gebhart/patrepeval huggingface dataset:
Overexpression ofbcl-2 inhibits sodium butyrate-induced apoptosis in Chinese hamster ovary cells resulting in enhanced humanized antibody production (2000)

Sodium butyrate (NaBu) can enhance the expression of genes from some of the mammalian promoters including cytomegalovirus (CMV) and simian virus 40 (SV40), but it can also inhibit cell growth and induce cellular apoptosis. Thus, the beneficial effect of using a higher concentration of NaBu on a foreign protein expression is compromised by its cytotoxic effect on cell growth. To overcome this cytotoxic effect of NaBu, a survival protein, human Bcl-2, was overexpressed in recombinant Chinese hamster ovary (CHO) cells (SH2-0.32), producing a humanized antibody directed against the S surface antigen of hepatitis B virus. When batch cultures of both control cells transfected with bcl-2-deficient plasmid (SH2-0.32-Deltabcl-2) and cells transfected with bcl-2 expression plasmid (14C6-bcl-2) were performed in the absence of NaBu, both cells showed similar profiles of cell viability and antibody production. Compared with the SH2-0.32-Deltabcl-2 culture, under the condition of NaBu addition at the exponential growth phase, overexpression of the bcl-2 gene considerably suppressed the NaBu-induced apoptosis of 14C6-bcl-2 by inhibiting caspase 3 activity and extending culture longevity by >2 days. As a result, the final antibody concentration of 14C6-bcl-2 culture was twofold higher than that of SH2-0.32-Deltabcl-2 culture in the presence of NaBu and threefold higher than that of SH2-0.32-Deltabcl-2 and 14C6-bcl-2 cultures in the absence of NaBu.
New CNN-Type Ruthenium Pincer NHC Complexes. Mild, Efficient Catalytic Hydrogenation of Esters (2011)

New pincer ruthenium complexes (2–6) based on the new bipyridine-NHC ligand 1 were prepared and studied, resulting in an efficient catalytic hydrogenation of esters to the corresponding alcohols under mild conditions. Reaction of the ligand 1 with RuH(Cl)CO(PPh3)3, followed by reaction with one equivalent of the base KHMDS, gave the mixed phosphine-NHC complex 2, incorporating a C–H-activated bipyridine ligand. Complex 2 has an octahedral structure containing two phosphorus atoms trans to each other, a hydride trans to the NHC ligand, and CO trans to the C–H-activated carbon of the bipyridine ligand. Using the precursor complex Ru(p-cymene)Cl2(CO), reaction with 1 followed by treatment of the intermediate product with one equivalent of KHMDS resulted in formation of the dichloride pincer complexes 3a and 3b, which are in equilibrium, as indicated by variable-temperature 1H NMR. Complex 3a is an octahedral, neutral, and symmetric complex with the CO ligand positioned trans to the central pyridine group of the pincer ligand and the two chlorides trans to each other, as indicated by single-crystal X-ray diffraction. Complex 3b is cationic, with an outer-sphere chloride. Reaction of the NHC ligand 1 with LiHMDS at low temperature followed by addition of RuH(Cl)CO(PPh3)3 resulted in the mixed phosphine-NHC complex 4, which has an octahedral structure containing phosphorus trans to the hydride, a CO trans to the NHC ligand, and an outer-sphere chloride. Chloride substitution by BArF– gave the X-ray-characterized complex 5. Deprotonation of complex 4 with KHMDS resulted in formation of the dearomatized complex 6. The in situ prepared 6 (from complex 4 and an equivalent of base) is among the best catalysts known for the hydrogenation of nonactivated esters to the corresponding alcohols under mild conditions.
2.2 Å refined crystal structure of the catalytic subunit of cAMP-dependent protein kinase complexed with MnATP and a peptide inhibitor (1993)

. The crystal structure of a ternary complex containing the catalytic subunit of cAMP-dependent protein kinase, ATP and a 20-residue inhibitor peptide was refined at a resolution of 2.2 A to an R value of 0.177. In order to identify the metal binding sites, the crystals, originally grown in the presence of low concentrations of Mg(2+), were soaked in Mn(2+). Two Mn(2+) ions were identified using an anomalous Fourier map. One Mn(2+) ion bridges the gamma- and beta-phosphates and interacts with Asp184 and two water molecules. The second Mn(2+) ion interacts with the side chains of Asn171 and Asp l84 as well as with a water molecule. Modeling a serine into the P site of the inhibitor peptide suggests a mechanism for phosphotransfer.
Regulation of prostatic growth and function by peptide growth factors (1996)

