gebhart/patrepeval huggingface dataset:
Induction of specific nonresponsiveness in unprimed human T cells by anti-CD3 antibody and alloantigen. (1990)

Fresh peripheral blood mononuclear cells exposed to alloantigen for 3-8 d in the presence of anti-CD3 antibodies showed no response after restimulation with cells from the original donor but remained capable of responding to third-party donors. Antigen-specific nonresponsiveness was induced by both nonmitogenic and mitogenic anti-CD3 antibodies but not by antibodies against CD2, CD4, CD5, CD8, CD18, or CD28. Nonresponsiveness induced by anti-CD3 antibody in mixed leukocyte culture was sustained for at least 34 d from initiation of the culture and 26 d after removal of the antibody. Anti-CD3 antibody also induced antigen-specific nonresponsiveness in cytotoxic T cell generation assays. Anti-CD3 antibody did not induce nonresponsiveness in previously primed cells. Nonresponsiveness induced by anti-CD3 did not appear to be associated with suppressor cell activation. Thus, co-stimulation of the T cell receptor-CD3 complex on unprimed T cells with a fluid phase anti-CD3 antibody and allogenic major histocompatibility complex antigens can induce either clonal anergy or clonal deletion. These results suggest novel approaches for achieving transplantation tolerance.
Seasonal changes in the transient expression of a 35S CaMV-GUS gene construct introduced into Scots pine buds (1995)

Seasonal changes in the transient expression of Beta-glucuronidase gene (GUS) driven by a constitutive 35S CaMV-promoter in Scots pine (Pinus sylvestris L.) buds were studied by the microprojectile DNA-delivery method. Buds were collected from 5-, 15- and 50-year-old trees. In buds from all age groups the amount of transient expression was dependent on the season; the highest values were found in March, and values were lowest both at the beginning and at the end of the growing season. Pretreatment with growth regulators increased both the amount of transient GUS expression and arginine decarboxylase (ADC) activity in buds indicating an increase in metabolic activity. These results confirm that the genetic transformation technique can be used to study seasonally dependent regulation in mature Scots pine tissues.
Epigenetic inactivation of the candidate tumor suppressorUSP44is a frequent and early event in colorectal neoplasia (2014)

In mouse models, loss of the candidate tumor suppressor gene Ubiquitin Specific Protease 44 (USP44) is associated with aneuploidy and cancer. USP44 is also transcriptionally silenced in human cancers. Here we investigated the molecular mechanism of USP44 silencing and whether this correlated with aneuploidy in colorectal adenomas. DNA methylation at the USP44 CpG island (CGI) promoter was measured using combined bisulfite restriction analysis (COBRA) in colorectal cancer (CRC) cell lines (n = 18), and with COBRA and bisulfite sequencing in colorectal adenomas (n = 89) and matched normal colonic mucosa (n = 51). The USP44 CGI was hypermethylated in all CRC cell lines, in most colorectal adenomas (79 of 89, 89%) but rarely in normal mucosa samples (3 of 51, 6%). USP44 expression was also compared between normal mucosa and paired hypermethylated adenomas in six patients using qRT-PCR. Hypermethylation of the USP44 CGI in adenomas was associated with a 1.8 to 5.5-fold reduction in expression compared with paired normal mucosa. Treatment of CRC cell lines with the DNA hypomethylating agent decitabine resulted in a 14 to 270-fold increase in USP44 expression. Whole genome SNP array data showed that gain or loss of individual chromosomes occurred in adenomas, but hypermethylation did not correlate with more aneuploidy. In summary, our data shows that USP44 is epigenetically inactivated in colorectal adenomas, but this alone is not sufficient to cause aneuploidy in colorectal neoplasia.
TCP congestion control with a misbehaving receiver (1999)

