gebhart/patrepeval huggingface dataset:
Glucocorticoids upregulate decreased IL-7 receptor expression in asthmatic patients and simian immunodeficiency virus-infected non-human primates. (2013)

Signaling through interleukin-7 receptor (IL-7R) is essential for regulation of T-cell homeostasis and survival. Previously, we and others have found diminished IL-7R levels in simian immunodeficiency virus (SIV) - infected non-human primates and human immunodeficiency virus (HIV) - infected patients. To date, it remains unknown whether changes in IL-7R expression could also be linked to non-infectious inflammatory diseases such as asthma or anti-inflammatory drug use. Here, we investigated through flow cytometry the levels of IL-7R expression on CD4+ and CD4- T-cells in asthmatic patients in relation to disease severity, immune status and glucocorticoid (GC) use. In addition, we sought to evaluate the effects of in vivo and in vitro GC treatment on IL-7R expression in both asthmatic patients and SIV-infected non-human primates. We demonstrated that expression of IL-7R on peripheral blood CD4+ T-cells was significantly decreased in clinically stable GC-naive mild and moderate asthmatic patients. Accordingly, the development of asthmatic reaction following bronchial allergen challenge performed in sensitized subjects was associated with a significant drop in levels of IL-7R on circulating CD4+ T-cells. In contrast, CD4+ T-cells from both, mild and moderate, but not severe asthmatics, treated with inhaled GC displayed levels of IL-7R similar to that seen in healthy controls. We did not find significant differences with serum or sputum interleukin-7 levels among healthy controls and GC-naïve and GC-treated asthmatic patients. Furthermore, both in vitro GC treatment and short-term oral GC administration to asthmatic patients resulted in a significant enhancement of IL-7R. Similarly, we demonstrated that GC-stimulated T-cells from SIV-infected non-human primates up-regulated IL-7R expression. Accordingly, experimental short-term systemic in vivo administration of GC to SIV-infected macaques led to enhancement of IL-7R expression on circulating T-cells. Our data indicate that GC bear potential to recover diminished IL-7R expression, as well in asthma as in lentiviral infection.
Possible Role of Amyloid Cross-Seeding in Evolvability and Neurodegenerative Disease (2019)

Aging-related neurodegenerative disorders are frequently associated with the aggregation of multiple amyloidogenic proteins (APs), although the reason why such detrimental phenomena have emerged in the post-reproductive human brain across evolution is unclear. Speculatively, APs might provide physiological benefits for the human brain during developmental/reproductive stages. Of relevance, it is noteworthy that cross-seeding (CS) of APs has recently been characterized in cellular and animal models of neurodegenerative disease, and that normal physiological CS of multiple APs has also been observed in lower organisms, including yeast and bacteria. In this context, our main objective is to discuss a possible involvement of the CS of APs in promoting evolvability, a hypothetical view regarding the function of APs as an inheritance of acquired characteristics against human brain stressors, which are transgenerationally transmitted to offspring via germ cells. Mechanistically, the protofibrils formed by the CS of multiple APs might confer hormesis more potently than individual APs. By virtue of greater encoded stress information in parental brains being available, the brains of offspring can cope more efficiently with forth-coming stressors. On the other hand, subsequent neurodegeneration caused by APs in parental brain through the antagonistic pleiotropy mechanism in aging, may suggest that synergistically, multiple APs might be more detrimental compared to singular AP in neurodegeneration. Taken together, we suggest that the CS of multiple APs might be involved in both evolvability and neurodegenerative disease in human brain, which may be mechanistically and therapeutically important.
Systemic RNAi in the small hive beetle Aethina tumida Murray (Coleoptera: Nitidulidae), a serious pest of the European honey bee Apis mellifera (2016)

This is the first study to show evidence for systemic RNAi in A. tumida in response to injected dsRNA, but further research is required to develop methods to induce RNAi effects via ingestion. © 2016 Crown copyright. Pest Management Science © 2016 Society of Chemical Industry.
Quantitative analysis on the revealed comparative advantage of Chinese manufacturing (2002)

On the basis of the suggested formula of RCA index by Balassa, this paper makes a quantitative analysis on the revealed comparative advantage of Chinese manufacturing export goods, analyses the evolution trend of manufacturing RCA from 1980, evaluates the advantages and disadvantages of international competition of Chinese manufacturing industries and puts forward the difference between the RCA of China with USA, Japan and EU.
Predicting the presence of colon cancer in members of a health maintenance organisation by evaluating analytes from standard laboratory records (2017)

Information taken from routine blood tests can be used to predict the risk of being diagnosed with CRC in the near future.
Efficacy of the Self-inflating Bulb in Detecting Esophageal Intubation Does the Presence of a Nasogastric Tube or Cuff Deflation Make a Difference? (1994)

