gebhart/patrepeval huggingface dataset:
Current Interruption—Instrumentation and Applications (1987)

This paper describes an electronic circuit for periodic interruption of current to a cell with simultaneous observation of closed‐circuit and open‐circuit electrode potentials. The open‐circuit potential may be observed at interruption times ranging from 2.0 μs to 2.0s or longer. The duty cycle of the cell may be adjusted between 40 and 99.93%. Application of the circuit to observe relaxation of polarization is demonstrated with simple electrical test circuits, with commercial dry cells, and with a mass‐transfer controlled rotating disk electrode. The latter example shows that interruption can provide not only resistance measurements but also estimates of mass‐transfer parameters.
Supplementary Table 2 from Enhanced Radiation Sensitivity in HPV-Positive Head and Neck Cancer (2023)

&lt;p&gt;XLSX - 46K, Table of Primer sequences used and probes.&lt;/p&gt;
Raman Spectroscopy for Chemical Analysis (2000)

Many scientists have a passing familiarity with Raman spectroscopy and those of us who have tried using it, say 15 years ago, to identify chemical groups were probably disappointed. At the time, a long recording time and poor signal/noise ratios did not inspire strong recommendations for chemical analysis. This was disappointing because there was always a deep-seated feeling that here was a technique that could be capable of detailed chemical analysis, indeed chemical imaging. How things have changed! The more widespread use of infrared lasers, CCD detectors and signal processing using powerful PCs have all reduced the recording times from around one hour to about 30 seconds. The general convenience of the technique is bringing it to the attention of a wider audience of chemists and materials scientists. This volume by McCreery is another in the excellent Wiley series of monographs on Analytical Chemistry. These have provided a very high standard, indeed a `flagship' of authority and quality in this broad area. The treatment given here will capture the attention of both the novice who wants to find out how Raman spectroscopy works, and the expert practitioner who requires some original sources of information. It will be very useful to all researchers who use, or wish to use, the Raman technique. The introductory sections really do highlight the differences to be expected between modern Raman techniques and the `rival' techniques of near infrared (NIR) and Fourier transform infrared (FTIR) spectroscopies. The treatment is a no-nonsense, pragmatic approach, with comparable spectra for the techniques, warts and all! Later sections then go on to give a rigorous analysis of signal levels, signal/noise ratios and practical details of the lasers, detectors and software that are best suited to specific needs and applications. There are several extensions of Raman spectroscopy that have been made possible by improved software and instrumentation in recent years, but probably the ability to form images is the one that will capture a large share of devotees. In conclusion, McCreery gives a very well balanced and authoritative account of Raman microscopy in all its different variants. He repeats this very effectively for its application via fibre-optic probes, and the examples that he has selected are clear, simple and useful. The section on surface enhanced Raman spectroscopy (SERS) is a model of clarity and one that I will use in future lectures. I can recommend this volume without hesitation. P J Dobson
J0240203 Evaluation of Wall Shear Stresses and Energy Loss in Aortic Aneurysms with Consideration of Wall Deformations (2014)

Hemodynamics can be a key factor associated with the onset and progress of aortic aneurysms, which are normally triggered by atherosclerosis. This study is aiming to clarify the aortic aneurysm hemodynamics with consideration of wall deformations and to evaluate the wall shear stresses and energy loss with rigid and deformable vessels by introducing two indices of the pulsatile pressure index (PPI) and the pulsatile energy loss index (PELI). A realistic three-dimensional computational fluid dynamic model of aortic aneurysm is constructed based on medical images and is further connected to a 0-1D model for the whole cardiovascular system, which provides both boundary conditions of pressure and flow-volumetric rate waveforms at inlet and outlet as well as vessel wall deformations. Our result shows that the wall deformation can result in significant differences in a three-dimensional, and hence points to the importance of considering the influence of vessel compliance in evaluation of the pulsatile flow energy loss.
CSO distortions due to the combined effects of self- and external-phase modulations in long-distance 1550-nm AM-CATV systems (1999)

