for the collection of patient-reported data in rheumatoid arthritis. Integral sensors within smartphones can be harnessed to provide novel end points, and the novel wrist range of movement test warrants further clinical validation. </sec>
Volume-selective magnetic resonance imaging using an adjustable, single-sided, portable sensor (2008)

Portable, single-sided NMR sensors can operate under conditions inaccessible to conventional NMR while featuring lower cost, portability, and the ability to analyze arbitrary-sized objects. Such sensors can nondestructively probe the interior of samples by collecting images and measuring relaxation and diffusion constants, and, given careful shimming schemes, even perform chemical analysis. The inherently strong magnetic-field gradients of single-sided sensors developed so far has prevented imaging of materials with high water content, such as biological tissues, over large volumes whereas designs with more homogeneous fields suffer from low field strength and typically cannot probe volumes larger than approximately 10 cm(3). We present a design with a continuously adjustable sensitive volume, enabling the effective volume to be enlarged several fold. This capability allows for imaging in reasonable times of much bigger objects and opens the door to the possibility of clinical imaging with portable sensors. We demonstrate MRI in axial and sagittal planes, at different depths of the sensitive volume and T(1)-weighted contrast in a tissue sample.
Timing of Adjunctive Azithromycin for Unscheduled Cesarean Delivery and Postdelivery Infection (2022)

ClinicalTrials.gov, NCT01235546.
The Role of Mass Spectrometry and Proteogenomics in the Advancement of HLA Epitope Prediction (2018)

A challenge in developing personalized cancer immunotherapies is the prediction of putative cancer-specific antigens. Currently, predictive algorithms are used to infer binding of peptides to human leukocyte antigen (HLA) heterodimers to aid in the selection of putative epitope targets. One drawback of current epitope prediction algorithms is that they are trained on datasets containing biochemical HLA-peptide binding data that may not completely capture the rules associated with endogenous processing and presentation. The field of MS has made great improvements in instrumentation speed and sensitivity, chromatographic resolution, and proteogenomic database search strategies to facilitate the identification of HLA-ligands from a variety of cell types and tumor tissues. As such, these advances have enabled MS profiling of HLA-binding peptides to be a tractable, orthogonal approach to lower throughput biochemical assays for generating comprehensive datasets to train epitope prediction algorithms. In this review, we will highlight the progress made in the field of HLA-ligand profiling enabled by MS and its impact on current and future epitope prediction strategies.
Modulation of the proteolytic activity of the complement protease C1s by polyanions: implications for polyanion-mediated acceleration of interaction between C1s and SERPING1 (2009)

The complement system plays crucial roles in the immune system, but incorrect regulation causes inflammation and targeting of self-tissue, leading to diseases such as systemic lupus erythematosus, rheumatoid arthritis and age-related macular degeneration. In vivo, the initiating complexes of the classical complement and lectin pathways are controlled by SERPING1 [(C1 inhibitor) serpin peptidase inhibitor, clade G, member 1], which inactivates the components C1s and MASP-2 (mannan-binding lectin serine peptidase 2). GAGs (glycosaminoglycan) and DXS (dextran sulfate) are able to significantly accelerate SERPING1-mediated inactivation of C1s, the key effector enzyme of the classical C1 complex, although the mechanism is poorly understood. In the present study we have shown that C1s can bind to DXS and heparin and that these polyanions enhanced C1s proteolytic activity at low concentrations and inhibited it at higher concentrations. The recent determination of the crystal structure of SERPING1 has given rise to the hypothesis that both the serpin (serine protease inhibitor)-polyanion and protease-polyanion interactions might be required to accelerate the association rate of SERPING1 and C1s. To determine what proportion of the acceleration was due to protease-polyanion interactions, a chimaeric mutant of alpha1-antitrypsin containing the P4-P1 residues from the SERPING1 RCL (reactive-centre loop) was produced. Like SERPING1, this molecule is able to effectively inhibit C1s, but is unable to bind polyanions. DXS exerted a biphasic effect on the association rate of C1s which correlated strongly with the effect of DXS on C1s proteolytic activity. Thus, whereas polyanions are able to bind C1s and modulate its activity, polyanion interactions with SERPING1 must also play a vital role in the mechanism by which these cofactors accelerate the C1s-SERPING1 reaction.
Galiellalactone induces cell cycle arrest and apoptosis through the ATM/ATR pathway in prostate cancer cells (2015)