In this paper, we explore the operation of TCP congestion control when the receiver can misbehave, as might occur with a greedy Web client. We first demonstrate that there are simple attacks that allow a misbehaving receiver to drive a standard TCP sender arbitrarily fast, without losing end-to-end reliability. These attacks are widely applicable because they stem from the sender behavior specified in RFC 2581 rather than implementation bugs. We then show that it is possible to modify TCP to eliminate this undesirable behavior entirely, without requiring assumptions of any kind about receiver behavior. This is a strong result: with our solution a receiver can only reduce the data transfer rate by misbehaving, thereby eliminating the incentive to do so.
Novel mechanism of post-transcriptional modification of tRNA. Insertion of bases of Q precursors into tRNA by a specific tRNA transglycosylase reaction. (1979)

The guanine insertion enzyme isolated from Escherichia coli (tRNA transglycosylase) catalyzed the incorporation of bases of Q (queuosine) precursors into E. coli undermodified tRNAAsn and tRNATyr. These bases of Q precursors were inserted in the first position of the anticodon of tRNASn and tRNATyr, replacing guanine originally located in that position. This is a novel type of post-transcriptional modification, inserting a modified base into the polynucleotide chain by cleavage of the N--C glycoside bond without breakage of the phosphodiester bond. One of the bases of Q precursors, 7-(aminomethyl)-7-deazaguanine, was found in the acid-soluble fraction of E. coli cells, supporting the conclusion that formation of Q, 7-(3,4-trans-4,5-cis-dihydroxy-1-cyclopenten-3-ylaminomethyl)-7-deazaguanosine, in tRNA in vivo actually proceeds by the tRNA transglycosylase reaction.
TDP-43 Is a Transcriptional Repressor (2011)

TDP-43 is an evolutionarily conserved ubiquitously expressed DNA/RNA-binding protein. Although recent studies have shown its association with a variety of neurodegenerative disorders, the function of TDP-43 remains poorly understood. Here we address TDP-43 function using spermatogenesis as a model system. We previously showed that TDP-43 binds to the testis-specific mouse acrv1 gene promoter in vitro via two GTGTGT-motifs and that mutation of these motifs led to premature transcription in spermatocytes of an otherwise round spermatid-specific promoter. The present study tested the hypothesis that TDP-43 represses acrv1 gene transcription in spermatocytes. Plasmid chromatin immunoprecipitation demonstrated that TDP-43 binds to the acrv1 promoter through GTGTGT motifs in vivo. Reporter gene assays showed that TDP-43 represses acrv1 core promoter-driven transcription via the N-terminal RRM1 domain in a histone deacetylase-independent manner. Consistent with repressor role, ChIP on physiologically isolated germ cells confirmed that TDP-43 occupies the endogenous acrv1 promoter in spermatocytes. Surprisingly, however, TDP-43 remains at the promoter in round spermatids, which express acrv1 mRNA. We show that RNA binding-defective TDP-43, but not splice variant isoforms, relieve repressor function. Transitioning from repressive to active histone marks has little effect on TDP-43 occupancy. Finally, we found that RNA polymerase II is recruited but paused at the acrv1 promoter in spermatocytes. Because mutation of TDP-43 sites caused premature transcription in spermatocytes in vivo, TDP-43 may be involved in pausing RNAPII at the acrv1 promoter in spermatocytes. Overall, our study shows that TDP-43 is a transcriptional repressor and that it regulates spatiotemporal expression of the acrv1 gene during spermatogenesis.
Fractionation of suspensions using synchronized ultrasonic and flow fields (1993)

Abstract A fractionation method for fine‐particle suspensions using resonant ultrasonic fields coordinated with bidirectional fluid flow fields is described. The basis for the separation is differences in the speed of response of particles to the imposition of a resonant acoustic field. As such, the method is sensitive to the particle size and the acoustic contrast between the solid particles and their suspending fluid. Both batch and continuous fractionation processes can be developed from a two‐step acoustic‐flow cycle. An analytical model was constructed from equations that describe the trajectories of particles as they respond to the acoustic and flow fields. Model predictions indicate how the fractionation can be controlled through choice of cycle parameters. The method was implemented experimentally. Results for the fractionation of 325‐mesh polystyrene spheres indicate that sharp fractionations can be achieved. The experimental results are generally in agreement with the model predictions.
The High Output Maximum Efficiency Resonator (HOMER) Developed for Long Life, Space-Based Altimetry (2006)

