gebhart/patrepeval huggingface dataset:
Imipramine Inhibits Migration and Invasion in Metastatic Castration-Resistant Prostate Cancer PC-3 Cells via AKT-Mediated NF-κB Signaling Pathway (2020)

Imipramine (IMI) is a tricyclic synthetic antidepressant that is used to treat chronic psychiatric disorders, including depression and neuropathic pain. IMI also has inhibitory effects against various cancer types, including prostate cancer; however, the mechanism of its anticancer activity is not well understood. In the present study, we investigated the antimetastatic and anti-invasive effects of IMI in metastatic castration-resistant prostate cancer PC-3 cells, with an emphasis on the serine/threonine protein kinase AKT-mediated nuclear factor kappa B (NF-κB) signaling pathway. While IMI did not induce cell death, it attenuated PC-3 cell proliferation. According to the wound healing assay and invasion assay, migration and invasion in PC-3 cells were significantly inhibited by IMI in a dose-dependent manner. IMI significantly downregulated p-AKT protein expression but upregulated phospho-extracellular signal-regulated kinase (ERK1)/2 protein expression levels. Furthermore, IMI treatment resulted in decreased AKT-mediated downstream signaling, including p-inhibitor of κB kinase (IKK)α/β, p-inhibitor of κB (IκBα), and p-p65. Inhibited NF-κB signaling reduced the secretion of several proinflammatory cytokines and chemokine by PC-3 cells. Overall, our study explored the negative correlation between the use of antidepressants and prostate cancer progression, showing that IMI attenuated cell viability, migration, and invasion of PC-3 cells by suppressing the expression of AKT and NF-κB-related signaling proteins and secretion of tumor necrosis factor-<i>α</i> (<i>TNF-α</i>), interleukin-1β (<i>IL-1β</i>), and monocyte chemoattractant protein-1 (<i>MCP-1</i><i>)</i>.
Human Cytomegalovirus Induces Monocyte Differentiation and Migration as a Strategy for Dissemination and Persistence (2004)

Human cytomegalovirus (HCMV) pathogenesis is characterized by multiple organ system involvement due to viral spread to host organs after a cell-associated viremia. The cell type responsible for HCMV dissemination is unknown. Monocytes are the most likely candidate since they are the predominant cell type infected in the blood. However, monocytes are not productive for viral replication and are abortively infected. The results presented here provide a potential answer to this conundrum. We report that primary HCMV infection of monocytes induces transendothelial migration and monocyte-to-macrophage differentiation and that these HCMV-differentiated macrophages are productive for viral replication. Together, our data suggest a novel mechanism for HCMV pathogenesis; HCMV induces cellular changes in monocytes to promote viral replication and spread to host organs.
Determination of Naringin and Neohesperidin in Orange Juice by Liquid Chromatography with UV Detection to Detect the Presence of Grapefruit Juice: Collaborative Study (2000)

Fifteen collaborating laboratories were sent 9 samples of citrus juice mixtures as blind duplicates for determination of naringin and neohesperidin by liquid chromatography. Two sample pairs were 100% orange juice and did not contain any naringin or neohesperidin. The remaining 7 sample pairs contained naringin at levels ranging from 3.9 to 46.5 ppm and neohesperidin at levels ranging from 0.14 to 35.6 ppm. Five sample pairs consisted of orange juice mixtures containing 1, 3, and 5% grapefruit juice; 5% sour orange; and 5% K-Early citrus variety. Two sample pairs were orange juice spiked with naringin, neohesperidin, sodium benzoate, and potassium sorbate. Data were received from 13 laboratories. Data from 1 collaborator were eliminated because the method protocol was not followed. Neohesperidin values from another laboratory were also not used because of problems with a coeluting component. Repeatability relative standard deviations ranged from 2.95 to 15.23% for naringin and from 3.00 to 11.74% for neohesperidin. Reproducibility relative standard deviations ranged from 11.34 to 31.94% for naringin and from 10.45 to 26.17% for neohesperidin. The method is reliable for detecting the presence of grapefruit juice in orange juice as indicated by a finding of > or =10 ppm naringin and < or =2 ppm neohesperidin. The method was adopted First Action by AOAC INTERNATIONAL.
A parallel implementation of iterative-deepening-A (1987)

