gebhart/patrepeval huggingface dataset:
Changes in the deep subsurface microbial biosphere resulting from a field-scale CO2 geosequestration experiment (2014)

Subsurface microorganisms may respond to increased CO2 levels in ways that significantly affect pore fluid chemistry. Changes in CO2 concentration or speciation may result from the injection of supercritical CO2 (scCO2) into deep aquifers. Therefore, understanding subsurface microbial responses to scCO2, or unnaturally high levels of dissolved CO2, will help to evaluate the use of geosequestration to reduce atmospheric CO2 emissions. This study characterized microbial community changes at the 16S rRNA gene level during a scCO2 geosequestration experiment in the 1.4 km-deep Paaratte Formation of the Otway Basin, Australia. One hundred and fifty tons of mixed scCO2 and groundwater was pumped into the sandstone Paaratte aquifer over 4 days. A novel U-tube sampling system was used to obtain groundwater samples under in situ pressure conditions for geochemical analyses and DNA extraction. Decreases in pH and temperature of 2.6 log units and 5.8°C, respectively, were observed. Polyethylene glycols (PEGs) were detected in the groundwater prior to scCO2 injection and were interpreted as residual from drilling fluid used during the emplacement of the CO2 injection well. Changes in microbial community structure prior to scCO2 injection revealed a general shift from Firmicutes to Proteobacteria concurrent with the disappearance of PEGs. However, the scCO2 injection event, including changes in response to the associated variables (e.g., pH, temperature and salinity), resulted in increases in the relative abundances of Comamonadaceae and Sphingomonadaceae suggesting the potential for enhanced scCO2 tolerance of these groups. This study demonstrates a successful new in situ sampling approach for detecting microbial community changes associated with an scCO2 geosequestration event.
An alternative for pre‐treatment of high‐strength raw whey wastewaters: submerged membrane bioreactors (2004)

Abstract The direct treatment of whey wastewater at various sludge ages (10–75 days) and high biomass concentration (above 50 g mixed liquor suspended solid (MLSS) dm −3 ) in a submerged membrane bioreactor (sMBR) is described. The chemical oxygen demand (COD) of raw whey varied in the range of 60 and 90 g dm −3 . After feeding the sMBR with raw whey, effluent COD reduced to about 20 g dm −3 . The effluent was free of suspended solids and total coliform bacteria. Total phosphorus (TP) and orthophosphate (Ortho‐P) in the influent varied between 204 and 880 mg dm −3 and between 180 and 620 mg dm −3 , and effluent TP and Ortho‐P reduced to 113 and 109 mg dm −3 , respectively. The ammonium and nitrate concentrations in the influent were in the ranges of 3.4 and 120 mg dm −3 and 10 and 503 mg dm −3 , respectively. The effluent ammonium concentration varied between 17.6 and 198 mg dm −3 and nitrate concentrations varied between 0.9 and 69 mg dm −3 . Effluent turbidity varied between 23 and 111 FAU (Formazin Attenuation Unit). The results show that sMBR is an effective pre‐treatment system for high‐strength agro‐wastewaters because of its ability to reduce the pollution load. Copyright © 2004 Society of Chemical Industry
Microjet printing of micro-optical waveguides (2002)

The development of a novel technology for drop-on-demand microjet printing of microlenses, ranging in configuration from spherical to hyperbolic and anamorphic, has been described earlier. This presentation focuses on the utilization of this technology for the printing of hemi-cylindrical ridge waveguides for multimode optical interconnections.
A method to reduce the Gibbs ringing artifact in MRI scans while keeping tissue boundary integrity (2002)

Gibbs ringing is a well known artifact that effects reconstruction of images having discontinuities. This is a problem in the reconstruction of magnetic resonance imaging (MRI) data due to the many different tissues normally present in each scan. The Gibbs ringing artifact manifests itself at the boundaries of the tissues, making it difficult to determine the structure of the brain tissue. The Gegenbauer reconstruction method has been shown to effectively eliminate the effects of Gibbs ringing in other applications. This paper presents the application of the Gegenbauer reconstruction method to neuro-imaging.
Exploring the tertiary gene pool of bread wheat: sequence assembly and analysis of chromosome 5M<sup>g</sup> of <i>Aegilops geniculata</i> (2015)

