gebhart/patrepeval huggingface dataset:
Drivers of archaeal ammonia-oxidizing communities in soil (2012)

Soil ammonia-oxidizing archaea (AOA) are highly abundant and play an important role in the nitrogen cycle. In addition, AOA have a significant impact on soil quality. Nitrite produced by AOA and further oxidized to nitrate can cause nitrogen loss from soils, surface and groundwater contamination, and water eutrophication. The AOA discovered to date are classified in the phylum Thaumarchaeota. Only a few archaeal genomes are available in databases. As a result, AOA genes are not well annotated, and it is difficult to mine and identify archaeal genes within metagenomic libraries. Nevertheless, 16S rRNA and comparative analysis of ammonia monooxygenase sequences show that soils can vary greatly in the relative abundance of AOA. In some soils, AOA can comprise more than 10% of the total prokaryotic community. In other soils, AOA comprise less than 0.5% of the community. Many approaches have been used to measure the abundance and diversity of this group including DGGE, T-RFLP, q-PCR, and DNA sequencing. AOA have been studied across different soil types and various ecosystems from the Antarctic dry valleys to the tropical forests of South America to the soils near Mount Everest. Different studies have identified multiple soil factors that trigger the abundance of AOA. These factors include pH, concentration of available ammonia, organic matter content, moisture content, nitrogen content, clay content, as well as other triggers. Land use management appears to have a major effect on the abundance of AOA in soil, which may be the result of nitrogen fertilizer used in agricultural soils. This review summarizes the published results on this topic and suggests future work that will increase our understanding of how soil management and edaphoclimatic factors influence AOA.
Etiology of the Metabolic Syndrome: Potential Role of Insulin Resistance, Leptin Resistance, and Other Players (1999)

Obesity and Type 2 diabetes are now major public health issues in developed nations and have reached epidemic proportions in many developing nations, as well as disadvantaged groups in developed countries, e.g., Mexican-Americans, African-Americans, and Australian Aborigines. These groups all show hyperinsulinemia and insulin resistance, which have been demonstrated to be future predictors of Type 2 diabetes and have also been suggested as key factors in the etiology of the Metabolic Syndrome. It is now increasingly recognized that Type 2 diabetes is part of a cluster of cardiovascular disease (CVD) risk factors comprising the Metabolic Syndrome. This group is at very high risk of atherosclerosis because each of the risk factors in the Metabolic Syndrome cluster in its own right is an important CVD risk factor. They also contribute cumulatively to atherosclerosis. A key strategy in reducing macrovascular disease lies in the better understanding of the Metabolic Syndrome--glucose intolerance, hypertension, hyperlipidemia, and central obesity. Although it has been suggested that hyperinsulinemia/insulin resistance is the central etiological factor for the Metabolic Syndrome, epidemiological data do not support the idea that this can account for all of the cluster abnormalities. We have animal and human data suggesting that hyperleptinemia rather than, or synergistically with, hyperinsulinemia may play a central role in the genesis of the CVD risk factor cluster that constitutes the syndrome. Studies in Psammomys obesus (the Israeli sand rat) suggest hyperinsulinemia/insulin resistance is an early metabolic lesion in the development of obesity and Type 2 diabetes. This animal also develops other features of the Metabolic Syndrome, making it an excellent model to investigate etiology. Psammomys, when placed on an ad libitum laboratory diet, develops hyperinsulinemia, insulin resistance, impaired glucose tolerance, diabetes, and dyslipidemia. It also develops hyperleptinemia and leptin insensitivity, and hyperleptinemia is correlated with insulin resistance independent of changes in body weight. It is likely that a similar sequence occurs in the transition from the prediabetic state to Type 2 diabetes in humans. More recently, other potential players in the etiology of the Metabolic Syndrome have been suggested including endothelial dysfunction and acetylation-stimulating protein (ASP). It has been suggested that endothelial dysfunction may be an antecedent for both Type 2 diabetes and the Metabolic Syndrome. In addition, ASP is a serious new candidate for an important role in insulin resistance. The ASP pathway plays a critical role in fatty acid metabolism and storage, and it has been suggested that ineffective storage of fatty acids by adipocytes due to a defect in the ASP pathway may lead to insulin resistance and Type 2 diabetes.
Probabilistic Inference of Viral Quasispecies Subject to Recombination (2013)