Galiellalactone (GL) is a fungal metabolite that presents antitumor activities on prostate cancer in vitro and in vivo. In this study we show that GL induced cell cycle arrest in G2/M phase, caspase-dependent apoptosis and also affected the microtubule organization and migration ability in DU145 cells. GL did not induce double strand DNA break but activated the ATR and ATM-mediated DNA damage response (DDR) inducing CHK1, H2AX phosphorylation (fH2AX) and CDC25C downregulation. Inhibition of the ATM/ATR activation with caffeine reverted GL-induced G2/M cell cycle arrest, apoptosis and DNA damage measured by fH2AX. In contrast, UCN-01, a CHK1 inhibitor, prevented GL-induced cell cycle arrest but enhanced apoptosis in DU145 cells. Furthermore, we found that GL did not increase the levels of intracellular ROS, but the antioxidant N-acetylcysteine (NAC) completely prevented the effects of GL on fH2AX, G2/M cell cycle arrest and apoptosis. In contrast to NAC, other antioxidants such as ambroxol and EGCG did not interfere with the activity of GL on cell cycle. GL significantly suppressed DU145 xenograft growth in vivo and induced the expression of fH2AX in the tumors. These findings identify for the first time that GL activates DDR in prostate cancer.
Mass absorption coefficient of tungsten and tantalum, 1450 eV to 2350 eV: Experiment, theory, and application (2003)

The mass absorption coefficients of tungsten and tantalum were measured with soft x-ray photons from 1450 eV to 2350 eV using an undulator source. This region includes the M3, M4, and M5 absorption edges. X-ray absorption fine structure was calculated within a real-space multiple scattering formalism; the predicted structure was observed for tungsten and to a lesser degree tantalum as well. Separately, the effects of dynamic screening were observed as shown by an atomic calculation within the relativistic time-dependent local-density approximation. Dynamic screening effects influence the spectra at the 25 % level and are observed for both tungsten and tantalum. We applied these results to characterize spatially-resolved spectra of a tungsten integrated circuit interconnect obtained using a scanning transmission x-ray microscope. The results indicate tungsten fiducial markers were deposited into silica trenches with a depths of 50 % and 60 % of the markers' heights.
Epidermal growth factor‐dependent growth of human KB cells in a defined medium and altered growth factor requirements of KB mutants resistant to EGF‐<i>Pseudomonas</i> exotoxin conjugates (1988)

A serum-free culture system was established for human KB carcinoma (HeLa) cells that consisted of a chemically defined medium and several growth factors including epidermal growth factor (EGF), insulin, transferrin, hydrocortisone, and ethanolamine. EGF and insulin showed the greatest effects on the growth rate of KB cells. Insulin-like growth factor I (IGF-I) at the same concentration as insulin stimulated cell growth less than insulin. Transferrin, hydrocortisone, or ethanolamine had no growth-stimulatory effects alone but were stimulatory when combined with EGF and/or insulin. Transforming growth factor-beta inhibited growth and triiodothyronine stimulated growth. The growth factor requirements were established for several KB mutants with low EGF receptor levels that had been selected for resistance to a conjugate of EGF with Pseudomonas exotoxin (EGF-PE). Three of five KB mutants did not respond to EGF; two other mutants responded to a lesser extent than the parental KB cells. Four mutants had a reduced response to insulin and responded to T3; one mutant (ET-30) responded to neither. These results indicate that KB cells selected for EGF-PE resistance have lost their growth response to EGF and illustrate the usefulness of serum-free medium for studying the growth factor requirements of mutants with altered receptor levels.
Genetic variants in the <scp><i>IL12B</i></scp> gene are associated with inflammatory bowel diseases in the <scp>K</scp>orean population (2013)

This study is first to identify SNP rs2288831 in the IL12B gene as a susceptible variation for CD. Further studies in other ethnic groups are warranted to validate the association of this genetic variant with IBD.
Differential Interactions of Na+ Channel Toxins with T-type Ca2+ Channels (2008)

