gebhart/patrepeval huggingface dataset:
Experimental Infection of Rhesus Monkeys with Lassa Virus and a Closely Related Arenavirus, Mozambique Virus (1982)

As a model for the pathogenesis of Lassa fever in humans, nine rhesus monkeys were inoculated with Lassa virus. Three monkeys had had a previous asymptomatic experimental infection with Mozambique virus, a closely related arenavirus; these monkeys were protected from illness and viremia and manifested only mild pathologic lesions. The other animals developed severe disease and viremia. At necropsy, hepatocellular necrosis, interstitial pneumonia, a unique pulmonary arteritis, adrenal gland necrosis, encephalitis, and uveitis were prominent pathologic lesions which correlated with the organ titers of virus. One animal infected with Lassa virus developed prolonged viremia, a typical immune response, and sudden onset of lower limb paralysis after recovery; at necropsy chronic proliferative arteritis of the spinal cord, brain, and heart was evident. Similarities and differences in the pathologic lesions in this model and Lassa fever in humans indicate that care must be taken in interpreting the results of experiments concerning immune prophylaxis, pathogenesis, and treatment in rhesus monkeys.
Synthesis and Biological Activity of the Superestrogen (E)-17-Oximino-3-O-sulfamoyl-1,3,5(10)-estratriene:  X-ray Crystal Structure of (E)-17-Oximino-3-hydroxy-1,3,5(10)-estratriene (1999)

Steroid sulfatases regulate the formation of estrogenic steroids which can support the growth of endocrine-dependent breast tumors. Therefore, the development of potent steroid sulfatase inhibitors could have considerable therapeutic potential. Several such inhibitors have now been developed including estrone 3-O-sulfamate (EMATE, 1), which shows potent active site-directed inhibition. However, EMATE was subsequently shown to be also a potent estrogen. In an attempt to reduce the estrogenicity while retaining the potent sulfatase inhibitory properties associated with this type of molecule, (E)-17-oximino-3-O-sulfamoyl-1,3,5(10)-estratriene (5) (estrone oxime 3-O-sulfamate, OMATE) was synthesized. The X-ray crystal structure of (E)-17-oximino-3-hydroxy-1,3,5(10)-estratriene (4) (estrone oxime) demonstrated the presence of only one geometrical isomer [anti-isomer, (E)]. OMATE potently inhibited estrone sulfatase (E1-STS) activity and was similar to EMATE (>99% inhibition at 0.1 μM in MCF-7 breast cancer cells). It was also evaluated in vivo for its estrogenicity and ability to inhibit sulfatase activity. While it was equipotent with EMATE in vivo as a sulfatase inhibitor, it surprisingly had a stimulatory effect on uterine growth in ovariectomized rats about 1.5-fold greater than that of EMATE. Thus, OMATE possesses potential as a superestrogen and modification at C-17 is identified as a useful route for enhancement of estrogenicity in sulfamate-based estrogens.
An Equivalence Between Network Coding and Index Coding (2015)

We show that the network coding and index coding problems are equivalent. This equivalence holds in the general setting which includes linear and nonlinear codes. Specifically, we present a reduction that maps a network coding instance to an index coding instance while preserving feasibility, i.e., the network coding instance has a feasible solution if and only if the corresponding index coding instance is feasible. In addition, we show that one can determine the capacity region of a given network coding instance with colocated sources by studying the capacity region of a corresponding index coding instance. Previous connections between network and index coding were restricted to the linear case.
Treatment of Malignant Brain Tumors with Controlled-Release Local-Delivery Polymers (2005)

Central nervous system (CNS) tumors account for tremendous morbidity and mortality. In the United States, the annual incidence of primary brain tumors approaches 16,800 people and corresponds with 13,100 lesion-related deaths (1). Histopathological classification deconstructs primary brain tumors into several categories based on grade and cell of origin. Gliomas, for example, derive from glial cells and constitute half of all primary brain tumors. Astrocytomas, in turn, encompass three-quarters of all gliomas, and define a heterogeneous tumor class ranging from low-grade to high-grade anaplastic variants. Glioblastoma multiforme (GBM) represents the most common and aggressive form of astrocytoma.
Modulation of gene expression by Pseudomonas aeruginosa during chronic infection in the adult cystic fibrosis lung (2013)