We report on the status of the high output maximum efficiency resonator (HOMER), a prototype space-flight Nd:YAG, diode pumped, unstable resonator. HOMER, the 3 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rd</sup> generation of this design based on the high efficiency laser transmitter, is a stand-alone oscillator that has achieved ~2 billion 10 ns q-switched pulses at 17-15 mJ. In this configuration HOMER achieves an excellent optical efficiency of ~16%. It is currently the lead candidate for the biomass monitoring mission (BioMM); a global vegetation instrument currently under design and pre-proposal at NASA-GSFC
Retaining cell–cell contact enables preparation and culture of spheroids composed of pure primary cancer cells from colorectal cancer (2011)

Primary culture of the cancer cells from patients' tumors can provide crucial information of individual tumors, yet the technology has not been optimized until now. We developed an innovative culture method for primary colorectal cancer cells, based on the principle that cell-cell contact of cancer cells was maintained throughout the process. When tumor tissue was dissociated into cell clusters, in which cell-cell contact was retained, they rapidly formed spheroids that we termed cancer tissue-originated spheroids (CTOSs). CTOSs of colorectal cancer consisted of highly purified and viable cancer cells, and they were prepared with high efficiency. In immunodeficient mice, CTOSs formed xenograft tumors that retained the features of the parental tumors. Moreover, CTOSs were able to be cultured and expanded in vitro using a 3D culture system and stem cell culture medium. This method allowed evaluation of chemosensitivity and signal pathway activation in cancer cells from individual patients. Easy preparation and culture of pure primary cancer cells provides an innovative platform for studying cancer biology and developing personalized medicine.
Clustered OFDM with channel estimation for high rate wireless data (2003)

Clustered OFDM can provide in-band diversity gain for wideband wireless channels. It is a promising technique for high-rate wireless packet data access, such as mobile multimedia communications. Due to the smaller size of each cluster for clustered OFDM than for classical (non-clustered) OFDM, edge effects can be very large. In this paper, we present new transforms for channel estimators in clustered OFDM systems. The new transforms are independent of the channel delay profiles and can effectively mitigate the edge effects. Computer simulation shows that the performance of clustered OFDM with the estimator using the new transforms is very close to the performance with the optimum estimator that depends on the channel delay profile. For the typical-urban or hilly-terrain delay profiles, clustered OFDM using the new transform based estimator is almost as good as classical OFDM with transmitter diversity.
A model-based approach to attributed graph clustering (2012)

Graph clustering, also known as community detection, is a long-standing problem in data mining. However, with the proliferation of rich attribute information available for objects in real-world graphs, how to leverage structural and attribute information for clustering attributed graphs becomes a new challenge. Most existing works take a distance-based approach. They proposed various distance measures to combine structural and attribute information. In this paper, we consider an alternative view and propose a model-based approach to attributed graph clustering. We develop a Bayesian probabilistic model for attributed graphs. The model provides a principled and natural framework for capturing both structural and attribute aspects of a graph, while avoiding the artificial design of a distance measure. Clustering with the proposed model can be transformed into a probabilistic inference problem, for which we devise an efficient variational algorithm. Experimental results on large real-world datasets demonstrate that our method significantly outperforms the state-of-art distance-based attributed graph clustering method.
The asialoglycoprotein receptor in human hepatocellular carcinomas: its expression on proliferating cells (1999)