This paper presents a parallel version of the Iterative-Deepening-A* (IDA*) algorithm. Iterative-Deepening-A* is an important admissible algorithm for state-space search which has been shown to be optimal both in time and space for a wide variety of state-space search problems. Our parallel version retatins all the nice properties of the sequential IDA* and yet does not appear to be limited in the amount of parallelism. To test its effectiveness, we have implemented this algorithm on Sequent Balance 21000 parallel processor to solve the 15-puzzle problem, and have been able to obtain almost linear speedups on the 30 processors that are available on the machine. On machines where larger number of processors are available, we expect that the speedup will still grow linearly. The parallel version seems suitable even for loosely coupled architectures such as the Hypercube.
Multi-design variable optimization for a fixed pumping power of a water-cooled cold plate for high power electronics applications (2012)

The current trend in microelectronic systems has made thermal management a critical design phase with the increase in the number of transistors per chip and decrease in system footprint. For high end systems, it has become increasingly difficult to rely on air cooling. As a result, liquid cooling has grown in prominence as a method for cooling high density interconnect (HDI) devices. Water cooling in particular has multiple advantages over air cooling as it has a greater heat carrying capacity. Cold plates will play a prominent role in cooling such high end systems. As a way of demonstrating the proposed methodology, the performance of the cold plate previously employed in IBM's Enterprise System/9000 water-cooled mainframes is optimized. By varying multiple design parameters, such as the channel dimensions, a conjugate CFD model is deployed to optimize the thermal resistance for a fixed pumping power. This will serve as an indicator for future studies into the design of robust cold plates for energy-efficient thermal management and packaging of high power single and multi-chip planar modules.
CP4ACS - Feedback report on guideline adherence for STEMI - 2nd edition (2016)

status: Published
An adaptive power conservation scheme for heterogeneous wireless sensor networks with node redeployment (2005)

We introduce a new modelling assumption in wireless sensor networks, that of node redeployment (addition of sensor devices during the protocol evolution) and we extend the modelling assumption of heterogeneity (having sensor devices of various types). These two features further increase the highly dynamic nature of such networks and adaptation becomes a powerful technique for protocol design. Under this model, we design, implement and evaluate a power conservation scheme for efficient data propagation. Our protocol is adaptive: it locally monitors the network conditions (density, energy) and accordingly adjusts the sleep-awake schedules of the nodes towards best operation choices. Our protocol operates does not require exchange of control messages between nodes to coordinate.Implementing our protocol we combine it with two well-known data propagation protocols and evaluate the achieved performance through a detailed simulation study using our extended version of Ns2. We focus in highly dynamic scenarios with respect to network density, traffic conditions and sensor node resources. We propose a new general and parameterized metric capturing the trade-off between delivery rate, energy efficiency and latency. The simulation findings demonstrate significant gains (such as more than doubling the success rate of the well-known Directed Diffusion propagation paradigm) and good trade-offs. Furthermore, redeployment of sensors during network evolution and/or heterogeneous deployment of sensors drastically improve (when compared to equal total "power" simultaneous deployment of identical sensors at the start) the protocol performance (the success rate increases up to four times while reducing energy dissipation and, interestingly, keeping latency low).
Registered report: Systematic identification of genomic markers of drug sensitivity in cancer cells (2016)

The Reproducibility Project: Cancer Biology seeks to address growing concerns about the reproducibility in scientific research by conducting replications of selected experiments from a number of high-profile papers in the field of cancer biology. The papers, which were published between 2010 and 2012, were selected on the basis of citations and Altmetric scores (Errington et al., 2014). This Registered Report describes the proposed replication plan of key experiments from "Systematic identification of genomic markers of drug sensitivity in cancer cells" by Garnett and colleagues, published in Nature in 2012 (Garnett et al., 2012). The experiments to be replicated are those reported in Figures 4C, 4E, 4F, and Supplemental Figures 16 and 20. Garnett and colleagues performed a high throughput screen assessing the effect of 130 drugs on 639 cancer-derived cell lines in order to identify novel interactions for possible therapeutic approaches. They then tested this approach by exploring in more detail a novel interaction they identified in which Ewing's sarcoma cell lines showed an increased sensitivity to PARP inhibitors (Figure 4C). Mesenchymal progenitor cells (MPCs) transformed with the signature EWS-FLI1 translocation, the hallmark of Ewing's sarcoma family tumors, exhibited increased sensitivity to the PARP inhibitor olaparib as compared to MPCs transformed with a different translocation (Figure 4E). Knockdown mediated by siRNA of EWS-FLI1 abrogated this sensitivity to olaparib (Figure 4F). The Reproducibility Project: Cancer Biology is a collaboration between the Center for Open Science and Science Exchange, and the results of the replications will be published by eLife.
Isoamylene Trimerization in Liquid-Phase over Ion Exchange Resins and Zeolites (2010)

