gebhart/patrepeval huggingface dataset:
MPTH-29CONNECTING MUTANT GENOTYPES TO ABERRANT TRANSCRIPTIONAL SIGNATURES ACROSS SERIAL SECTIONS OF A HUMAN TUMOR (2015)

Identifying the transcriptional consequences of mutations that cause tumors may reveal new targets for the development of cancer therapies. However, this task is complicated by the variability that characterizes tumors from different individuals, which arise from unique genetic backgrounds, consist of various cell types in different proportions, and often exhibit clonal heterogeneity. Here we present a novel strategy to connect mutant genotypes to aberrant transcriptional signatures within individual human tumors. This strategy deconstructs a tumor by extracting RNA from serial sections and comparing genome-wide gene coexpression relationships to control samples analyzed in a similar fashion. In parallel, quantitative genomic analysis of the same serial sections enables identification and mapping of clonal populations within the tumor. We apply this strategy to a single grade II human astrocytoma and identify tumor-specific transcriptional signatures. Genomic analysis reveals clonal heterogeneity, including a dominant clone marked by mutations in IDH1 and TP53. Expression patterns of the two largest tumor-specific transcriptional signatures are almost perfectly associated with the spatial distribution of the dominant clone and consist of genes that are activated or repressed within malignant cells and their microenvironment. Our experimental strategy offers an unbiased and personalized method for identifying aberrant transcriptional signatures that are associated with specific mutant genotypes in any solid tumor while preserving the complex cellular milieu of the tumor microenvironment. More generally, this strategy can reveal shared and distinct patterns of transcriptional organization between any pair of tissue samples, thereby facilitating novel comparisons of diverse biological systems in health and disease.
Tracking Hydrocarbon Plume Transport and Biodegradation at Deepwater Horizon (2010)

The Deepwater Horizon blowout is the largest offshore oil spill in history. We present results from a subsurface hydrocarbon survey using an autonomous underwater vehicle and a ship-cabled sampler. Our findings indicate the presence of a continuous plume of oil, more than 35 kilometers in length, at approximately 1100 meters depth that persisted for months without substantial biodegradation. Samples collected from within the plume reveal monoaromatic petroleum hydrocarbon concentrations in excess of 50 micrograms per liter. These data indicate that monoaromatic input to this plume was at least 5500 kilograms per day, which is more than double the total source rate of all natural seeps of the monoaromatic petroleum hydrocarbons in the northern Gulf of Mexico. Dissolved oxygen concentrations suggest that microbial respiration rates within the plume were not appreciably more than 1 micromolar oxygen per day.
Interaction of interleukin-11 with cytotoxic therapiesin vitro against CEM cells andin vivo against EMT-6 murine mammary carcinoma (1996)

Interleukin-11(rhIL-11) is a cytokine that has been shown to enhance the recovery of bone marrow and intestinal crypt cells after cytotoxic insult with radiation or anticancer drugs. The current study examined the effects of rhIL-11 on the response of CEM human lymphoblastic leukemia cells and on the EMT-6 murine mammary carcinoma in vivo to cytotoxic anticancer therapies. Exposure of CEM cells to rhIL-11 for 24 hr did not alter the cytotoxicity of melphalan or radiation, increased the cytotoxicity of CDDP (100 muM) and 4-hydroperoxycyclophosphamide (50 betaM) and decreased the cytotoxicity of 5-fluorouracil and ara-C toward the cells. Treatment of mice bearing the EMT-6 tumor with rhIL-11 twice daily for 4 days prior to and the day of cytotoxic therapy resulted in no significant change in the tumor cell killing or bone marrow CFU-GM killing by melphalan, cyclophosphamide, thiotepa, CDDP, radiation, 5-fluorouracil or ara-C. Administration of rhIL-11 twice per day on days 7-18 to EMT-6 tumor bearing animals receiving high dose chemotherapy (melphalan, thiotepa or cyclophosphamide) as a single dose on day 7 followed by mobilized peripheral blood cells on day 8 and rhG-CSF on days 8-20, tended to prolong the tumor growth delay produced by the drugs. This rhIL-11 treatment also resulted in a more rapid recovery of white blood cells and granulocytes in the animals. Furthermore, animals treated with rhIL-11 had improved survival rates compared with animals receiving all other normal tissue support without rhIL-11.
Microfluidics and microbial engineering (2015)

