gebhart/patrepeval huggingface dataset:
Injection of Antibodies against Immunodominant Epitopes Tunes Germinal Centers to Generate Broadly Neutralizing Antibodies (2019)

Broadly neutralizing antibodies are crucial for the control of many life-threatening viral infections like HIV, influenza, or hepatitis. Their induction is a prime goal in vaccine research. Using computer simulations, we identify strategies to promote the generation of broadly neutralizing antibodies in natural germinal center (GC) reactions. The simulations predict a feedback loop based on antibodies and memory B cells from previous GC reactions that promotes GCs to focus on new epitopes. Memory-derived or injected antibodies specific for immunodominant epitopes control epitope availability, suppress the participation of memory B cells in the GC reaction, and allow for the evolution of other B cells to affinity mature for hidden or rare epitopes. This defines a natural selection mechanism for GC B cells to concentrate on new epitopes rather than refine affinity to already-covered epitopes. This principle can be used for the design and testing of future therapies and vaccination protocols.
Cornifin, a cross-linked envelope precursor in keratinocytes that is down-regulated by retinoids. (1992)

In this study, we have characterized the cDNA clone SQ37 that was isolated previously from a rabbit squamous cell library. The gene encodes a 14-kDa protein that appears to function as a component of the cross-linked envelope in squamous differentiating cells. The protein, which has been named cornifin, has a high content of proline (31%), glutamine (20%), and cysteine (11%) and contains 13 repeats of an octapeptide (consensus sequence, EPCQPKVP) at its C terminus. SQ37 mRNA and protein are induced during squamous differentiation of rabbit tracheal (RbTE) cells and human epidermal keratinocytes. This induction is repressed by retinoids. Immunohistochemical studies reveal SQ37 immunoreactivity in fragmented cross-linked envelopes from squamous-differentiated RbTE cells and in the suprabasal layers of the epidermis. In situ hybridization analysis showed that the presence of SQ37 mRNA is restricted to the suprabasal layers. Treatment of RbTE cells with a Ca2+ ionophore induces cross-linking of the SQ37 protein into higher molecular weight complexes. This cross-linking reaction appears to be mediated by transglutaminase type I. Our observations suggest that the protein encoded by SQ37 participates in the assembly of the cross-linked envelope.
Effects of increasing the intake of dietary β-glucans by exchanging wheat for barley on nutrient digestibility, nitrogen excretion, intestinal microflora, volatile fatty acid concentration and manure ammonia emissions in finishing pigs (2007)

An experiment (complete randomised design) was conducted to investigate the linear and quadratic effects of barley β-glucan inclusion level on total tract nutrient apparent digestibility, nitrogen excretion, intestinal microflora, volatile fatty acid (VFA) profile and manure ammonia emissions in pigs. Twenty-four boars (66 kg) were assigned to one of four treatments: (T1) 0 g/kg barley (control diet) (5.6 g/kg β-glucan), (T2) 222 g/kg barley (12.1 g/kg β-glucan), (T3) 444 g/kg barley (18.9 g/kg β-glucan) and (T4) 666 g/kg barley (25 g/kg β-glucan). Barley was substituted for wheat in the diet. The diets were formulated to contain similar concentrations of digestible energy and digestible lysine. There was a linear decrease (P < 0.001) in the total tract apparent digestibility of dry matter, organic matter, gross energy and neutral-detergent fibre with increasing β-glucan concentration. Faecal nitrogen excretion was affected by dietary β-glucan concentration (quadratic P < 0.05). There was a linear decrease in Enterobacteria concentrations (P < 0.05) with increasing dietary β-glucan concentration. Increasing dietary barley levels caused a linear decrease in colonic (P < 0.01) and caecal pH (P < 0.001). Total caecal VFA and propionic acid were affected by dietary β-glucan concentration (quadratic, P < 0.05). There was a linear decrease in the proportion of acetic acid (P < 0.001), isobutyric acid (P < 0.01) and isovaleric acid (P < 0.05) with increasing levels of dietary barley in both the caecum and colon. There was a linear increase in the proportion of propionic acid (P < 0.001) and butyric acid (P < 0.05) with increasing barley in the colon. In conclusion, high level of dietary β-glucan (25 g/kg) is required to reduce offensive odour forming branched-chain VFAs; however, diet digestibility is compromised at such levels.
A Solid Phase Antibody Screen (1984)

