gebhart/patrepeval huggingface dataset:
Pleiotropic effects of PipX, PipY, or RelQ overexpression on growth, cell size, photosynthesis, and polyphosphate accumulation in the cyanobacterium Synechococcus elongatus PCC7942 (2023)

The cyanobacterial protein PipY belongs to the Pyridoxal-phosphate (PLP)-binding proteins (PLPBP/COG0325) family of pyridoxal-phosphate-binding proteins, which are represented in all three domains of life. These proteins share a high degree of sequence conservation, appear to have purely regulatory functions, and are involved in the homeostasis of vitamin B<sub>6</sub> vitamers and amino/keto acids. Intriguingly, the genomic context of the <i>pipY</i> gene in cyanobacteria connects PipY with PipX, a protein involved in signaling the intracellular energy status and carbon-to-nitrogen balance. PipX regulates its cellular targets <i>via</i> protein-protein interactions. These targets include the PII signaling protein, the ribosome assembly GTPase EngA, and the transcriptional regulators NtcA and PlmA. PipX is thus involved in the transmission of multiple signals that are relevant for metabolic homeostasis and stress responses in cyanobacteria, but the exact function of PipY is still elusive. Preliminary data indicated that PipY might also be involved in signaling pathways related to the stringent stress response, a pathway that can be induced in the unicellular cyanobacterium <i>Synechococcus elongatus</i> PCC7942 by overexpression of the (p)ppGpp synthase, RelQ. To get insights into the cellular functions of PipY, we performed a comparative study of PipX, PipY, or RelQ overexpression in <i>S. elongatus</i> PCC7942. Overexpression of PipY or RelQ caused similar phenotypic responses, such as growth arrest, loss of photosynthetic activity and viability, increased cell size, and accumulation of large polyphosphate granules. In contrast, PipX overexpression decreased cell length, indicating that PipX and PipY play antagonistic roles on cell elongation or cell division. Since ppGpp levels were not induced by overexpression of PipY or PipX, it is apparent that the production of polyphosphate in cyanobacteria does not require induction of the stringent response.
Synthetic and Mechanistic Studies of a Versatile Heteroaryl Thioether Directing Group for Pd(II) Catalysis (2019)

A weakly coordinating monodentate heteroaryl thioether directing group has been developed for use in Pd(II) catalysis to orchestrate key elementary steps in the catalytic cycle that require conformational flexibility in a manner that is difficult to accomplish with traditional strongly coordinating directing groups. This benzothiazole thioether, (BT)S, directing group can be used to promote oxidative Heck reactivity of internal alkenes providing a wide range of products in moderate to high yields. To demonstrate the broad applicability of this directing group, arene C–H olefination was also successfully developed. Reaction progress kinetic analysis provides insights into the role of the directing group in each reaction, which is supplemented with computational data for the oxidative Heck reaction. Furthermore, this (BT)S directing group can be transformed into a number of synthetically useful functional groups, including a sulfone for Julia olefination, allowing it to serve as a “masked olefin” directing group in synthetic planning. In order to demonstrate this synthetic utility, natural products (+)-salvianolic acid A and salvianolic acid F are formally synthesized using the (BT)S directed C–H olefination as the key step.
Binding of SH2-B Family Members within a Potential Negative Regulatory Region Maintains JAK2 in an Active State (2006)

The tyrosine kinase Janus kinase 2 (JAK2) transduces signaling for the majority of known cytokine receptor family members and is constitutively activated in some cancers. Here we examine the mechanisms by which the adapter proteins SH2-Bbeta and APS regulate the activity of JAK2. We show that like SH2-Bbeta, APS binds JAK2 at multiple sites and that binding to phosphotyrosine 813 is essential for APS to increase active JAK2 and to be phosphorylated by JAK2. Binding of APS to a phosphotyrosine 813-independent site inhibits JAK2. Both APS and SH2-Bbeta increase JAK2 activity independent of their N-terminal dimerization domains. SH2-Bbeta-induced increases in JAK2 dimerization require only the SH2 domain and only one SH2-Bbeta to be bound to a JAK2 dimer. JAK2 mutations and truncations revealed that amino acids 809 to 811 in JAK2 are a critical component of a larger regulatory region within JAK2, most likely including amino acids within the JAK homology 1 (JH1) and JH2 domains and possibly the FERM domain. Together, our data suggest that SH2-Bbeta and APS do not activate JAK2 as a consequence of their own dimerization, recruitment of an activator of JAK2, or direct competition with a JAK2 inhibitor for binding to JAK2. Rather, they most likely induce or stabilize an active conformation of JAK2.
Vehicle Reidentification and Travel Time Measurement, Part I: Congested Freeways (2001)