We found that the combined effects of self- and external-phase modulations must be considered in order to precisely predict the composite second-order distortions in a long-distance 1550-nm externally modulated AM-cable TV (CATV) system, especially when the applied phase modulation index and modulating tone frequency to the integrated phase modulator are high. This result has important implications to the optimum design of 1550-nm transmitter for long-distance AM and QAM-CATV systems.
Rule based fuzzy classification using squashing functions (2008)

In this paper we are dealing with the construction of a fuzzy rule based classifier. A three-step method is proposed based on Łukasiewicz logic for the description of the rules and the fuzzy memberships to construct concise and highly comprehensible fuzzy rules. In our method, a genetic algorithm is applied to evolve the structure of the rules and then a gradient based optimization to fine tune the fuzzy membership functions. The introduced squashing function allows us not only to handle the approximation of the operators and the memberships in the same way, but also to efficiently calculate the derivatives of the membership functions. We also show applications of the model on the UCI machine learning database.
The Seed Proteome Web Portal (2012)

The Seed Proteome Web Portal (SPWP; http://www.seed-proteome.com/) gives access to information both on quantitative seed proteomic data and on seed-related protocols. Firstly, the SPWP provides access to the 475 different Arabidopsis seed proteins annotated from two dimensional electrophoresis (2DE) maps. Quantitative data are available for each protein according to their accumulation profile during the germination process. These proteins can be retrieved either in list format or directly on scanned 2DE maps. These proteomic data reveal that 40% of seed proteins maintain a stable abundance over germination, up to radicle protrusion. During sensu stricto germination (24 h upon imbibition) about 50% of the proteins display quantitative variations, exhibiting an increased abundance (35%) or a decreasing abundance (15%). Moreover, during radicle protrusion (24-48 h upon imbibition), 41% proteins display quantitative variations with an increased (23%) or a decreasing abundance (18%). In addition, an analysis of the seed proteome revealed the importance of protein post-translational modifications as demonstrated by the poor correlation (r(2) = 0.29) between the theoretical (predicted from Arabidopsis genome) and the observed protein isoelectric points. Secondly, the SPWP is a relevant technical resource for protocols specifically dedicated to Arabidopsis seed proteome studies. Concerning 2D electrophoresis, the user can find efficient procedures for sample preparation, electrophoresis coupled with gel analysis, and protein identification by mass spectrometry, which we have routinely used during the last 12 years. Particular applications such as the detection of oxidized proteins or de novo synthesized proteins radiolabeled by [(35)S]-methionine are also given in great details. Future developments of this portal will include proteomic data from studies such as dormancy release and protein turnover through de novo protein synthesis analyses during germination.
CHAPTER 20: Biotechnology Aspects of Cucumber Mosaic Virus (2019)

Plants have been considered an excellent platform for producing important foreign proteins and provide some advantages over animal and bacterial cells. Because cucumber mosaic virus (CMV) can multiply efficiently in plant cells and has a broad host range, it has the potential to be developed as a promising viral vector for gene expression. In addition, it has been demonstrated that CMV vectors can be used for virus-induced gene silencing and thus in functional genomics as a research tool. A substantial number of CMV vectors have already been developed. In this chapter, the development of different CMV vectors is described by explaining the nature of each construct, its uses, and its limitations.
PRELOAD OPTIMIZATION USING “STARLING CURVE” GENERATION DURING SHOCK RESUSCITATION: CAN IT BE DONE? (2004)