Two types of voltage-dependent Ca(2+) channels have been identified in heart: high (I(CaL)) and low (I(CaT)) voltage-activated Ca(2+) channels. In guinea pig ventricular myocytes, low voltage-activated inward current consists of I(CaT) and a tetrodotoxin (TTX)-sensitive I(Ca) component (I(Ca(TTX))). In this study, we reexamined the nature of low-threshold I(Ca) in dog atrium, as well as whether it is affected by Na(+) channel toxins. Ca(2+) currents were recorded using the whole-cell patch clamp technique. In the absence of external Na(+), a transient inward current activated near -50 mV, peaked at -30 mV, and reversed around +40 mV (HP = -90 mV). It was unaffected by 30 microM TTX or micromolar concentrations of external Na(+), but was inhibited by 50 microM Ni(2+) (by approximately 90%) or 5 microM mibefradil (by approximately 50%), consistent with the reported properties of I(CaT). Addition of 30 microM TTX in the presence of Ni(2+) increased the current approximately fourfold (41% of control), and shifted the dose-response curve of Ni(2+) block to the right (IC(50) from 7.6 to 30 microM). Saxitoxin (STX) at 1 microM abolished the current left in 50 microM Ni(2+). In the absence of Ni(2+), STX potently blocked I(CaT) (EC(50) = 185 nM) and modestly reduced I(CaL) (EC(50) = 1.6 microM). While TTX produced no direct effect on I(CaT) elicited by expression of hCa(V)3.1 and hCa(V)3.2 in HEK-293 cells, it significantly attenuated the block of this current by Ni(2+) (IC(50) increased to 550 microM Ni(2+) for Ca(V)3.1 and 15 microM Ni(2+) for Ca(V)3.2); in contrast, 30 microM TTX directly inhibited hCa(V)3.3-induced I(CaT) and the addition of 750 microM Ni(2+) to the TTX-containing medium led to greater block of the current that was not significantly different than that produced by Ni(2+) alone. 1 microM STX directly inhibited Ca(V)3.1-, Ca(V)3.2-, and Ca(V)3.3-mediated I(CaT) but did not enhance the ability of Ni(2+) to block these currents. These findings provide important new implications for our understanding of structure-function relationships of I(CaT) in heart, and further extend the hypothesis of a parallel evolution of Na(+) and Ca(2+) channels from an ancestor with common structural motifs.
Older Adults Living With Social Robots: Promoting Social Connectedness in Long-Term Communities (2019)

Social robots have been used to investigate human-to-robot engagement-but connection between one person and another is the real key for human emotional wellness. This work explores the role and impact of a social robot in facilitating human-to-human engagement in an assisted-living community. Older adults, in particular, are a population in need of sufficient social connectedness to promote their well-being. While several studies have sought to investigate how social robots can help to improve older adults? quality of life, not many have studied their long-term impact on community-level engagement.
Identification of a DNA region from lactococcal phage sk1 protecting phage 712 from the abortive infection mechanism AbiF (2000)

Bacteriophage 712 is a small isometric-headed phage which is sensitive to the lactococcal abortive infection mechanism AbiF. Its 29.6-kb DNA genome was characterized by restriction mapping and transcriptional analysis. Construction of a gene bank of lactococcal phage sk1, which is insensitive to the action of AbiF, in Lactococcus lactis containing AbiF resulted in the identification of a 324-bp DNA fragment which reduced the effect of the abortive infection mechanism on phage 712. Analysis of this region provided evidence that the action of AbiF is related to the cos ends of small isometric-headed phages. Sequence analysis of a 3.2-kb segment containing the middle operon and the cos ends of phage 712 genome allowed comparison of this part of the phage 712 genome with the equivalent sequences of four other small isometric-headed phages.
Simultaneous Pancreas-Kidney Transplantation From Donation After Cardiac Death (2005)

SPK transplantation using selected DCD donors is a safe and viable method to expand the organ pool for transplantation.
Changes of Components in Salt-Fermented Anchovy, Engraulis Japonicus Sauce during Fermentation (2000)

To investigate changes of components in salt-fermented anchovy, Engraulis japonims sauce during fermentation, various chemical properties were examined at months interval during 18 months fermentation. Moisture content and pH were decreased slightly, but the contents of VBN and crude protein, total and amino nitrogen, hydrolytic degree and absorbance at 453 nm were increased gradually during fermentation. On the other hand, ash content and salinity showed almost no change. Hk and uric acid were the most abundant in ATP related compounds, ranging from in salt-fermented anchovy sauce during the fermentation, After 18 months of fermentation the sauce was rich in free amino acids, such as glutamic acid, leucine, alanine, lysine, isoleucine, valine in that order.
Three-Dimensionally Complex Phase Behavior and Collective Phenomena in Mixtures of Acoustically Powered Chiral Microspinners (2023)

The process of dynamic self-organization of small building blocks is fundamental to the emergent function of living systems and is characteristic of their out-of-equilibrium homeostasis. The ability to control the interactions of synthetic particles in large groups could lead to the realization of analogous macroscopic robotic systems with microscopic complexity. Rotationally induced self-organization has been observed in biological systems and modeled theoretically, but studies of fast, autonomously moving synthetic rotors remain rare. Here, we report switchable, out-of-equilibrium hydrodynamic assembly and phase separation in suspensions of acoustically powered chiral microspinners. Semiquantitative modeling suggests that three-dimensionally (3D) complex spinners interact through viscous and weakly inertial (streaming) flows. The interactions between spinners were studied over a range of densities to construct a phase diagram, which included gaseous dimer pairing at low density, collective rotation and multiphase separation at intermediate densities, and ultimately jamming at high density. The 3D chirality of the spinners leads to self-organization in parallel planes, forming a three-dimensionally hierarchical system that goes beyond the 2D systems that have so far been modeled computationally. Dense mixtures of spinners and passive tracer particles also show active-passive phase separation. These observations are consistent with recent theoretical predictions of the hydrodynamic coupling between rotlets generated by autonomous spinners and provide an exciting experimental window to the study of colloidal active matter and microrobotic systems.
Dielectric response of multiwalled carbon nanotubes as a function of applied ac-electric fields (2008)