The paper presents an algorithm for matching individual vehicles measured at a freeway detector with the vehicles' corresponding measurements taken earlier at another detector located upstream. Although this algorithm is potentially compatible with many vehicle detector technologies, the paper illustrates the method using existing dual-loop-detectors to measure vehicle lengths. This detector technology has seen widespread deployment for velocity measurement. Since the detectors were not developed to measure vehicle length, these measurements can include significant errors. To overcome this problem, the algorithm exploits drivers' tendencies to retain their positions within dense platoons. The otherwise complicated task of vehicle reidentification is carried-out by matching these platoons rather than individual vehicles. Of course once a vehicle has been matched across neighboring detector stations, the difference in its arrival time at each station defines the vehicle's travel time on the intervening segment. Findings from an application of the algorithm over a 1/3 mile long segment are presented herein and they indicate that a sufficient number of vehicles can be matched for the purpose of traffic surveillance. As such, the algorithm extracts travel time data without requiring the deployment of new detector technologies. In addition to the immediate impacts on traffic monitoring, the work provides a means to quantify the potential benefits of emerging detector technologies that promise to extract more detailed information from individual vehicles.
Video S2 from Evidencing a Pancreatic Ductal Adenocarcinoma Subpopulation Sensitive to the Proteasome Inhibitor Carfilzomib (2023)

&lt;p&gt;Supplementary Video S2&lt;/p&gt;
Using handheld devices for real-time wireless teleconsultation (2005)

Recent advances in the hardware of handheld devices, opened up the way for newer applications in the healthcare sector, and more specifically, in the teleconsultation field. Out of these devices, this paper focuses on the services that personal digital assistants and smartphones can provide to improve the speed, quality and ease of delivering a medical opinion from a distance and laying the ground for an all-wireless hospital. In that manner, PDAs were used to wirelessly support the viewing of digital imaging and communication in medicine (DICOM) images and to allow for mobile videoconferencing while within the hospital. Smartphones were also used to carry still images, multiframes and live video outside the hospital. Both of these applications aimed at increasing the mobility of the consultant while improving the healthcare service.
Increased pattern similarity in two major olfactory cortices despite higher sparseness levels (2021)

Abstract Pattern separation is a fundamental process that enhances discrimination of similar stimuli and can be achieved by sparsening the neural activity and expanding the coding space. Odor stimuli evoke patterns of activity in the olfactory bulb (OB) and these activity patterns are projected to several cortical regions that contain larger numbers of neurons and show sparser activity levels. However, whether these projected patterns are better separated is still unclear. Here we compared odor responses in the OB, anterior piriform cortex (aPC) and anterior olfactory nucleus (AON) to the exact same odor stimuli. We found that odor representations are more similar, noisier and less distinctive in aPC and AON than in the OB. The increase in similarity was observed for both similar and dissimilar odors. Modeling odor transformation from the OB to the olfactory cortex using simulated as well as actual OB odor responses as inputs, demonstrates that the observed rise in odor representation similarity can be explained by assuming biologically plausible variation in the number of OB inputs each cortical neuron receives. We discuss the possible advantages of our findings to odor processing in the aPC and AON. Highlights Odor representations in the aPC and AON are more correlated despite increase in sparseness levels. Odor identity is best represented in the OB. Variance in the number of inputs from OB can explain the reduction in odor separation.
Served Portion Sizes Affect Later Food Intake Through Social Consumption Norms (2019)