These results confirm that a nasogastric tube or cuff deflation does not interfere with the reliability of the self-inflating bulb in detecting esophageal intubation and thus does not contribute to false positive results. Confirmation of tracheal tube placement by this simple method makes it ideal for use with other recognized methods both in and outside the operating rooms and enables physicians and emergency personnel to proceed with other resuscitative measures.
Cost Total Colorings of Trees (2004)

A total coloring of a graph G is to color all vertices and edges of G so that no two adjacent or incident elements receive the same color. Let C be a set of colors, and let ω be a cost function which assigns to each color c in C a real number ω(c) as a cost of c. A total coloring f of G is called an optimal total coloring if the sum of costs ω( f (x)) of colors f (x) assigned to all vertices and edges x is as small as possible. In this paper, we give an algorithm to find an optimal total coloring of any tree T in time O(n∆3) where n is the number of vertices in T and ∆ is the maximum degree of T . key words: cost total coloring, dynamic programming, matching, total coloring, tree
Converting Faces by Preserving the Expression from the Actor's Viewpoint Based on Examples Obtained from User Interactions (2001)

This article discusses how to realize the process of converting the user's face into an avatar's face by preserving the expression. The objective of this work is to make this process reflect the user's subjective view about correspondence between the facial images of the user and the avatar. In this article, it is proposed to adapt the process to the user's view through interactions with the user. This is realized by an example-based approach, in which the correspondence between the facial images of the user and the avatar is estimated from its examples obtained from the interactions with the user. The process increasingly reflects the user's view with the number of examples.
Strong Correlations between the Binding Antibodies against Wild-Type and Neutralizing Antibodies against Omicron BA.1 and BA.2 Variants of SARS-CoV-2 in Individuals Following Booster (Third-Dose) Vaccination (2022)

This study examined the neutralizing activity and receptor-binding domain (RBD) antibody levels against wild-type and omicron BA.1 and BA.2 variants in individuals who received three doses of COVID-19 vaccination. The relationship between the anti-RBD IgG against wild-type and live virus neutralizing antibody titers against omicron BA.1 and BA.2 variants was examined. In total, 310 sera samples from individuals after booster vaccination (third-dose) were tested for specific IgG wild-type SARS-CoV-2 RBD and the omicron BA.1 surrogate virus neutralization test (sVNT). The live virus neutralization assay against omicron BA.1 and BA.2 was performed using the foci-reduction neutralization test (FRNT50). The anti-RBD IgG strongly correlated with FRNT50 titers against BA.1 and BA.2. Non-linear regression showed that anti-RBD IgG at the cut-off value ≥148 BAU/mL and ≥138 BAU/mL were related to the threshold for FRNT50 titers ≥20 against BA.1 and BA.2, respectively. A moderate correlation was observed between the sVNT and FRNT50 titers. At FRNT50 titers ≥20, the predicted sVNT for BA.1 and BA.2 was ≥10.57% and ≥11.52%, respectively. The study identified anti-RBD IgG and sVNT levels that predict detectable neutralizing antibodies against omicron variants. Assessment and monitoring of protective immunity support vaccine policies and will help identify optimal timing for booster vaccination.
Profiling of Nutrient Transporter Expression in Human Stem Cell–Derived Cardiomyocytes Exposed to Tyrosine Kinase Inhibitor Anticancer Drugs Using RBD Ligands (2014)

We applied a novel profiling approach using receptor binding domain (RBD) ligands to cell surface domains of a panel of nutrient transporters to characterize the impact of a number of tyrosine kinase inhibitor anticancer drugs on human stem cell-derived cardiomyocytes. High-content screening and flow cytometry analysis showed diagnostic changes in nutrient transporter expression correlating with glycolysis and oxidative phosphorylation-based cell metabolism in glucose and galactose media. Cluster analysis of RBD binding signatures of drug-treated cells cultured in glucose medium showed good correlation with sensitization of mitochondrial toxicity in cells undergoing oxidative phosphorylation in galactose medium. These data demonstrate the potential for RBD ligands as profiling tools to improve the clinical predictivity of in vitro cell assays for drug toxicity.
Figure S5 from Mitochondrial Reprogramming Regulates Breast Cancer Progression (2023)

&lt;p&gt;Impact of SH3GL2 overexpression in vivo.&lt;/p&gt;
Extending FLAVERS to Check Properties on Infinite Executions of Concurrent Software Systems (2000)

Finite state verication techniques can be used for detecting the presence or proving the absence of certain kinds of errors in software systems. These approaches are based on reason-ing about a nite, abstracted model of a system&amp;apos;s behaviors.
The mechanism of exogenous B7.1‐enhanced IL‐12‐mediated complete regression of tumors by a single electroporation delivery (2006)