The complex dielectric constant (ε∗) is reported for multiwalled carbon nanotubes (MWCNTs) up to 105 Hz as a function of ac-electric field amplitudes Erot (in phase and same frequency as the measurement) and Eac (different phase and fixed frequency with respect to the measurement). A slow relaxation process (mode 1) is observed, which shifts to higher frequency with increasing Erot but is independent of Eac. A fast relaxation process (mode 2) is also observed, which is independent of Erot but shifts to higher frequency with increasing Eac (opposite to that of mode 1). An ac-conductivity analysis of MWCNT reveals insights on how Erot and Eac influence the dissipation.
Optimization of optical spin readout of the nitrogen-vacancy center in diamond based on spin relaxation model (2022)

For quantum sensing, it is vital to develop an efficient technique for determining the quantum state of the sensor. We optimize the weighting of the photoluminescence intensity for readout of the spin state of the nitrogen-vacancy (NV) center in diamond. We find that adopting a physical model that considers the optical transitions and relaxations of the NV center allows for an efficient readout. Our method improves the signal-to-noise ratio of the readout by 5.4% in a short time of 3 s, while the existing methods typically require 1 min of integration time. We also show that our technique enhances the readout of the nuclear spin memory. The demonstrated way is helpful for a wide range of measurements, from a few minutes to several days.
Temporal and Topographic Profiles of Tissue Hypoxia Following Transient Focal Cerebral Ischemia in Rats (2006)

Intravascular accumulation of blood cells after brain ischemia-reperfusion can cause obstruction of cerebral blood flow and tissue hypoxia/ischemia as a consequence. In the present study, we examined temporal and topographic changes of tissue hypoxia/ischemia after occlusion of the middle cerebral artery (MCA) for 60 min in rats with immunohistochemical staining for hypoxia (2-nitroimidazole hypoxia marker: hypoxyprobe-1 adducts). Our results showed that tissue hypoxia expressed as positive staining for hypoxyprobe-1 adducts preceded neuronal degeneration. Platelets and granulocytes were detected close to the hypoxyprobe-1 adducts positive area. These results suggested that the hypoxic environment could persist even after reperfusion of MCA, because of vascular obstruction with accumulation of platelets and granulocytes.
How evaporation and condensation lead to self-oscillations in the single-branch pulsating heat pipe (2019)

The physics behind the instability at the source of oscillations in a single-branch pulsating heat pipe is investigated. Oscillations produced by the resonator increase in amplitude when pressure induced by evaporation-condensation (positive feedback mechanism) overcomes the viscous losses (dissipation).
An Adaptive WLAN Interference Mitigation Scheme for ZigBee Sensor Networks (2015)

We propose an adaptive interference avoidance scheme that enhances the performance of ZigBee networks by adapting ZigBees' transmissions to measured wireless local area network (WLAN) interference. Our proposed algorithm is based on a stochastic analysis of ZigBee operation that is interfered with by WLAN transmission, given ZigBee and WLAN channels are overlaid in the industrial, scientific, and medical (ISM) band. We assume that WLAN devices have higher transmission power than ZigBee devices. Then, the high transmission power of WLAN devices causes the capture effect when WLAN and ZigBee transmit simultaneously. On the other hand, ZigBee performs backoff during clear channel assessment (CCA) operation if the WLAN is transmitting its frames on the channel. We adopt a widely used WLAN queueing/transmission model that is based on a Markov chain concept. We model a ZigBee device's operation using the Markov chain that includes WLAN interference statistically derived from the WLAN queueing/transmission model. Our proposed algorithm is evaluated in a simulated ZigBee network in the presence of varying WLAN interference. Numerical results show that our WLAN interference mitigation scheme finds the ZigBee control parameters, among a candidate set, which enhances ZigBee network performance compared to the conventional ZigBee operation.
Manifold-enhanced Segmentation through Random Walks on Linear Subspace Priors (2012)

In this paper we propose a novel method for knowledge-based segmentation. Our contribution lies on the introduction of linear sub-spaces constraints within the random-walk segmentation framework. Prior knowledge is obtained through principal component analysis that is then combined with conventional boundary constraints for image segmentation. The approach is validated on a challenging clinical setting that is multicomponent segmentation of the human upper leg skeletal muscle in Magnetic Resonance Imaging, where there is limited visual differentiation support between muscle classes.