Liquid-phase trimerization of 2-methyl-1-butene and 2-methyl-2-butene mixtures over solid acid catalysts was carried out in a batch-stirred tank reactor in the temperature range 333−373 K. Diisoamylenes and triisoamylenes were the main products. Cracking products among C6−C9 and C11−C14 were also obtained under the assayed conditions. The catalityc performance of five different acidic ion exchange resins (Amberlyst 15, Amberlyst 35, Amberlyst 70, Purolite CT-252, Purolite CT-276) and four zeolites (H-BEA-25, H-FAU-30, H-FAU-6 and H-MOR-20) was assessed. Experimental results showed that Amberlyst 15 and H-FAU-30 were the best catalysts for isoamylene trimerization, with selectivities above 40% at 373 K. The most influencing physical properties of the catalysts on the selectivity toward dimers and trimers were acid capacity, acid strength, and specific surface area for resins, and microporous surface area for zeolites. Isoamylene trimerization extent was larger at higher temperature. The most probable mechanism of formation of these compounds involves the reaction between one molecule of dimer with one molecule of isoamylenes, although trimers could also be formed directly from three molecules of isoamylenes.
High repetition rate, high energy, actively Q-switched all-in-fiber laser (2010)

We report an actively Q-switched Ytterbium-doped all-in-fibre laser delivering 10ns pulses with high repetition rate (from 100kHz to 1MHz). The laser operation has been validated at three different wavelengths (1040, 1050 and 1064nm). The laser can deliver up to 20Watts average power with an high beam quality (M<sup>2</sup> = 1).
The Implementation of the 65nm Dual-Core 64b Merom Processor (2007)

Merom is a dual-core 64b processor implementing the Coretrade architecture. The 143mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> die has 291M transistors in a 65nm 8M process. The shared 4MB 16-way L2 cache uses PMOS power gating to minimize leakage. The processor operates in a wide core frequency range of 1 to 3GHz, a bus frequency range of 666 to 1333MHz and voltage range of 0.85 to 1.325V, while providing 40% better power performance.
The genetic basis of aminoglycoside ototoxicity: The search for susceptibility genes (1994)

The susceptibility to aminoglycoside ototoxicity appears to be genetically determined. Recently we identified a mutation in the small ribosomal RNA gene of the mitochondrial DNA that can cause deafness after aminoglycoside treatment in families with maternally-inherited susceptibility to the ototoxic effect of these antibiotics. The mutation produces a structural change in the 12S rRNA, which allows increased binding of aminoglycosides, mistranslation of mitochondrial proteins, decreased energy production, and cell death. Because only a minority of sporadic patients have mutations in the 12S rRNA gene, we anticipate the involvement of other genes in ototoxic deafness. We have developed a model system in the yeast Saccharomyces cerevisiae to functionally identify genes whose products interact with aminoglycosides. Besides its small genome size and well-developed genetic tools, a unique advantage of using this haploid organism is that recessive drug-responsive mutations will not be missed. An additional advantage is that yeast can be grown in either fermentative or respiratory media, allowing the functional categorization of mutants. Over 100 antibiotic-resistant mutants have now been isolated. The majority of these mutations (69%) are dominant and are being sorted by segregation tests. The 31% of mutations that are recessive have been sorted into two major complementation groups, indicatingmore » that two genes appear to be responsible for most of the recessive cases. Our strategy is to isolate the yeast genes that most commonly acquire mutations, clone the human homologs, and screen patients for susceptibility mutations.« less
Acquisition and Evolution of SXT-R391 Integrative Conjugative Elements in the Seventh-Pandemic Vibrio cholerae Lineage (2014)