The expression of the asialoglycoprotein receptor (ASGP-R) on human hepatocellular carcinoma (HCC) cells might be exploited to reduce the extrahepatic toxicity of DNA synthesis inhibitors by their conjugation with galactosyl-terminating peptides. In the present study we first assessed the frequency of ASGP-R expression in 60 HCCs. Secondly, we investigated whether the receptor was maintained on the plasma membranes of DNA synthesizing cancer cells. Needle biopsies of HCC were evaluated. Diagnosis and grading of HCC were performed on routine haematoxylin and eosin-stained sections according to Edmondson and Steiner (1953). Thirty-five tumours were grade I and II and were classified as well differentiated, while 25 tumours were grade III and IV and were classified as poorly differentiated. Sections from formalin-fixed, paraffin-embedded samples were incubated, after antigen retrieval, with an anti-ASGP-R monoclonal antibody revealed by secondary biotinylated antibody and streptavidin-biotin-peroxidase-diaminobenzidine reaction. A clear immunolabelling of plasma membranes of HCC cells was observed in 28 out of 35 (80%) well differentiated (grade I and II) and in five out of 25 (20%) poorly differentiated (grade III and IV) HCCs. The presence of the ASGP-R on the surface of DNA synthesizing cancer cells was also investigated after in vitro bromodeoxyuridine (BrdU) labelling of HCC samples by immunohistochemical visualization of both the ASGP-R and incorporated BrdU on the same section. The results obtained clearly demonstrated that DNA synthesizing cancer cells expressed the ASGP-R on their surface. The presence of ASGP-R on cell plasma membrane in the majority of differentiated HCCs and its maintenance on proliferating cells encourages studies in order to restrict the action of the inhibitors of DNA synthesis of HCC cells by their conjugation with galactosyl-terminating carriers internalized through this receptor.
Failure of immunological cells to eradicate tumor and cancer cells: an overview (2014)

Inflammation can be broadly understood as a successive immune response of an organism's immune system towards nonnative or foreign antigens. This is a protective mechanism of the immune system, mediated by diverse immunological cells, to ensure homeostasis of an individual. Once activated, these immunological cells release a number of cytokines, chemokines, reactive oxygen species, reactive nitrogen species, histamines, prostaglandins, and other materials leading to inflammation. Tumor cells express altered proteins due to mutations of their genes, DNA modifications such as histone modification, DNA methylation, or other mechanisms of altered protein expression. The body's immunological cells actively recognize these altered proteins, now acting as tumor antigens, and eliminate the tumor cell; this is popularly known as tumor immunosurveillance. However, in unmanaged or inexorable circumstances, tumor cells escape from immunosurveillance mechanisms. This ultimately leads to the cascading events of cancer development and progression. T regulatory cells, tumor-associated macrophages, and myeloid-derived suppressor cells are pronounced cells involved in immunosuppression. These cells not only dodge the immune system's surveillance but also significantly increase the survival, proliferation, and metastasis rates of tumor cells. They hinder T cytotoxic activation by secreting inhibitory cytokines (which inhibit the antitumor activity of natural killer cells) along with dendritic cells and disrupt presentation of antigens, ultimately leading to cancer development. On their own, these cells have emerged as promising therapeutic targets in cancer immunotherapy. This review highlights some of the mechanisms by which these cells escape immunosurveillance and mediate immune suppression.
Joint myocardial T1 and T2 mapping using a combination of saturation recovery and T2‐preparation (2015)

The proposed sequence allows joint estimation of accurate and coregistered quantitative myocardial T1 and T2 maps in a single breath-hold. Magn Reson Med 76:888-896, 2016. © 2015 Wiley Periodicals, Inc.
Fetal DNA in Maternal Plasma (2001)