An automated solid phase antibody screen (SPAS) in microplates has been developed. Red blood cell (RBC) adherence was used as the end point instead of agglutination. Consequently, positive and negative reactions were readily distinguished by a microplate spectrophotometer. The SPAS performed as well as conventional antiglobulin methods for detecting IgG antibodies in donor sera and had increased sensitivity as determined by serial dilutions of antibodies.
Standardization of rebar manufacturing for rebar work (2009)

Due to a shortage of professional labor and the stagnant construction industry in recent days, there has been an increasing demand for securing profitability through cost reduction. Though its importance in the cost and its great influence on the safety and durability of structures, the labor intensiveness of rebar work has caused a serious problem of rising cost accompanied by the loss of rebar materials. In the plant manufacturing process, rebar is cut and bent at the automated facilities and conveyed to the construction site, which makes it possible to manufacture higher-quality bars and to reduce the losses from rebar materials. Different from the expectation, however, this type of plant manufacturing still has not been active since its first introduction in 1990s. In this study, a research on the actual condition of rebar manufacturing plant has been implemented and a standardized rebar manufacturing has been provided as a way to activate rebar manufacturing.
INFLUENCE OF PLANT POPULATION ON PERFORMANCE OF SUNFLOWER HYBRIDS (1978)

Hybrid sunflowers (Helianthus annuus L.) have rapidly replaced open-pollinated cultivars in the United States in the past 5 yr. Because of differential performance or economic considerations, hybrids of several other crops are grown at different plant populations than the standard cultivars that they replaced. This study was conducted to ascertain whether previous recommendations at plant populations for open-pollinated cultivars are appropriate for hybrids. The performance of three hybrids was compared with the major open-pollinated cv. Peredovik, at plant populations of 36,000, 48,000, and 72,000 plants/ha over 3 yr, 1973–1975. A nonsignificant cultivar × population interaction indicated that the three hybrids and Peredovik responded similarly to changes in plant population for each of the 3 yr of testing. Yield, oil content, and test weight were not significantly altered by the three plant populations evaluated. As plant population increased, head size and seed weight decreased and plant height of the hybrids and days to flowering increased. It was concluded that plant population recommendations for Peredovik of about 48,000 plants/ha are also appropriate for the growing of hybrids.
Sexualité En Milieu Psychiatrique (1994)

The main goal of this paper is to describe the problems associated with the expression of sexuality of patients in a psychiatric setting. The problem is analyzed according to the normalization principle. The staff's attitude is considered to be a determining factor in this situation. The authors present the principal conclusions of their study and make some practical recommendations.
Comparison of the Kinetics of Acyclic Diene Metathesis Promoted by Grubbs Ruthenium Olefin Metathesis Catalysts (2001)

The kinetics of acyclic diene metathesis (ADMET) promoted by (PCy3)2Cl2RuCHPh (2), and the more recently developed catalyst 3, which contains the 1,3-bis(mesityl)imidazolidene-2-ylidene (SIMes) ligand, were measured and compared. Complex 3 is clearly the more active catalyst at temperatures of 45−75 °C, while complex 2 is actually the faster catalyst at 30 °C. Although no induction period was observed for complex 2, a conspicuous delay in activity was observed at the onset of ADMET with complex 3 at all temperatures studied. We propose that this behavior is due to the rates of phosphine dissociation for these catalysts, as is consistent with new mechanistic data in the context of other olefin metathesis reactions.
Principles of Modern Radar: Advanced techniques (2012)