The combination of microbial engineering and microfluidics is synergistic in nature. For example, microfluidics is benefiting from the outcome of microbial engineering and many reported point-of-care microfluidic devices employ engineered microbes as functional parts for the microsystems. In addition, microbial engineering is facilitated by various microfluidic techniques, due to their inherent strength in high-throughput screening and miniaturization. In this review article, we firstly examine the applications of engineered microbes for toxicity detection, biosensing, and motion generation in microfluidic platforms. Secondly, we look into how microfluidic technologies facilitate the upstream and downstream processes of microbial engineering, including DNA recombination, transformation, target microbe selection, mutant characterization, and microbial function analysis. Thirdly, we highlight an emerging concept in microbial engineering, namely, microbial consortium engineering, where the behavior of a multicultural microbial community rather than that of a single cell/species is delineated. Integrating the disciplines of microfluidics and microbial engineering opens up many new opportunities, for example in diagnostics, engineering of microbial motors, development of portable devices for genetics, high throughput characterization of genetic mutants, isolation and identification of rare/unculturable microbial species, single-cell analysis with high spatio-temporal resolution, and exploration of natural microbial communities.
Growth responses of male broilers subjected to increasing air velocities at high ambient temperatures and a high dew point (2005)

This study examined live performance responses of male broilers to increasing air velocity of 120 and 180 m/min reared under high cyclic temperatures (25-35-25 degrees C) with a 23 degrees C dew point from 21 to 49 d. Birds were reared in an environmental facility containing 2 wind tunnels (4 pens/tunnel) and 6 floor pens (control). At 21 d, 53 birds were placed in each pen of the wind tunnels and control group, respectively, and growth performance was determined weekly. Increasing air velocity from 120 to 180 m/min improved BW and BW gain from 29 to 35, 36 to 42, and 43 to 49 d of age leading to a cumulative advantage of 287 g in BW gain and a 10-point difference in feed conversion from 21 to 49 d of age. Subjecting birds to air velocity improved growth rate, feed consumption, and feed conversion at each weekly interval from 28 to 49 d over the control birds. These results indicate that male broilers approximating 2.0 to 3.0 kg respond to an air velocity of 180 m/min when exposed to high cyclic temperatures.
Respiratory Physiology in Pregnancy (2009)

Pregnancy is a normal but altered physiologic state that results in significant hormonal, mechanical, and circulatory changes. The increases in progesterone and estrogen associated with pregnancy contribute to vascular and central nervous system effects, changes in the balance of bronchoconstrictor and bronchodilator prostanoids, and increases in peptide hormones that alter connective tissue characteristics. The course of pregnancy is accompanied by structural changes to the ribcage and abdominal compartments as a consequence of the hormonal changes and the enlarged uterus. Cardiac output, pulmonary blood flow, and circulating blood volume are all increased due to increased metabolic demands. This increase in blood volume without an increase in red cell mass results in a decreased hemoglobin concentration.
New Indicators for Visualizing Pattern Formation in Uncatalyzed Bromate Oscillatory Systems (1998)

Many uncatalyzed bromate oscillators (UBO's) undergo oscillations in electrochemical potential without any observable color change in a closed, stirred (batch) system. We have investigated the effects of adding a wide variety of redox indicators, including diphenylamine derivatives, azo dyestuffs, triphenylmethane derivatives, diimine chelate complexes, and methylene blue to UBO's. We find that in many cases the indicators make the batch oscillations strikingly visible and also allow observation of spatial pattern formation (concentric rings and spirals) in a thin, unstirred layer of solution. In some systems, the indicators act merely to make visible changes in redox potential, while in others they play an active role in the chemistry, and added indicator can lengthen the duration of oscillations or regenerate oscillations or patterns once this behavior has ceased.
Genotyping on ALDH2: Comparison of Four Different Technologies (2015)

