gebhart/patrepeval huggingface dataset:
Poly(A) addition during maturation of frog oocytes: distinct nuclear and cytoplasmic activities and regulation by the sequence UUUUUAU. (1989)

In frog oocytes, certain maternal mRNAs receive poly(A) in the cytoplasm during progesterone-induced maturation. To analyze this reaction and to compare it to poly(A) addition in the nucleus, we injected short, synthetic RNA substrates into Xenopus oocytes. These RNAs contain only portions of the 3'-untranslated regions of appropriate mRNAs and end at the natural poly(A) site. We demonstrate that the nuclear and maturation-specific polyadenylation activities are distinct in substrate specificity and subcellular location. The sequence AAUAAA, contained in virtually all pre-mRNAs, is necessary for both activities. A second sequence element, UUUUUAU, activates poly(A) addition during maturation. UUUUUAU and AAUAAA are both necessary and virtually sufficient for maturation-specific polyadenylation: Poly(A) tails of between 50 and 300 nucleotides are added during maturation to RNAs containing both sequences but not to RNAs that lack either sequence. Before maturation, RNAs that contain AAUAAA are extended by just 10 nucleotides, presumably adenosines. The maturation-specific activity first appears within 1 hr of the time the nucleus breaks down but apparently does not require a nuclear component, as it is unaffected by enucleation. These observations, combined with those of others, lead us to speculate that polyadenylation may be responsible for the translational activation of a family of mRNAs essential for maturation.
A genetic perspective of male germ cell tumors. (1998)

Adult human male germ cell tumors (GCTs) arise by transformation of germ cells (GCs). The transformed GCs exhibit pluripotentiality to differentiate into embryonic, extra-embryonic, and somatic tissue types, and are highly sensitive to cisplatin-based chemotherapy. Recent investigations into the genetics of GCTs have advanced methods of diagnosis and provided leads to the understanding of molecular basis of transformation, differentiation, and sensitivity/resistance. Cytogenetic and molecular cytogenetic studies have identified multiplication of 12p, manifested in i(12p) or tandem duplication of 12p, as a unique change in GCTs which serves as a diagnostic marker. Ectopic over-expression of cyclin D2, a gene mapped to 12p, as early as in carcinoma in situ identifies a candidate gene in GC transformation. Genetic alterations identified in the tumor suppressor genes deleted in colorectal cancer, retinoblastoma 1 and non-metastatic protein 23 (NME) in GCT suggest that their inactivation play a key role in transformation or differentiation. A number of regions of chromosomal deletion have been identified including those previously known to be deleted in various tumor types and novel candidate tumor suppressor gene sites such as 12q13, 12q22, and 5p15.1-15.2. Identification and characterization of the genes in these sites will provide important clues in understanding the biology of GCT. The molecular studies have also enumerated several possible differentiation controls such as switching of KIT and mast cell growth factor gene expression in a lineage-associated manner, and loss of certain types of genes such as NME in teratomas that may act in a dominant negative fashion in differentiation. The exquisite sensitivity of these tumors to chemotherapy is reflected in their over-expression of wild-type p53 protein and lack of TP53 mutations. These data indicate that multiple genetic events play a role in distinct pathways in the development of GCT, and further elucidation of the underlying genetic and biochemical mechanisms is central to unraveling biology and improving treatment of GCT.
A Useful One-Step Synthesis of β-Trihaloacetylvinyl Ethers and Trihaloacetylketene Acetals (1986)

Synthese respectivement a partir de l'orthoacetate de triethyle et de dialkylacetals de l'acetone et acetophenone
An Introduction to Arithmetic Coding (1984)

Arithmetic coding is a data compression technique that encodes data (the data string) by creating a code string which represents a fractional value on the number line between 0 and 1. The coding algorithm is symbolwise recursive; i.e., it operates upon and encodes (decodes) one data symbol per iteration or recursion. On each recursion, the algorithm successively partitions an interval of the number line between 0 and 1, and retains one of the partitions as the new interval. Thus, the algorithm successively deals with smaller intervals, and the code string, viewed as a magnitude, lies in each of the nested intervals. The data string is recovered by using magnitude comparisons on the code string to recreate how the encoder must have successively partitioned and retained each nested subinterval. Arithmetic coding differs considerably from the more familiar compression coding techniques, such as prefix (Huffman) codes. Also, it should not be confused with error control coding, whose object is to detect and correct errors in computer operations. This paper presents the key notions of arithmetic compression coding by means of simple examples.
SentencePiece: A simple and language independent subword tokenizer and detokenizer for Neural Text Processing (2018)

