gebhart/patrepeval huggingface dataset:
Foliar and root applications of the rare sugar tagatose control powdery mildew in soilless grown cucumbers (2021)

Powdery mildew is a constant threat to cucumber production in soilless systems requiring the intensive use of chemical fungicides to limit yield losses. However, the toxicity risks for the growers and the food safety issues linked to fungicide residues represent a major concern for crops with a frequent and extended harvest period, like cucumber, and create an urgent need of eco-friendly alternatives. The objective of this study was to assess the effectiveness of foliar and root applications of the rare sugar tagatose, against naturally occurring powdery mildew (Podosphaera xanthii and Golovinomyces cichoracearum) on cucumber plants grown in a soilless system under commercial-like greenhouse conditions. Foliar and root applications of tagatose reduced powdery mildew severity and incidence under conditions of low severity in untreated plants, but tagatose and the chemical standard strategy lost their effect in the control of powdery mildew when the disease severity was increasing steadily. The combination of sulphur with foliar applications of tagatose effectively reduced powdery mildew under high severity conditions. Overall, under high disease pressure, foliar and root applications of tagatose were more effective than the standard chemical treatment reducing powdery mildew disease incidence and severity. Foliar application of tagatose directly inhibited P. xanthii conidial germination. After root application, tagatose was translocated to the leaves guaranteeing a systemic protection with no accumulation in cucumber fruits. Root applications of tagatose represent a novel strategy for cucumber protection against powdery mildew and reduce fungicide applications.
A Systematic Meta-analysis of Immune Signatures in Patients With Acute Chikungunya Virus Infection (2015)

To our knowledge, this is the first study that associated levels of CHIKV load with arthralgia as an indicator of acute CHIKV infection. Importantly, our findings also revealed specific immune mediator signatures that can be used to better define CHIKV infection.
Isochores and Heat Capacity of Liquid Water in Terms of the Ion–Molecular Model (2023)

Thermodynamics of liquid water in terms of a non-standard approach-the ion-molecular model-is considered. Water is represented as a dense gas of neutral H<sub>2</sub>O molecules and single charged H<sub>3</sub>O<sup>+</sup> and OH<sup>-</sup> ions. The molecules and ions perform thermal collisional motion and interconvert due to ion exchange. The energy-rich process-vibrations of an ion in a hydration shell of molecular dipoles-well known to spectroscopists with its dielectric response at 180 cm<sup>-1</sup> (5 THz), is suggested to be key for water dynamics. Taking into account this ion-molecular oscillator, we compose an equation of state of liquid water to obtain analytical expressions for the isochores and heat capacity.
Molecular characterization of wheat antigens involved in celiac disease (71.13) (2012)

Abstract Wheat gliadins trigger a hypersensitive immune response in genetically susceptible individuals causing celiac disease (CD). The small intestinal mucosa of CD patients is characterised by presence of numerous infiltrating CD4+ T cells. These T cells proliferate and secrete IFN-γ when stimulated with gliadin extracts and are implicated in the mucosal damage and production of anti-gliadin antibodies. Peptide sequences in the Pro(P) and Glub(Q) rich regions of gliadins are known to be T cell-stimulatory but due to the heterogeneity of gliadin sequences, several potential stimulatory epitopes and the individual protein antigens are yet to be identified and characterized. Thus our aim was to identify and characterize wheat antigens with ability to initiate and sustain celiac disease. Due to their complex biochemistry the three subtypes of gliadins α/β, γ, and ω-gliadins are difficult to isolate into pure fractions. Hence, we developed a method wherein the alcohol extracted gliadins was sub-fractionated ion-exchange chromatography and each sub-fraction’s reactivity to serum IgA, from clinically well defined CD (active/diet) patients and non-CD patients was analyzed. We identified and generated recombinant gliadins that were CD specific. Epitope mapping studies revealed major immune-reactive regions. Recombinant gamma-gliadins will be useful for characterizing the immune response to wheat antigens and to develop reliable diagnostic and therapeutic strategies.
Hybrid Bayesian Networks for Reasoning about Complex Systems (2002)

Many real-world systems are naturally modeled as hybrid stochastic processes, i.e., stochastic processes that contain both discrete and continuous variables. Examples include speech recognition, target tracking, and monitoring of physical systems. The task is usually to perform probabilistic inference, i.e., infer the hidden state of the system given some noisy observations. For example, we can ask what is the probability that a certain word was pronounced given the readings of our microphone, what is the probability that a submarine is trying to surface given our sonar data, and what is the probability of a valve being open given our pressure and flow readings. Bayesian networks are
Component based design of fault-tolerance (1999)