Preload-directed resuscitation is the standard of care in U.S. trauma centers. As part of our standardized protocol for traumatic shock resuscitation, patients who do not respond to initial interventions of hemoglobin replacement and fluid volume loading have optimal preload determined using a standardized algorithm to generate a "Starling curve." We retrospectively analyzed data from 147 consecutive resuscitation protocol patients during the 24 months ending August 2002. Fifty (34%) of these patients required preload optimization, of which the optimization algorithm was completed in 36 (72%). The average age of those who required preload optimization was 44 +/- 3 years vs. 34 +/- 1 years for patients who did not. Execution of the algorithm caused PCWP to increase from 18 +/- 1 mmHg to a maximum of 25 +/- 2 mmHg and CI to increase from 3.2 +/- 0.1 L/min m(-2) to 4.5 +/- 0.4 L/min m(-2). Algorithm logic determined PCWP = 24 +/- 2 to be optimal preload at the maximum CI = 4.8 +/- 0.4, and as the volume loading threshold for the remaining time of the resuscitation process. Starling curve preload optimization was begun 6.5 +/- 0.8 h after start of the resuscitation protocol and required 36 +/- 5 min and 4 +/- 0.4 fluid boluses (1.6 +/- 0.2 L). Comparison of early response of those patients who required preload optimization and those who did not indicated hemodynamic compromise apparent in the 1st 4 h of standardized resuscitation. We conclude that preload optimization using sequential fluid bolus and PCWP-CI measurement to generate a Starling curve is feasible during ICU shock resuscitation, but that there is the disadvantage that increasing and maintaining high PCWP may contribute to problematic tissue edema.
The Arabidopsis Rho of Plants GTPase AtROP6 Functions in Developmental and Pathogen Response Pathways (2013)

How plants coordinate developmental processes and environmental stress responses is a pressing question. Here, we show that Arabidopsis (Arabidopsis thaliana) Rho of Plants6 (AtROP6) integrates developmental and pathogen response signaling. AtROP6 expression is induced by auxin and detected in the root meristem, lateral root initials, and leaf hydathodes. Plants expressing a dominant negative AtROP6 (rop6(DN)) under the regulation of its endogenous promoter are small and have multiple inflorescence stems, twisted leaves, deformed leaf epidermis pavement cells, and differentially organized cytoskeleton. Microarray analyses of rop6(DN) plants revealed that major changes in gene expression are associated with constitutive salicylic acid (SA)-mediated defense responses. In agreement, their free and total SA levels resembled those of wild-type plants inoculated with a virulent powdery mildew pathogen. The constitutive SA-associated response in rop6(DN) was suppressed in mutant backgrounds defective in SA signaling (nonexpresser of PR genes1 [npr1]) or biosynthesis (salicylic acid induction deficient2 [sid2]). However, the rop6(DN) npr1 and rop6(DN) sid2 double mutants retained the aberrant developmental phenotypes, indicating that the constitutive SA response can be uncoupled from ROP function(s) in development. rop6(DN) plants exhibited enhanced preinvasive defense responses to a host-adapted virulent powdery mildew fungus but were impaired in preinvasive defenses upon inoculation with a nonadapted powdery mildew. The host-adapted powdery mildew had a reduced reproductive fitness on rop6(DN) plants, which was retained in mutant backgrounds defective in SA biosynthesis or signaling. Our findings indicate that both the morphological aberrations and altered sensitivity to powdery mildews of rop6(DN) plants result from perturbations that are independent from the SA-associated response. These perturbations uncouple SA-dependent defense signaling from disease resistance execution.
Glycolytic metabolism is essential for CCR7 oligomerization and dendritic cell migration (2018)

Dendritic cells (DCs) are first responders of the innate immune system that integrate signals from external stimuli to direct context-specific immune responses. Current models suggest that an active switch from mitochondrial metabolism to glycolysis accompanies DC activation to support the anabolic requirements of DC function. We show that early glycolytic activation is a common program for both strong and weak stimuli, but that weakly activated DCs lack long-term HIF-1α-dependent glycolytic reprogramming and retain mitochondrial oxidative metabolism. Early induction of glycolysis is associated with activation of AKT, TBK, and mTOR, and sustained activation of these pathways is associated with long-term glycolytic reprogramming. We show that inhibition of glycolysis impaired maintenance of elongated cell shape, DC motility, CCR7 oligomerization, and DC migration to draining lymph nodes. Together, our results indicate that early induction of glycolysis occurs independent of pro-inflammatory phenotype, and that glycolysis supports DC migratory ability regardless of mitochondrial bioenergetics.
miR‐146a regulates mechanotransduction and pressure‐induced inflammation in small airway epithelium (2012)