Chronic Pseudomonas aeruginosa infection is the leading cause of morbidity and mortality in cystic fibrosis (CF) patients. P. aeruginosa isolates undergo significant transcriptomic and proteomic modulation as they adapt to the niche environment of the CF lung and the host defences. This study characterized the in vitro virulence of isogenic strain pairs of P. aeruginosa epidemic or frequent clonal complexes (FCCs) and non-epidemic or infrequent clonal complexes (IFCCs) that were collected 5-8 years apart from five chronically infected adult CF patients. Strains showed a significant decrease in virulence over the course of chronic infection using a Caenorhabditis elegans slow-killing assay and in phenotypic tests for important virulence factors. This decrease in virulence correlated with numerous differentially expressed genes such as oprG, lasB, rsaL and lecB. Microarray analysis identified a large genomic island deletion in the IFCC strain pair that included type three secretion system effector and fimbrial subunit genes. This study presents novel in vitro data to examine the transcriptomic profiles of sequentially collected P. aeruginosa from CF adults. The genes with virulence-related functions identified here present potential targets for new therapies and vaccines against FCCs and IFCCs.
Comprehensive investigation and risk assessment of organic contaminants in Yellow River Estuary using suspect and nontarget screening strategies (2023)

Contaminants of emerging concerns (CECs) include numerous chemicals that may pose known and unknown risks to the ecosystem, and identification and risk ranking of these compounds is essential for the environmental management. In this study, liquid and gas chromatography time-of-flight mass spectrometry (LC-QTOF-MS and GC-QTOF-MS) were used to characterize the occurrence of CECs in the surface water of the Yellow River Estuary (YRE). A total of 295 and 315 chemicals were identified by LC-QTOF-MS and GC-QTOF-MS, respectively. The occurrence of two compounds, erucamide and 2-phenylquinoline, was for the first time reported in the aquatic environment in YRE. The concentrations of 121 CECs, including 35 antibiotics, 49 pesticides and veterinary, 16 polycyclic aromatic hydrocarbons and 21 phthalic acid esters were further quantified by target analysis, which showed the detection of 99 compounds in the surface water in the range of 7.07-4611.26 ng/L. Ecological risks of pollutants based on the risk quotient (RQ) method revealed that 13 pollutants posed ecological risks to the aquatic ecosystem (RQ > 1), and pesticides (n = 12) were the main risk contributors. Here, all CECs data sets were finally transformed and ranked in the framework of the toxicological priority index (ToxPi), and a total of 81 priority control pollutants were identified in the surface water of YRE. This study highlighted the necessity of suspect and nontarget screening for CECs in estuaries, and revealed the importance of localized contamination sources in urban and agricultural environment.
1291: Prognostic Impact of Cytogenetic Findings in Clear Cell Renal Cell Carcinoma: Improved Survival is Seen in Patients with Loss of Chromosome 3P (2007)

demonstrate an inverse correlation between BMI and adiponectin levels in our cohort however there was a clear trend for more aggressive tumour grade (3 + 4's) for BMI >30kglm 2 CONCLUSIONS: Lower blood levels of adiponectin and lower tumor expression of AdipoR2 are positively associated with renal cancer pathogenesis and aggressiveness. This observation may explain the link between obesity and RCC and may shed some new light on the pathogenesis of RCC. Studies on larger cohort of patients are ongoing.
ChemInform Abstract: Zero Thermal Expansion Fluid and Oriented Film Based on a Bistable Metal‐Cyanide Polymer. (2012)

Abstract Plate‐shaped microcrystals of Rb 0.97 Mn [Fe(CN) 6 ] 0.99 ·0.3H 2 O are synthesized by mixing an aqueous solution containing polyethylene glycol monolaurate, MnCl 2 , and RbCl with an aqueous solution of polyethylene glycol monolaurate, K 3 [Fe(CN) 6 ], and RbCl.
Emerging Research Nanoelectronic Devices: The Choice of Information Carrier (2007)

Many different approaches are being explored for information carriers that will enable continued geometrical scaling beyond the estimated physical limits of electron-based devices. In this paper we offer the proposition that as transistor channel length decreases below 5 nm, the mass of the information carrier must rapidly increase if acceptable ON-OFF switch characteristics are to be maintained. Several different possibilities for the realization of sub-5-nm switches are outlined.
A Distributed Markovian Parking Assist System (2018)