RNA viruses exist in their hosts as populations of different but related strains. The virus population, often called quasispecies, is shaped by a combination of genetic change and natural selection. Genetic change is due to both point mutations and recombination events. We present a jumping hidden Markov model that describes the generation of viral quasispecies and a method to infer its parameters from next-generation sequencing data. The model introduces position-specific probability tables over the sequence alphabet to explain the diversity that can be found in the population at each site. Recombination events are indicated by a change of state, allowing a single observed read to originate from multiple sequences. We present a specific implementation of the expectation maximization (EM) algorithm to find maximum a posteriori estimates of the model parameters and a method to estimate the distribution of viral strains in the quasispecies. The model is validated on simulated data, showing the advantage of explicitly taking the recombination process into account, and applied to reads obtained from a clinical HIV sample.
Alkaline Posttreatment of MFI Zeolites. From Accelerated Screening to Scale-up (2007)

The extraction of framework silicon, referred to as desilication, has been investigated for controlled mesoporosity development in commercial and synthesized MFI type zeolites. Several variables were successfully identified and optimized using a parallelization approach in the gram-scale. The framework Si/Al ratio of the treated zeolite is crucial for the susceptibility of the zeolite toward desilication. A NaOH solution has proven to be the most efficient medium to achieve substantial and controlled mesopore formation. Descriptors such as treatment temperature and time enable further tailoring of the porous characteristics. Importantly, the acidity and microporosity are preserved upon alkaline treatment under optimized conditions. Finally, the treatment has successfully been scaled up from gram-scale to kilogram-scale for both commercial zeolite powders and extrudates.
Merlin: A Language for Managing Network Resources (2018)

This paper presents Merlin, a framework for managing resources in software-defined networks. With Merlin, administrators express high-level policies using programs in a declarative language. The language includes logical predicates to identify sets of packets, regular expressions to encode forwarding paths, and arithmetic formulas to specify bandwidth constraints. The compiler maps these policies into a constraint problem that determines bandwidth allocations using parametrizable heuristics. It then generates a code that can be executed on the network elements to enforce the policies. To allow network tenants to dynamically adapt policies to their needs, Merlin provides mechanisms for delegating control of sub-policies and for verifying that modifications made to sub-policies do not violate global constraints. Experiments demonstrate the expressiveness and effectiveness of Merlin on realistic scenarios. Overall, Merlin simplifies network administration by providing high-level abstractions for specifying and enforcing network policies.
MHD modeling of rotating arc under restrike mode in ‘Kvaerner-type’ torch: part I. Dynamics at 1 bar pressure (2019)

Abstract This paper focuses on the 3D MHD modeling of an arc plasma at industrial level; the torch is a ‘Kvaerner-type’ one, made of two concentric graphite electrodes and where spots are displaced with an external magnetic field. Different phenomenologies in arc movement were observed, ranging from a gliding arc on electrodes surfaces to hopping arc foots, agreeing with previous experimental works at atmospheric pressure. These dynamics have non-negligible consequences in the plasma process: the hopping mode induces more erosion due to a higher heat flux at the electrodes surfaces in comparison to the gliding arc; the latter mode results also in a strong gas swirling inside the torch, thus longer particles residence time is predicted.
Evidence That Parietal Lobe Fatty Acids May Be More Profoundly Affected in Moderate Alzheimer’s Disease (AD) Pathology Than in Severe AD Pathology (2018)

