gebhart/patrepeval huggingface dataset:
Long Noncoding RNA and Protein Interactions: From Experimental Results to Computational Models Based on Network Methods (2019)

Non-coding RNAs with a length of more than 200 nucleotides are long non-coding RNAs (lncRNAs), which have gained tremendous attention in recent decades. Many studies have confirmed that lncRNAs have important influence in post-transcriptional gene regulation; for example, lncRNAs affect the stability and translation of splicing factor proteins. The mutations and malfunctions of lncRNAs are closely related to human disorders. As lncRNAs interact with a variety of proteins, predicting the interaction between lncRNAs and proteins is a significant way to depth exploration functions and enrich annotations of lncRNAs. Experimental approaches for lncRNA⁻protein interactions are expensive and time-consuming. Computational approaches to predict lncRNA⁻protein interactions can be grouped into two broad categories. The first category is based on sequence, structural information and physicochemical property. The second category is based on network method through fusing heterogeneous data to construct lncRNA related heterogeneous network. The network-based methods can capture the implicit feature information in the topological structure of related biological heterogeneous networks containing lncRNAs, which is often ignored by sequence-based methods. In this paper, we summarize and discuss the materials, interaction score calculation algorithms, advantages and disadvantages of state-of-the-art algorithms of lncRNA⁻protein interaction prediction based on network methods to assist researchers in selecting a suitable method for acquiring more dependable results. All the related different network data are also collected and processed in convenience of users, and are available at https://github.com/HAN-Siyu/APINet/.
An Erythropoietin Autocrine/Paracrine Axis Modulates the Growth and Survival of Human Prostate Cancer Cells (2009)

Abstract Erythropoietin receptors have been identified on a variety of cancer-derived cell lines and primary cancer cells, including those of prostate cancer. The functional status of these extrahematopoietic erythropoietin receptors remains a matter of some dispute. The publication of several important clinical trials suggesting a direct effect of erythropoietin on the growth and survival of primary tumors adds further importance to the question of whether erythropoietin receptors on cancer cells are functional. We have reported previously that human prostate cancer cell lines and primary prostate cancer cells express functional erythropoietin receptors that respond to exogenous erythropoietin by increased cell proliferation and STAT5 phosphorylation. We now show that prostate cancer cell lines express both the EPO gene and the biologically active erythropoietin. The coexpression of functional receptor and biologically active ligand in the cells has led us to hypothesize an autocrine/paracrine mechanism, driven by endogenous erythropoietin, which may modulate the growth and progression of prostate cancer. To test our hypothesis, we have knocked down, independently, erythropoietin receptor and erythropoietin on prostate cancer cells by transfection with short hairpin RNAs. Erythropoietin receptor knockdown cells grow significantly more slowly than their erythropoietin receptor-bearing counterparts in monolayer culture, produce fewer, smaller colonies in soft agar, and do not exhibit erythropoietin-induced signaling. Erythropoietin knockdown cells exhibit dramatically slower rates of growth, which could be restored by transfecting the cells with a murine erythropoietin gene. Taken together, our data suggest that the coordinated regulation of a functional erythropoietin/erythropoietin receptor axis in prostate cancer cells may be integral to the growth and progression of prostate cancer. (Mol Cancer Res 2009;7(7):OF1–8) (Mol Cancer Res 2009;7(7):1150–7)
Probing the impact of chromatin conformation on genome editing tools (2016)

Transcription activator-like effector nucleases (TALENs) and RNA-guided nucleases derived from clustered, regularly interspaced, short palindromic repeats (CRISPR)-Cas9 systems have become ubiquitous genome editing tools. Despite this, the impact that distinct high-order chromatin conformations have on these sequence-specific designer nucleases is, presently, ill-defined. The same applies to the relative performance of TALENs and CRISPR/Cas9 nucleases at isogenic target sequences subjected to different epigenetic modifications. Here, to address these gaps in our knowledge, we have implemented quantitative cellular systems based on genetic reporters in which the euchromatic and heterochromatic statuses of designer nuclease target sites are stringently controlled by small-molecule drug availability. By using these systems, we demonstrate that TALENs and CRISPR/Cas9 nucleases are both significantly affected by the high-order epigenetic context of their target sequences. In addition, this outcome could also be ascertained for S. pyogenes CRISPR/Cas9 complexes harbouring Cas9 variants whose DNA cleaving specificities are superior to that of the wild-type Cas9 protein. Thus, the herein investigated cellular models will serve as valuable functional readouts for screening and assessing the role of chromatin on designer nucleases based on different platforms or with different architectures or compositions.
Linear mitochondrial DNAs of yeasts: closed-loop structure of the termini and possible linear-circular conversion mechanisms. (1993)