In this dissertation, we defend the thesis that a fault-tolerant program is a composition of a fault-intolerant program and a set of fault-tolerance components. To validate this thesis, we identify a basis set of fault-tolerance components, namely detectors and correctors. We show that depending upon the desired level of fault-tolerance, detectors, correctors, or both are necessary and sufficient for designing a rich class of fault-tolerant programs. Moreover, the fault-tolerant programs designed using existing methods such as replication and Schneider's state machine approach can be alternatively designed in terms of detectors and correctors. 
Using these fault-tolerance components, we present a method for designing multi-tolerant programs, i.e., programs that tolerate multiple types of faults while providing potentially different levels of tolerance to each type of fault. Our method accommodates all types of faults, including process faults, communication faults, hardware and software faults, network failure and security intrusions, and it can be used in several application domains such as distributed systems, computer networks and parallel systems. 
Using several examples, we illustrate how our fault-tolerance components can be used in the design of several fault-tolerant programs. Among these examples, we discuss in detail the problem of distributed reset. A distributed reset operation reinitializes a distributed system to a given global state. Our distributed reset program is the first bounded state program that masks fail-stop and repair of processes and stabilizes in the presence of transient faults. In other words, it guarantees that if only fail-stop and repair faults occur then every reset operation is correct and if transient faults occur then eventually the program reaches a state from where subsequent reset operations are correct. Towards designing this distributed reset program, we have designed multitolerant components that are useful in adding multitolerance to several other applications. 
We also argue that the decomposition of a fault-tolerant program into its fault-tolerance components is useful in verification of that program. Towards this end, we present a case study that illustrates our experience in verifying Dijkstra's token ring program with the theorem prover PVS.
Application-dependent dynamic monitoring of distributed and parallel systems (1993)

Achieving high performance for parallel or distributed programs often requires substantial amounts of information about the programs themselves, about the systems on which they are executing, and about specific program runs. The monitoring system that collects, analyzes, and makes application-dependent monitoring information available to the programmer and to the executing program is presented. The system may be used for off-line program analysis, for on-line debugging, and for making on-line, dynamic changes to parallel or distributed programs to enhance their performance. The authors use a high-level, uniform data model for the representation of program information and monitoring data. They show how this model may be used for the specification of program views and attributes for monitoring, and demonstrate how such specifications can be translated into efficient, program-specific monitoring code that uses alternative mechanisms for the distributed analysis and collection to be performed for the specified views. The model's utility has been demonstrated on a wide variety of parallel machines.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Effects of TGFβ on bone ingrowth in the presence of polyethylene particles (1999)

We implanted bone harvest chambers (BHCs) bilaterally in ten mature male New Zealand white rabbits. Polyethylene particles (0.3+/-0.1 microm in diameter, 6.4 x 10(12) particles/ml) were implanted for two, four or six weeks bilaterally in the BHCs, with subsequent removal of the ingrown tissue after each treatment. In addition to the particles, one side also received 1.5 microg of recombinant transforming growth factor beta1 (TGFbeta1). At two weeks, the bone area as a percentage of total area was less in chambers containing TGFbeta compared with those with particles alone (7.8+/-1.3% v 16.9+/-2.7% respectively; 95% confidence interval (CI) for difference -14.0 to -4.30; p = 0.002). At four weeks, the percentage area of bone was greater in chambers containing TGFbeta compared with those with particles alone (31.2+/-3.4% v 22.5+/-2.0% respectively; 95% CI for difference 1.0 to 16.4; p = 0.03). There were no statistical differences at six weeks, despite a higher mean value with TGFbeta treatment (38.2+/-3.9% v 28.8 +/-3.5%; 95% CI for difference -4.6 to 23.3; p = 0.16). The number of vitronectin-receptor-positive cells (osteoclast-like cells) was greater in the treatment group with TGFbeta compared with that with particles alone; most of these positive cells were located in the interstitium, rather than adjacent to bone. TGFbeta1 is a pleotropic growth factor which can modulate cellular events in the musculoskeletal system in a time- and concentration-dependent manner. Our data suggest that there is an early window at between two and six weeks, in which TGFbeta may favourably affect bone ingrowth in the BHC model. Exogenous growth factors such as TGFbeta may be a useful adjunct in obtaining osseointegration and bone ingrowth, especially in revisions when there is compromised bone stock and residual particulate debris.
“On Water”‐Promoted Direct Coupling of Indoles with 1,4‐Benzoquinones without Catalyst (2005)

