gebhart/patrepeval huggingface dataset:
Comparisons between Transcriptional Regulation and RNA Expression in Human Embryonic Stem Cell Lines (2006)

Recent studies have focused on transcriptional regulation and gene expression profiling of human embryonic stem cells (hESCs). However, little information is available regarding the relationship between RNA expression and transcriptional regulation, which is critical in the complete understanding of pluripotency and differentiation of hESCs. In the current study, we determined RNA expression of three different hESC lines compared to Human universal reference RNA expression (HuU-RNA) using a full genome expression microarray, and compared our results to target genes previously identified using ChIP-on-chip analysis. The objective was to identify genes common between the two methods, and generate a more reliable list of embryonic signature genes. Even though hESCs were obtained from different sources and maintained under different conditions, a considerable number of genes could be identified as common between RNA expression and transcriptional regulation analyses. As an example, results from ChIP-on-chip studies show that OCT4, SOX2, and NANOG co-occupy SOX2, OCT4, TDGF1, GJA1, SET, and DPPA4 genes. The results are consistent with RNA expression analyses that demonstrate these genes as differently expressed in our hESC lines, further substantiating their role across cell types and confirming their importance as embryonic signatures. In addition, we report the differential expression of growth arrest-specific (GAS) family of genes in hESC. GAS2L1 and GAS3 members of this family appear to be transcriptionally regulated by OCT4, SOX2, or NANOG, whereas GAS5 and GAS6 are not; all of the genes are differentially expressed, as determined by microarray and validated via quantitative (Q)- PCR. Collectively, these data provide insight into the relationship between gene expression and transcriptional regulation, resulting in a reliable list of genes associated with hESCs.
The Widespread Impact of Mammalian MicroRNAs on mRNA Repression and Evolution (2005)

Thousands of mammalian messenger RNAs are under selective pressure to maintain 7-nucleotide sites matching microRNAs (miRNAs). We found that these conserved targets are often highly expressed at developmental stages before miRNA expression and that their levels tend to fall as the miRNA that targets them begins to accumulate. Nonconserved sites, which outnumber the conserved sites 10 to 1, also mediate repression. As a consequence, genes preferentially expressed at the same time and place as a miRNA have evolved to selectively avoid sites matching the miRNA. This phenomenon of selective avoidance extends to thousands of genes and enables spatial and temporal specificities of miRNAs to be revealed by finding tissues and developmental stages in which messages with corresponding sites are expressed at lower levels.
Augmentation of Tumor Immunity by 6-Mercaptopurine (6-MP) and Its Analogs in the Double Grafted Tumor System in Mice. (1995)

We investigated the antitumor effect of 6-mercaptopurine (6-MP) and its analogs using the double grafted tumor technique. BALB/c mice were inoculated intradermally with MethA fibrosarcoma cells at the right inguinal region on day 0 (the primary tumor) and at the left on day 10 (the secondary tumor). Intraperitoneal or intra-lesional administration of 6-MP, 6-mercaptopurine riboside (6-MP-r) and 6-mercaptopurine riboside triacetate (6-MPRTA) from day 3 to 7 dose-dependently inhibited growth of the secondary tumor. Without the primary inoculation, 6-MP showed no effect on growth of the tumor inoculated on day 10, indicating that the antitumor effect of 6-MP could not be attributable to its direct antimetabolic or tumoricidal action only, and that the primary tumor inoculation is necessary for these compounds to inhibits growth of the challenging tumor. 6-MP did not inhibit the secondary MethA growth in the BALB/c (nu/nu) mouse. Both CD4+ and CD8+ T cells increased in the spleen of mice treated with 6-MP. Meanwhile, delayed-type hypersensitivity (DTH) reaction to the methylated bovine serum albumin (MBSA) antigen at the footpad was not augmented but inhibited by 6-MP-r and 6-MPRTA in both normal and tumor-bearing mice. Thus, the immunomodulatory activity of 6-MP could be observed in two opposite directions, augmentation of tumor immunity and inhibition of DTH to MBSA. This indicates that the immune mechanism and/or the type of effector cells induced in these two cell-mediated immune systems are different from each other.
Quantum transport in sputtered, epitaxial Si/Si1−xGex heterostructures (1995)

