gebhart/patrepeval huggingface dataset:
Immunoaffinity Purification and Functional Characterization of Human Transcription Factor IIH and RNA Polymerase II from Clonal Cell Lines That Conditionally Express Epitope-tagged Subunits of the Multiprotein Complexes (1998)

Purification of multiprotein complexes such as transcription factor (TF) IIH and RNA polymerase II (pol II) has been a tedious task by conventional chromatography. To facilitate the purification, we have developed an effective scheme that allows human TFIIH and pol II to be isolated from HeLa-derived cell lines that conditionally express the FLAG-tagged p62 subunit of human TFIIH and the RPB9 subunit of human pol II, respectively. An approximate 2000-fold enrichment of FLAG-tagged TFIIH and a 1000-fold enhancement of total pol II are achieved by a one-step immunoaffinity purification. The purified complexes are functional in mediating basal and activated transcription, regardless of whether TATA-binding protein or TFIID is used as the TATA-binding factor. Interestingly, repression of basal transcription by the positive cofactor PC4 is alleviated by increasing amounts of TFIID, TFIIH, and pol II holoenzyme, suggesting that phosphorylation of PC4 by these proteins may cause a conformational change in the structure of PC4 that allows for preinitiation complex formation and initiation of transcription. Furthermore, pol II complexes with different phosphorylation states on the carboxyl-terminal domain of the largest subunit are selectively purified from the inducible pol II cell line, making it possible to dissect the role of carboxyl-terminal domain phosphorylation in the transcription process in a highly defined in vitro transcription system.
An Intervention Study on Mental Computation for Second Graders in Taiwan (2013)

ABSTRACT The authors compared the mental computation performance and mental strategies used by an experimental Grade 2 class and a control Grade 2 class before and after instructional intervention. Results indicate that students in the experimental group had better performance on mental computation. The use of mental strategies (counting, separation, aggregation, and holistic) and atypical strategies in the control group decreased or even disappeared after the intervention. However, students in the experimental group could apply higher level mental strategies, such as aggregation, holistic, short-jump, and atypical strategies after the intervention. These findings indicate that the teaching of the vertical addition/subtraction algorithm does not promote the development of mental computation.
Rapid monitoring of transesterification and assessing biodiesel fuel quality by near‐infrared spectroscopy using a fiber‐optic probe (1999)

Abstract Vegetable oil esters, particularly methyl esters, are being explored and used as alternative diesel fuel (biodiesel). The transesterification reaction which yields the methyl esters can be monitored for completion by near‐infrared (NIR) spectroscopy using a fiber‐optic probe. Although the NIR method is less sensitive than gas chromatography (GC) for quantifying minor components, by correlation with existing GC or other analytical data, biodiesel fuel quality can be assessed through the NIR method. The NIR method is easier and faster to use than GC.
Block assembly for global registration of building scans (2016)

We propose a framework for global registration of building scans. The first contribution of our work is to detect and use portals (e.g., doors and windows) to improve the local registration between two scans. Our second contribution is an optimization based on a linear integer programming formulation. We abstract each scan as a block and model the blocks registration as an optimization problem that aims at maximizing the overall matching score of the entire scene. We propose an efficient solution to this optimization problem by iteratively detecting and adding local constraints. We demonstrate the effectiveness of the proposed method on buildings of various styles and that our approach is superior to the current state of the art.
Micropore Distribution Change of Heated Powder Compacts Using Binary Alumina Powder Mixtures (1990)

The sintering behavior of bimodal alumina powders was investigated with reference to the change of open pore size distributions. Avarage particle sizes of fine and coarse alumina powders were 0.52μm (f particle) and 6.3μm (c particle). The coarse powder was spherical and polycrystalline. The open pore size distributions in green compacts were narrow for specimens with mixing ratios c:f=4:6-1:9, but were broad for c:f=9:1-5:5. When sintered at 1400°-1600°C, the open pore size increased with c:f=9:1-4:6, remained unchanged with c:f=3:7-1:9, and decreased with c:f=0:10. It is considered that the growth of pores was caused by the difference of sintering rates between tight and loose-packed parts, and also between c and f particles.
The Proteasome Distinguishes between Heterotypic and Homotypic Lysine-11-Linked Polyubiquitin Chains (2015)