Abstract A highly efficient direct coupling of indole compounds with 1,4‐benzoquinones was developed “on water” in the absence of any catalyst, organic co‐solvent, or additives. The “on‐water” conditions provided the best yields of the corresponding products and the only system to produce bis(coupling) products. (© Wiley‐VCH Verlag GmbH &amp; Co. KGaA, 69451 Weinheim, Germany, 2006)
Prednisolone promotes remission and gastric mucosal regeneration in experimental autoimmune gastritis (2006)

A cardinal feature of organ-specific autoimmunity is destructive pathology in the target organ. In human and experimental models of autoimmune gastritis, mononuclear cell infiltration and cellular destruction in the gastric mucosa are disease hallmarks. Strategies to cure autoimmune disease must not only establish immunological tolerance to autoantigen, but also rid the organ of pathogenic autoreactive cells. The present study has assessed the effect of prednisolone treatment in clearing the inflammatory infiltrate in experimental autoimmune gastritis and in preventing disease relapse in athymic compared with euthymic mice. Experimental autoimmune gastritis was induced by neonatal thymectomy or by transgenic expression of GM-CSF (PC-GMCSF mice). Groups of mice were treated with prednisolone (10 mg/kg per day) for 10 weeks or with prednisolone for 10 weeks followed by 10 weeks without prednisolone. Stomachs were examined for gross morphological changes, and by histology and immunohistochemistry for composition of inflammatory infiltrate and gastric mucosal integrity. Autoantibody to gastric H+/K+ ATPase was determined by ELISA. Prednisolone promoted remission of gastritis in both mouse models of experimental autoimmune gastritis, evident by reduction in stomach size, clearing of gastric inflammatory infiltrate, and regeneration of the gastric mucosa. Prednisolone withdrawal resulted in disease relapse in all PC-GMCSF mice, whereas approximately 40% of neonatal thymectomy mice retained normal stomach morphology and remained free of gastric pathology. It is concluded that prednisolone promotes remission and gastric mucosal regeneration in experimental autoimmune gastritis. Prolonged remission of autoimmune gastritis in some athymic mice suggests a role for the thymus in disease relapse.
The effect of bitumen polar groups adsorption on mastics properties at low temperatures (2013)

The current design standard for asphalt mixtures provides guidance on selection of aggregates and asphalt binder and includes requirements for the amount of mineral filler to be added in the mix. In the SuperPave system, the amount of filler that can be included is limited to a ratio in the range of 0.6–1.2 by mass of the filler to the binder (i.e. approximately 20–40% by volume of mastic). However, this range is based on experience rather than on scientific evaluation of the interaction between filler and binder. The experimental results collected in this study for mastics produced with two bitumens and a set of commonly used fillers indicate that the physico-chemical interaction effect is the result of adsorption of asphaltenes and resins (i.e. polar groups in asphalt) on the surface of the filler particles. This adsorption is partially responsible for the changes in the mechanical properties (e.g. stiffness and viscosity) and thermo-volumetric properties (e.g. coefficients of thermal contraction and glass transition temperature – T g) of the mastic. The amount of polar groups adsorbed was found to depend on the Braunauer–Emmett–Teller (BET) surface area of the filler, but not on the chemical composition of the filler or the bitumen. The higher the BET surface area, the greater the amount of polar groups adsorbed, and the lower the glass transition temperature. The significant reduction in the glass transition temperature indicates that this adsorption phenomenon results in softening the bitumen in the mastics.
Claudin-Low Breast Cancer; Clinical & Pathological Characteristics (2017)

Claudin-low breast cancer is a molecular type of breast cancer originally identified by gene expression profiling and reportedly associated with poor survival. Claudin-low tumors have been recognised to preferentially display a triple-negative phenotype, however only a minority of triple-negative breast cancers are claudin-low. We sought to identify an immunohistochemical profile for claudin-low tumors that could facilitate their identification in formalin fixed paraffin embedded tumor material. First, an in silico collection of ~1600 human breast cancer expression profiles was assembled and all claudin-low tumors identified. Second, genes differentially expressed between claudin-low tumors and all other molecular subtypes of breast cancer were identified. Third, a number of these top differentially expressed genes were tested using immunohistochemistry for expression in a diverse panel of breast cancer cell lines to determine their specificity for claudin-low tumors. Finally, the immunohistochemical panel found to be most characteristic of claudin-low tumors was examined in a cohort of 942 formalin fixed paraffin embedded human breast cancers with >10 years clinical follow-up to evaluate the clinico-pathologic and survival characteristics of this tumor subtype. Using this approach we determined that claudin-low breast cancer is typically negative for ER, PR, HER2, claudin 3, claudin 4, claudin 7 and E-cadherin. Claudin-low tumors identified with this immunohistochemical panel, were associated with young age of onset, higher tumor grade, larger tumor size, extensive lymphocytic infiltrate and a circumscribed tumor margin. Patients with claudin-low tumors had a worse overall survival when compared to patients with luminal A type breast cancer. Interestingly, claudin-low tumors were associated with a low local recurrence rate following breast conserving therapy. In conclusion, a limited panel of antibodies can facilitate the identification of claudin-low tumors. Furthermore, claudin-low tumors identified in this manner display similar clinical, pathologic and survival characteristics to claudin-low tumors identified from fresh frozen tumor material using gene expression profiling.
Electrostatic properties of antistatic cloth woven partly with electrically conductive fibers (1988)