In Brief OBJECTIVE To review the potential clinical diagnostic applications of fetal DNA analysis in maternal plasma or serum for noninvasive prenatal diagnosis and screening. DATA SOURCES We conducted a MEDLINE search of articles published between January 1970 and March 2000 using the key terms “fetal DNA,” “plasma,” and “serum.” METHODS OF STUDY SELECTION All 369 articles describing the detection of fetal DNA in maternal plasma were reviewed. RESULTS The diagnostic use of circulating fetal DNA in maternal plasma is currently limited to genes that are present in the fetus but not in the mother. From a clinical perspective, the most advanced application is for noninvasive detection of fetal rhesus D (Rh[D]) genotype. The results of studies performed by four different groups showed that prenatal diagnosis of fetal Rh(D) status by molecular analysis of maternal plasma or serum is routinely possible beginning in the second trimester. Noninvasive fetal genotyping should be useful for the treatment of sensitized Rh(D)-negative women whose partners are heterozygous for the Rh(D) gene because no further diagnostic or therapeutic procedures are necessary if the fetus is Rh(D) negative. Future clinical applications of fetal DNA may be in its use as a screening test for Down syndrome, preeclampsia, or preterm labor. However, these applications currently rely on the detection of Y chromosomal sequences and consequently are limited presently to male fetuses. CONCLUSION The recent discovery of high concentrations of fetal DNA in maternal plasma represents a promising noninvasive approach to prenatal diagnosis. Compared with the analysis of the cellular fraction of maternal blood, the analysis of fetal DNA extracted from maternal plasma has the advantage of being rapid, robust, and easy to perform. The fetal DNA detected is limited to the current pregnancy. However, universal fetal gene sequences must be identified that allow analysis of genetic material from both male and female fetuses. Study of fetal DNA in maternal plasma can improve our understanding of fetomaternal biology and physiology. The long-term effects of maternal exposure to relatively high amounts of foreign DNA are unknown but represent an exciting area for future inquiry. Large amounts of fetal DNA circulate in the plasma of pregnant women, providing a noninvasive source of material to determine the fetal genotype.
Optical anisotropy of polyimide (1990)

Abstract Optical anisotropy of polyimide films prepared from polyamic acid solutions was investigated by conoscopic observation and refractive index measurements. The conoscopic figure (crossed pattern) characteristic of a negative uniaxial crystal with its optic axis perpendicular to the film plane was observed for samples imidized on substrates. Uniaxial drawing of a polyamic acid cast film with 40 wt % solvent gave a highly oriented sample with an elongation of more than 80%. This sample had a conoscopic figure characteristic of a positive uniaxial crystal with its optic axis equivalent to the molecular c axis (parallel to the film plane). A large optical anisotropy (bire‐fringence 0.18) was observed in the film plane. The TE‐mode refractive index (parallel to the film plane) ranged from 1.64 to 1.82 at a wavelength of 633 nm according to the sample rotation. These values corresponded to the refractive indices perpendicular and parallel to the c axis, respectively. The optical system change of the polyimide film was explained in terms of the uniaxial orientation of the in‐plane oriented molecular c axis.
Biochemical characterization of a smaller form of recombinant Norwalk virus capsids assembled in insect cells (1997)

The expression of the single capsid protein of Norwalk virus (NV) in Spodoptera frugiperda (Sf9) insect cells infected with recombinant baculovirus results in the assembly of virus-like particles (VLPs) of two sizes, the predominant 38-nm, or virion-size VLPs, and smaller, 23-nm VLPs. Here we describe the purification and biochemical characterization of the 23-nm VLPs. The 23-nm VLPs were purified to 95% homogeneity from the medium of Sf9 cultures by isopycnic CsCl gradient centrifugation followed by rate-zonal centrifugation in sucrose gradients. The compositions of the purified 23- and 38-nm VLPs were compared by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and protein immunoblots. VLPs of both sizes showed a doublet at 58 kDa, the size of the full-length capsid protein. Upon alkaline treatment, the 23-nm VLPs underwent dissociation into soluble intermediates that were able to reassemble into 23- and 38-nm VLPs upon dialysis, suggesting that the assembly of both types of structures has a common pathway. Antigenic and biochemical properties of the 38- and 23-nm VLPs were examined and found to be conserved. Immunoprecipitation assays using polyclonal and monoclonal antibodies indicated that immunodominant epitopes on the capsid protein as well as conformational epitopes are conserved in the two types of particles. The trypsin cleavage site at residue 227 was protected in the assembled particles of both sizes but exposed after alkaline dissociation. These results, and the conservation of the binding activity of both forms of recombinant NV VLPs to cultured cells (L. J. White, J. M. Ball, M. E. Hardy, T. N. Tanaka, N. Kitamoto, and M. K. Estes, J. Virol. 70:6589-6597, 1996), suggest that the tertiary folding of the capsid protein responsible for these properties is conserved in the two structures. We hypothesize that the 23-nm VLPs are formed when 60 units of the NV capsid protein assembles into a structure with T=1 symmetry.