Electroporation-based mono-gene therapy has received great interest in recent years but coadministration of different therapeutic genes for treatment of tumors has not been well explored. We hypothesize that electroporation is capable of delivering multiple genes that induce an additive or synergistic antitumor effect. To test this hypothesis, we used mice that were bearing SCCVII or TRAMP tumors. Established tumors with a diameter of 4-5 mm were injected with control plasmid DNA or plasmid DNA encoding B7.1, IL-12 or both via electroporation. Tumor regression, CTL activity and the level of B7.1, IL-12 and Stat1 expression were determined in both wild-type mice and in mice with a knock-out of the Stat1 gene. Remarkably, a single coadministration of the plasmids that encoded IL-12 and B7.1 eradicated tumors in 80% of mice. The therapeutic effect was associated with high levels of endogenous B7.1 expression, activity of cytotoxic lymphocytes, and activation of Stat1. Both exogenous B7.1 and IL-12 were required for inducing a high level of Stat1 activation in tumors, which occurred through a mechanism that was independent of the host Stat1. Both stimulators were also required for inducing the strong cytotoxic lymphocyte activity and for increasing the level and extending the duration of endogenous B7.1 expression. We therefore propose a 2-signal stimulation model to explain the synergistic effect of the coadministration of IL-12 and B7.1 on the regression of the tumors.
Canonical Correlation Analysis of Video Volume Tensors for Action Categorization and Detection (2009)

This paper addresses a spatiotemporal pattern recognition problem. The main purpose of this study is to find a right representation and matching of action video volumes for categorization. A novel method is proposed to measure video-to-video volume similarity by extending Canonical Correlation Analysis (CCA), a principled tool to inspect linear relations between two sets of vectors, to that of two multiway data arrays (or tensors). The proposed method analyzes video volumes as inputs avoiding the difficult problem of explicit motion estimation required in traditional methods and provides a way of spatiotemporal pattern matching that is robust to intraclass variations of actions. The proposed matching is demonstrated for action classification by a simple Nearest Neighbor classifier. We, moreover, propose an automatic action detection method, which performs 3D window search over an input video with action exemplars. The search is speeded up by dynamic learning of subspaces in the proposed CCA. Experiments on a public action data set (KTH) and a self-recorded hand gesture data showed that the proposed method is significantly better than various state-of-the-art methods with respect to accuracy. Our method has low time complexity and does not require any major tuning parameters.
Amino acid usage and tRNA expression underlies proteome adaptation in Plasmodium falciparum (2023)

Abstract Parasites often depend on metabolic adaptation to the host environment. An adaptive feature of malaria-causing parasites is digestion of hemoglobin (HB) to acquire amino acids (AAs). Here we describe a link between nutrient availability and translation elongation-dependent regulation of gene expression as an adaptive strategy. We show that, unexpectedly, tRNA expression in P. falciparum does not match the decoding need as tRNAs decoding AAs that are rare in HB are lowly expressed. This discrepancy renders codons of HB-rare AAs inefficiently decoded and transcripts levels negatively correlated with the requirement of HB-rare AAs for protein synthesis, which are consistent with poor codon optimality causing co-translational mRNA decay. Intriguingly, proliferation-related genes have evolved to require a high level of HB-rare AAs in their encoded proteins, thereby allowing the parasite to control its proliferation by repressing protein synthesis of these genes during nutrient stress. We conclude that the parasite modulates translation elongation by maintaining a discordant tRNA profile as a mechanism to exploit variations in AA-composition among genes as an adaptation strategy.
Data speculation support for a chip multiprocessor (1998)

Thread-level speculation is a technique that enables parallel execution of sequential applications on a multiprocessor. This paper describes the complete implementation of the support for threadlevel speculation on the Hydra chip multiprocessor (CMP). The support consists of a number of software speculation control handlers and modifications to the shared secondary cache memory system of the CMP This support is evaluated using five representative integer applications. Our results show that the speculative support is only able to improve performance when there is a substantial amount of medium--grained loop-level parallelism in the application. When the granularity of parallelism is too small or there is little inherent parallelism in the application, the overhead of the software handlers overwhelms any potential performance benefits from speculative-thread parallelism. Overall, thread-level speculation still appears to be a promising approach for expanding the class of applications that can be automatically parallelized, but more hardware intensive implementations for managing speculation control are required to achieve performance improvements on a wide class of integer applications.
Performance and control optimisations using the adaptive torsion wing (2012)