Proteasome-mediated degradation occurs with proteins principally modified with lysine-48 polyubiquitin chains. Whether the proteasome also can bind atypical ubiquitin chains, including those linked by lysine-11, has not been well established. This is critically important, as lysine-11 polyubiquitination has been implicated in both proteasome-mediated degradation and non-degradative outcomes. Here we demonstrate that pure homotypic lysine-11-linked chains do not bind strongly to the mammalian proteasome. By contrast, heterotypic polyubiquitin chains, containing lysine-11 and lysine-48 linkages, not only bind to the proteasome but also stimulate the proteasomal degradation of the cell-cycle regulator cyclin B1. Thus, while heterotypic lysine-11-linked chains facilitate proteasomal degradation, homotypic lysine-11 linkages adopt conformations that prevent association with the proteasome. Our data demonstrate the capacity of the proteasome to bind ubiquitin chains of distinct topology, with implications for the recognition and diverse biological functions of mixed ubiquitin chains.
Pseudorejection and True Rejection after Kidney Transplantation: Classification and Clinical Significance (2012)

'Pseudorejection' has been described only once, for the first time in 1976 in the USA, and there have been no other reports since then. Multiple factors, mainly hyperglycemia, may induce a pseudorejection, presenting with an elevation of serum creatinine level and leading the clinician to an erroneous diagnosis of true rejection initially, resulting in inappropriate management.
Scanning Eye Movements in Homonymous Hemianopia Documented by Scanning Laser Ophthalmoscope Retinal Perimetry (2003)

Sparing or partial recovery of visual fields in hemianopic patients is frequently difficult to document. This is because when testing large field losses, the standard automated or manual visual field testing systems have limited fixation controls. Measured visual field recovery in these cases may not be real but instead may be due to an artifact such as scanning eye movement. This article illustrates a way to separate the actual visual field sparing from scanning eye movement artifact by using perimetry testing with the scanning laser ophthalmoscope (SLO). During the SLO perimetry, the examiner has a direct and magnified view of the retinal fixation locus. This direct view allows for the added ability to monitor the fixation stability during target presentation. When eye movements larger than 1 degrees are noted, the examiner can repeat the trial. During static perimetry, our SLO records the retinal position of the fixation target at the end of the stimulus presentation and corrects scanning eye movements that occur during stimulus presentation. These special features enable us to identify when the apparent sparing of the visual field is due to the artifact of scanning. To demonstrate this, we selected the records of four hemianopic patients whose fields were examined by both standard perimetry and the SLO. We then compared the clinical visual fields with the SLO perimetry fields. One of the patients had a complete homonymous hemianopia on both the clinical perimetry and the SLO perimetry. A second patient was found by the SLO to have unstable fixation during testing. The SLO perimetry revealed that the apparent spared fields seen in standard perimetry were the result of eye scanning and not an actual enlargement of the visual field. Two other patients were confirmed by the SLO findings to have valid partial recovery of the visual field, one with and one without scanning eye movements. The advantages and limitations of SLO perimetry in analyzing hemianopic field sparing are discussed.
Probabilistic and Holistic Prediction of Vehicle States Using Sensor Fusion for Application to Integrated Vehicle Safety Systems (2014)

This paper presents a probabilistic and holistic prediction algorithm for vehicle states using multisensor fushion. Three concerns are mainly considered in this paper, i.e, reliable and reasonable information fusion, extension of predicted states, and real-time evaluation of prediction uncertainties. The main idea of this paper is that a state-prediction problem can be solved as a multistage optimal estimation problem based on the current vehicle motion, a road geometry description in the current body-fixed frame, a path-following behavior model, and the error covariance of each. The prediction algorithm consists of two sequential parts. The first part is estimation, which contains a vehicle filter that estimates the current vehicle states, and a road geometry filter, which approximates the road geometry. The second part is prediction, which consists of a path-following model that generates the future desired yaw rate, which acts as a virtual measurement, and a vehicle predictor, which predicts the future vehicle states by a maximum-likelihood filtering method. The prediction performance of the proposed method has been investigated via vehicle tests. Moreover, its applicability to integrated vehicle safety system (IVSS) has been validated via computer simulation studies. It is shown that the state-prediction performance can be significantly enhanced by the proposed prediction algorithm compared with conventional methods. The enhancement of the prediction performance allows for the improvement of driver assistance functions of an IVSS by providing accurate predictions about the future driving environment.
Genetic polymorphisms of p21 are associated with risk of squamous cell carcinoma of the head and neck (2005)