Brain is a lipid-rich tissue, and fatty acids (FAs) play a crucial role in brain function, including neuronal cell growth and development. This study used GC-MS to survey all detectable FAs in the human parietal cortex (Brodmann area 7). These FAs were accurately quantified in 27 cognitively normal age-matched controls, 16 cases of moderate Alzheimer's disease (AD), 30 severe AD, and 14 dementia with Lewy bodies (DLB). A total of 24 FA species were identified. Multiple comparison procedures, using stepdown permutation tests, noted higher levels of 13 FAs but the majority of changes were in moderate AD and DLB, rather than severe AD. Subjects with moderate AD and DLB pathology exhibited significantly higher levels of a number of FAs (13 FAs and 12 FAs, respectively). These included nervonic, lignoceric, <i>cis</i>-13,16-docosadienoic, arachidonic, <i>cis</i>-11,14,17-eicosatrienoic, erucic, behenic, α-linolenic, stearic, oleic, <i>cis</i>-10-heptanoic, and palmitic acids. The similarities between moderate AD and DLB were quite striking-arachidic acid was the only FA which was higher in moderate AD than control, and was not similarly affected in DLB. Furthermore, there were no significant differences between moderate AD and DLB. The associations between each FA and a number of variables, including diagnosis, age, gender, Aβ plaque load, tau load, and frontal tissue pH, were also investigated. To conclude, the development of AD or DLB pathology affects brain FA composition but, intriguingly, moderate AD neuropathology impacts this to a much greater extent. Post-mortem delay is a potential confounding factor, but the findings here suggest that there could be a more dynamic metabolic response in the earlier stages of the disease pathology.
Measurement of the total hadronic cross section ine+e−annihilation ats=29GeV (1991)

A precise measurement of the ratio $R$ of the total cross section ${e}^{+}{e}^{\ensuremath{-}}\ensuremath{\rightarrow}\mathrm{hadrons}$ to the pointlike cross section ${e}^{+}{e}^{\ensuremath{-}}\ensuremath{\rightarrow}{\ensuremath{\mu}}^{+}{\ensuremath{\mu}}^{\ensuremath{-}}$ at a center-of-mass energy of 29.0 GeV is presented. The data were taken with the upgraded Mark II detector at the SLAC storage ring PEP. The result is $R=3.92\ifmmode\pm\else\textpm\fi{}0.05\ifmmode\pm\else\textpm\fi{}0.09$. The luminosity has been determined with three independent luminosity monitors measuring Bhabha scattering at different angular intervals. Recent calculations of higher-order QED radiative corrections are used to estimate the systematic error due to missing higher-order radiative corrections in the Monte Carlo event generators.
Quantification of MII Egg-specific Transcripts in Single Polar Bodies Provides a Non-Invasive Tool to Measure Embryo Potential. (2011)

Background: Non-invasive tests of mature egg quality and embryo potential are extremely limited but urgently needed. Oocyte-specific genes play important roles in oogenesis, fertilization and at the time of implantation. Detection and abundance of oocyte-derived mRNAs may provide insight into oocyte competence. We tested the hypothesis that mRNAs originating from expression in the metaphase II (MII) oocyte are present and detectable in single polar body. Results: Secondary mouse follicles were grown in vitro using an alignate-based three-dimensional culture system. Oocytes were isolated at the end of culture and MII eggs matured. The first polar body was removed from all oocytes followed by reverse transcription and sibling oocytes were similarly prepared. Real-time PCR was performed to detect and quantify relative gene expression levels. Six oocyte-specific genes (GDF9, BMP15, Nlrp5, ZP3, H1foo and TCL1) were detected in the polar body. There is a linear correlation between the abundance of mRNA transcripts in the oocyte and in its polar body (P<0.01) and as expected, the abundance of these gene products was lower in the polar body when compared to their sibling oocyte (fold change between 0.20 and 0.76).Conclusion: The ability to detect and compare differences in gene expression from individual polar bodies may provide a non-invasive tool to select embryos of high quality from a pool of MII eggs. (poster)
Pulmonary disease in selected protozoal infections. (1997)

Protozoa of the phylum Apicomplexa, including the genera Plasmodium, Babesia, Toxoplasmosis, and Cryptosporidium, are a group of closely related organisms that seldom cause pulmonary disease. All but Babesia are members of the subclass Coccidiasina ("Coccidians"). (The fungal organism Coccidioides immitis, a frequent cause of pulmonary disease in endemic areas, was first believed by Rixsford and Gilchrist to be a member of the subclass Coccidiasina; hence its name, meaning coccidioidal-like). Some species, such as Toxoplasma gondii, occasionally cause pulmonary disease by directly infecting lung parenchyma, whereas others, such as Cryptosporidium and Microsporidium, can be occasionally visualized in respiratory secretions or lung biopsy specimens, but their role in causing respiratory disease in human beings is more questionable. In contrast, pulmonary disease associated with infections caused by Malaria and Babesia is often the result of a systemic inflammatory response.
Integrating Visual Representaiton of Knowledge with Learning Management Systems (2011)