Next-generation sequencing (NGS) provides a powerful tool for the discovery of important genes and alleles in crop plants and their wild relatives. Despite great advances in NGS technologies, whole-genome shotgun sequencing is cost-prohibitive for species with complex genomes. An attractive option is to reduce genome complexity to a single chromosome prior to sequencing. This work describes a strategy for studying the genomes of distant wild relatives of wheat by isolating single chromosomes from addition or substitution lines, followed by chromosome sorting using flow cytometry and sequencing of chromosomal DNA by NGS technology. We flow-sorted chromosome 5M(g) from a wheat/Aegilops geniculata disomic substitution line [DS5M(g) (5D)] and sequenced it using an Illumina HiSeq 2000 system at approximately 50 × coverage. Paired-end sequences were assembled and used for structural and functional annotation. A total of 4236 genes were annotated on 5M(g) , in close agreement with the predicted number of genes on wheat chromosome 5D (4286). Single-gene FISH indicated no major chromosomal rearrangements between chromosomes 5M(g) and 5D. Comparing chromosome 5M(g) with model grass genomes identified synteny blocks in Brachypodium distachyon, rice (Oryza sativa), sorghum (Sorghum bicolor) and barley (Hordeum vulgare). Chromosome 5M(g) -specific SNPs and cytogenetic probe-based resources were developed and validated. Deletion bin-mapped and ordered 5M(g) SNP markers will be useful to track 5M-specific introgressions and translocations. This study provides a detailed sequence-based analysis of the composition of a chromosome from a distant wild relative of bread wheat, and opens up opportunities to develop genomic resources for wild germplasm to facilitate crop improvement.
Alloreactive cytotoxic T cells recognize MHC class I antigen without peptide specificity (1991)

In this report, experiments are described to differentiate between three potential models of class I MHC allorecognition, namely 1) recognition of peptide-free MHC, 2) peptide-MHC-specific recognition, and 3) peptide-MHC-nonspecific recognition. Using a nucleoprotein peptide (NPP) with a sequence derived from influenza virus nucleoprotein with high affinity for Kd class I MHC molecules, it is shown that target cells rapidly become lysable by Kd-NPP self-restricted cytotoxic T (Tc) cells, and retain sufficient Kd-NPP complexes for at least 72 h. Kd-specific alloreactive Tc cells at the clonal and polyclonal level do not show decreased lysis of Kd-bearing targets in the continuous long term (48 h) presence of NPP. Kd-stimulator cells modified with NPP are able to induce potent Kd-NPP-specific self-restricted Tc cells, however Kd-NPP stimulator cells do not generate Kd-NPP specific alloreactive Tc cells from CBA and B10.A (5R) mouse strains as tested by limiting dilution split clone experiments. Human cells infected with the vaccinia virus recombinant coding for the murine Kd class I MHC Ag can be lysed by murine Kd-specific alloreactive Tc cells. In addition the rate of reemergence of alloreactive and self-restricted Tc cell epitopes on virally infected target cells that had their cell-surface class I MHC Ag removed is identical. These results are consistent with model 3 namely that the majority of Tc precursor and effector cells recognize class I MHC Ag without peptide specificity.
Antisense inhibition of macrophage inflammatory protein 1-α blocks bone destruction in a model of myeloma bone disease (2001)