SXT-R391 ICEs have been recognized as key vectors of antibiotic resistance in the seventh-pandemic lineage of V. cholerae, which remains a major cause of mortality and morbidity on a global scale. ICEs were acquired only recently in this clade and are acknowledged to be major contributors to horizontal gene transfer and the acquisition of new traits in bacterial species. We have reconstructed the temporal dynamics of SXT-R391 ICE acquisition and spread and have identified subsequent recombination events generating significant diversity in ICEs currently circulating among V. cholerae clinical strains. Our results showed that acquisition of SXT-R391 ICEs provided the V. cholerae seventh-pandemic lineage not only with a multidrug resistance phenotype but also with a powerful molecular tool for rapidly accessing the pan-genome of a large number of gammaproteobacteria.
Neutrophil infiltrations compared between types 1 and 2 autoimmune pancreatitis (2018)

【背景】自己免疫性膵炎（Autoimmune pancreatitis; AIP）はわが国から提唱された疾患概念である．2011年に国際コンセンサス診断基準が作成されIgG4の関与するものを1型自己免疫性膵炎，好中球病変が主体とするものを2型自己免疫性膵炎と分類することとなった．2型自己免疫性膵炎の組織像として，好中球が膵管内腔や上皮に集簇し，管腔の破壊や閉塞をきたすことが特徴的である．2型自己免疫性膵炎は好中球が重要な役割を果たしていると言われているが，好中球が遊走されるメカニズムや自然免疫の関与については解明されておらず，1型自己免疫性膵炎との免疫学的相違は全く不明である．そこで今回我々は好中球遊走に関わるケモカインなどの差異について検討した．
Neuronal-Hematopoietic Cell Fusion in Diabetic Neuropathy (2023)

Diabetic neuropathy is a major complication of diabetes mellitus that occurs during the early stages of the disease. Many pathogenic mechanisms are related and induced by hyperglycemia. However, even if these factors improve, diabetic neuropathy cannot go into remission and progresses slowly. Furthermore, diabetic neuropathy often progresses even with proper glycemic control. Recently, bone marrow-derived cells (BMDCs) were reported to be involved in the pathogenesis of diabetic neuropathy. BMDCs expressing proinsulin and TNFα migrate to the dorsal root ganglion and fuse with neurons, and this neuronal-hematopoietic cell fusion induces neuronal dysfunction and apoptosis. The CD106-positive lineage-sca1+c-kit+ (LSK) stem cell fraction in the bone marrow is strongly involved in cell fusion with neurons, leading to diabetic neuropathy. Surprisingly, when CD106-positive LSK stem cells obtained from diabetic mice were transplanted into nondiabetic mice, they fused with dorsal root ganglion neurons and induced neuropathy in non-hyperglycemic normal mice. The transplanted CD106-positive LSK fraction inherited the trait even after transplantation; this "progeny effect" may explain the irreversibility of diabetic neuropathy and is a significant finding for determining the target of radical treatments and provides new directions for developing therapeutic methods for diabetic neuropathy.
Detection of specific antibodies in gingival crevicular transudate by enzyme-linked immunosorbent assay for diagnosis of human immunodeficiency virus type 1 infection (1992)

