gebhart/patrepeval huggingface dataset:
Data from The Tumor Microenvironment Shapes Lineage, Transcriptional, and Functional Diversity of Infiltrating Myeloid Cells (2023)

&lt;div&gt;Abstract&lt;p&gt;Myeloid cells play important regulatory roles within the tumor environment by directly promoting tumor progression and modulating the function of tumor-infiltrating lymphocytes, and as such, they represent a potential therapeutic target for the treatment of cancer. Although distinct subsets of tumor-associated myeloid cells have been identified, a broader analysis of the complete myeloid cell landscape within individual tumors and also across different tumor types has been lacking. By establishing the developmental and transcriptomic signatures of infiltrating myeloid cells from multiple primary tumors, we found that tumor-associated macrophages (TAM) and tumor-associated neutrophils (TAN), while present within all tumors analyzed, exhibited strikingly different frequencies, gene expression profiles, and functions across cancer types. We also evaluated the impact of anatomic location and circulating factors on the myeloid cell composition of tumors. The makeup of the myeloid compartment was determined by the tumor microenvironment rather than the anatomic location of tumor development or tumor-derived circulating factors. Protumorigenic and hypoxia-associated genes were enriched in TAMs and TANs compared with splenic myeloid-derived suppressor cells. Although all TANs had an altered expression pattern of secretory effector molecules, in each tumor type they exhibited a unique cytokine, chemokine, and associated receptor expression profile. One such molecule, haptoglobin, was uniquely expressed by 4T1 TANs and identified as a possible diagnostic biomarker for tumors characterized by the accumulation of myeloid cells. Thus, we have identified considerable cancer-specific diversity in the lineage, gene expression, and function of tumor-infiltrating myeloid cells. &lt;i&gt;Cancer Immunol Res; 2(7); 655–67. ©2014 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Prevalence of Escherichia coli O157:H7 and Salmonella in traditional meats derived from game animals in Nunavik (2010)

These results represent a first step towards the creation for future reference of a database on the prevalence of the pathogens E. coli O157 and Salmonella.
Recent progress in investigating optical rogue waves (2013)

Some of the latest advancements in investigating optical rogue waves are discussed. This subject has been rapidly expanding from 2007 with many published works in different fields: supercontinuum generation in a fiber, nonlinear waves in optical cavities,
Monotonicity Properties and Spectral Characterization of Power Redistribution in Cascading Failures (2017)

In this work, we apply spectral graph theory methods to study the monotonicity and structural properties of power redistribution in a cascading failure process. We demonstrate that in contrast to the lack of monotonicity in physical domain, there is a rich collection of monotonicity one can explore in the spectral domain, leading to a systematic way to define topological metrics that are monotonic. It is further shown that many useful quantities in cascading failure analysis can be unified into a spectral inner product, which itself is related to graphical properties of the transmission network. Such graphical interpretations precisely capture the Kirchhoff's law expressed in terms of graph structural properties and gauge the impact of a line when it is tripped.
CGG‐repeat polymorphism of the BCR gene rules out predisposing alleles leading to the philadelphia chromosome (1994)

The Philadelphia chromosome (Ph) is associated with leukemia, most frequently of the chronic myelogenous variety. The Ph chromosome is a translocation chromosome which gains oncogenic potential through the fusion of the ABL oncogene of chromosome 9 with the BCR gene of chromosome 22. The Ph is believed to arise from random chromosome rearrangement with a subsequent selective advantage of the malignant cell line. However, alleles may be present in the population which predispose toward this specific rearrangement. We used a highly polymorphic CGG-repeat polymorphism within the first exon of the BCR gene to determine BCR allele frequencies among 26 leukemia patients with the Ph chromosome and 63 control individuals. Eight BCR alleles of variable CGG-repeat length were present in both groups at statistically similar frequencies and in Hardy-Weinberg equilibrium. We therefore concluded that there are no alleles of the BCR gene that have a major predisposing influence on the development of the Ph chromosome and subsequent leukemia.
Antibody Response to a Human Diploid Cell Rabies Vaccine (1974)