This paper proposes a congestion balancing parking guidance system that suggests to a driver a sequence of streets to follow around the desired destination with the aim to reduce the total distance that is travelled while searching for a free parking spot. The system requires only limited infrastructure information, and neither requires parking spaces to be instrumented, nor vehicles to communicate with each other. Specifically, the system utilizes parking vacancy information on each street. The system also accounts for the added cost of not finding a free space, which is typically expressed as the additional distance that needs to be travelled to find an available parking spot. To avoid local congestion, different drivers respond to different suggestions based on a probability distribution that considers the total distance that needs to be travelled. A mobility simulator is used to model the searching behaviors of vehicles for parking spaces with and without the smart parking algorithm and experimental results are provided using the road network of the city of Dublin, Ireland.
Ovarian stromal hyperplasia and ovarian vein steroid levels in relation to endometrioid endometrial cancer (2003)

In endometrioid endometrial cancer, higher degrees of ovarian stromal hyperplasia were found and with increasing degrees of ovarian stromal hyperplasia, levels of ovarian vein androgens were higher. A causal relationship in the origin of hormone-dependent endometrial pathology may exist between ovarian stromal hyperplasia, ovarian vein androgen levels and endometrioid endometrial carcinoma.
IRAC: Insecticide Resistance, and Mode of Action Classification of Insecticides (2011)

This chapter contains sections titled: Introduction Objectives of the IRAC Structure and Organization of the IRAC Activities Principles of Resistance The Mode of Action (MoA) Classification Scheme v7.0, August 2010 Effective IRM Strategies and Approved Principles Future Market Trends Conclusions References
Comparison of in vivo protective activity of interleukin-1.ALPHA. with that of interferon and tumor necrosis factor against systemic Candida albicans infection in mice. (1991)

Treatments with recombinant human interleukin-1α (IL-1α), tumor necrosis factor a (TNFα) or interferon-α-A/D (IFNα) greatly enhanced the resistance of mice to systemic infection with Candida albicans. IL-1α was the most active of these three cytokines, followed by IFNα and TNFα. IL-1α was more active when treatment was begun before the infection. In contrast, IFN was most effective when given within 24 hrs before or after C. albicans challenge, while the anti candidal activity of TNFα was maximal when administered after infection. Analyses of the effectors which are active in the resistance induced by IL-1α treatment indicated the important role of macrophages.
More precisely defining risk peri-HCT in pediatric ALL: pre- vs post-MRD measures, serial positivity, and risk modeling (2019)

Detection of minimal residual disease (MRD) pre- and post-hematopoietic cell transplantation (HCT) for pediatric acute lymphoblastic leukemia (ALL) has been associated with relapse and poor survival. Published studies have had insufficient numbers to: (1) compare the prognostic value of pre-HCT and post-HCT MRD; (2) determine clinical factors post-HCT associated with better outcomes in MRD+ patients; and (3) use MRD and other clinical factors to develop and validate a prognostic model for relapse in pediatric patients with ALL who undergo allogeneic HCT. To address these issues, we assembled an international database including sibling (n = 191), unrelated (n = 259), mismatched (n = 56), and cord blood (n = 110) grafts given after myeloablative conditioning. Although high and very high MRD pre-HCT were significant predictors in univariate analysis, with bivariate analysis using MRD pre-HCT and post-HCT, MRD pre-HCT at any level was less predictive than even low-level MRD post-HCT. Patients with MRD pre-HCT must become MRD low/negative at 1 to 2 months and negative within 3 to 6 months after HCT for successful therapy. Factors associated with improved outcome of patients with detectable MRD post-HCT included acute graft-versus-host disease. We derived a risk score with an MRD cohort from Europe, North America, and Australia using negative predictive characteristics (late disease status, non-total body irradiation regimen, and MRD [high, very high]) defining good, intermediate, and poor risk groups with 2-year cumulative incidences of relapse of 21%, 38%, and 47%, respectively. We validated the score in a second, more contemporaneous cohort and noted 2-year cumulative incidences of relapse of 13%, 26%, and 47% (P < .001) for the defined risk groups.
57‐4: Invited Paper: Progress on Key Innovations in Direct‐View μLED Display Manufacturing (2022)