This second of three volumes in the Principles of Modern Radar series offers a much-needed professional reference for practicing radar engineers. It provides the stepping stones under one cover to advanced practice with overview discussions of the most commonly used techniques for radar design, thereby bridging readers to single-topic advanced books, papers, and presentations. It spans a gamut of exciting radar capabilities from exotic waveforms to ultra-high resolution 2D and 3D imaging methods, complex adaptive interference cancellation, multi-target tracking in dense scenarios, multiple-input, multiple-output (MIMO) and much more. All of this material is presented with the same careful balance of quantitative rigor and qualitative insight of Principles of Modern Radar: Basic Principles. Each chapter is likewise authored by recognized subject experts, with the rigorous editing for consistency and suggestions of numerous volunteer reviewers from the radar community applied throughout. Advanced academic and training courses will appreciate the sets of chapter-end problems for students, as well as worked solutions for instructors. Extensive reference lists show the way for further study.
Animal Models of Francisella tularensis Infection (2007)

The increased incidence of emerging infections has caused a resurgence in the development of animal models in order to study their pathophysiology and develop therapeutics against them. Optimizing these models and improving our ability to extrapolate information from animals to humans is critical because in many cases the animal model will represent the only modality for efficacy testing. Francisella tularensis (F. tularensis) is an emerging pathogen that fits this category. While there is a significant body of literature that has examined infections with F. tularensis in a variety of species, the optimal small animal model has yet to be defined. A vast majority of studies have used two strains of F. tularensis, the more virulent type A strain commonly found in North America and the less virulent type B strain common to Europe. None of the small animal models described in the literature thus far behave in a fashion identical to humans with respect to their sensitivity to SCHU S4 (type A) or live vaccine strains (LVS) (attenuated type B) and an ability of LVS vaccination to consistently protect against a SCHU S4 aerosol challenge, suggesting that significant work on animal model development still remains. This report briefly describes the parameters important for animal model development and reviews the literature related to animal models of F. tularensis, including the human model, and the characterization performed for those models.
HEAT-SHOCK PROTEINS, MOLECULAR CHAPERONES, AND THE STRESS RESPONSE: Evolutionary and Ecological Physiology (1999)

▪ Abstract Molecular chaperones, including the heat-shock proteins (Hsps), are a ubiquitous feature of cells in which these proteins cope with stress-induced denaturation of other proteins. Hsps have received the most attention in model organisms undergoing experimental stress in the laboratory, and the function of Hsps at the molecular and cellular level is becoming well understood in this context. A complementary focus is now emerging on the Hsps of both model and nonmodel organisms undergoing stress in nature, on the roles of Hsps in the stress physiology of whole multicellular eukaryotes and the tissues and organs they comprise, and on the ecological and evolutionary correlates of variation in Hsps and the genes that encode them. This focus discloses that (a) expression of Hsps can occur in nature, (b) all species have hsp genes but they vary in the patterns of their expression, (c) Hsp expression can be correlated with resistance to stress, and (d) species' thresholds for Hsp expression are correlated with levels of stress that they naturally undergo. These conclusions are now well established and may require little additional confirmation; many significant questions remain unanswered concerning both the mechanisms of Hsp-mediated stress tolerance at the organismal level and the evolutionary mechanisms that have diversified the hsp genes.
Glucocorticoid (GC)-Mediated Down-Regulation of Urokinase Plasminogen Activator Expression via the Serum and GC Regulated Kinase-1/Forkhead Box O3a Pathway (2008)