The p21 (Waf1/Cip1/CDKN1A) protein regulates the transition from the G1 to the S phase and has an important role in modulating cell-cycle control, apoptosis and cell growth. Two polymorphisms of the p21 gene at codon 31 (p21 C98A, dbSNP rs1801270) and at the 3' untranslated region (p21 T70C, dbSNP rs1059234) may have an effect on the protein function and may thus play a role in the development of cancer. We hypothesized that these two p21 polymorphisms are associated with the risk of squamous cell carcinoma of the head and neck (SCCHN). We tested this hypothesis in a hospital-based case-control study of 712 patients newly diagnosed with SCCHN and 1222 cancer-free controls who were frequency-matched by age, sex and ethnicity. All subjects were non-Hispanic whites. Our results showed that the variant alleles and genotypes were more common among cases than among controls (P < 0.001 and P = 0.013 for p21C70T, and P < 0.001 and P = 0.035 for p21C98A, respectively). Compared with the p21 70CC genotype, there was a significantly greater risk of SCCHN associated with the variant p21 70TC [odds ratio (OR) = 1.47, 95% confidence interval (CI) = 1.12-1.93] and combined p21 70TC/TT (OR = 1.49, 95% CI = 1.14-1.95) genotypes. Similarly, compared with the p21 98CC genotype, there was also a significantly greater SCCHN risk associated with the variant p21 98AC (OR = 1.32, 95% CI = 1.00-1.73) and combined p21 98AC/AA (OR = 1.37, 95% CI = 1.05-1.79) genotypes. When these two polymorphisms were evaluated together by the number of risk alleles, there was a significant increase in SCCHN risk that was dependent on the number of risk alleles (P(trend) = 0.001). Our results suggest that the presence of these two p21 polymorphisms may be a marker of genetic susceptibility to SCCHN.
Synthesis of oxazolo[4,5‐<i>c</i>]quinolones by thermolytic degradation of 4‐azido‐2(1<i>H</i>)‐quinolones (1994)

Abstract 4‐Azido‐2(1 H )‐quinolones 1 are thermolyzed in the presence of carboxylic acids and polyphosphoric acid to yield oxazolo[4,5‐ c ]quinolones 3. Formation of other possible isomeric ring closure products such as oxazolo[5,4‐ c ]quinolones 2 or isoxazolo[4,3‐ c ]quinolones 4 could be excluded by independent syntheses.
A large-scale CRISPR screen and identification of essential genes in cellular senescence bypass (2019)

Cellular senescence is an important mechanism of autonomous tumor suppression, while its consequence such as the senescence-associated secretory phenotype (SASP) may drive tumorigenesis and age-related diseases. Therefore, controlling the cell fate optimally when encountering senescence stress is helpful for anti-cancer or anti-aging treatments. To identify genes essential for senescence establishment or maintenance, we carried out a CRISPR-based screen with a deliberately designed single-guide RNA (sgRNA) library. The library comprised of about 12,000 kinds of sgRNAs targeting 1378 senescence-associated genes selected by integrating the information of literature mining, protein-protein interaction network, and differential gene expression. We successfully detected a dozen gene deficiencies potentially causing senescence bypass, and their phenotypes were further validated with a high true positive rate. RNA-seq analysis showed distinct transcriptome patterns of these bypass cells. Interestingly, in the bypass cells, the expression of SASP genes was maintained or elevated with CHEK2, HAS1, or MDK deficiency; but neutralized with MTOR, CRISPLD2, or MORF4L1 deficiency. Pathways of some age-related neurodegenerative disorders were also downregulated with MTOR, CRISPLD2, or MORF4L1 deficiency. The results demonstrated that disturbing these genes could lead to distinct cell fates as a consequence of senescence bypass, suggesting that they may play essential roles in cellular senescence.
Reaction Mechanism and Kinetics of the Traceless Staudinger Ligation (2006)