An experimentally killed rabies virus vaccine prepared in a human diploid cell strain (WI-38)-Wyeth rabies vaccine (WRV)-was used by various injection schedules in two separate studies to define more closely in human volunteer subjects an effective vaccination schedule for pre- or postexposure immunization, particularly for donors of rabies-hyperimmune plasma. To permit valid comparisons between our results and those of other workers, antibody levels achieved were expressed in terms of international units (IU) per milliliter of serum. Antibody response of previously nonvaccinated persons were only modest after a single dose of WRV, never reaching a level higher than 0.80 IU/ml over a 56-day testing period. Moreover, antibody was not detected at 0.16 IU/ml before the 14th day, either after a single dose or after two doses given 3 days apart. The best response followed four doses of WRV given within 4 weeks. This schedule resulted in the highest rate of seroconversion to the >/=6 IU/ml antibody level required of potential rabies-immune plasma donors. Giving the first vaccine dose in aluminum hydroxide diluent did not enhance the antibody response. There was a definite suggestion in the various injection schedules that higher and more sustained antibody levels were reached when the interval between the first and second vaccine doses was longest. The greater immunogenicity of WRV as compared with duck embryo vaccine was best demonstrated by the fact that a single booster dose of duck embryo vaccine to previously vaccinated individuals resulted in only a sevenfold antibody rise during the following 56 days, whereas a booster dose of WRV elicited a 69-fold rise. Al(OH)(3) in the first dose of WRV had no effect, but the enhancing effect of a longer interval between vaccine doses was noted once again; 20 of 20 subjects who received three doses of WRV with 4 weeks between doses developed good levels of rabies antibody, and 19 exceeded 6 IU/ml.
Aberrant Expression of TIMP-2 and PBEF Genes in the Placentae of Cloned Mice Due to Epigenetic Reprogramming Error (2016)

Cloned mice derived from somatic or ES cells show placental overgrowth (placentomegaly) at term. We had previously analyzed cloned and normal mouse placentae by using two-dimensional gel electrophoresis and mass spectrometry to identify differential protein expression patterns. Cloned placentae showed upregulation of tissue inhibitor of metalloproteinase-2 (TIMP-2), which is involved in extracellular matrix degradation and tissue remodeling, and downregulation of pre-B cell colony enhancing factor 1 (PBEF), which inhibits apoptosis and induces spontaneous labor. Here, we used Western blotting to further analyze the protein expression levels of TIMP-2 and PBEF in cloned placentae derived from cumulus cells, TSA-treated cumulus cells, intracytoplasmic sperm injection (ICSI), and natural mating (NM control). Cloned and TSA-treated cloned placentae had higher expression levels of TIMP-2 compared with NM control and ICSI-derived placentae, and there was a positive association between TIMP-2 expression and the placental weight of cloned mouse concepti. Conversely, PBEF protein expression was significantly lower in cloned and ICSI placentae compared to NM controls. To examine whether the observed differences were due to abnormal gene expression caused by faulty epigenetic reprogramming in clones, we investigated DNA methylation and histone modification in the promoter regions of the genes encoding TIMP-2 and PBEF. Sodium bisulfite sequencing did not reveal any difference in DNA methylation between cloned and NM control placentae. However, ChIP assays revealed that the level of H3-K9/K14 acetylation at the TIMP-2 locus was higher in cloned placentae than in NM controls, whereas acetylation of the PBEF promoter was lower in cloned and ICSI placenta versus NM controls. These results suggest that cloned placentae appear to suffer from failure of histone modification-based reprogramming in these (and potentially other) developmentally important genes, leading to aberrant expression of their protein products. These changes are likely to be involved in generating the abnormalities seen in cloned mouse placentae, including enlargement and/or a lack of proper placental function.
A Real/Complex Logarithmic Number System ALU (2010)