Portion sizes of commercially available foods have increased, and there is evidence that exposure to portion sizes recalibrates what is perceived as 'normal' and subsequently, how much food is selected and consumed. The present study aims to explore the role of social (descriptive and injunctive) and personal portion size norms in this effect. Across two experiments, participants were either visually exposed to (Study 1, <i>N</i> = 329) or actually served (Study 2, <i>N</i> = 132) a smaller or larger than normal food portion. After 24 h, participants reported their intended consumption (Study 1) or served themselves and consumed (Study 2) a portion of that food and reported perceived portion size norms. In Study 1, visual exposure to portion size did not significantly affect intended consumption and perceived portion size norms. In Study 2, participants consumed a smaller portion of food when they were served a smaller rather than a larger portion the previous day, which was mediated by perceived descriptive and injunctive social (but not personal) portion size norms. Results suggest that being served (but not mere visual exposure to) smaller (relative to larger) portions changes perceived social norms about portion size and this may reduce future consumption of that food.
Assessment of the effects of a topical product containing glycosaminoglycans in cutaneous hydration. (1988)

The hydrating power of a topically applied mixture of glycosaminoglycans has been evaluated by means of an electrical impedance method. The electrical parameters investigated, namely angle alpha and R infinity, are related to the permeability and the hydration of deeper tissues. The study revealed lowering of alpha levels after the application of the product, thus signifying an accumulation of electrical charges in the epidermis consistent with the penetration of glycosaminoglycans. After 15 days of treatment, significant reduction of R infinity levels was recorded. The relationship between R infinity levels, dermal water content and glycosaminoglycans is discussed.
「崇高」在電影音樂中的跨文化作法：李安的《少年Pi的奇幻漂流》 (2015)

This paper focuses on the sublime in the film Life of Pi from Ang Lee’s cross-cultural perspective. The sublime has been a popular topic among musicological studies. In most of these studies, the sublime refers to either the feelings aroused by a particular religion, or the aesthetic value mentioned in Kant’s Critique of Judgment. Their research subjects center on the late eighteenth-century Western repertories, such as works from Handel, Haydn, Mozart and Beethoven. Little has the musical sublime of non-Western music been discussed. In addition, despite growing concerns about film music, few studies have examined the notion of the sublime in film music. Ang Lee’s film, Life of Pi, (Ang Lee, 2012) involves the issues of religion, natural disaster, which are also commonly referred to in discussion of the sublime in Western tradition. However, both the concept and musical signification of the sublime in Life of Pi are distinctly different from the ones discussed so far in the academia. Different from “a process of self-transcendence aroused by reason” (as in the Kantian sublime), Pi’s attitude toward the limitless and the overwhelming power shows “introversion”, “letting go”, and “self-salvation”. Except for mild tempo, the film music uses “stasis chord progression”, “repeated melodies”, and “plagal cadence” to express “introversion” and “letting go”. Through detailed analysis, I try to explore (1) the concept of sublime being presented in Life of Pi (2) the ways of how this concept is connected with the music, sound and intermedia (medias including music/sound, image, synopsis, plots, etc.) interaction in the film (3) the differences between the sublime in Life of Pi and what is hitherto found in the academia. With this multimedia analysis I hope to bring up a discussion of the sublime in film music from a cross- cultural perspective.
Association of blood-cell-based inflammatory markers with gut microbiota and cancer incidence in the Rotterdam Study (2023)