The traceless Staudinger ligation enables the formation of an amide bond between a phosphinothioester (or phosphinoester) and an azide without the incorporation of residual atoms. Here, the coupling of peptides by this reaction was characterized in detail. Experiments with [(18)O]H(2)O indicated that the reaction mediated by (diphenylphosphino)methanethiol proceeded by S-->N acyl transfer of the iminophosphorane intermediate to form an amidophosphonium salt, rather than by an aza-Wittig reaction and subsequent hydrolysis of the resulting thioimidate. A continuous (13)C NMR-based assay revealed that the rate-determining step in the Staudinger ligation of glycyl residues mediated by (diphenylphosphino)methanethiol was the formation of the initial phosphazide intermediate. Less efficacious coupling reagents and reaction conditions led to the accumulation of an amine byproduct (which resulted from a Staudinger reduction) or phosphonamide byproduct (which resulted from an aza-Wittig reaction). The Staudinger ligation mediated by (diphenylphosphino)methanethiol proceeded with a second-order rate constant (7.7 x 10(-3) M(-1) s(-1)) and yield (95%) that was unchanged by the addition of exogenous nucleophiles. Ligations mediated by phosphinoalcohols had lower rate constants or less chemoselectivity. Accordingly, (diphenylphosphino)methanethiol was judged to be the most efficacious known reagent for effecting the traceless Staudinger ligation.
Autolytic enzyme-deficient mutants of Bacillus subtilis 168 (1976)

Mutants of Bacillus subtilis strain 168 have been isolated that are at least 90 to 95% deficient in the autolytic enzymes N-acetylmuramyl-L-alanine amidase and endo-beta-N-acetylglucosaminidase. These mutants grow at normal rates as very long chains of unseparated cells. The length of the chains is directly related to the growth rates. They are nonmotile and have no flagella, but otherwise appear to have normal cell morphology. Their walls are fully sysceptible to enzymes formed by the wild type and have the same chemical composition as the latter. Cell wall preparations from the mutants lyse at about 10% of the rate of those from the isogenic wild type, with the correspondingly small liberation of both the amino groups of alanine at pH 8.0 and of reducing groups at pH 5.6. Likewise, Microcococcus luteus walls at pH 5.6 and B. subtilis walls at pH 8 are lysed only very slowly by LiCl extracts made from the mutants as compared with rates obtained with wild-type extracts. Thus, the activity of both autolytic enzymes in the mutants is depressed. The frequencies of transformation, the isolation of revertants, and observations with a temperature-sensitive mutant all point to the likelihood that the pleiotropic, phenotypic properties of the strains are due to a single mutation. The mutants did not produce more protease or amylase than did the wild type. They sporulate and the spores germinate normally. The addition of antibiotics to exponentially growing cultures prevents wall synthesis but leads to less lysis than is obtained with the wild type. The bacteriophage PBSX can be induced in the mutants by treatment with mitomycin C.
Identification of Gaussian Process State Space Models (2017)

The Gaussian process state space model (GPSSM) is a non-linear dynamical system, where unknown transition and/or measurement mappings are described by GPs. Most research in GPSSMs has focussed on the state estimation problem, i.e., computing a posterior of the latent state given the model. However, the key challenge in GPSSMs has not been satisfactorily addressed yet: system identification, i.e., learning the model. To address this challenge, we impose a structured Gaussian variational posterior distribution over the latent states, which is parameterised by a recognition model in the form of a bi-directional recurrent neural network. Inference with this structure allows us to recover a posterior smoothed over sequences of data. We provide a practical algorithm for efficiently computing a lower bound on the marginal likelihood using the reparameterisation trick. This further allows for the use of arbitrary kernels within the GPSSM. We demonstrate that the learnt GPSSM can efficiently generate plausible future trajectories of the identified system after only observing a small number of episodes from the true system.
A Reconfigurable Multi-Mode Architecture for Reed-Solomon Codec (2010)