All of the referred methods can be used for genotyping ALDH2 rs671 with the same accuracy compared to Sanger sequencing. In small size of clinical samples, HRM and AS-PCR outperform over others due to their lower cost and less hands-on operation, which are suitable for clinical application.
Analysis of a Questionnaire Survey Administered to Determine the Periodontal Condition (2018)

Periodontal disease is an infectious disease that occurs at a high prevalence, although many periodontitis patients do not have any subjective symptoms and the disease often goes untreated. Recognition of periodontitis in its early (mild) stage is extremely useful for effective treatment and prophylaxis. Therefore, the purpose of the present study was to identify appropriate questions to be asked in the screening for periodontal disease.
Genome-Wide Mapping of Cystitis Due to Streptococcus agalactiae and Escherichia coli in Mice Identifies a Unique Bladder Transcriptome That Signifies Pathogen-Specific Antimicrobial Defense against Urinary Tract Infection (2012)

The most common causes of urinary tract infections (UTIs) are Gram-negative pathogens such as Escherichia coli; however, Gram-positive organisms, including Streptococcus agalactiae, or group B streptococcus (GBS), also cause UTI. In GBS infection, UTI progresses to cystitis once the bacteria colonize the bladder, but the host responses triggered in the bladder immediately following infection are largely unknown. Here, we used genome-wide expression profiling to map the bladder transcriptome of GBS UTI in mice infected transurethrally with uropathogenic GBS that was cultured from a 35-year-old women with cystitis. RNA from bladders was applied to Affymetrix Gene-1.0ST microarrays; quantitative reverse transcriptase PCR (qRT-PCR) was used to analyze selected gene responses identified in array data sets. A surprisingly small significant-gene list of 172 genes was identified at 24 h; this compared to 2,507 genes identified in a side-by-side comparison with uropathogenic E. coli (UPEC). No genes exhibited significantly altered expression at 2 h in GBS-infected mice according to arrays despite high bladder bacterial loads at this early time point. The absence of a marked early host response to GBS juxtaposed with broad-based bladder responses activated by UPEC at 2 h. Bioinformatics analyses, including integrative system-level network mapping, revealed multiple activated biological pathways in the GBS bladder transcriptome that regulate leukocyte activation, inflammation, apoptosis, and cytokine-chemokine biosynthesis. These findings define a novel, minimalistic type of bladder host response triggered by GBS UTI, which comprises collective antimicrobial pathways that differ dramatically from those activated by UPEC. Overall, this study emphasizes the unique nature of bladder immune activation mechanisms triggered by distinct uropathogens.
Intelligent Snow Plow: How to Calibrate the Volumetric Box (2021)

&lt;p&gt;[[Video(https://youtube.com/watch?v=y-qkNFw6EzQ)]]&lt;/p&gt; &lt;p&gt;To perform accurate calibration of road salt spreading equipment the volumetric box must be calibrated to account for variation in salt densities and moisture content.&amp;nbsp; This calibration ensures accurate application amounts during de-icing activities.&lt;/p&gt; &lt;p&gt;The information provided in this resource is based on the intelligent snowplow database for Indiana managed by the Joint Transportation Research Program (JTRP). The database itself is not available for download in PURR because it is both prohibitively large and continually updated, but this resource is part of a series of tools based on those data.&lt;/p&gt; &lt;p&gt;For fleet management and training, Automatic Vehicle Location devices were installed on all 1,100 Indiana Department of Transportation (INDOT) fleet trucks beginning in October 2020.&amp;nbsp; The resulting intelligent snowplow database stores real-time vehicle location, salt spreader controller and vehicle data, and dash images every minute, allowing agencies to actively monitor and deploy their assets. INDOT manages and maintains over 28,000 miles of roadways. Maintenance of the roadways includes pavement repair in the summer as well as snow removal and de-icing in the winter. The prioritization of assets during winter storm events is crucial and impacts travel and safety. The objective of this project was to identify and develop tools INDOT could provide its operators to effectively perform winter operation de-icing activities. This project examined application methods and data to provide analytics and make data-driven decisions for state-wide deployment and operations. Discovery of calibration metrics partnered with fleetwide telematics enabled the development of analytic dashboards that allowed real-time evaluations and adjustments to be made during winter operation activities. These tools will allow the agency to better treat and enhance safety for road users.&lt;/p&gt;
A Balloon-Borne Grating Spectrometer (1967)