The real Logarithmic Number System (LNS) offers fast multiplication but uses more expensive addition. Cotransformation and higher order table methods allow real LNS ALUs with reasonable precision on Field-Programmable Gate Arrays (FPGAs). The Complex LNS (CLNS) is a generalization of LNS, which represents complex values in log-polar form. CLNS is a more compact representation than traditional rectangular methods, reducing bus and memory cost in the FFT; however, prior CLNS implementations were either slow CORDIC-based or expensive 2D-table-based approaches. Instead, we reuse real LNS hardware for CLNS, with specialized hardware (including a novel \log \sin that overcomes singularity problems) that is smaller than the real-valued LNS ALU to which it is attached. All units were derived from the Floating-Point-Cores (FloPoCo) library. FPGA synthesis shows our CLNS ALU is smaller than prior fast CLNS units. We also compare the accuracy of prior and proposed CLNS implementations. The most accurate of the proposed methods increases the error in radix-two FFTs by less than half a bit, and a more economical FloPoCo-based implementation increases the error by only one bit.
SSOI technology for integrated Schottky barrier diode (2002)

In fabricating MMICs on silicon, a conflict arises between the requirement of low resistivity silicon (LRS) for active device fabrication, and very high resistivity silicon (VHRS) for low interconnect loss. Two differing solutions are presented here. Low loss CPW lines have been fabricated on oxidised porous silicon (OPS) formed on 1-3 /spl Omega/cm silicon wafers, yielding typical losses of 8.5 dB/cm at 30 GHz. Alternatively, silicon on insulator (SOI) substrates, produced by bonding 1-3 /spl Omega/cm silicon wafers to 2-4 k/spl Omega/ "handle" wafers, give CPW line losses of 2.2 dB/cm at 30 GHz. In addition, by incorporating a buried tungsten layer to form a silicon-on-silicide-on-insulator (SSOI) structure, integrated Schottky barrier diodes, with low and controllable C/sub j/ and R/sub s/, can be produced.
Generation of a Convalescent Model of Virulent Francisella tularensis Infection for Assessment of Host Requirements for Survival of Tularemia (2012)

Francisella tularensis is a facultative intracellular bacterium and the causative agent of tularemia. Development of novel vaccines and therapeutics for tularemia has been hampered by the lack of understanding of which immune components are required to survive infection. Defining these requirements for protection against virulent F. tularensis, such as strain SchuS4, has been difficult since experimentally infected animals typically die within 5 days after exposure to as few as 10 bacteria. Such a short mean time to death typically precludes development, and therefore assessment, of immune responses directed against virulent F. tularensis. To enable identification of the components of the immune system that are required for survival of virulent F. tularensis, we developed a convalescent model of tularemia in C57Bl/6 mice using low dose antibiotic therapy in which the host immune response is ultimately responsible for clearance of the bacterium. Using this model we demonstrate αβTCR(+) cells, γδTCR(+) cells, and B cells are necessary to survive primary SchuS4 infection. Analysis of mice deficient in specific soluble mediators shows that IL-12p40 and IL-12p35 are essential for survival of SchuS4 infection. We also show that IFN-γ is required for survival of SchuS4 infection since mice lacking IFN-γR succumb to disease during the course of antibiotic therapy. Finally, we found that both CD4(+) and CD8(+) cells are the primary producers of IFN-γand that γδTCR(+) cells and NK cells make a minimal contribution toward production of this cytokine throughout infection. Together these data provide a novel model that identifies key cells and cytokines required for survival or exacerbation of infection with virulent F. tularensis and provides evidence that this model will be a useful tool for better understanding the dynamics of tularemia infection.
Trauma Triage (1989)