Radio–frequency magnetron sputter epitaxy was employed for the synthesis of n–type modulation doped Si/Si1−xGex heterostructures. Si channels were grown coherently on sputtered, compositionally graded Si1−xGex buffers of low defect density, and remotely doped with phosphorus by plasma assisted gas phase doping. Magnetotransport measurements on these films revealed Shubnikov–de Haas oscillations in the longitudinal and the integer quantum Hall effect in the transverse magnetoresistance, demonstrating the presence of a two–dimensional electron gas. At T=1.6 K and sheet densities of 1012 cm−2, electron mobilities as high as 15 800 cm2/V s give evidence of the excellent structural and electronic properties achievable by the sputter growth technique.
The photoelectrolysis of water using iron titanate anodes (1977)

Single-crystal and polycrystalline samples of the iron titanates FeTiO3, Fe2TiO4, and Fe2TiO5 have been studied as anodes for the photoelectrolysis of water. Band gaps and flatbands for the various compositions have been determined and aging studies have been conducted which indicate electrochemical leaching of iron atoms from the surface.
Optical Coherence Tomography and Its Role in Mohs Micrographic Surgery: A Case Report (2012)

Optical coherence tomography (OCT) is an imaging technology with the potential to provide high-resolution images of the skin non-invasively. With this device, it is possible to identify a host of skin structures including tumors. In this case report, we demonstrate the use of an OCT device in delineating a lateral tumor margin of an ill-defined basal cell carcinoma prior to Mohs micrographic surgery. Following surgery, the OCT images are compared to histologic sections to confirm their accuracy. OCT technology has the potential to be a vital tool for dermatologists and particularly Mohs surgeons in identifying tumor margins and potentially reducing the number of invasive procedures needed.
Clinical potential of new antiestrogens. (1997)

Although many of these compounds appear promising, further evaluation will be necessary to determine the role these compounds may serve as preventive agents, adjuvant therapies, treatments for advanced disease, or other medical indications such as osteoporosis.
RUN-OFF-ROAD COLLISION AVOIDANCE COUNTERMEASURES USING IVHS COUNTERMEASURES, TASK 3. VOLUME 2 (1995)

The Run-Off-Road Collision Avoidance Using IVHS Countermeasures program is to address the single vehicle crash problem through application of technology to prevent and/or reduce the severity of these crashes. This report describes the findings of the Task 3 effort. Task 3 focused on testing of existing technology to meet the functional goals for run-off-road countermeasures identified in Task 2. These tests included all aspects of countermeasure performance, including sensing functions, algorithm or decision making functions and driver interface functions. Tests of existing technology were performed using a range of techniques and facilities, including laboratory experiments, in-vehicle tests and driving simulator tests. Two primary categories of run-off-road countermeasure technologies were tested in this effort - lateral countermeasures and longitudinal countermeasures. Lateral countermeasures are designed to prevent run-off-road crashes in which the vehicle drifts from its lane because of driver inattention or because the driver relinquishes steering control due to drowsiness, intoxication or some other medical condition. Technology tested in this category included forward and downward looking vision systems for sensing the vehicle's lateral position on the roadway. Longitudinal countermeasures are designed to prevent run-off-road crashes in which the vehicle departs the road due to excessive speed for the roadway geometry or pavement conditions. Technology tested in this category included a combination of Global Positioning System (GPS) and digital maps for sensing the distance to, and the severity of, upcoming curves.
A warning from an ancient oasis: intensive human activities are leading to potential ecological and social catastrophe (2008)