We recently identified macrophage inflammatory protein 1- (MIP-1) as a factor produced by multiple myeloma (MM) cells that may be responsible for the bone destruction in MM (1).To investigate the role of MIP-1 in MM bone disease in vivo, the human MM-derived cell line ARH was stably transfected with an antisense construct to MIP-1 (AS-ARH) and tested for its capacity to induce MM bone disease in SCID mice.Human MIP-1 levels in marrow plasma from AS-ARH mice were markedly decreased compared with controls treated with ARH cells transfected with empty vector (EV-ARH).Mice treated with AS-ARH cells lived longer than controls and, unlike the controls, they showed no radiologically identifiable lytic lesions.Histomorphometric analysis demonstrated that osteoclasts (OCLs) per square millimeter of bone and OCLs per millimeter of bone surface of AS-ARH mice were significantly less than in EV-ARH mice, and the percentage of tumors per total bone area was also significantly decreased.AS-ARH cells demonstrated decreased adherence to marrow stromal cells, due to reduced expression of the 5 1 integrin and diminished homing capacity and survival.These data support an important role for MIP-1 in cell homing, survival, and bone destruction in MM.
High Dynamic Range Camera using Reflective Liquid Crystal (2007)

High dynamic range images (HDRIs) are needed for capturing scenes that include drastic lighting changes. This paper presents a method to improve the dynamic range of a camera by using a reflective liquid crystal. The system consists of a camera and a reflective liquid crystal placed in front of the camera. By controlling the attenuation rate of the liquid crystal, the scene radiance for each pixel is adaptively controlled. After the control, the original scene radiance is derived from the attenuation rate of the liquid crystal and the radiance obtained by the camera. A prototype system has been developed and tested for a scene that includes drastic lighting changes. The radiance of each pixel was independently controlled and the HDRIs were obtained by calculating the original scene radiance from these results.
Genetics of childhood-onset inflammatory bowel disease (2010)

Nearly a third of inflammatory bowel disease (IBD) patients present in childhood or adolescence, with epidemiological and natural history studies clearly demonstrating a rising incidence in this population. Although early-onset disease has a distinct phenotype, such as more extensive disease at onset and rapid progression, two recent genome-wide association studies (GWAS) carried out exclusively in this age group have demonstrated marked genetic similarities to adult disease. Although these parallels exist, this review will focus on the novel regions associated with early-onset IBD susceptibility identified by these early-onset GWAS. These new loci reaffirm the dysregulated pathways previously implicated in adult IBD pathogenesis and provide further insight into the pathophysiology of intestinal inflammation. The newly identified loci and expression data suggest mutations in genes encoding IL-27, which is involved in Th17 effector cell physiology; MTMR3, which we demonstrate is an essential component of autophagy; and CAPN10, which is necessary in regulating endoplasmic reticulum stress. In addition, the roles of PSMG1, TNFRSF6B, ZMIZ1 and SMAD3 are also discussed in relation to abnormal protein degradation and the secondary immune response. It is clear that with increasing technology our understanding of IBD pathogenesis is deepening at the genomic level and that the use of early patient selection coupled with ongoing work on therapeutic targets will lead to improved disease-modifying treatments in the near future.
Amyloid β peptide as a vaccine for Alzheimer's disease involves receptor-mediated transport at the blood–brain barrier (2001)

Much research is now focused on a potential vaccine for Alzheimer's disease (AD). Current studies involve administering the amyloid β peptide (Aβ) in Freund's complete adjuvant, which cannot be used in humans. Our studies show that the immune complex of Aβ is taken up by a receptor-mediated process at the blood–brain barrier (BBB). The success of immunization for AD, therefore, may be critically dependent on circulating Aβ levels which are lower in AD patients compared to AD transgenic mice. Moreover, we have found that modifying the antibody with polyamine increases its BBB permeability and may provide a better approach to passive immunization for Alzheimer's disease.
Prenylated Benzophenones and Xanthones from <i>Hypericum </i><i>s</i><i>cabrum</i> (2004)

Two new polyprenylated benzophenones, a new polyprenylated phloroglucinol, and six new xanthone derivatives were isolated from the aerial parts of the Uzbekistan medicinal plant Hypericum scabrum. Their structures were elucidated on the basis of spectroscopic evidence. The isolated compounds showed moderate cytotoxicity for human tumor cells.
Demand responsive pricing and competitive spectrum allocation via a spectrum server (2005)