A balloon-borne, 0.5-m, Czerny-Turner grating spectrometer has been designed and constructed at the University of Denver and has measured atmospheric transmittance in several spectral regions between 2 micro and 14 micro. These data have been obtained on a series of eleven balloon flights at three geographic locations over a period of thirty months. The solar pointing system, spectrometer optics, electronics and recording system are described. The preflight and flight performance of the spectrometer is discussed and sample data presented.
ChemInform Abstract: Novel Synthesis of the Ocular Age Pigment A2‐E: New Method for Substituted Pyridine Synthesis via Azaelectrocyclization. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Biodegradable drug delivery systems based on aliphatic polyesters: application to contraceptives and narcotic antagonists. (1981)

The classes of polymer which form the basis of different types of drug delivery systems are discussed, and the relationships between the chemical structure of the polymer and its permeability, morphology, biodegradability, and mechanical properties are considered, using polyesters as specific examples. Studies of the permeability and biodegradability of poly epsilon-caprolactone), poly(DL-lactic acid), and various copolymers are described and used to illustrate how these properties may be varied by the choice of polymer structure. An induction period prior to bioerosion of these polymers, coupled with high permeability, permits their use as reservoir devices (capsules) which exhibit constant, diffusion-controlled drug release rates and which erode after the drug is exhausted. The applications of this approach to the long term delivery (1 year) of levonorgestrel, a contraceptive agent, and the short term delivery (1-2 months) of naltrexone, a narcotic antagonist, are described.
Growth and Composition of Maize Kernels Cultured in Vitro with Varying Supplies of Carbon and Nitrogen (1989)

This study employed in vitro seed culture to determine how C and N supply influence the growth (i.e. starch accumulation) and protein composition of maize (Zea mays L.) endosperm. Immature kernels were grown to maturity on liquid medium containing various concentrations of C (sucrose at 234 millimolar [low] and 468 millimolar [high]) and N (amino acid mixture ranging in N from 0 to 144 millimolar). Low C supply limited starch, but not N, accumulation in the endosperm. With high C, endosperm starch and protein content increased concomitantly as N supply increased from 0 to 13.4 millimolar. Endosperm growth was unaffected by additional N until concentrations exceeding approximately 72 millimolar reduced starch accumulation. A similar inhibition of starch deposition occurred with lower N concentrations when kernels were grown with low C. Endosperm total N content reached a point of saturation with approximately 36 millimolar N in the medium, regardless of C supply. Zein synthesis in the endosperm responded positively across all N levels, while glutelin content remained static and albumin/globulin proteins were reduced in amount when N supply was greater than 36 millimolar. A reciprocal, inverse relationship was observed in mature endosperm tissue between the concentrations of free amino acids and soluble sugars. Our data suggest that under N stress starch and protein accumulation in the endosperm are interdependent, at least in appearance, but are independent otherwise.
A COGNITIVE MODEL OF IMITATIVE DEVELOPMENT IN HUMANS AND MACHINES (2007)

Several algorithms and models have recently been proposed for imitation learning in humans and robots. However, few proposals offer a framework for imitation learning in noisy stochastic environments where the imitator must learn and act under real-time performance constraints. We present a novel probabilistic framework for imitation learning in stochastic environments with unreliable sensors. Bayesian algorithms, based on Meltzoff and Moore's AIM hypothesis for action imitation, implement the core of an imitation learning framework. Our algorithms are computationally efficient, allowing real-time learning and imitation in an active stereo vision robotic head and on a humanoid robot. We present simulated and real-world robotics results demonstrating the viability of our approach. We conclude by advocating a research agenda that promotes interaction between cognitive and robotic studies of imitation.
Borehole Acoustic Reflection Survey for high resolution imaging (2006)