Abstract The Shiyang River Basin is an inland river basin in the Hexi Corridor, Gansu Province, northwest China. Shiyang is the largest basin in terms of human population density and has the highest exploitation of water resources in the northwest. Serious water shortages constrain social and economic development, and the area has some of the worst ecological and environmental deterioration in China. From historical data and recent observations, we have analysed changes in water systems in the Minqin oasis, at the end of the river basin, and assessed impacts and consequences of a changing climate and intensive human activity. Historically, climate change has been the main cause of changes in the oasis. In the last 50 years, however, a major influence has been intense human activity in the basin. With increasing population (159% in 50 years), the amount of cultivated land has been greatly expanded (by 51%). Many reservoirs have been built by damming rivers and large-scale irrigation has been introduced in the middle reaches of the basin. The introduction of leakage-free canals and more extensive exploitation of underground water have further expanded the irrigated area. Water use by humans has exceeded the carrying capacity of the water resources of the basin, which has led to a dramatic shift in water allocation between the upper and lower reaches and a rapid drop in the water table in the Minqin oasis (by as much as 14 m). The oasis is shrinking, natural vegetation that relies on underground water is disappearing, and desertification is accelerating. An ancient oasis that can be traced back 2000 years is disappearing and this must be a warning sign for future generations. Keywords: OASISWATER RESOURCESIRRIGATIONCLIMATE CHANGESHIYANG RIVER BASIN
Compositional Determination of rf Co-Sputtered Multicomponent Systems (1971)

A technique of synthesis of nearly complete two- and three-component systems is described, which consists of one-cathode, multiple-target, rf co-sputtering of the constituent elements onto one large substrate. A new and simple approximate method of compositional determination of co-sputtered films is introduced which is based on the assumptions of superposition of the sputtered species and the constancy of geometry-dependent deposition profiles. Compositional analysis of any portion of the deposited film can be obtained from film thickness measurements and the knowledge of the deposition profiles, which need to be determined only once for a given sputtering geometry.
Expression and function of adenosine receptors in human dendritic cells (2001)

Dendritic cells (DCs) are specialized antigen-presenting cells characterized by their ability to migrate into target sites, process antigens, and activate naive T cells. In this study, we analyzed the biological activity and intracellular signaling of adenosine by using reverse transcriptase-polymerase chain reaction assays to investigate mRNA expression of A(1), A(2a) and A(3) adenosine receptors in immature and mature human DCs. Functional experiments on adenosine stimulation showed chemotaxis, intracellular calcium transients, and actin polymerization, but no activation of adenylate cyclase in immature DCs. Experiments with receptor isotype-selective agonists and antagonists as well as pertussis toxin revealed that chemotaxis, calcium transients, and actin polymerization were mediated via G(i-) or G(0-)protein-coupled A(1) and A(3) receptors. Maturation of DCs induced by lipopolysaccharide (LPS) resulted in down-regulation of A(1) and A(3) receptor mRNAs, although A(2a) receptor mRNA was still expressed. However, in LPS-differentiated DCs, adenosine and an A(2a) receptor agonist stimulated adenylate cyclase activity, enhanced intracellular cAMP levels, and inhibited interleukin 12 (IL-12) production. These effects could be completely prevented by pretreatment with A(2) receptor antagonist. These findings strongly suggest that adenosine has important but distinct biological effects in DCs activity as a chemotaxin for immature DCs and as a modulator of IL-12 production in mature DCs. These effects can be explained by differential expression of adenosine receptor subtypes.
Hacking SIEMs to Catch Hackers: Decreasing the Mean Time to Respond to Network Security Events with a Novel Threat Ontology in SIEM Software (2016)