This paper describes SentencePiece, a language-independent subword tokenizer and detokenizer designed for Neural-based text processing, including Neural Machine Translation. It provides open-source C++ and Python implementations for subword units. While existing subword segmentation tools assume that the input is pre-tokenized into word sequences, SentencePiece can train subword models directly from raw sentences, which allows us to make a purely end-to-end and language independent system. We perform a validation experiment of NMT on English-Japanese machine translation, and find that it is possible to achieve comparable accuracy to direct subword training from raw sentences. We also compare the performance of subword training and segmentation with various configurations.
Driving the Adoption of High Voltage Gallium Nitride Field-Effect Transistors [Expert View] (2017)

Expert View High-voltage (HV) gallium nitride field-effect transistors (FETs) are becoming the next standard for power conversion. They provide cost competitive, easy-to-embed solutions that reduce energy loss by more than 50%, shrink system size by more than 40%, and simplify power converter/inverter design and manufacturing.
cSSMD: assessing collective activity for addressing off-target effects in genome-scale RNA interference screens (2011)

Supplementary data are available at Bioinformatics online.
Shaping the light amplified in a multimode fiber (2016)

Propagation of light in multimode optical fibers usually gives a spatial and temporal randomization of the transmitted field similar to the propagation through scattering media. Randomization still applies when scattering or multimode propagation occurs in gain media. We demonstrate that appropriate structuration of the input beam wavefront can shape the light amplified by a rare-earth-doped multimode fiber. Profiling of the wavefront was achieved by a deformable mirror in combination with an iterative optimization process. We present experimental results and simulations showing the shaping of a single sharp spot at different places in the output cross-section of an ytterbium-doped fiber amplifier. Cleaning and narrowing of the amplifier far-field pattern was realized as well. Tailoring the wavefront to shape the amplified light can also serve to improve the effective gain. The shaping approach still works under gain saturation, showing the robustness of the method. Modeling and experiments attest that the shaping is effective even with a highly multimode fiber amplifier carrying up to 127 modes.
Separation by &#x201C;humming&#x201D;: User-guided sound extraction from monophonic mixtures (2009)

In this paper we present a novel approach for isolating and removing sounds from dense monophonic mixtures. The approach is user-based, and requires the presentation of a guide sound that mimics the desired target the user wishes to extract. The guide sound can be simply produced from a user by vocalizing or otherwise replicating the target sound marked for separation. Using that guide as a prior in a statistical sound mixtures model, we propose a methodology that allows us to efficiently extract complex structured sounds from dense mixtures.
Bone marrow stromal cells enhance differentiation of cocultured neurosphere cells and promote regeneration of injured spinal cord (2003)

Transplantation of bone marrow stromal cells (MSCs) has been regarded as a potential approach for promoting nerve regeneration. In the present study, we investigated the influence of MSCs on spinal cord neurosphere cells in vitro and on the regeneration of injured spinal cord in vivo by grafting. MSCs from adult rats were cocultured with fetal spinal cord-derived neurosphere cells by either cell mixing or making monolayered-feeder cultures. In the mixed cell cultures, neuroshpere cells were stimulated to develop extensive processes. In the monolayered-feeder cultures, numerous processes from neurosphere cells appeared to be attracted to MSCs. In an in vivo experiment, grafted MSCs promoted the regeneration of injured spinal cord by enhancing tissue repair of the lesion, leaving apparently smaller cavities than in controls. Although the number of grafted MSCs gradually decreased, some treated animals showed remarkable functional recovery. These results suggest that MSCs might have profound effects on the differentiation of neurosphere cells and be able to promote regeneration of the spinal cord by means of grafting.
<title>Correlation between particle defects and electrical faults determined with laser scattering systems and digital measurements on checkerboard test structures</title> (1996)