Polypeptide growth factors are positive and negative regulators of prostatic growth and function. Expression and biological effects of epidermal growth factor (EGF), transforming growth factors (TGFs) alpha and beta, fibroblast growth factors (FGFs), and insulin-like growth factors (IGFs) in the prostate have been extensively studied. EGF and TGF alpha, which share the same receptor, are strong mitogens for prostatic epithelial and stromal cells. Their paracrine mode of action in normal tissue and early-stage tumors is apparently altered towards an autocrine stimulation in hormone-independent tumors, which gain the ability to produce TGF alpha by themselves. TGF beta has a dual role in the regulation of prostatic growth. It inhibits growth of prostatic epithelial cells in culture and mediates programmed cell death after androgen withdrawal. However, advanced prostatic carcinomas become insensitive to the inhibitory effect of TGF beta. Several members of the FGF family have been identified in the prostate. They are mainly or exclusively expressed in the stromal cells, and stimulate the epithelial cells. In the rat Dunning tumor model, progression is accompanied by distinct changes in the expression of FGFs and their receptors. In the hyperplastic tissue, basic FGF (bFGF) is accumulated. This growth factor is also a potent angiogenic inducer, expression of which may determine the metastatic capability of a tumor. IGFs are paracrine growth stimulators in the normal and hyperplastic prostate. It is still under consideration whether prostatic cancer cells gain the ability to produce IGF-I by themselves and thus shift to an autocrine mode of IGF-I stimulation. Growth factors also interact with the androgen-signaling pathway. IGF-I in particular, other growth factors as well, can activate the androgen receptor.
A model of head-related transfer functions based on principal components analysis and minimum-phase reconstruction (1992)

Free-field to eardrum transfer functions (HRTFs) were measured from both ears of 10 subjects with sound sources at 265 different positions. A principal components analysis of the resulting 5300 HRTF magnitude functions revealed that the HRTFs can be modeled as a linear combination of five basic spectral shapes (basis functions), and that this representation accounts for approximately 90% of the variance in the original HRTF magnitude functions. HRTF phase was modeled by assuming that HRTFs are minimum-phase functions and that interaural phase differences can be approximated by a simple time delay. Subjects' judgments of the apparent directions of headphone-presented sounds that had been synthesized from the modeled HRTFs were nearly identical to their judgments of sounds synthesized from measured HRTFs. With fewer than five basis functions used in the model, a less faithful reconstruction of the HRTF was produced, and the frequency of large localization errors increased dramatically.
Use of a novel marker, calponin, for myoepithelial cells in fine-needle aspirates of papillary breast lesions (2000)

Benign and malignant papillary lesions of the breast (PBL) can be difficult to distinguish in fine-needle aspirates (FNA). This study evaluates the use of smooth muscle actin (SMA) and a new smooth muscle-specific protein, calponin, for identifying myoepithelial cells (MEC) by immunohistochemical methods in paraffin-embedded cell blocks of FNA of PBL. Formalin-fixed, paraffin-embedded cell blocks of 40 cases of PBL were stained using SMA and calponin, steam heat-induced epitope retrieval, and an avidin biotin-complex technique. Staining was evaluated in MEC, epithelial, and stromal cells. The diagnosis of benign vs. malignant papillary lesion was made by using cytomorphological criteria and the presence/absence of MEC in the cell block. These results were compared to the original cytologic and subsequent histologic diagnoses. Of 40 cases of FNA diagnosed as PBL, there were 27 intraductal papillomas (IP), 6 papillary lesions with atypical features (PLAF), and 7 papillary carcinomas (PC). In all of the IP, MEC stained both with SMA and calponin. None of the PC cases was positive for MEC with calponin, and 2 out of 7 cases were weakly positive by SMA. In 6 cases of PLAF, 2 were negative for MEC, both by SMA and calponin, and a malignant papillary lesion was confirmed by histology. The remaining 4 cases were positive for MEC with both markers and were confirmed to be benign by histology. SMA stained stromal cells strongly in all of the cases where stroma was present (18 of a total of 40 cases of PBL), while calponin stained stroma focally in only 7 cases. More than half of all cases had nuclear staining of epithelial cells with SMA; calponin did not show any nuclear staining.
Unequal VH Gene Rearrangement Frequency Within the Large VH7183 Gene Family Is Not Due to Recombination Signal Sequence Variation, and Mapping of the Genes Shows a Bias of Rearrangement Based on Chromosomal Location (2001)