The terminal structure of the linear mitochondrial DNA (mtDNA) from three yeast species has been examined. By enzymatic digestion, alkali denaturation, and sequencing of cloned termini, it was shown that in Pichia pijperi and P. jadinii, both termini of the linear mtDNA were made of a single-stranded loop covalently joining the two strands, as in the case of vaccinia virus DNA. The left and right loop sequences were in either of two orientations, suggesting the existence of a flip-flop inversion mechanism. Contiguous to the terminal loops, inverted terminal repeats were present. The mtDNA from Williopsis mrakii seems to have an analogous structure, although terminal loops could not be directly demonstrated. Electron microscopy revealed the presence, among linear molecules, of a small number of circular DNAs, mostly of monomer length. Linear and circular models of replication are considered, and possible conversion mechanisms between linear and circular forms are discussed. A flip-flop inversion mechanism between the inverted repeat sequences within a circular intermediate may be involved in the generation of the linear form of mtDNA.
Photoacoustic cell for reflection and transition measurements (1981)

A photoacoustic cell is described in which the sample can constitute one of the cell walls. The cell, which can be used alone or in a combined unit with a reference cell, allows nondestructive investigation of a variety of samples either in a normal reflection mode (pressure wave generated at illuminated surface) or in a thermal or elastic transmission mode (pressure wave generated at opposite surface). Simultaneous sample illumination from both sides is possible, too. The cell sensitivity, as measured for an electrically-generated thermal wave, is about 10−2 V/W at 34 Hz. Use of the cell is illustrated by the dependence of the photoacoustic signal, generated by transmitted thermal and/or elastic waves, on the thickness of copper plates, and by the photoacoustic spectrum resulting from illumination through Begonia leaves.
Nonlinear optical polymer films (1988)

Orientationally ordered polymer films combine the attractive properties of organic nonlinear optical materials (large molecular susceptibilities, tailoring properties by molecular engineering) with attractive properties of glassy polymers (high optical quality, low dielectric constant and dielectric loss, processability, fabrication flexibility). Using the thermodynamic model, improvements in the pertinent parameters are realized. Such improvements, along with the linear optical properties and fabrication flexibility inherent to glassy polymers, makes this material class a promising one for use in integrated optics.
Novel Insights into the Role of Interleukin-27 and Interleukin-23 in Human Malignant and Normal Plasma Cells (2011)

Multiple myeloma is a monoclonal postgerminal center tumor that has phenotypic features of plasmablasts and/or plasma cells and usually localizes at multiple sites in the bone marrow. The pathogenesis of multiple myeloma is complex and dependent on the interactions between tumor cells and their microenvironment. Different cytokines, chemokines, and proangiogenic factors released in the tumor microenvironment are known to promote multiple myeloma cell growth. Here, we report recent advances on the role of 2 strictly related immunomodulatory cytokines, interleukin-27 (IL-27) and IL-23, in human normal and neoplastic plasma cells, highlighting their ability to (i) act directly against multiple myeloma cells, (ii) influence the multiple myeloma microenvironment by targeting osteoclast and osteoblast cells, and (iii) modulate normal plasma cell function. Finally, the therapeutic implication of these studies is discussed.
<i>Mycobacterium</i>-Inducible<i>Nramp</i>in Striped Bass (<i>Morone saxatilis</i>) (2004)