To improve accuracy of defect densities, yield prediction and failure analysis, this paper compares data on defects and faults collected by electrical measurement methods and laser scattering systems. For that we choose the checkerboard test structure design to partition the whole chip area into a large number of subchips, each containing defect sensitive comb lines. A digital tester based measurement procedure enables the detection and separation of faults. Additional analysis procedures guarantee a layer- specific fault localization inside specific subchips. manufacturing of test chips at Thesys Gesellschaft fur Mikroelektronik was accompanied by laser scattering after selected processed layers. Finally wafer maps based on electrically detected faults and optically detected particle defects were analyzed to determine correlations between defects and faults.
4-Hydroxypyrrolo[2,3-d]pyrimidine: Mannich Reaction (1961)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXT4-Hydroxypyrrolo[2,3-d]pyrimidine: Mannich ReactionROBERT A. WESTCite this: J. Org. Chem. 1961, 26, 12, 4959–4961Publication Date (Print):December 1, 1961Publication History Published online1 May 2002Published inissue 1 December 1961https://doi.org/10.1021/jo01070a044RIGHTS & PERMISSIONSArticle Views407Altmetric-Citations16LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (382 KB) Get e-Alerts Get e-Alerts
Antigen-Presenting Cell-Intrinsic PD-1 Neutralizes PD-L1 in cis to Attenuate PD-1 Signaling in T Cells (2018)

Summary: The PD-1 pathway, consisting of the co-inhibitory receptor PD-1 on T cells and its ligand (PD-L1) on antigen-presenting cells (APCs), is a major mechanism of tumor immune evasion. PD-1 and PD-L1 blockade antibodies have produced remarkable clinical activities against a subset of cancers. Binding between T cell-intrinsic PD-1 and APC-intrinsic PD-L1 triggers inhibitory signaling to attenuate the T cell response. Here, we report that PD-1 is co-expressed with PD-L1 on tumor cells and tumor-infiltrating APCs. Using reconstitution and cell culture assays, we demonstrate that the co-expressed PD-1 binds to PD-L1 in cis. Such interaction inhibits the ability of PD-L1 to bind T cell-intrinsic PD-1 in trans and, in turn, represses canonical PD-L1/PD-1 inhibitory signaling. Selective blockade of tumor-intrinsic PD-1 frees up tumor-intrinsic PD-L1 to inhibit T cell signaling and cytotoxicity. Our study uncovers another dimension of PD-1 regulation, with important therapeutic implications. : Zhao et al. show that the T cell inhibitory receptor PD-1 expressed on tumor cells and tumor-infiltrating APCs neutralizes its ligand, PD-L1, in cis to inhibit canonical PD-1 signaling. Selective blockade of tumor-intrinsic PD-1 frees up tumor PD-L1 for T cell suppression. Keywords: PD-1, PD-L1, cis-interaction, trans-interaction, reconstitution, T cell signaling
Analysis of 16S libraries of mouse gastrointestinal microflora reveals a large new group of mouse intestinal bacteria b bThe GenBank accession numbers for the clone sequences reported in this paper can be found in Table 1 T1 ; the accession number for isolate MIB-CB3 is AJ418059. (2002)

Total genomic DNA from samples of intact mouse small intestine, large intestine, caecum and faeces was used as template for PCR amplification of 16S rRNA gene sequences with conserved bacterial primers. Phylogenetic analysis of the amplification products revealed 40 unique 16S rDNA sequences. Of these sequences, 25% (10/40) corresponded to described intestinal organisms of the mouse, including Lactobacillus spp., Helicobacter spp., segmented filamentous bacteria and members of the altered Schaedler flora (ASF360, ASF361, ASF502 and ASF519); 75% (30/40) represented novel sequences. A large number (11/40) of the novel sequences revealed a new operational taxonomic unit (OTU) belonging to the Cytophaga-Flavobacter-Bacteroides phylum, which the authors named 'mouse intestinal bacteria'. 16S rRNA probes were developed for this new OTU. Upon analysis of the novel sequences, eight were found to cluster within the Eubacterium rectale-Clostridium coccoides group and three clustered within the Bacteroides group. One of the novel sequences was distantly related to Verrucomicrobium spinosum and one was distantly related to Bacillus mycoides. Oligonucleotide probes specific for the 16S rRNA of these novel clones were generated. Using a combination of four previously described and four newly designed probes, approximately 80% of bacteria recovered from the murine large intestine and 71% of bacteria recovered from the murine caecum could be identified by fluorescence in situ hybridization (FISH).
In vivo fiber‐based multicolor photoacoustic detection and photothermal purging of metastasis in sentinel lymph nodes targeted by nanoparticles (2009)