Abstract Background Gut microbiota play a crucial role in defining the immune response. The immune response – gut microbiota interaction is implicated in various human diseases including cancer. Identifying the link between gut microbiota and systemic inflammatory markers, and their association with cancer, will be important to our understanding of cancer etiology. Results The current study was performed on 8,090 participants from the population-based Rotterdam Study. We found a significant association (false discovery rate [FDR] ≤ 0.05) between three gut-microbial taxa, namely the family Streptococcaceae , genus Streptococcus , and the order Lactobacillales with lymphocytes. In addition, we identified 95 gut-microbial taxa associated with inflammatory markers ( P-value &lt; 0.05). Analyzing the cancer data, we observed a significant association between higher SII levels at baseline (HR: 1.65 [95% CI; 1.10–2.46, P -value ≤ 0.05]) and the higher count of lymphocytes (HR: 1.38 [95% CI; 1.15–1.65, P-value ≤ 0.05]) and granulocytes (HR: 1.69 [95% CI; 1.40–2.03, P -value ≤ 0.05]) with increased risk of lung cancer after adjusting for age, sex, body mass index (BMI), and study cohort. This association was lost for SII and lymphocytes after additional adjustment for smoking (SII = HR:1.46 [95%CI; 0.96–2.22, P -value = 0.07] and lymphocytes = HR: 1.19 [95%CI; 0.97–1.46, P -value = 0.08]). In the stratified analysis, higher count of lymphocytes and granulocytes at baseline were associated with an increased risk of lung cancer in smokers after adjusting for age, sex, BMI, and study cohort (HR: 1.33 [95%CI; 1.09–1.62, P-value ≤ 0.05] and HR: 1.57 [95%CI; 1.28–1.92, P-value ≤ 0.05], respectively). Conclusion Our study revealed a positive association between gut-microbiota, higher SII levels and higher count of lymphocytes and granulocytes with an increased risk of developing lung cancer.
Catalytic Conversion of Glycerol into Aromatic Hydrocarbons, Acrolein, and Glycerol Ethers on Zeolite Catalysts (2018)

The effect of the nature of zeolite catalysts H-ZSM-5, H-BETA, and SAPO-34 on the activity and selectivity in the conversion of glycerol into aromatic hydrocarbons, acrolein, and oxygenates (various glycerol ethers) was studied. H-ZSM-5 was found to be the most effective catalyst for the conversion of glycerol into aromatic hydrocarbons and mono-, di-, and trisubstituted glycerol ethers with methanol and isobutylene. These products are effective gasoline additives increasing its octane number. Zeolite SAPO-34 shows the lowest activity in aromatization and alkylation reactions; the main product formed on this catalyst was acrolein.
[VEGF in therapeutic coronary and peripheral artery angiogenesis]. (1999)

An overview is presented of the various steps of angiogenesis, to which an important contributor is Vascular Endothelial Growth Factor (VEGF), a substance capable of increasing both the permeability and the mitosis rate of endothelial cells. VEGF is also a potent vasodilating agent. The beneficial effects of these properties on the ischemic vasculature have been documented in numerous animal models, leading to the concept of angiogenesis-enhancement as a therapeutic tool. The first clinical trials are under way. This area is discussed based on a literature review.
A Simple and Effective High-Order Shock-Capturing Limiter for Discontinuous Galerkin Methods (2015)

The discontinuous Galerkin (DG) finite element method when applied to hyperbolic conservation laws requires the use of shock-capturing limiters in order to suppress unphysical oscillations near large solution gradients. In this work we develop a novel shock-capturing limiter that combines key ideas from the limiter of Barth and Jespersen [AIAA-89-0366 (1989)] and the maximum principle preserving (MPP) framework of Zhang and Shu [Proc. R. Soc. A, 467 (2011), pp. 2752--2776]. The limiting strategy is based on traversing the mesh element-by-element in order to (1) find local upper and lower bounds on user-defined variables by sampling these variables on neighboring elements, and (2) to then enforce these local bounds by minimally damping the high-order corrections. The main advantages of this limiting strategy is that it is simple to implement, effective at shock capturing, and retains high-order accuracy of the solution in smooth regimes. The resulting numerical scheme is applied to several standard numerical tests in both one and two-dimensions and on both Cartesian and unstructured grids. These tests are used as benchmarks to verify and assess the accuracy and robustness of the method.
Advances in Asthma, Allergy and Immunology Series 2005 Advances in pediatric and adult asthma (2005)