In mammals, the natural resistance-associated macrophage protein 1 gene, Nramp1, plays a major role in resistance to mycobacterial infections. Chesapeake Bay striped bass (Morone saxatilis) is currently experiencing an epizootic of mycobacteriosis that threatens the health of this ecologically and economically important species. In the present study, we characterized an Nramp gene in this species and obtained evidence that there is induction following Mycobacterium exposure. The striped bass Nramp gene (MsNramp) and a 554-amino-acid sequence contain all the signal features of the Nramp family, including a topology of 12 transmembrane domains (TM), the transport protein-specific binding-protein-dependent transport system inner membrane component signature, three N-linked glycosylation sites between TM 7 and TM 8, sites of casein kinase and protein kinase C phosphorylation in the amino and carboxy termini, and a tyrosine kinase phosphorylation site between TM 6 and TM 7. Phylogenetic analysis most closely grouped MsNramp with other teleost Nramp genes and revealed high sequence similarity with mammalian Nramp2. MsNramp expression was present in all tissues assayed by reverse transcription-PCR. Within 1 day of injection of Mycobacterium marinum, MsNramp expression was highly induced (17-fold higher) in peritoneal exudate (PE) cells compared to the expression in controls. The levels of MsNramp were three- and sixfold higher on days 3 and 15, respectively. Injection of Mycobacterium shottsii resulted in two-, five-, and threefold increases in gene expression in PE cells over the time course. This report is the first report of induction of an Nramp gene by mycobacteria in a poikilothermic vertebrate.
2018광주비엔날레 ‘상상된 경계들’ 연구 - 경계에 대한 담론과 경계 형상화 작품 중심으로- (2018)

1995년 창설되어 24년 간 현대미술의 발신지로서 역할을 했던 광주비엔날레가 올해로 제 12회를 맞는다. 2018광주비엔날레는 9월 7일부터 11월 11일까지 66일 간 광주 비엔날레 전시관과 국립아시아문화전당 등지에서 개최될 예정이다.
2018광주비엔날레 ‘상상된 경계들(Imagined Borders)’은 46개국 작가 163명의 참여로 인류 역사와 사회적·정치적 경계에 있는 동시대 어젠다인 현재까지 잔존하는 전쟁과 분단, 냉전, 독재 등 근대의 잔상과 21세기 포스트인터넷 시대에서의 새로운 격차와 소외를 고찰해보는데 본 소논문에서는 경계에 대한 다양한 관점 중 과거와 현재, 타자, 실재와 가상, 국가와 이주의 문제를 담고 있는 작품을 분석해보았다.
1995년 광주비엔날레가 창설되어 선보인 제1회 광주비엔날레 ‘경계를 넘어’가 세계화로 인한 이동성과 하나의 지구촌 공동체의 변화상을 다뤘다면, 2018광주비엔날레 ‘상상된 경계들’은 지난 20세기 근대적 관점을 회고하고 현재까지 잔존하는 근대의 잔상과 새로운 격차와 소외 등의 경계를 고찰하고 있다.
근대 이후 글로벌화되고 국제적인 시대에 살고 있다 하더라도 인간과 인종, 국가가 체제를 유지하기 위한 수단으로 구축해놓은 일종의 ‘상상된 경계들’은 더욱 굳건해지고 다양해지고 확대 재생산됨을 알 수 있다.
즉 2018광주비엔날레는 근대 이후 글로벌 시대의 새로운 구별짓기와 편가르기 등이 성행하고 있는 동시대 현상의 반영이라 할 수 있다. 현대미술 미술제도로서 시대의 패러다임과 함께 국제 미술 및 현안의 흐름과 보폭을 측정하게 하는 지진계 역할을 하고 있는 비엔날레로서 경계에 대한 시의적 담론을 통해 새로운 공동체가 형성되길 기대해본다. 2018광주비엔날레 ‘상상된 경계들’을 통해 평등의 가치와 문화의 다양성을 극대화하고 실현하면서 이를 뛰어넘은 미래적 가치와 상상력을 제안하기를 바란다.
Power Saving Efficiency of a novel Packet Aggregation Scheme for high-throughput WLAN stations at different data rates (2005)

Multiple MCS and receiver aggregation (MMRA) is a method to aggregate several MAC protocol data units (MPDUs) that are intended for different receivers and can be transmitted at different modulation and coding schemes (MCS) in the next generation of WLAN, the IEEE 802.11n protocol. Traditional aggregation schemes only link MPDUs between the same source and destination device pair together. The main purpose of aggregation is to reduce the number of access attempts to the medium and thereby significantly increase the protocol efficiency and data throughput. Analytical computations show that MMRA performs better not only in time efficiency compared to other single-rate aggregation schemes, where MPDUs aggregates belonging to different receivers are limited to the lowest MCS, but above all MMRA outperforms single-rate aggregation schemes in terms of power efficiency. MMRA provides a power saving frame format structure, which will allow receiving stations to reduce power consumption and save battery life, crucial for small handled devices.
Pregnancy associated glycoprotein‐1, ‐6, ‐7, and ‐17 are major products of bovine binucleate trophoblast giant cells at midpregnancy (2005)