Borehole Acoustic Reflection Survey (BARS) data were acquired in the Brent formation in the Norwegian North Sea in an exploration well for Hydro. In total, an interval of approximately 300 m was logged. Initial near‐wellbore formation images were obtained within 24 hours. The quality of the sonic waveform data was very good. However, significant uncertainties in the actual tool depth caused by rough weather conditions during the time of logging, affected to some extent the coherence and the range of the formation images. The high‐resolution image shows an interface dipping at 5° and clearly visible for at least 45 ft away from the well bore. The dip of the interface is in agreement with the expected local geology at the well location. The high‐resolution event can be correlated to a 1 m thin coal bed intersecting the borehole and indicated by the petrophysical logs. The coal bed is interpreted as the Top Etive Formation. The BARS images helped characterizing the local geology and the reservoir. In addition, the high‐resolution sonic images augment the understanding of the seismic responses in the reservoir section.
Kalman Consensus Strategies and Their Application to Cooperative Control (2004)

Sponsorship: AFOSR, NSF. In this paper, we propose discrete-time and continuous-time consensus update schemes motivated by the discrete-time and continuous-time Kalman filters. With certainty information encoded into each agent, the proposed consensus schemes explicitly account for relative confidence in the information that is communicated from each agent in the team. We show mild sufficient conditions under which consensus can be achieved using the proposed schemes in the presence of switching interaction topologies. The Kalman consensus scheme is shown to be input-to-state stable. We show how to exploit this fact in multi-agent cooperative control scenarios.
CDX2 is involved in microRNA‑associated inflammatory carcinogenesis in gastric cancer (2017)

The development of gastric cancer is significantly associated with chronic inflammation, such as caused by <i>Helicobacter pylori (H. pylori)</i> infection. Caudal-type homeobox 2 (CDX2) is a homeobox protein involved in intestinal differentiation in normal and in aberrant locations, and is associated with inflammation. The authors of the present study have previously reported that CDX2 may have a suppressive role in the progression and carcinogenesis of gastric carcinoma. In the present study, the authors initially confirmed that a decreased expression of CDX2, as detected by immunohistochemistry, is associated with poor cancer-specific survival in 210 gastric cancer cases, which is consistent with several previously published studies. To elucidate the potential mechanisms underlying this association, the authors investigated the mechanism of CDX2 suppression, which included interleukin (IL)-6/signal transducer and activator of transcription 3 (STAT3) and p53 signaling pathways. The present study confirmed that CDX2 was suppressed by activation of the IL-6/STAT3 signaling pathway via miR-181b <i>in vitro</i>. It was further revealed that gastric cancer with negative CDX2 expression is associated with negative p53 staining, and this association was particularly significant in undifferentiated gastric cancer. The activation of the IL-6/STAT3 signaling pathway suppressed miR-34a, which is induced by p53. This suggests that the activation of the IL-6/STAT3 signaling pathway inflammation signaling pathway suppresses the p53 signaling pathway in tumors without <i>TP53</i> mutation, which results in poor prognostic outcomes. In conclusion, CDX2 may be a useful prognostic biomarker for gastric cancer and is associated with p53 inactivation.
Effects of physical and chemical pressure on charge density wave transitions in LaAg1-xAuxSb2 single crystals (2022)

The structural characterization and electrical transport measurements at ambient and applied pressures of the compounds of the La(Ag1-xAux)Sb2 family are presented. Up to two charge density wave (CDW) transitions could be detected upon cooling from room temperature and an equivalence of the effects of chemical and physical pressure on the CDW ordering temperatures was observed with the unit cell volume being a salient structural parameter. As such La(Ag1-xAux)Sb2 is a rare example of a non-cubic system that exhibits good agreement between the effects of applied, physical, pressure and changes in unit cell volume from steric changes induced by isovalent substitution. Additionally, for La(Ag0.54Au0.46)Sb2 anomalies in low temperature electrical transport were observed in the pressure range where the lower charge density wave is completely suppressed.