In this paper we develop a framework for competition of future operators likely to operate in a mixed commons/property-rights regime under the regulation of a spectrum policy server (SPS). The operators dynamically compete for customers as well as portions of available spectrum. The operators are charged by the SPS for the amount of bandwidth they use in their services. Through demand responsive pricing, the operators try to come up with convincing service offers for the customers, while trying to maximize their profits. We first consider a single-user system as an illustrative example. We formulate the competition between the operators as a non-cooperative game and propose an SPS-based iterative bidding scheme that results in a Nash equilibrium of the game. Numerical results suggest that, competition increases the user's (customer's) acceptance probability of the offered service, while reducing the profits achieved by the operators. It is also observed that as the cost of unit bandwidth increases relative to the cost of unit infrastructure (fixed cost), the operator with superior technology (higher fixed cost) becomes more competitive. We then extend the framework to a multiuser setting where the operators are competing for a number of users at once. We propose an SPS-based bandwidth allocation scheme in which the SPS optimally allocates bandwidth portions for each user-operator session to maximize its overall expected revenue resulting from the operator payments. Comparison of the performance of this scheme to one in which the bandwidth is equally shared between the user-operator pairs reveals that such an SPS-based scheme improves the user acceptance probabilities and the bandwidth utilization in multiuser systems
Sustainable Separations of C<sub>4</sub>‐Hydrocarbons by Using Microporous Materials (2017)

Petrochemical refineries must separate hydrocarbon mixtures on a large scale for the production of fuels and chemicals. Typically, these hydrocarbons are separated by distillation, which is extremely energy intensive. This high energy cost can be mitigated by developing materials that can enable efficient adsorptive separation. In this critical review, the principles of adsorptive separation are outlined, and then the case for C<sub>4</sub> separations by using zeolites and metal-organic frameworks (MOFs) is examined. By analyzing both experimental and theoretical studies, the challenges and opportunities in C<sub>4</sub> separation are outlined, with a focus on the separation mechanisms and structure-selectivity correlations. Zeolites are commonly used as adsorbents and, in some cases, can separate C<sub>4</sub> mixtures well. The pore sizes of eight-membered-ring zeolites, for example, are in the order of the kinetic diameters of C<sub>4</sub> isomers. Although zeolites have the advantage of a rigid and highly stable structure, this is often difficult to functionalize. MOFs are attractive candidates for hydrocarbon separation because their pores can be tailored to optimize the adsorbate-adsorbent interactions. MOF-5 and ZIF-7 show promising results in separating all C<sub>4</sub> isomers, but breakthrough experiments under industrial conditions are needed to confirm these results. Moreover, the flexibility of the MOF structures could hamper their application under industrial conditions. Adsorptive separation is a promising viable alternative and it is likely to play an increasingly important role in tomorrow's refineries.
On Rate Control of Wireless Multicasting (2006)

Abstract This paper studies wireless multicast communication, where a source of common information is trans-mitted to a group of receivers over fading channels. Communication between the transmitter and each of the receivers is implemented by specifying a minimum signal to noise ratio (SNR) threshold; if the threshold is met, the communi-cation is successful at a corresponding rate, otherwise the communication fails. The determination of SNR threshold that maximizes the effective multicast communication rate is termed rate control. By modeling the channel from the transmitter to each of the receivers as an erasure channel and assuming only channel distribution information at the transmitter, the optimal SNR threshold under a given transmit power is derived. It is shown that, in the low transmit power regime, the optimal ratio between the SNR threshold and the transmit power is determined only by the channel distributions. Key words multicast, rate control 1
The in-vitro antibiotic susceptibility of <i>Chlamydia pneumoniae</i> (1990)

A cell culture technique was used to test the in-vitro susceptibility of the type strain of Chlamydia pneumoniae to 23 antibiotics including macrolides, tetracyclines and quinolones. The activity of the antibiotics tested was similar to previous findings with C. trachomatis. Clarythromycin had the lowest MIC overall (0.007 mg/l). Other macrolides were found to have similar MICs to erythromycin (0.06 mg/l). Both the macrolides and the tetracyclines were more active than the quinolones. It is proposed that the tetracyclines and erythromycin should be the drugs of choice for treating infections with C. pneumoniae; however several other antibiotics need to be evaluated.
[Reconstruction of great vessel for patients with advanced lung cancer or malignant mediastinal tumor]. (1999)