After a review of literature pertaining to representative constituent parts of contemporary learning management systems (LMS) and features of other systems that support visual representations of information and knowledge in support of learning, a summarization of desirable design elements for a system that is meant to support distance learning is developed and elaborated. These elements include the potential benefits of having an explicit realization of a viable pedagogical theory as the underlying basis for the software, the possible benefits of integrating a variety of capabilities in as simple and usable a fashion as possible, the value of presenting a customizable interface, and the desirability of providing for sharing and reuse of instructional resources. The chapter concludes with a description of a prototype system that embodies many of the principles laid out in the paper.
Heavy chain variable region allotypic subspecificities of rabbit immunoglobulins. II. Selective escape of the a1-AB Ig subpopulation after the induction of auto anti-a1 antibody. (1979)

An a1a2 rabbit (P286-3), neonatally suppressed for the expression of the a1 allotype, was immunized with autologous a1 IgG at 2 months of age. Both auto anti-a1 Ab and a1 IgG molecules were found in the serum of this rabbit after the auto-immunization. The auto anti-a1 Ab and the IgG from the auto anti-a1 Ab-depleted serum were isolated. Of the previously defined a1-AB, a1-AC, and a1-AD Ig subpopulations, the a1 IgG in the IgG preparation from the rabbit P286-3 were all of the a1-AB Ig subpopulation. The auto anti-a1 Ab from rabbit P286-3 did not react with the a1-A, a1-B, and a1-C allotypic subspecificities; thus, it was presumably specific for the a1-AC and a1-D allotypic subspecificity. Thus, the a1-AB Ig subpopulation escaped from allotype suppression in rabbit P286-3, whereas the a1-AD Ig subpopulation remained suppressed. The a1-AD Ig subpopulation will probably remain suppressed for a long time and perhaps permanently since rabbit P286-3 has produced circulating auto-Ab specific for the a1-D allotypic subspecificity. These results indicate that the a1 Ig subpopulations are synthesized by distinct clones of lymphocytes under separate control.
Determination of cadmium in urine and observations on urinary cadmium and protein excretion in men exposed to cadmium oxide dust (1955)

Prolonged exposure of workmen in the alkaline- accumulator industry to cadmium oxide dust led in many cases to the appearance of protein in the urine As part of a study of the pizoteinuria of cadmium poisoning an acciirate method for the measurement of cadmium in urine was obligatory. This paper describes a sensitive and specific dithizone procedure and presents data on the incidence and degree of proteinuria in relation to cadmium exposure and excretion.
Analysis of Tissue and Serum MicroRNA Expression in Patients with Upper Urinary Tract Urothelial Cancer (2015)

MicroRNA expression is altered in UUTUC. The analysis of circulating miR-141 may be useful to identify patients with UUTUC.
Enteric Viruses in Diarrheic Turkey Poults (1985)

Thirty-three intestinal samples from 10-to-21-day-old diarrheic turkey poults were examined for the presence of enteric viruses by electron microscopy. Samples originated from 32 flocks in six commercial operations located in six states. Mortality in these flocks ranged from 3 to 15%, and birds from recovered flocks varied greatly in size. Rotavirus-like agents (RVLA) were the most common viruses associated with diarrhea outbreaks in the flocks examined, occurring in five out of six operations. Other viruses detected either singly or in combination, in order of prevalence, were astroviruses, reoviruses, rotaviruses, enteroviruses, and adenoviruses. With the exception of RVLA and rotaviruses, the other viruses were identified solely on the basis of morphology. Salmonellae were isolated from only one of the intestinal samples. By electron microscopy, RVLA were morphologically indistinguishable from rotaviruses, occurring as both 55-nm single-shelled and 70-nm double-shelled particles. However, immune electron microscopy was useful for antigenic differentiation of these two viruses. Turkey rotaviruses reacted with antisera to porcine and bovine rotaviruses, whereas turkey RVLA did not. Neither turkey rotaviruses nor RVLA reacted with antisera to porcine para-rotavirus or an antigenically distinct bovine rotavirus (bovine rotavirus-like agent). Similarly, convalescent anti-turkey RVLA serum (from recovered specific-pathogen-free poults) reacted with homologous virus but did not react with mammalian or avian rotaviruses or reoviruses. Further, RVLA were found to possess RNA electrophoretic migration patterns unlike those of conventional rotaviruses or reoviruses. This trait was used as an additional means of differentiating these viruses.
Widening the Voltammetric Window Using Regular Arrays of Microdisk Electrodes (2007)