Information security is plagued with increasingly sophisticated and persistent threats to communication networks. The development of new threat tools or vulnerability exploits often outpaces advancements in network security detection systems. As a result, detection systems often compensate by over reporting partial detections of routine network activity to security analysts for further review. Such alarms seldom contain adequate forensic data for analysts to accurately validate alerts to other stakeholders without lengthy investigations. As a result, security analysts often ignore the vast majority of network security alarms provided by sensors, resulting in security breaches that may have otherwise been prevented. Security Information and Event Management (SIEM) software has been introduced recently in an effort to enable data correlation across multiple sensors, with the intent of producing a lower number of security alerts with little forensic value and a higher number of security alerts that accurately reflect malicious actions. However, the normalization frameworks found in current SIEM systems do not accurately depict modern threat activities. As a result, recent network security research has introduced the concept of a "kill chain" model designed to represent threat activities based upon patterns of action, known indicators, and methodical intrusion phases. Such a model was hypothesized by many researchers to result in the realization of the desired goals of SIEM software. The focus of this thesis is the implementation of a "kill chain" framework within SIEM software. A novel "Kill chain" model was developed and implemented within a commercial SIEM system through modifications to the existing SIEM database. These modifications resulted in a new log ontology capable of normalizing security sensor data in accordance with modern threat research. New SIEM correlation rules were developed using the novel log ontology compared to existing vendor recommended correlation rules using the default model. The novel log ontology produced promising results indicating improved detection rates, more descriptive security alarms, and a lower number of false positive alarms. These improvements were assessed to provide improved visibility and more efficient investigation processes to security analysts ultimately reducing the mean time required to detect and escalate security incidents.
Fluoride and Casein Phosphopeptide-Amorphous Calcium Phosphate (2008)

Casein phosphopeptide-amorphous calcium phosphate (CPP-ACP) slows the progression of caries and remineralizes enamel subsurface lesions. The aim of this study was to determine the ability of CPP-ACP to increase the incorporation of fluoride into plaque and to promote enamel remineralization in situ. Randomized, double-blind, cross-over studies involved mouthrinses and dentifrices containing CPP-ACP and fluoride. The mouthrinses were used for 60 sec, three times/day for 5 days, and supragingival plaque was collected and analyzed for F. The dentifrices were rinsed as a water slurry for 60 sec four times/day for 14 days in an in situ model. The addition of 2% CPP-ACP to the 450-ppm-F mouthrinse significantly increased the incorporation of fluoride into plaque. The dentifrice containing 2% CPP-ACP produced a level of remineralization similar to that achieved with a dentifrice containing 2800 ppm F. The dentifrice containing 2% CPP-ACP plus 1100 ppm F was superior to all other formulations.
Chitinase activity in human serum and leukocytes (1995)

Using colloidal [3H] chitin as a substrate, we provide the first demonstration of a chitinase in human leukocytes; chitinolytic activity in whole and disrupted leukocyte preparations (approximately 0.6 and 5.5 nmol of N-acetylglucosamine [GlcNAc] released min-1 mg of protein-1, respectively) was partially inhibited by the specific chitinase inhibitor allosamidin (9 microM). Following fractionation of the leukocytes, much higher levels of chitinase activity were detected in granulocyte-rich homogenates (approximately 7.2 nmol of GlcNAc released min-1 mg of protein-1) than in lymphocyte- and monocyte-rich homogenates (approximately 0.22 and 0.26 nmol of GlcNAc released min-1 mg of protein-1, respectively). Low levels of chitinase activity were detected in human serum (approximately 4 pmol of GlcNAc released min-1 mg of protein-1). Chitinolytic activity in granulocyte-rich homogenates and serum was partially inhibited by allosamidin (9 microM). Proteins with chitinolytic activities (approximate molecular masses, 48 and 56 kDa) distinct from lysozyme (14.3 kDa) were detected on polyacrylamide gels following the electrophoresis of human granulocyte-rich preparations. Chitinase activity, detected consistently in serum and leukocytes from all human volunteers investigated, may contribute to the protection of the host by cleaving chitin in the cell walls of fungal pathogens.
Immune Hyperactivation of HIV-1-Infected T Cells Mediated by Tat and the CD28 Pathway (1997)

Human immunodeficiency virus-type 1 (HIV-1) infection is characterized by a chronic state of immune hyperactivation in patients. Infection of human peripheral blood lymphocytes with HIV-1 in vitro resulted in increased interleukin-2 (IL-2) secretion in response to T cell activation via the CD3 and CD28 receptors. Expression of the HIV-1 transactivator Tat recapitulated this phenotype and was associated with increased IL-2 secretion in response to costimulation with CD3 plus CD28. IL-2 superinduction by Tat occurred at the transcriptional level, was mediated by the CD28-responsive element in the IL-2 promoter, and was exclusively dependent on the 29 amino acids encoded by the second exon of Tat.
Differentiation of Human Hematopoietic Cells Increases Expression of a Gene Transferred by a Retroviral Vector (1989)