The glucocorticoid receptor (GR) and its ligand, cortisol, play a central role in human physiology. The exact mechanisms by which GR activation regulates these processes are the subject of intensive investigation. We and others have shown that GR activation can indirectly down-regulate specific genes via serum and glucocorticoid (GC) regulated kinase-1-mediated inhibition of forkhead box O3a (FOXO3a) transcriptional activity. We previously used gene expression microarrays, together with bioinformatic analyses, to identify putative FOXO3a target genes in breast epithelial cells. In this paper we refine our analysis through the use of FOXO3a chromatin immunoprecipitation (ChIP) microarrays. ChIP microarray results reveal urokinase plasminogen activator (uPA) as a putative novel target of FOXO3a in breast epithelial and breast cancer cell lines. We further show that uPA down-regulation after GC treatment requires serum and GC regulated kinase-1-mediated inactivation of FOXO3a activity. ChIP and luciferase assays confirm that FOXO3a can both occupy and transactivate the uPA promoter. Our data suggest that inactivation of FOXO3a after GR activation is an important mechanism contributing to GC-mediated repression of uPA gene expression in breast epithelial and cancer cells.
Comparative Cost-Effectiveness of Gastroesophageal Reflux Disease Centric and Population Based Barrett’s Esophagus Screening: Fellows-in-Training Award (Esophagus Category) (2018)

Introduction: Current Barrett’s esophagus (BE) screening recommendations are gastroesophageal reflux disease (GERD) centric, but 40-50% of patients with BE or esophageal adenocarcinoma deny GERD. With the development of minimally invasive tests for BE screening, the prospect of population screening (all adults age ≥50) instead of targeted screening (white, male, age ≥50, GERD) has arisen. We aimed to evaluate the comparative cost effectiveness of current tests utilizing recently published data on prevalence, accuracy, screening uptake, and costs. Methods: Decision analytic methods were used to compare six screening strategies to no screening: sEGD, Cytosponge with TFF3 biomarker, Sponge on String (SoS) with methylated DNA markers, breath testing (E-Nose), hospital-based transnasal endoscopy (hTNE), and mobile unit-based transnasal endoscopy (mTNE). The Markov model simulated a hypothetical cohort of 100,000 individuals aged ≥50 followed up for 40 years. Patients could follow seven distinct health states: no BE, non-dysplastic BE, low grade dysplasia, high grade dysplasia, intramucosal cancer, symptomatic cancer, and death. sEGD was used as a confirmatory test of positive findings for all other diagnostic tests. Mean costs (direct as well as indirect costs resulting from missed or false positive diagnoses and cost of test uptake) were calculated for each strategy. Effectiveness of each option was assessed using quality adjusted life years (QALYs) from the extant literature. Results: Screening (GERD centric: prevalence 8%, and population prevalence 1.6%) was associated with gains in QALYs compared to no screening (Table 1). Under the general population analysis, mean costs ranged from $120 (mTNE) to $554 (E-Nose). While mTNE was the dominant strategy, both the Cytosponge and SoS tests had the lowest incremental cost effectiveness ratios (ICERs) (Table 1). Under the GERD centric screening analysis, mean costs ranged from $212 (mTNE) to $768 (E-Nose). Cytosponge, SoS, hTNE, and mTNE were all dominant strategies compared to no screening. Of those, mTNE was the least costly and most effective strategy. The E-Nose had the highest ICER primarily due to lower accuracy estimates. Conclusion: While mTNE was the dominant strategy for both screening scenarios, this technique is not widely utilized and has been only evaluated in one center. Both Cytosponge and SoS strategies had very favorable ICERs in both strategies and may make population-based BE screening regardless of GERD status feasible.316 Figure 1. Main Results of the simulation models
Adversarial collision attacks on image hashing functions (2020)

Hashing images with a perceptual algorithm is a common approach to solving duplicate image detection problems. However, perceptual image hashing algorithms are differentiable, and are thus vulnerable to gradient-based adversarial attacks. We demonstrate that not only is it possible to modify an image to produce an unrelated hash, but an exact image hash collision between a source and target image can be produced via minuscule adversarial perturbations. In a white box setting, these collisions can be replicated across nearly every image pair and hash type (including both deep and non-learned hashes). Furthermore, by attacking points other than the output of a hashing function, an attacker can avoid having to know the details of a particular algorithm, resulting in collisions that transfer across different hash sizes or model architectures. Using these techniques, an adversary can poison the image lookup table of a duplicate image detection service, resulting in undefined or unwanted behavior. Finally, we offer several potential mitigations to gradient-based image hash attacks.
Expression and molecular diversity of Tcf7l2 in the developing murine cerebellum and brain (2009)