Abstract This work explores, through mathematical modeling and numerical simulation, the use of regular arrays of microdisk electrodes wired in parallel as a means to increase the width of the electrochemical window in which one can carry out electrochemical experiments.
Shear Alignment Mechanisms of Close-Packed Spheres in a Bulk ABA Triblock Copolymer (2022)

The alignment and shear-induced microstructural changes of closed-packed spheres observed in a poly(styrene-b-lauryl acrylate-b-styrene) triblock copolymer were quantified with a combination of in situ small-angle X-ray scattering (SAXS) and Fourier-transform (FT) rheology. Disordered spheres produced through compression molding were transformed to close-packed spheres through the application of nonlinear oscillatory shear. FT rheology identified strain amplitude regimes for small-, medium-, and large-amplitude oscillatory shear behaviors (SAOS, MAOS, and LAOS, respectively) at fixed temperature and frequency. The presence of oscillatory shear induced orientational changes in the hexagonally-closed packed (HCP) layers. Increasing the strain amplitude produced faster ordering and higher degree of orientation, quantified through fitting a stretched exponential function to in situ SAXS and FT rheology data. In the MAOS regime, shear thinning behavior was observed, with decrease in the storage modulus (G′) due to the formation of HCP layers that exhibited less resistance to flow. The third-order harmonic (I3/1) increased with the square of the strain amplitude, hypothesized to originate from the presence of sharp grain interphase boundaries (due to defects), and Chebyshev coefficients indicated intracycle shear thickening and strain stiffening. In the LAOS regime, HCP layers adopted a parallel orientation with a zigzag path sliding mechanism, and both G′ and the loss modulus (G″) decreased with increasing strain amplitude. Interestingly, at higher strain amplitude, shear deordering was observed for the first time in close-packed spheres under oscillatory shear, as evidenced by characteristic signatures in both in situ SAXS and FT rheology data. Structural rearrangements were consistent with the domain dissolution and reformation mechanism.
Approximate Value Trees in Structured Dynamic Programming. (1996)

We propose and examine a method of approximate dynamic programming for Markov decision processes based on structured problem representations. We assume an MDP is represented using a dynamic Bayesian network, and construct value functions using decision trees as our function representation. The size of the representation is kept within acceptable limits by pruning these value trees so that leaves represent possible ranges of values, thus approximating the value functions produced during optimization. We propose a method for detecting convergence,prove errors bounds on the resulting approximately optimal value functions and policies, and describe some preliminary experimental results.
Protective role of vanilloid receptor type 1 in HCl‐induced gastric mucosal lesions in rats (2004)

The results of this study suggest that VR1 plays a protective role in the gastric defensive mechanism in rats.
Systematic condition-dependent annotation of metabolic genes (2007)

The task of deriving a functional annotation for genes is complex as their involvement in various processes depends on multiple factors such as environmental conditions and genetic backup mechanisms. This study employs a large-scale model of the metabolism of Saccharomyces cerevisiae to investigate the function of yeast genes and derive a condition-dependent annotation (CDA) for their involvement in major metabolic processes under various genetic and environmental conditions. The resulting CDA is validated on a large scale and is shown to be superior to the corresponding Gene Ontology (GO) annotation, by showing that genes annotated with the same CDA term tend to be more coherently conserved in evolution and display greater expression coherency than those annotated with the same GO term. The CDA gives rise to new kinds of functional condition-dependent metabolic pathways, some of which are described and further examined via substrate auxotrophy measurements of knocked-out strains. The CDA presented is likely to serve as a new reference source for metabolic gene annotation.