Fifteen lung cancer (LC) and 11 malignant mediastinal tumor (MMT) patients who received surgical treatment in association with a reconstruction of great vessel from 1981 to 1997 were retrospectively reviewed. The aorta was resected in 7 (AO group) of 15 LC patients and the superior vena cava in the remaining 8 patients (SVC group). Pathological examination revealed actual tumor invasion in one (14%) of AO group and 6 (75%) of SVC group. In 7 p-T4 patients, 6 (85.7%) were p-N2 or N3 diseases. Five of the 6 patients belonged to SVC group and one to AO group. Five-year survival rate was 10% in all LC patients, 20% in p-T3 patients, 0% in p-T4 cancers, 50% in p-N0 patients and 0% in p-N2 or N3 patients. Eleven MMT patients included 5 thymomas, 2 thymic cancers and 4 germ cell tumors. SVC was resected and replaced with ringed PTFE graft in all patients. Invasion of vessel wall was diagnosed pathologically in 10 of 11 patients. Fifteen-year survival rate was 60% in 5 thymoma patients but 4 of whom had distant metastasis. Five-year survival rate was 50% in thymic cancers and 0% in germ cell tumors. Since the prognosis of LC and MMT patients who have tumor invasion of the great vessel is very poor, induction therapy based on preoperatively pathological diagnosis is recommended.
Foamy virus vector integration sites in normal human cells (2006)

Foamy viruses (FVs) or spumaviruses are retroviruses that have been developed as vectors, but their integration patterns have not been described. We have performed a large-scale analysis of FV integration sites in unselected human fibroblasts (n = 1,008) and human CD34(+) hematopoietic cells (n = 1,821) by using a bacterial shuttle vector and a comparable analysis of lentiviral vector integration sites in CD34(+) cells (n = 1,331). FV vectors had a distinct integration profile relative to other types of retroviruses. They did not integrate preferentially within genes, despite a modest preference for integration near transcription start sites and a significant preference for CpG islands. The genomewide distribution of FV vector proviruses was nonrandom, with both clusters and gaps. Transcriptional profiling showed that gene expression had little influence on integration site selection. Our findings suggest that FV vectors may have desirable integration properties for gene therapy applications.
Homeodomain transcription factor NKX2.2 functions in immature cells to control enteroendocrine differentiation and is expressed in gastrointestinal neuroendocrine tumors (2008)

The homeodomain transcription factor NKX2.2 is necessary for neuroendocrine (NE) differentiation in the central nervous system and pancreas. NE tumors derived from the gut are defined by their NE phenotype, which is used for diagnosis and contributes to tumorigenicity. We hypothesized that NKX2.2 is important for NE differentiation in normal and neoplastic gut. NKX2.2 and NE marker expression was investigated in the small intestine of embryonic and adult mice using immunofluorescence (IF). To determine the role of NKX2.2 in NE differentiation of the intestine, the phenotype of Nkx2.2 (-/-) mice was examined by IF and real-time (RT)-PCR. NKX2.2 and NE marker expression in human NE tumors of the gut and normal tissues were evaluated by immunohistochemistry and qRT-PCR. NKX2.2 expression was detected in the intervillus/crypt regions of embryonic and adult mouse intestine. Co-expression of Nkx2.2 with neurogenin3 (NEUROG3) and hormones was observed in the adult intestinal crypt compartment, suggesting NKX2.2 functions in NEUROG3-positive endocrine progenitors and newly differentiated endocrine cells. In the intestine of Nkx2.2 (-/-) mice, we found a dramatic reduction in the number of cells producing numerous hormones, such as serotonin, gastrin, cholecystokinin, somatostatin, glucagon-like peptide 1 (GLP-1), and secretin, but an increase in cells producing ghrelin. NKX2.2 was expressed in most (24 of 29) human NE tumors derived from diverse primary sites. We conclude NKX2.2 functions in immature endocrine cells to control NE differentiation in normal intestine and is expressed in most NE tumors of the gut, and is therefore a novel target of diagnosis for patients with gastrointestinal NE tumors.