In order to save the hardware cost and reduce the power consuming in Reed-Solomon codec, a reconfigurable multi-mode codec is presented, which provides support to encoder and decoder. The reconfigurable calculation module (RCM) in the codec can be reconfigured to perform as a linear feedback shift register (LFSR), syndrome generator and Chien's search algorithm calculator and can handle variable error correction capability (0 <; t ≤ 8). The design, written in hardware description language (HDL), was realized by using Altera's FPGA. The result proves that the codec could operation at a max frequency of 90 MHz, and the total logic element count is 2887. This design is suitable for systems such as cable modem and digital video broadcasting (DVB).
Clinical Respiratory Physiology (1989)

Clinical respiratory physiology , Clinical respiratory physiology , کتابخانه مرکزی دانشگاه علوم پزشکی ایران
The T-cell antigen receptor utilizes Lck, Raf-1, and MEK-1 for activating mitogen-activated protein kinase. Evidence for the existence of a second protein kinase C-dependent pathway in an Lck-negative Jurkat cell mutant. (1994)

T-cell antigen receptor (TCR) ligation of an Lck-deficient Jurkat mutant, J.CaM1, with anti-CD3 or anti-TCR beta monoclonal antibodies failed to induce tyrosine phosphorylation and activation of p42MAPK. The same stimuli activated mitogen-activated protein (MAP) kinase in J.CaM1 cells transfected with Lck, demonstrating that Lck plays a critical role in MAP kinase activation. Utilizing immunocomplex kinase assays, we demonstrated that TCR/CD3 ligation activated a MAP kinase kinase kinase (Raf-1) as well as a MAP kinase kinase (MEK-1) in Jurkat but not in J.CaM1 cells. It was possible, however, to activate Raf-1, MEK-1, and p42MAPK in J.CaM1 cells during treatment with the phorbol ester phorbol 12-myristate 13-acetate, which activates protein kinase C (PKC). This demonstrates the presence of a PKC-dependent pathway which functions independently from Lck in MAP kinase activation. Stimulation of Jurkat cells with either anti-TCR beta or anti-CD3 monoclonal antibody failed to induce substantial tyrosine phosphorylation of Shc proteins or their association with Grb2 which forms a complex with the guanine nucleotide exchange factor hSOS. However, the same stimuli induced tyrosine phosphorylation of another putative guanine nucleotide exchange factor, p95Vav, in Jurkat but not J.CaM1 cells. Moreover, Lck was reversibly co-immunoprecipitated with p95Vav, and the stoichiometry of binding increased in anti-CD3-treated Jurkat cells. Phorbol 12-myristate 13-acetate did not induce tyrosine phosphorylation of p95Vav. These data show that the TCR activates MAP kinase by way of a signaling cascade, which depends upon Lck, and may be mediated by downstream events involving PKC or p95Vav which act on Raf-1 and MEK-1.
Metal‐Organic‐Framework‐Based Vaccine Platforms for Enhanced Systemic Immune and Memory Response (2016)

Nanoparticulate delivery platforms have shown promising advantages for vaccines in many aspects. However, their application was limited so far by lengthy synthetic protocols, the requirement of specific modification of antigen, and by the low efficiency in inducing antigen‐specific cytotoxic T‐lymphocyte responses. This study demonstrates for the first time the construction of metal‐organic‐framework (MOF) based vaccines by encapsulating ovalbumin (OVA) and attaching the cytosine‐phosphate‐guanine oligodeoxynucleotides (CpG ODNs) in/on zeolitic imidazolate framework‐8 (ZIF‐8) nanoparticles. The pH responsive decomposition feature enables the system to release the protein antigens and CpG ODNs in the same antigen presenting cells more efficiently. More importantly, in addition to the induction of a potent immune memory response, both in vitro and in vivo experiments show that the vaccines can induce strong humoral and cellular immunity. These findings suggest that the MOF‐based vaccine platforms can be used to produce effective vaccines against a range of ailments, which will facilitate the application of MOFs in biomedical areas.