Applied Materials reported earlier on an innovative approach to μLED‐based front plane technology using a single wavelength GaN LED emitter with Cd‐free quantum dots for color conversion. This proprietary μLED front plane technology incorporates several key innovations such as the use of high external quantum efficiency dice in ultraviolet wavelength spectrum (vs. red/green/blue), highest photon extraction efficiency at small die‐size, fewer number of mass transfer steps with high yield, and a four‐subpixel backplane architecture to allow for a simple, cost‐effective repair strategy. A picture of this display is shown below.
PHGDH heterogeneity potentiates cancer cell dissemination and metastasis (2022)

Cancer metastasis requires the transient activation of cellular programs enabling dissemination and seeding in distant organs<sup>1</sup>. Genetic, transcriptional and translational heterogeneity contributes to this dynamic process<sup>2,3</sup>. Metabolic heterogeneity has also been observed<sup>4</sup>, yet its role in cancer progression is less explored. Here we find that the loss of phosphoglycerate dehydrogenase (PHGDH) potentiates metastatic dissemination. Specifically, we find that heterogeneous or low PHGDH expression in primary tumours of patients with breast cancer is associated with decreased metastasis-free survival time. In mice, circulating tumour cells and early metastatic lesions are enriched with Phgdh<sup>low</sup> cancer cells, and silencing Phgdh in primary tumours increases metastasis formation. Mechanistically, Phgdh interacts with the glycolytic enzyme phosphofructokinase, and the loss of this interaction activates the hexosamine-sialic acid pathway, which provides precursors for protein glycosylation. As a consequence, aberrant protein glycosylation occurs, including increased sialylation of integrin α<sub>v</sub>β<sub>3</sub>, which potentiates cell migration and invasion. Inhibition of sialylation counteracts the metastatic ability of Phgdh<sup>low</sup> cancer cells. In conclusion, although the catalytic activity of PHGDH supports cancer cell proliferation, low PHGDH protein expression non-catalytically potentiates cancer dissemination and metastasis formation. Thus, the presence of PHDGH heterogeneity in primary tumours could be considered a sign of tumour aggressiveness.
Low Antigen Dose in Adjuvant-Based Vaccination Selectively Induces CD4 T Cells with Enhanced Functional Avidity and Protective Efficacy (2017)

T cells with high functional avidity can sense and respond to low levels of cognate Ag, a characteristic that is associated with more potent responses against tumors and many infections, including HIV. Although an important determinant of T cell efficacy, it has proven difficult to selectively induce T cells of high functional avidity through vaccination. Attempts to induce high-avidity T cells by low-dose in vivo vaccination failed because this strategy simply gave no response. Instead, selective induction of high-avidity T cells has required in vitro culturing of specific T cells with low Ag concentrations. In this study, we combined low vaccine Ag doses with a novel potent cationic liposomal adjuvant, cationic adjuvant formulation 09, consisting of dimethyldioctadecylammonium liposomes incorporating two immunomodulators (monomycolyl glycerol analog and polyinosinic-polycytidylic acid) that efficiently induces CD4 Th cells, as well as cross-primes CD8 CTL responses. We show that vaccination with low Ag dose selectively primes CD4 T cells of higher functional avidity, whereas CD8 T cell functional avidity was unrelated to vaccine dose in mice. Importantly, CD4 T cells of higher functional avidity induced by low-dose vaccinations showed higher cytokine release per cell and lower inhibitory receptor expression (PD-1, CTLA-4, and the apoptosis-inducing Fas death receptor) compared with their lower-avidity CD4 counterparts. Notably, increased functional CD4 T cell avidity improved antiviral efficacy of CD8 T cells. These data suggest that potent adjuvants, such as cationic adjuvant formulation 09, render low-dose vaccination a feasible and promising approach for generating high-avidity T cells through vaccination.
Supplementary Figure Legends 1-4 from Methylation Mediated Silencing of MicroRNA-1 Gene and Its Role in Hepatocellular Carcinogenesis (2023)

Supplementary Figure Legends 1-4 from Methylation Mediated Silencing of MicroRNA-1 Gene and Its Role in Hepatocellular Carcinogenesis
Iron/Iron Oxide Nanoparticle Sequestration of Catalytic Metal Impurities from Aqueous Media and Organic Reaction Products (2007)