Field triage of injured patients has the objective of rapid identification of that 5-10% with injuries serious enough to pose a risk to life. The process requires not only the identification of patients with abnormal physiology, but also those whose physiology is normal despite the fact that significant anatomic injury may exist. This paper defines relationships by which vehicle damage information available at the accident may augment the physiologic measures used for triage decisions. Vehicle velocity changes of 20 m.p.h. or more in direct frontal collisions, 22 m.p.h. or more in offset frontal collisions, and 15 m.p.h. or more in side impacts captured 90% of the patients with Injury Severity Scores of 16 or greater. The amount of vehicle damage observed with these velocity changes was found to be 20 inches of crush in direct frontal collisions, 28 inches of crush in offset frontal collisions, and 15 inches of damage in side impacts. Incorporating these findings into triage of trauma patients who exhibit normal vital signs at the accident scene may provide a more structured basis for field triage.
Anticipatory Radio Resource Management for Mobile Video Streaming with Linear Programming (2016)

In anticipatory networking, channel prediction is used to improve communication performance. This paper describes a new approach for allocating resources to video streaming traffic while accounting for quality of service. The proposed method is based on integrating a model of the user's local play-out buffer into the radio access network. The linearity of this model allows to formulate a Linear Programming problem that optimizes the trade-off between the allocated resources and the stalling time of the media stream. Our simulation results demonstrate the full power of anticipatory optimization in a simple, yet representative, scenario. Compared to instantaneous adaptation, our anticipatory solution shows impressive gains in spectral efficiency and stalling duration at feasible computation time while being robust against prediction errors.
Differentially Expressed RNA from Public Microarray Data Identifies Serum Protein Biomarkers for Cross-Organ Transplant Rejection and Other Conditions (2010)

Serum proteins are routinely used to diagnose diseases, but are hard to find due to low sensitivity in screening the serum proteome. Public repositories of microarray data, such as the Gene Expression Omnibus (GEO), contain RNA expression profiles for more than 16,000 biological conditions, covering more than 30% of United States mortality. We hypothesized that genes coding for serum- and urine-detectable proteins, and showing differential expression of RNA in disease-damaged tissues would make ideal diagnostic protein biomarkers for those diseases. We showed that predicted protein biomarkers are significantly enriched for known diagnostic protein biomarkers in 22 diseases, with enrichment significantly higher in diseases for which at least three datasets are available. We then used this strategy to search for new biomarkers indicating acute rejection (AR) across different types of transplanted solid organs. We integrated three biopsy-based microarray studies of AR from pediatric renal, adult renal and adult cardiac transplantation and identified 45 genes upregulated in all three. From this set, we chose 10 proteins for serum ELISA assays in 39 renal transplant patients, and discovered three that were significantly higher in AR. Interestingly, all three proteins were also significantly higher during AR in the 63 cardiac transplant recipients studied. Our best marker, serum PECAM1, identified renal AR with 89% sensitivity and 75% specificity, and also showed increased expression in AR by immunohistochemistry in renal, hepatic and cardiac transplant biopsies. Our results demonstrate that integrating gene expression microarray measurements from disease samples and even publicly-available data sets can be a powerful, fast, and cost-effective strategy for the discovery of new diagnostic serum protein biomarkers.
Induction of Redox Instability of Bovine Myoglobin by Adduction with 4-Hydroxy-2-nonenal (2003)