Abstract This paper presents the Adaptive Torsion Wing (ATW) concept and performs two multidisciplinary design optimisation (MDO) studies by employing this novel concept across the wing of a representative UAV. The ATW concept varies the torsional stiffness of a two-spar wingbox by changing the enclosed area through the relative chordwise positions of the front and rear spar webs. The first study investigates the use of the ATW concept to improve the aerodynamic efficiency (lift-to-drag ratio) of the UAV. In contrast, the second study investigates the use of the concept to replace conventional ailerons and provide roll control. In both studies, the semi-span of the wing is split into five equal partitions and the concept is employed in each of them. The partitions are connected through thick ribs that allow the spar webs of each partition to translate independently of the webs of adjacent partitions and maintain a continuous load path across the wing span. An MDO suite consisting of a Genetic Algorithm (GA) optimiser coupled with a high-end low-fidelity aero-structural model was developed and employed in this paper.
How are 1,2,3-triazoles accommodated in helical secondary structures? (2018)

1,4-Disubstituted-1,2,3-triazole (Tz) is widely used in peptides as a trans-amide bond mimic, despite having hazardous effects on the native peptide activity. The impact of amide bond substitution by Tz on peptide secondary structures is scarcely documented. We performed a Tz scan, by systematically replacing peptide bonds following the Aib residues with Tz on two model peptaibols: alamethicin F50/5 and bergofungin D, which adopt stable α- and 310 helices, respectively. We observed that the Tz insertion, whatever its position in the peptide sequences, abolished their antimicrobial activity. The structural consequences of this insertion were further investigated using CD, NMR and X-ray diffraction. Importantly, five crystal structures that were incorporated with Tz were solved, showing various degrees of alteration of the helical structures, from minor structural perturbation of the helix to partial disorder. Together, these results showed that Tz insertions impair helical secondary structures.
PCR MP Method for Differentiation of Clavibacter michiganensis Subsp. sepedonicus Isolates (2019)

Abstract The published data indicate that the bacterium Clavibacter michiganensis subsp. sepedonicus ( Cms ) shows a notably low degree of intraspecific variation, and most of the molecular diagnostic methods could differentiate among subspecies groups but lacked the resolution to detect genetic diversity within subspecies. The present study describes effective differentiation of 50 isolates of C. michiganensis subsp. sepedonicus by the PCR MP method using five restriction enzymes ( Apa I , Pst I , Bam HI , Xma I , Hind III). By analysing the electrophoretic patterns obtained by the PCR MP method performed with the applied restriction enzymes, each of the 50 tested isolates could be identified and distinguished from the remaining isolates. The PCR MP method of bacterial strain identification can be used in epidemiological studies, particularly for excluding the isolates of C. michiganensis subsp. sepedonicus as a source of primary infection.
A 2GHz-to-7.5GHz quadrature clock-generator using digital delay locked loops for multi-standard I/Os in 14nm CMOS (2014)

A highly digital quadrature clock generator using a digital DLL that employs a digital loop filter and digitally-calibrated replica-based regulator is presented. The proposed DLL combines the advantages of both analog and digital loop-filters of conventional architectures to implement a wide-range, energy efficient, highly digital, and high performance quadrature clock generator. To suppress supply-noise, we propose an LDO that combines fast/slow paths with a replica-load to achieve better than 20dB rejection with small area and low power. Fabricated in Intel's 14nm CMOS process, the proposed digital DLL operates over a wide range of output frequencies (2GHz-to-7.5GHz). At 7GHz, it achieves 176fs <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rms</inf> /2.7ps <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">pp</inf> long-term jitter while consuming 4.4mW. The DLL is 4X smaller than state-of-the art designs and occupies an active area of 0.0024mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Plume Dispersion Anomalies in a Nocturnal Urban Boundary Layer in Complex Terrain (2008)

Abstract The URBAN 2000 experiments were conducted in the complex urban and topographical terrain in Salt Lake City, Utah, in stable nighttime conditions. Unexpected plume dispersion often arose because of the interaction of complex terrain and mountain–valley flow dynamics, drainage flows, synoptic influences, and urban canopy effects, all within a nocturnal boundary layer. It was found that plume dispersion was strongly influenced by topography, that dispersion can be significantly different than what might be expected based upon the available wind data, and that it is problematic to rely on any one urban-area wind measurement to predict or anticipate dispersion. Small-scale flows can be very important in dispersion, and their interaction with the larger-scale flow field needs to be carefully considered. Some of the anomalies observed include extremely slow dispersion, complicated recirculation dispersion patterns in which plume transport was in directions opposed to the measured winds, and flow decoupling. Some of the plume dispersion anomalies could only be attributed to small-scale winds that were not resolved by the existing meteorological monitoring network. The results shown will make clear the difficulties in modeling or planning for emergency response to toxic releases in a nocturnal urban boundary layer within complex terrain.
A retrospective cohort study to evaluate the development of comorbidities, including psychiatric comorbidities, among a pediatric psoriasis population (2019)

The incidence rates of many comorbid conditions were higher for patients with pediatric psoriasis compared with patients without pediatric psoriasis, and similar between patients with moderate-to-severe and mild pediatric psoriasis.