Mechanical ventilation generates biophysical forces, including high transmural pressures, which exacerbate lung inflammation. This study sought to determine whether microRNAs (miRNAs) respond to this mechanical force and play a role in regulating mechanically induced inflammation. Primary human small airway epithelial cells (HSAEpCs) were exposed to 12 h of oscillatory pressure and/or the proinflammatory cytokine TNF-α. Experiments were also conducted after manipulating miRNA expression and silencing the transcription factor NF-κB or toll-like receptor proteins IRAK1 and TRAF6. NF-κB activation, IL-6/IL-8/IL-1β cytokine secretion, miRNA expression, and IRAK1/TRAF6 protein levels were monitored. A total of 12 h of oscillatory pressure and TNF-α resulted in a 5- to 7-fold increase in IL-6/IL-8 cytokine secretion, and oscillatory pressure also resulted in a time-dependent increase in IL-6/IL-8/IL-1β cytokine secretion. Pressure and TNF-α also resulted in distinct patterns of miRNA expression, with miR-146a being the most deregulated miRNA. Manipulating miR-146a expression altered pressure-induced cytokine secretion. Silencing of IRAK1 or TRAF6, confirmed targets of miR-146a, resulted in a 3-fold decrease in pressure-induced cytokine secretion. Cotransfection experiments demonstrate that miR-146a's regulation of pressure-induced cytokine secretion depends on its targeting of both IRAK1 and TRAF6. MiR-146a is a mechanosensitive miRNA that is rapidly up-regulated by oscillatory pressure and plays an important role in regulating mechanically induced inflammation in lung epithelia.
Vibration Analysis of Elevator Rope with Vibration Suppressor (2007)

The lateral vibration of elevator ropes for high-rise buildings, which is forcibly excited by the displacement of the building induced by wind force, is numerically analyzed, and a new practical method of reducing rope vibration by using vibration suppressors is proposed for relaxing the restricted elevator operation. Finite difference analyses of rope vibration with/without vibration suppressors are performed. The advantage of using vibration suppressors for reducing lateral vibration of the rope is demonstrated through numerical calculation: The resonant position of a rope with vibration suppressors greatly depends on the position of the vibration suppressors. When the vibration suppressors are uniformly installed along the full length of the rope, the maximum rope deflection becomes smaller as the number of vibration suppressors is made greater. It is also shown that the calculated results of the reaction force from the vibration suppressor are in fairly good agreement with the experimental results.
Anatomic Variants of the Hepatic Arteries (1986)

The anatomic variants of the hepatic arteries observed in 216 abdominal arteriographies were analysed. A comparison was made with MICHELS' work based upon 200 anatomic dissections, and SUZUKI'S investigation of 200 abdominal arteriographies. Seven not previously classified anatomic variants of the hepatic arteries were found. The large number of variants may be ascribed to intricacies in the development of the vascular supply in the embryo and to the normal caudal displacement of the liver taking place in the embryo and fetus. Knowledge concerning existing variants is important in performing surgery, embolization and intra-arterial infusion chemotherapy in the hepatic region.
Extracting Adverse Drug Effects from User Experiences: A Baseline (2018)

It has been proved that pharmacovigilance benefits from the analysis and extraction of user generated data from blogs, medical forums or other social networks, regarding adverse effect mentions or complaints that occur from taking certain drugs. Data mining, machine learning, pattern recognition, content summarization and natural language processing techniques are often used in this field with promising results. However, there are still several difficulties concerning the extraction, as the highly domain-specific vocabulary presents a few challenges. This is mainly because patients like to use idiomatic or vernacular expressions along with descriptive symptom explanations, which tend to deviate from grammatical rules or expected terms. To address this issue, we propose a well-curated baseline. We believe that building a specific lexicon, identifying common linguistic patterns and observing certain phrasal structures is key to first understanding how a user generates contents online. From there, we can later develop sets of tailored rules that will allow data classification/extraction systems to potentially improve their efficiency at these tasks.
Growth factor‐like effects of placental alkaline phosphatase in human fetus and mouse embryo fibroblasts (2000)