This report introduces a novel diagnostic and therapeutic platform for in vivo non-invasive detection and treatment of metastases in sentinel lymph nodes (SLNs) at single cell level using an integrated system of multicolor photoacoustic (PA) lymph flow cytometry, PA lymphography, absorption image cytometry, and photothermal (PT) therapy. A melanoma-bearing mouse model was used to demonstrate the capability of this platform for real-time lymphatic mapping, counting of disseminated tumor cells (DTCs) in prenodal lymphatics, and detecting metastasis in SLNs and its purging. The detection and ablation of non-pigmented breast cancer cells in SLNs was achieved by labeling them with nanoparticles. The association between DTC count and SLN metastasis progression supports lymphatic DTCs as a novel prognostic marker of metastasis. The fiber-based portable PA device may replace the conventional SLN(s) excision and histology-based staging. The earliest detection of DTCs in the lymphatic vessels before the establishment of nodal metastasis may prevent metastasis by well-timed ablation of DTCs.
Java and the shift to net-centric computing (1996)

Java is an object-oriented programming language with a syntax similar to C and C++, only simpler. Because Java is an interpreted language, the typical C or C++ compile-link-load-test-debug cycle is reduced. Java development environments actually let the entire software-development life cycle take place within a Web browser. The author discusses some basic and advanced features of Java, including garbage collection, multithreading and application programming interfaces.
Purification and Characterization of Two Related but Distinct Metalloproteinase Inhibitors Secreted by Bovine Aortic Endothelial Cells (1989)

Two metalloproteinase inhibitors were purified from serum-free medium conditioned by bovine aortic endothelial cells. One of these inhibitors, with a molecular weight of 30,000-34,000 (reduced) is identified as tissue inhibitor of metalloproteinases; the second inhibitor has a molecular weight of 27,500 (reduced) and 20,400 (unreduced), is not recognized by an antiserum against bovine tissue inhibitor of metalloproteinases, appears unglycosylated, and has 51% identity with tissue inhibitor of metalloproteinases by NH2-terminal amino acid sequence analysis. This inhibitor has antiproteinase activities similar to those of tissue inhibitor of metalloproteinases, with inhibition of classical collagenase, type IV collagenase, and gelatinases but not trypsin, plasmin, or bacterial collagenase. Other properties shared with tissue inhibitor of metalloproteinases include trypsin sensitivity, acid and heat resistance, and inactivation by reduction-alkylation. The presence of these inhibitors in endothelial cells suggests that they may play important roles in protecting the integrity of the vascular basement membrane.
ChemInform Abstract: Synthesis of Substituted 6‐(3′,5′‐Dimethyl‐1H‐pyrazol‐1′‐yl)quinolines and Evaluation of Their Biological Activities. (1990)

Abstract All products obtained starting from (I) are screened for their antibacterial activity.
The 5'-untranslated region of p23 mRNA from the Ehrlich ascites tumor is involved in translation control of the growth related protein p23. (1991)

The growth-related protein p23 of the Ehrlich ascites tumor (EAT) is preferentially expressed in the exponentially growing tumor; its synthesis is translationally controlled. p23 mRNA is efficiently translated in the wheat germ cell-free lysate. In contrast, p23 mRNA present in poly(A)+RNA isolated from EAT is not translated in cell-free systems of EAT and reticulocytes. Moreover, translation of a p23 transcript is inhibited in the presence of total poly(A)+RNA. This inhibition is abolished by the removal of the 5'-UTR of the p23 transcript. Solution hybridization/RNase protection experiments point to the presence of a nucleotide sequence complementary to the 5'-UTR of p23 mRNA which might be involved in p23 mRNA inhibition.
Bragg gratings fabricated in monomode photosensitive optical fiber by UV exposure through a phase mask (1993)