The Wingless family of secreted proteins impinges on multiple aspects of vertebrate nervous system development, from early global patterning and cell fate decision to synaptogenesis. Here, we mapped the developmental expression of the Tcf7l2, which is key to the canonical Wingless signaling cascade, in the developing cerebellum. The exclusive and transient expression of Tcf7l2 in ventricular and Olig2-defined precursor cells within the cerebellar anlage, and its predominant expression in postmitotic neurons in the midbrain/inferior colliculus allowed us to ask whether cell type-specific differences are also reflected in splice isoform variability. We also included in this analysis intestinal epithelia, where Tcf7l2 function has been intensively studied. Our data reveal extensive variability of Tcf7l2 splicing in the central nervous system. Additional variability in brain-expressed Tcf7l2 is generated by a length polymorphism of expressed mRNAs in a stretch of normally nine adenines found at the beginning of exon 18, reminiscent of variability observed at the same site in cancers with microsatellite instability. A consensus emerging from our data is that the expression of isoforms comprising or lacking the C-clamp motif, which has been linked by in vitro studies to the regulation of cell growth, is indeed tightly correlated with the proliferative status in vivo.
Design and test of the Stirling-type pulse tube cryocooler (2017)

Stirling type pulse tube cryocoolers are very attractive for cooling of diverse application because it has it has several inherent advantages such as no moving part in the cold end, low manufacturing cost and long operation life. To develop the Stirling-type pulse tube cryocooler, we need to design a linear compressor to drive the pulse tube cryocooler. A moving magnet type linear motor of dual piston configuration is designed and fabricated, and this compressor could be operated with the electric power of 100 W and the frequency up to 60 Hz. A single stage coaxial type pulse tube cold finger aiming at over 1.5 W at 80K is built and tested with the linear compressor. Experimental investigations have been conducted to evaluate their performance characteristics with respect to several parameters such as the phase shifter, the charging pressure and the operating frequency of the linear compressor.
Online Assessment of Transient Stability of Grid Connected PV Generator With DC Link Voltage and Reactive Power Control (2020)

The proliferation of Photovoltaic (PV) generation has brought several changes in the transient stability analysis of power systems. The rotor angle dynamics based stability analysis used for synchronous generators may not be applicable for PV generators. In the existing literature, the transient stability of a grid connected PV generator with dc link voltage and reactive power control (Vdc and Q control) is analyzed from the coupled nonlinear functions corresponding to PV control loops, Phase Locked Loop (PLL) and network dynamics. The existing method may not be suitable for online transient stability assessment because it is computationally heavy. This paper proposes an online transient stability criterion for a PV generator (with Vdc and Q control) connected to grid modelled as infinite bus. The PV generator is considered to have Low Voltage Ride Through (LVRT) capability, but does not provide voltage support. In this study, the relation between the ac and dc side dynamics is explored. A stability criterion is proposed to assess the transient stability by monitoring the swing in the energy of the dc link capacitor. The proposed criterion requires the dc link voltage trajectory only till the first swing of the dc link voltage. As a result, the proposed assessment criterion is computationally less demanding and less prone to measurement errors in comparison to existing methods. Thus, the proposed criterion is suitable for online transient stability assessment. The effectiveness of the proposed criterion is verified for single-stage as well as two-stage converter configurations of PV generator. The proposed criterion is also verified on a modified IEEE 39 bus system. Time-domain simulations are carried out to validate the proposed criterion. The proposed approach is compared with an existing transient stability criterion for Vdc and Q control based grid connected PV generator. The advantages of the proposed method as compared to the existing method are discussed.