Human placental alkaline phosphatase (PALP) is synthesized in the placenta during pregnancy and is also expressed in many cancer patients; however, its physiological role is unknown. Here we show that in human fetus fibroblasts as well as normal and H-ras-transformed mouse embryo fibroblasts PALP stimulates DNA synthesis and cell proliferation in synergism with insulin, zinc and calcium. The mitogenic effects of PALP are associated with the activation of c-Raf-1, p42/p44 mitogen-activated protein kinases, p70 S6 kinase, Akt/PKB kinase and phosphatidylinositol 3'-kinase. The results suggest that in vivo PALP may promote fetus development as well as the growth of cancer cells which express oncogenic Ras.
Sirolimus vs. Paclitaxel Stents: Little Difference in REALITY (2006)

In this randomized trial (known as REALITY), researchers compared the two most widely used drug-eluting stents, sirolimus-eluting and
Molecular characteristics of advanced colorectal cancer and multi-hit PIK3CA mutations. (2022)

3535 Background: Approximately 20% of colorectal cancer (CRC) has an activating mutation in the PIK3CA oncogene. PIK3CA codes for the catalytic subunit of phosphoinositide 3-kinase alpha (PI3Kα), which ultimately activates the AKT and mammalian target of rapamycin (mTOR) pathway. The PI3Kα inhibitor alpelisib has been approved for breast cancer where a single PIK3CA activating mutation is sufficient for response. However, two activating mutations (multi-hit) in the PIK3CA allele substantially increases PI3Kα signaling compared to single hot spot mutations and results in exceptional response to PI3Kα inhibition. We aimed to identify the prevalence of PIK3CA multi-hit mutations in CRC to identify patients potentially susceptible to PI3K inhibitors. Methods: Tissue-based comprehensive genomic profiling (CGP) was performed in a Clinical Laboratory Improvement Amendments (CLIA)-certified, CAP (College of American Pathologists)-accredited laboratory (Foundation Medicine Inc., Cambridge, MA, USA) on all-comers during the course of routine clinical care from 2013-2021. Approval was obtained from the Western Institutional Review Board (Protocol No. 20152817). Hybrid capture was carried out for at least 324 cancer-related genes, including PIK3CA. Results: We identified 48,836 patients with advanced CRC who underwent Foundation Medicine testing and 846 (1.7%) patients with multi-hit PIK3CA mutations. Additional clinical and molecular data was available for 41,154 of these patients of which 710 (1.7%) had multi-hit PIK3CA and 7627 (19%) had any deleterious PIK3CA mutation . The local colon tumor was used for sequencing in 70% of cases and a separate site in 30% of cases. Patients with PIK3CA multi-hit mutations were 53% male with a median age of 60 (interquartile range 50-70). The microsatellite status was available for 697 of 710 patients with multi-hit PIK3CA and 123/697 (18%) were microsatellite instability-high. The Table outlines the genes with cooccurring mutations of &gt;10% prevalence for multi-hit PIK3CA CRC, including the clinically relevant mutations in KRAS (65%) and BRAF (13%). The four most common PIK3CA variants were H1047R (9.8%), E545K (9.2%), E542K (9.0%) and R88Q (7.1%). The most common variant pair was E542K with E545K in 4.7% of multi-hit cases. Conclusions: Double-hit mutations in PIK3CA are seen in 1.7% of advanced CRC patients and may represent a subset of patients that may have enhanced sensitivity to PI3K inhibitors. Given the high prevalence of CRC in the United States and worldwide this represents a clinically meaningful prevalence of multi-hit PIK3CA. Future investigation on the clinical utility of PI3K inhibitors may be warranted in multi-hit PIK3CA CRC.[Table: see text]
Molecular mechanisms of nonablative fractionated laser resurfacing (2010)

Nonablative fractionated laser resurfacing induces a well-organized wound-healing response that leads to substantial dermal remodelling and collagen induction. Surprisingly, only minimal differences were observed between lower and higher microbeam energy settings. These data suggest that lower microbeam energy/higher microbeam density treatment parameters, which are generally better tolerated by patients, may yield dermal changes similar to those that result from higher microbeam energy/lower microbeam density treatment parameters.