Last year’s review on adult and pediatric asthma highlighted reports related to asthma genetics, the importance of upper airway management, the costs of asthma, and the importance of early recognition and intervention. This year we will organize our discussion to review recent reports related to the origins and persistence of asthma in both adults and children. We highlight Journal publications from 2004, along with recent key publications from other medical journals, to provide a perspective on the rapidly developing areas of genetics, including pharmacogenetics, respiratory infection, biomarker measurements, and asthma pharmacotherapy. This new understanding of the pathogenesis of asthma combined with clinical applications of genetics and biomarkers should lead to new management strategies. Asthma management is likely to change in the coming years from a strategy directed to the best outcome in groups of patients to an individualized approach to assessment and management. (J Allergy Clin Immunol 2005;115:470-7.)
Coupling Between Hybrid Mode Dielectric Resonators (1987)

Methods for the rigorous numerical calculation of the coupling coefficient between dual hybrid mode dielectric resonators in a circular waveguide are developed. A simplified model for the approximate calculation of the coupling is also presented. Experimental measurements performed to verify the models are found to be in excellent agreements with the calculations.
Design and Preparation of a Nanoprobe for Imaging Inflammation Sites (2012)

To image inflammation sites, we developed a novel nanoparticle, hydroxylamine-containing nanoparticle (HANP), which emits an intense electron spin resonance (ESR)-signal triggered by enzymatic oxidation reaction and pH-sensitive self-disintegration. The nanoparticle was prepared from an amphiphilic block copolymer, poly(ethylene glycol)-b-poly[4-(2,2,6,6-tetramethylpiperidine-1-hydroxyl)aminomethylstyrene] (PEG-b-PMNT-H), which spontaneously forms a core-shell type polymeric micelle (particle diameter = ca. 50 nm) in aqueous media. Because the PMNT-H segment in the block copolymer possesses amino groups in each repeating unit, the particle can be disintegrated by protonation of the amino groups in an acidic pH environment such as inflammation sites, which is confined to the hydrophobic core of HANP. Mixing HANP with horseradish peroxidase (HRP)/H(2)O(2) mixture resulted in enzymatic oxidization of the hydroxylamines in the PEG-b-PMNT-H and converted the hydroxylamine to the stable nitroxide radical form in PEG-b-poly[4-(2,2,6,6-tetramethylpiperidine-1-oxyl)aminomethylstyrene] (PEG-b-PMNT), which shows an intense ESR signal. It is interesting to note that the ESR signal increased at a greater rate under acidic conditions (pH 5.6) than that under neutral conditions (pH 7.4), although the enzymatic activity of HRP under neutral conditions is known to be much higher than that under acidic conditions. This indicates that enzymatic oxidation reaction was accelerated by synchronizing the disintegration of HANP under acidic conditions. On the basis of these results, HANP can be used as a high-performance ESR probe for imaging of inflammation sites.
Temporal and spatial relationships between segmentation and homeotic gene expression in Drosophila embryos: distributions of the fushi tarazu, engrailed, Sex combs reduced, Antennapedia, and Ultrabithorax proteins. (1988)

The specification of segment number and identity in the Drosophila embryo requires the activity of several classes of genes that may be grouped according to the array of pattern elements that they control. Double-label immunofluorescence was used to simultaneously localize the products of genes representative of the pair-rule segmentation class (fushi tarazu), the segment polarity class (engrailed), and the homeotic class (Sex combs reduced, Antennapedia, and Ultrabithorax) of pattern-regulating genes. The temporal order of appearance of each class of proteins and the precise spatial relationships between the products of the different genes are described with single-cell resolution. Boundaries of gene expression, particularly the parasegmental boundaries, are established by early-acting genes such as fushi tarazu and subsequently respected by the expression patterns of later appearing gene products such as engrailed and Ultrabithorax, suggesting regulatory relationships between certain pairs of genes. In addition, the dynamic transitions observed in spatial relationship among the Sex combs reduced, Antennapedia, and Ultrabithorax homeotic protein patterns during the early period of embryogenesis may reflect cross-regulatory interactions among these genes. Finally, some cells contain a single homeotic product, whereas other cells simultaneously contain several, suggesting that certain cells may be determined by the combinatorial action of homeotic genes.