An electrically conductive fiber and an antistatic cloth woven partly with electrically conductive fibers have a high electrostatic elimination effect in wet as well as dry atmospheres. The electrostatic elimination effect of the antistatic cloth does not decay with repeated washing. Antistatic cloth has been widely used in industry to prevent the electrostatic risk caused by electrification of fiberware. Charge densities and discharge characteristics of various antistatic cloths, controlled primarily by weaving electrically conductive fibers into the cloth, have been investigated experimentally. The electrostatic elimination effect of these is evaluated.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Stress induced polarization currents and electromagnetic emission from rocks and ionic crystals, accompanying their deformation (2004)

Abstract. A crucial question of the scientific community nowadays, concerns the existence of electric signals preceding earthquakes. In order to give a plausible answer to this question, we carried out two kinds of laboratory experiments of uniaxial deformation of ionic crystals and rock samples: a) In the first kind, stress induced polarization currents are detected and recorded. Our experimental results showed not only the existence of stress induced polarization currents before the fracture of the samples, but the possibility of the propagation of these signals, as well, through conductive channels, for distances much longer than the source dimensions. b) In the second, acoustic and electromagnetic signals are detected and recorded in the frequency range from 1KHz to some MHz. The mechanism of generation of these signals is shown to be different for those emitted from piezoelectric and from non-piezoelectric materials. A plausible model is also suggested, on the compatibility of our laboratory results with the processes occurring in the earth during the earthquake preparatory stage.
Lung evolution as a cipher for physiology (2009)

In the postgenomic era, we need an algorithm to readily translate genes into physiologic principles. The failure to advance biomedicine is due to the false hope raised in the wake of the Human Genome Project (HGP) by the promise of systems biology as a ready means of reconstructing physiology from genes. like the atom in physics, the cell, not the gene, is the smallest completely functional unit of biology. Trying to reassemble gene regulatory networks without accounting for this fundamental feature of evolution will result in a genomic atlas, but not an algorithm for functional genomics. For example, the evolution of the lung can be "deconvoluted" by applying cell-cell communication mechanisms to all aspects of lung biology development, homeostasis, and regeneration/repair. Gene regulatory networks common to these processes predict ontogeny, phylogeny, and the disease-related consequences of failed signaling. This algorithm elucidates characteristics of vertebrate physiology as a cascade of emergent and contingent cellular adaptational responses. By reducing complex physiological traits to gene regulatory networks and arranging them hierarchically in a self-organizing map, like the periodic table of elements in physics, the first principles of physiology will emerge.
Partial Sequence Homogenization in the 5S Multigene Families May Generate Sequence Chimeras and Spurious Results in Phylogenetic Reconstructions (2013)

Multigene families have provided opportunities for evolutionary biologists to assess molecular evolution processes and phylogenetic reconstructions at deep and shallow systematic levels. However, the use of these markers is not free of technical and analytical challenges. Many evolutionary studies that used the nuclear 5S rDNA gene family rarely used contiguous 5S coding sequences due to the routine use of head-to-tail polymerase chain reaction primers that are anchored to the coding region. Moreover, the 5S coding sequences have been concatenated with independent, adjacent gene units in many studies, creating simulated chimeric genes as the raw data for evolutionary analysis. This practice is based on the tacitly assumed, but rarely tested, hypothesis that strict intra-locus concerted evolution processes are operating in 5S rDNA genes, without any empirical evidence as to whether it holds for the recovered data. The potential pitfalls of analysing the patterns of molecular evolution and reconstructing phylogenies based on these chimeric genes have not been assessed to date. Here, we compared the sequence integrity and phylogenetic behavior of entire versus concatenated 5S coding regions from a real data set obtained from closely related plant species (Medicago, Fabaceae). Our results suggest that within arrays sequence homogenization is partially operating in the 5S coding region, which is traditionally assumed to be highly conserved. Consequently, concatenating 5S genes increases haplotype diversity, generating novel chimeric genotypes that most likely do not exist within the genome. In addition, the patterns of gene evolution are distorted, leading to incorrect haplotype relationships in some evolutionary reconstructions.