A photolithographic method is described for fabricating refractive index Bragg gratings in photosensitive optical fiber by using a special phase mask grating made of silica glass. A KrF excimer laser beam (249 nm) at normal incidence is modulated spatially by the phase mask grating. The diffracted light, which forms a periodic, high-contrast intensity pattern with half the phase mask grating pitch, photoimprints a refractive index modulation into the core of photosensitive fiber placed behind, in proximity, and parallel, to the mask; the phase mask grating striations are oriented normal to the fiber axis. This method of fabricating in-fiber Bragg gratings is flexible, simple to use, results in reduced mechanical sensitivity of the grating writing apparatus and is functional even with low spatial and temporal coherence laser sources.
Impact of serum SP-A and SP-D levels on comparison and prognosis of idiopathic pulmonary fibrosis (2017)

Serum SP-A/D detection might be useful for differential diagnosis and prediction of survival in patients with IPF.
Gene Therapy for a Mucopolysaccharidosis Type I Murine Model with Lentiviral-IDUA Vector (2005)

Mucopolysaccharidosis type I is a lysosomal disease due to mutations in the IDUA gene, resulting in deficiency of alpha-L-iduronidase and accumulation of glycosaminoglycans (GAGs). Bone marrow transplantation and enzyme replacement are two therapies considered only moderately successful for affected patients, making the development of novel treatments necessary. We have previously shown the efficacy of lentivirus-mediated gene transfer to correct patient fibroblasts in vitro. Here we tested lentiviral-IDUA vector gene therapy in vivo on a murine MPS I model. Eight- to 10 week-old mice were injected with increasing lentiviral doses via the tail vein and analyzed 1 month after treatment. A single injection of lentiviral-IDUA vector resulted in transgene expression in several murine tissues, with the highest level reached in liver and spleen. Expression of 1% normal activity was sufficient in treated animals to normalize the GAG level in urine, liver, and spleen and was able to reduce the GAG level in kidney, heart, and lung. Polymerase chain reaction assays showed integration of the viral genome only in liver and spleen of treated animals, suggesting that the correction of the pathology in other tissues was due to secretion into the plasma by liver and spleen and uptake of corrective enzyme by distant tissues. Long-term (6 months) analysis showed the presence of enzyme-specific antibodies and the loss of enzyme activity and vector sequence in the target tissue, suggesting that the transgene-specific immune response interfered with long-term therapeutic correction and led to clearance of transduced cells. In conclusion, our results show the promising potential and the limitations of lentiviral-IDUA vector-mediated gene therapy in an in vivo model.
Resistive training can reduce coronary risk factors without altering VO2max or percent body fat (1988)

HURLEY, B. F., J. M. HAGBERG, A. P. GOLDBERG, D. R. SEALS, A. A. EHSANI, R. E. BRENNAN, and J. O. HOLLOSZY. Resistive training can reduce coronary risk factors without altering VO2max or percent body fat. Med. Sci. Sports Exerc., Vol. 20, No. 2, pp. 150–154, 1988. Eleven healthy, untrained males (age = 44 ± 1 yr; range = 40 to 55 yr) were studied to determine the effects of 16 wk of high-intensity resistive training on risk factors for coronary artery disease. Lipoprotein-lipid profiles, plasma glucose and insulin responses during an oral glucose tolerance test, and blood pressure at rest were determined before and after training. The training program resulted in a 13% increase in high-density lipoprotein-cholesterol (39 ± 2 vs 44 ± 3 mg·dl−1, P < 0.05), a 43% increase in high-density lipoprotein-cholesterol2 (7 ± 2 vs 10 ± 2 mg-dl−1, P < 0.05), a 5% reduction in low-density lipoprotein cholesterol (129 ± 5 vs 122 ± 5 mg·dl−1, P< 0.05), and an 8% decrease in the total cholesterol/high- density lipoprotein-cholesterol ratio (5.1 ± 0.3 vs 4.7 ± 0.3, P < 0.01), despite no changes in VO2max body weight, or percent body fat. Glucose-stimulated plasma insulin concentrations during oral glucose tolerance testing were significantly lower, and supine diastolic blood pressure was reduced (P < 0.05) as a result of the training program. No changes in any of these variables occurred in a sedentary control group. These findings indicate that resistive training can lower risk factors for coronary artery disease independent of changes in VO2max, body weight, or body composition.