The purpose of this open and multicenter trial was to determine the usefulness of antibody detection by enzyme-linked immunosorbent assay (ELISA) in gingival crevicular transudate (GCT), which was collected with an investigational device (Orasure; Epitope, Beaverton, Oreg.), for the diagnosis of human immunodeficiency virus type 1 (HIV-1) infection and to compare it with antibody detection in serum. A total of 1,880 individuals were tested, as follows: 354 HIV-1-infected individuals (111 asymptomatics individuals and 243 individuals with AIDS), 46 individuals with autoimmune diseases (AD), 296 individuals with dental diseases, 42 individuals with other chronic diseases, and 1,142 healthy individuals. Sera from 356 individuals and GCT from 354 individuals were positive for HIV-1 antibodies. There were two false-negative gingival samples, one from an HIV-1-positive asymptomatic individual and one from a patient with AIDS. HIV-1 antibodies were unexpectedly detected in both serum and GCT of two individuals, one with dental disease and one with pulmonary tuberculosis. None of the sera or GCTs from healthy subjects or patients with AD were positive. Compared with the serum assay, the sensitivity, specificity, and positive and negative predictive values of the GCT assay were 99.5, 100, 100, and 99.9%, respectively. Of 355 paired serum-GCT samples that were HIV-1 positive by ELISA and that were tested by Western blot (immunoblot), all were positive for HIV-1 by using the U.S. Public Health Service interpretation criteria, while among gingival samples, 301 were positive, 52 were indeterminate, and 2 were negative. Of 82 negative paired samples selected at random, 80 were negative by Western blotting of serum and GCT and 2 were indeterminate by Western blotting of serum and negative by Western blotting of GCT (a healthy blood donor and a patient with dermatopolymyositis). Testing for HIV-1 antibodies in GCT is a simple and reliable screening procedure in populations with high and low prevalences of infection because of the high sensitivity and specificity of the method, and it offers improved safety for hospital personnel.
Transcription of Ehrlichia chaffeensis Genes Is Accomplished by RNA Polymerase Holoenzyme Containing either Sigma 32 or Sigma 70 (2013)

Bacterial gene transcription is initiated by RNA polymerase containing a sigma factor. To understand gene regulation in Ehrlichia chaffeensis, an important tick-transmitted rickettsiae responsible for human monocytic ehrlichiosis, we initiated studies evaluating the transcriptional machinery of several genes of this organism. We mapped the transcription start sites of 10 genes and evaluated promoters of five genes (groE, dnaK, hup, p28-Omp14 and p28-Omp19 genes). We report here that the RNA polymerase binding elements of E. chaffeensis gene promoters are highly homologous for its only two transcription regulators, sigma 32 and sigma 70, and that gene expression is accomplished by either of the transcription regulators. RNA analysis revealed that although transcripts for both sigma 32 and sigma 70 are upregulated during the early replicative stage, their expression patterns remained similar for the entire replication cycle. We further present evidence demonstrating that the organism's -35 motifs are essential to transcription initiations. The data suggest that E. chaffeensis gene regulation has evolved to support the organism's growth, possibly to facilitate its intraphagosomal growth. Considering the limited availability of genetic tools, this study offers a novel alternative in defining gene regulation in E. chaffeensis and other related intracellular pathogens.
Gut Microbiota Characteristics in Ulcerative Colitis and other Gastrointestinal Diseases (2021)

Gut microbiota refers to the collective assembly of micro-organisms in a given host ‎environment. It includes, in addition to the well characterized bacterial communities, different ‎life forms of viruses and fungi. Knowledge of these life forms and their functions is currently ‎expanding paralleling with advances in microbiological next generation methodologies which ‎enabled to recognize even unculturable organisms. In the normal health state, these life forms ‎are in a symbiotic relationship with the host where they can provide some biological functions ‎not executed by the host. Vitamin K biosynthesis is a well-known example of this. On the other ‎hand, in disease state, these microbiota communities become disturbed where beneficial ‎members are lost in favour of some pathological forms which may increase the pathological ‎process. In this regard, the gastrointestinal tract is the best model to study these interactions ‎given the direct contact of these microbiota communities with the host mucosal surfaces. In this ‎review, we would revise some of these microbiota changes in different gastrointestinal diseases. ‎ Gut microbiota changes in different gastrointestinal diseases provides an insight into the ‎possible role of gut microbiota in the development of different GI diseases. However, the main ‎question is “are these changes a cause or a result of a disease process”. Moreover, trying to alter ‎gut microbiota with a therapeutic intent is the best way to prove such a causal relationship ‎where improvement of the disease process, after gut microbiota modulation, is a strong ‎indicator of gut microbiota role in the pathogenesis of this disease‎‎‎.
Simultaneous inversion of pre-stack seismic data (2005)

We present a new approach to the simultaneous pre-stack inversion of PP and, optionally, PS angle gathers for the estimation of P-impedance, S-impedance and density. Our algorithm is based on three assumptions. The first is that the linearized approximation for reflectivity holds. The second is that PP and PS reflectivity as a function of angle can be given by the Aki-Richards equations (Aki and Richards, 2002).