Pregnancy associated glycoproteins (PAGs) are extensively glycosylated secretory proteins of ruminant trophoblast cells. In cattle placenta several PAG cDNAs are expressed, but the variety of correspondent proteins and their degree of glycosylation are not well characterized. Thus, we purified PAGs by using a protocol which included a lectin (Vicia villosa agglutinin) affinity chromatography. Due to their specific glycosylation pattern, PAGs derived from binucleate trophoblast giant cells were highly enriched by this protocol. PAGs were purified from cotyledons of 2 day 100 placentas and from a single placenta at day 155 and 180. In all samples three major bands (75; 66; 56 kDa) were detected by one-dimensional SDS-PAGE. Mass-spectrometric analysis identified the 75 kDa band as a mixture of PAG-7 and PAG-6, the 66 kDa band as PAG-1 and the 56 kDa band as PAG-17. N-terminal sequencing of the day 100 sample confirmed the mass spectrometric identifications. Enzymatic release of N-glycans with peptide-N-glycanase-F from PAGs reduced the molecular weight to approximately 37 kDa which corresponds to the theoretical molecular mass of PAGs. Limited peptide-N-glycanase-F treatment revealed that all four N-glycosylation sites are quantitatively occupied in PAG-1. Compared to PAG-1 the number of potential N-glycosylation sites is lower in PAG-17 (three sites) and higher in PAG-6 and -7 (five and six sites, respectively). This suggests that the number of attached N-glycans is the main determinant of molecular mass of bovine PAGs. The degree of glycosylation may be a major factor regulating the plasma half life of PAGs.
Conversion of Sugars to 1,2-Propanediol by Thermoanaerobacterium thermosaccharolyticum HG-8 (2001)

The purpose of this study was to explore a fermentation route for the production of 1,2-propanediol (1,2-PD) from renewable sugars: lactose found in cheese whey, and D-glucose, D-galactose, L-arabinose, and D-xylose found in corn and wood byproducts. Thermoanaerobacterium thermosaccharolyticum, a naturally occurring organism, was found to ferment a wider range of sugars to 1,2-PD than previously reported. The specific sugar had a significant effect on the selectivity for 1,2-PD vs other fermentation products such as ethanol, D- and L-lactate, and acetate. T. thermosaccharolyticum potentially provides an environmentally friendly route to a major commodity chemical now made from petrochemicals.
RGB-‘D’ Saliency Detection With Pseudo Depth (2018)

Recent studies have shown the effectiveness of using depth information in salient object detection. However, the most commonly seen images so far are still RGB images that do not contain the depth data. Meanwhile, the human brain can extract the geometric model of a scene from an RGB-only image and hence provides a 3D perception of the scene. Inspired by this observation, we propose a new concept named RGB-'D' saliency detection, which derives pseudo depth from the RGB images and then performs 3D saliency detection. The pseudo depth can be utilized as image features, prior knowledge, an additional image channel, or independent depth-induced models to boost the performance of traditional RGB saliency models. As an illustration, we develop a new salient object detection algorithm that uses the pseudo depth to derive a depth-driven background prior and a depth contrast feature. Extensive experiments on several standard databases validate the promising performance of the proposed algorithm. In addition, we also adapt two supervised RGB saliency models to our RGB-'D' saliency framework for performance enhancement. The results further demonstrate the generalization ability of the proposed RGB-'D' saliency framework.
Study on the Preparation and Stabilization of Pyrene Labeled Polymer Particles in Nonpolar Media (2003)