A host of transition metal ions (Co2+, Cu2+, Ni2+, RuX+, RhX+, Pd2+, Ag+, and Pt4+) were sequestered from aqueous media upon exposure to FexOy@Fe nanoparticles. Concentrations were lowered from approximately 100 ppm to below 40 ppb. This technique was extended to the removal of catalytic ions from the products of a "Click" cycloaddition and a Heck coupling in organic solvents. Residual metal concentrations in organic reaction products matched or exceeded pharmaceutical standards.
Pump-Probe Experiments in Organic Solutions for Optical Limiting (1996)

We report a series of picosecond excite-probe and femtosecond continuum excite-probe experiments performed on solutions of organic dyes. These experiments show the dynamics and spectral range of utility for these materials which have shown promise for applications in optical limiting devices. The metallo-organic dye solutions used were: Silicon Naphthalocyanine (SiNc) in methanol, tetrakis(β-cumylphenoxy) Lead Phthalocyanine (PbPc(β-CP) 4 ) in chloroform and Zinc meso-Tetra(p-methoxyphenyl)Tetrabenzporphyrin (ZnTMOTBP) in tetrahydrofuran (THF). Initial studies involved Z-Scan and picosecond pump-probe measurements on these solutions at 532 nm.[1-3] All of these materials exhibited large reverse saturable absorption (RSA), i.e. the excited-state cross-section is larger than that of the ground-state.
Roles ofVibrio fischeriand Nonsymbiotic Bacteria in the Dynamics of Mucus Secretion during Symbiont Colonization of theEuprymna scolopesLight Organ (2002)

During light organ colonization of the squid Euprymna scolopes by Vibrio fischeri, host-derived mucus provides a surface upon which environmental V. fischeri forms a biofilm and aggregates prior to colonization. In this study we defined the temporal and spatial characteristics of this process. Although permanent colonization is specific to certain strains of V. fischeri, confocal microscopy analyses revealed that light organ crypt spaces took up nonspecific bacteria and particles that were less than 2 micro m in diameter during the first hour after hatching. However, within 2 h after inoculation, these cells or particles were not detectable, and further entry by nonspecific bacteria or particles appeared to be blocked. Exposure to environmental gram-negative or -positive bacteria or bacterial peptidoglycan caused the cells of the organ's superficial ciliated epithelium to release dense mucin stores at 1 to 2 h after hatching that were used to form the substrate upon which V. fischeri formed a biofilm and aggregated. Whereas the uncolonized organ surface continued to shed mucus, within 48 h of symbiont colonization mucus shedding ceased and the formation of bacterial aggregations was no longer observed. Eliminating the symbiont from the crypts with antibiotics restored the ability of the ciliated fields to secrete mucus and aggregate bacteria. While colonization by V. fischeri inhibited mucus secretion by the surface epithelium, secretion of host-derived mucus was induced in the crypt spaces. Together, these data indicate that although initiation of mucus secretion from the superficial epithelium is nonspecific, the inhibition of mucus secretion in these cells and the concomitant induction of secretion in the crypt cells are specific to natural colonization by V. fischeri.
Sustained Activation of AMPK Enhances Differentiation of Human iPSC-Derived Cardiomyocytes via Sirtuin Activation (2020)

Recent studies suggest that metabolic regulation may improve differentiation of cardiomyocytes derived from induced pluripotent stem cells (iPSCs). AMP-activated protein kinase (AMPK) is a master regulator of metabolic activities. We investigated whether AMPK participates in iPSC-derived cardiomyocyte differentiation. We observed that AMPK phosphorylation at Thr172 increased at day 9 but then decreased after day 11 of differentiation to cardiomyocytes. Inhibition of AMPK with compound C significantly reduced mRNA and protein expression of cardiac troponins TNNT2 and TNNI3. Moreover, sustained AMPK activation using AICAR from days 9 to 14 of differentiation increased mRNA and protein expression of both TNNT2 and TNNI3. AICAR decreased acetylation of histone 3 at Lys9 and 56 and histone 4 at Lys16 (known target sites for nuclear-localized sirtuins [SIRT1, SIRT6]), suggesting that AMPK activation enhances sirtuin activity. Sustained AMPK activation during days 9-14 of differentiation induces sirtuin-mediated histone deacetylation and may enhance cardiomyocyte differentiation from iPSCs.