To study expression of a retroviral vector in human hematopoietic lineages, two established human hematopoietic cell lines (HL60 and K562) and a human adherent stromal cell line (KM101) were infected with the vector pZIP-SV(X). Expression of the transferred neomycin resistance gene (neor) of pZIP-SV(X) was evaluated as the ability of the cells to form colonies (greater than 50 cells) in an agar assay in the presence of the neomycin analogue, G418. After infection, all three cell lines produced colonies resistant to G418. The level of neor mRNA in separate colonies was analyzed by Northern blot analysis. The neor gene transferred by the vector pZIP-SV(X) was expressed in both human hematopoietic and stromal cell lines. In addition, primary adherent human stromal cells infected with pZIP-SV(X) grew in the presence of G418. To determine if differentiation of hematopoietic cells affects expression of the retroviral vector, HL60 cells infected with pZIP-SV(X) were induced to differentiate, and the level of neor mRNA measured. The amount of neor mRNA increased when HL60 cells were induced to differentiate along the granulocytic pathway. Conversely, when HL60 cells were induced toward monocytoid differentiation (TPA), the level of neor mRNA did not significantly increase. We conclude that the neor gene transferred by a retroviral vector, pZIP-SV(X), is functionally expressed. In addition, expression of the transferred neor gene is regulated during myeloid differentiation of HL60 cells.
Prevalence of TMPRSS2-ERG Fusion Prostate Cancer among Men Undergoing Prostate Biopsy in the United States (2009)

This is the first prospective North American multicenter study to characterize TMPRSS2-ERG prostate cancer prevalence in a cohort of patients undergoing needle biopsy irrespective of whether or not they subsequently undergo prostatectomy. Our results show that this gene rearrangement is common among North American men who have prostate cancer on biopsy, is absent in benign prostate biopsy, and is associated with specific morphologic features. These findings indicate a need for prospective studies to evaluate the relationship of TMPRSS2-ERG rearrangement with clinical course of screening-detected prostate cancer in North American men, and a need for the development of noninvasive screening tests to detect TMPRSS2-ERG rearrangement.
Colloidal synthesis of nanocrystals and nanocrystal superlattices (2001)

This paper provides an overview of the synthetic techniques used to prepare colloidal nanocrystals (NCs) of controlled composition, size, shape, and internal structure and the methods for manipulation of these materials into ordered NC assemblies (superlattices). High-temperature solution-phase synthesis (100–300°C) is followed by size-selective separation techniques in the preparation of monodisperse NC samples tunable in size from ∼1 to 15 nm in diameter with <5% standard deviation. Each NC consists of a crystalline inorganic core coordinated by an organic monolayer. These monodisperse NC samples enable systematic studies of structural, electronic, magnetic, and optical properties of materials as a function of size evolution from molecular species (<100 atoms) to bulk solids (>100 000 atoms). We illustrate size-dependent properties for magnetic materials using Co and for semiconducting materials using PbSe. These NC samples are sufficiently uniform in size to self-assemble into close-packed, ordered NC superlattices, also known as colloidal crystals.
Control of central and peripheral tolerance by Aire (2011)

The negative selection of self-reactive thymocytes depends on the expression of tissue-specific antigens by medullary thymic epithelial cells. The autoimmune regulator (Aire) protein plays an important role in turning on these antigens, and the absence of even one Aire-induced tissue-specific antigen in the thymus can lead to autoimmunity in the antigen-expressing target organ. Recently, Aire protein has been detected in peripheral lymphoid organs, suggesting that peripheral Aire plays a complementary role here. In these peripheral sites, Aire was found to regulate the expression of a group of tissue-specific antigens that is distinct from those expressed in the thymus. Furthermore, transgenic antigen expression in extrathymic Aire-expressing cells (eTACs) can mediate deletional tolerance, but the immunological relevance of Aire-dependent, endogenous tissue-specific antigens remains to be determined.