Abstract Two routes have been studied for the preparation of pyrene labeled polymer particles in non‐polar medium. In route I, polystyrene‐pyrene particles were first prepared by emulsion polymerization. Incorporation of pyrene in the particles was proved by fluorescence measurement. An attempt was then made to transfer the particles from the aqueous continuous phase into isopar. In route II, the direct dispersion polymerization in isopar, polybutadiene‐b‐polyisoprene was successfully used as stabilizer. In the case of polystyrene particles the average diameter was above 1 µm whereas in case of poly(methyl methacrylate) the average diameter was only about 0.2 µm. Based on this result a dispersion polymerization of methyl methacrylate was then carried out in presence of pyrene under the same conditions. Incorporation of pyrene was found to be pretty high as measured by fluorescence spectroscopy and the particles were also colloidally stable. Keywords: Polymer dispersions in nonpolar mediaReactive stabilizerPyrene labeled latex particles Acknowledgments One of the authors (H. A.) acknowledges the financial support from AvH Foundation, Germany. We are also grateful to Mrs. S. Pitschke, Mrs. M. Gräwert, and Mrs. U. Lubahn for analytical and preparative assistance.
A ROM-based high-accuracy line frequency and line frequency deviation meter (1990)

The meter is based entirely on basic digital circuits and does not include a microprocessor. A large-capacity ROM is used to convert the data, which are proportional to the line period, into line frequency and line frequency deviation. The meter provides 0.001-Hz resolution and an updating speed of 4 times per second. A computer algorithm for developing the ROM memory map is also presented. A prototype of the meter has been constructed and found to work well.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Degradation and Stabilization of Poly(propylene carbonate) (2002)

Low-molecular-weight poly(propylene carbonate) resins, useful for polyurethane preparation, surfactant production and many other purposes, were obtained by copolymerization of CO2 and propylene oxide. This study describes an investigation into their stability against thermal degradation, offers details of the random chain-breaking and “unzipping” processes, and suggests possible methods to avoid degradation.
Sensitivity of next-generation sequencing assays detecting oncogenic fusions in plasma cell-free DNA (2019)

Focusing on complex, clinically actionable mutations using tumor as a reference standard allows for evaluation of technical differences in plasma NGS assays that may impact clinical performance. Noting the heterogeneity of fusion sequences observed in NSCLC, we hypothesize that differences in hybrid capture techniques and bioinformatic calling may be sources of variations in sensitivity among these assays.
APEC Meeting Provides Wider Platform for Chinese Enterprises (2014)

The attention APEC paid to small and medium enterprises In 1998,the APEC Kuala Lumpur Summit in Malaysia has agreed to build a foundation of sustainable development by strengthening the contact with business community,perfecting the financial system and establishing a social insurance net,etc.which is also mentioned in a programmatic document called Agenda of APEC Industrial Cooperation in the 21st Century.Till today,APEC has been keeping an eye
A Long-term Dose-Response Study of Mitomycin in Glaucoma Filtration Surgery (1997)

A possible dose-response relationship seemed to exist between the concentration of and duration of exposure to mitomycin. Length of exposure seems to be more important than concentration. The benefits of additional decreases in IOP must be weighed against the potential for increases in the risk of complications.
Fault-coverage analysis techniques of crosstalk in chip interconnects (2003)

This paper addresses the problem of evaluating the effectiveness of test sets to detect crosstalk defects in system-level interconnects and buses of deep submicron (DSM) chips. The fast and accurate estimation technique will enable: 1) evaluation of different existing tests, like functional, scan, logic built-in self-test (BIST), and delay tests, for effective testing of crosstalk defects in core-to-core interconnects and 2) development of crosstalk tests if the existing tests are not sufficient, thereby minimizing the cost of interconnect testing. Based on a covering relationship we distinguish between transition tests in detecting crosstalk defects and develop an abstract crosstalk fault model for chip interconnects. With this fault model and the covering relationship, we develop a fast and efficient method to estimate the fault coverage of any general test set. We also develop a simulation-based technique to calculate the probability of occurrence of the defects corresponding to each fault, which enables the fault-coverage analysis technique to produce accurate estimates of the actual crosstalk defect coverage of a given test set. The crosstalk test and fault properties, as well as the accuracy of the proposed crosstalk coverage analysis techniques, have been validated through extensive simulation experiments. The experiments also demonstrate that the proposed crosstalk techniques are orders of magnitude faster than the alternative method of SPICE-level simulation. Finally, we demonstrate the practical applicability of the proposed fault-coverage analysis technique by using it to evaluate the crosstalk fault coverage of logic BIST tests for the system-level interconnects and buses in a digital signal processor core.