The redox stability of myoglobin (Mb) is compromised by many factors, including lipid oxidation and its products. 4-Hydroxy-2-nonenal (HNE) is an alpha,beta-unsaturated aldehyde derived from the oxidation of omega-6 polyunsaturated fatty acids and is highly reactive and cytotoxic. Our objective was to study potential binding of HNE to Mb and determine how it affects redox stability. OxyMb (0.15 mM) was incubated with HNE (1 mM) at 4, 25, and 37 degrees C at pH 7.4 or 5.6. Samples were analyzed for MetMb formation and by Western blot analyses, LC-MS, LC-MS-MS, circular dichroism (CD), and differential scanning calorimetry (DSC). MetMb formation increased with increasing temperature and was greater at pH 5.6 than at pH 7.4 (P < 0.05). At 37 degrees C, HNE accelerated oxidation at pH 7.4 but not at pH 5.6 (P < 0.05). At both 25 and 4 degrees C, HNE accelerated oxidation at pH 7.4 and 5.6 (P < 0.05). LC-MS revealed the covalent binding of HNE to Mb at both pH values via Michael addition, while Western blot analysis indicated that HNE was bound to histidine (HIS) residues. LC-MS-MS identified six histidine residues of Mb that were readily adducted by HNE, including the proximal (HIS 93) and distal (HIS 64) histidine associated with the heme group. Secondary structure differences between control Mb and Mb incubated with HNE were not detected by CD. However, DSC revealed a decreased T(m) for Mb reacted with HNE at pH 7.4, indicating Mb tertiary structure was altered in a manner consistent with destabilization. These results suggest that HNE accelerates bovine skeletal muscle OxyMb oxidation in vitro by covalent modification at histidine residues.
Syntheses of the enantiomers of carnitine and 4-methylcarnitine via the chromatographic resolution of .gamma.-(dimethylamino)-.beta.-hydroxy ester precursors (1987)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSyntheses of the enantiomers of carnitine and 4-methylcarnitine via the chromatographic resolution of .gamma.-(dimethylamino)-.beta.-hydroxy ester precursorsRobert N. Comber and Wayne J. BrouilletteCite this: J. Org. Chem. 1987, 52, 11, 2311–2314Publication Date (Print):May 1, 1987Publication History Published online1 May 2002Published inissue 1 May 1987https://pubs.acs.org/doi/10.1021/jo00387a041https://doi.org/10.1021/jo00387a041research-articleACS PublicationsRequest reuse permissionsArticle Views169Altmetric-Citations18LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Bias of Tedlar Bags in the Measurement of Agricultural Odorants (2006)

Odor regulations typically specify the use of dynamic dilution olfactometery (DDO) as a method to quantify odor emissions, and Tedlar bags are the preferred holding container for grab samples. This study was conducted to determine if Tedlar bags affect the integrity of sampled air from animal operations. Air samples were collected simultaneously in both Tedlar bags and Tenax thermal desorption tubes. Sample sources originated from either a hydrocarbon-free air tank, dynamic headspace chamber (DHC), or swine-production facility, and were analyzed by gas chromatography-mass spectrometry-olfactometry (GC-MS-O). Several background contaminants were identified from Tedlar bags, which included the odorous compounds N,N-dimethyl acetamide (DMAC), acetic acid, and phenol. Samples from the DHC demonstrated that recovery of malodor compounds was dependent on residence time in the Tedlar bag with longer residence time leading to lower recovery. After 24 h of storage, recovery of C3-C6 volatile fatty acids (VFA) averaged 64%, 4-methylphenol and 4-ethylphenol averaged 10%, and indole and 3-methylindole were below the detection limits of GC-MS-O. The odor activity value (OAV) of grab samples collected in Tedlar bags were 33 to 65% lower following 24 h of storage. These results indicate that significant odorant bias occurs when using Tedlar bags for the sampling of odors from animal production facilities.
Integrating Bayesian Networks into Knowledge-Intensive CBR (1998)

In this paper we propose an approach to knowledge intensive CBR, where explanations are generated from a domain model consisting partly of a semantic network and partly of a Bayesian network (BN). The BN enables learning within this domain model based on the observed data. The domain model is used to focus the retrieval and reuse of past cases, as well as the indexing when learning a new case. Essentially, the BN-powered submodel works in parallel with the semantic network model to generate a statistically sound contribution to case indexing, retrieval and explanation. 1. Introduction and background In knowledge-intensive CBR a model of general domain knowledge is utilized to support the processes of retrieval and reuse of past cases, as well as to learn new cases. The role of the general domain knowledge is to explain why two cases are similar based on semantic and pragmatic criteria, how a past solution may be adapted to a new problem case, and/or what to retain from a case just sol...