Much of the nonrandom usage of V, D, and J genes in the Ab repertoire is due to different frequencies with which gene segments undergo V(D)J rearrangement. The recombination signal sequences flanking each segment are seldom identical with consensus sequences, and this natural variation in recombination signal sequence (RSS) accounts for some differences in rearrangement frequencies in vivo. Here, we have sequenced the RSS of 19 individual V(H)7183 genes, revealing that the majority have one of two closely related RSS. One group has a consensus heptamer, and the other has a nonconsensus heptamer. In vitro recombination substrate studies show that the RSS with the nonconsensus heptamer, which include the frequently rearranging 81X, rearrange less well than the RSS with the consensus heptamer. Although 81X differs from the other 7183-I genes at three positions in the spacer, this does not significantly increase its recombination potency in vitro. The rearrangement frequency of all members of the family was determined in microMT mice, and there was no correlation between the in vitro recombination potential and V(H) gene rearrangement frequency in vivo. Furthermore, genes with identical RSS rearrange at different frequencies in vivo. This demonstrates that other factors can override differences in RSS potency in vivo. We have also determined the gene order of all V(H)7183 genes in a bacterial artificial chromosome contig and show that most of the frequently rearranging genes are in the 3' half of the region. This suggests that chromosomal location plays an important role in nonrandom rearrangement of the V(H)7183 genes.
监控式资本主义：垄断金融资本、军工复合体和数字时代 (2015)

第二次世界大战后美国雄踞全球制造业首位，生成巨大的“经济剩余”，但其国内市场毕竟有限、不足以吸纳庞大的“经济剩余”，为此，当局启动“军工复合体”和“促销活动”两大战略机制。20世纪70年代再次陷入经济滞涨后，经济金融化则成为吸纳“经济剩余”的第三个主要机制。随着计算机和互联网的发展，“数字时代”又助推了经济金融化。为维持“资本统治”，美国以国家安全为由与垄断金融资本合作、。全网监控”美国及世界人民，促使当代资本主义新样态——监控式资本主义——走上历史舞台。
Lysine Succinylation and Lysine Malonylation in Histones (2012)

Histone protein post-translational modifications (PTMs) are significant for gene expression and DNA repair. Here we report the identification and validation of a new type of PTM in histones, lysine succinylation. The identified lysine succinylated histone peptides were verified by MS/MS of synthetic peptides, HPLC co-elution, and isotopic labeling. We identified 13, 7, 10, and 7 histone lysine succinylation sites in HeLa, mouse embryonic fibroblast, Drosophila S2, and Saccharomyces cerevisiae cells, respectively. We demonstrated that this histone PTM is present in all eukaryotic cells we examined. Mutagenesis of succinylation sites followed by functional assays implied that histone lysine succinylation can cause unique functional consequences. We also identified one and two histone lysine malonylation sites in HeLa and S. cerevisiae cells, respectively. Our results therefore increase potential combinatorial diversity of histone PTMs and suggest possible new connections between histone biology and metabolism.
Simple and Reliable Factor V Genotyping by PNA-Mediated PCR Clamping (1998)

Resistance to activated protein C (APC resistance) is the most common cause of thrombophilia and linked to a single point mutation in the factor V gene (G-->A transition at nucleotide 1691). In the past, several PCR based methods have been proposed to determine the allelostatus of individual patients from small amounts of blood DNA including PCR followed by restriction fragment length polymorphism detection (PCR-RFLP), PCR using sequence-specific primers (PCR-SSP) and oligonucleotide ligation assay (OLA). Here, we present a novel approach based on the method of peptide nucleic acid(PNA)-mediated PCR clamping which is extremely sensitive to base pair mismatches. If PNAs specific for the two allelic variants are applied separately in each case a clear discrimination between a heterozygous or homozygous normal or homozygous Factor V Leiden status is possible and no further confirmation step is required. In a prospective study, 60 patients with suspected venous thrombosis events were tested and compared to the conventional PCR-RFLP technique. The concordance between both methods was 100%. PNA-based factor V genotyping, therefore, should be considered for large scale screening of those patients considered to be at risk for deep venous thrombosis.
Designed Ankyrin Repeat Proteins (DARPins) as Novel Isoform-Specific Intracellular Inhibitors of c-Jun N-Terminal Kinases (2012)

The c-Jun N-terminal kinases (JNKs) are involved in many biological processes such as proliferation, differentiation, apoptosis, and inflammation and occur in highly similar isoforms in eukaryotic cells. Isoform-specific functions and diseases have been reported for individual JNK isoforms mainly from gene-knockout studies in mice. There is, however, a high demand for intracellular inhibitors with high selectivity to improve the understanding of isoform-specific mechanisms and for use as therapeutic tools. The commonly used JNK inhibitors are based on small molecules or peptides that often target the conserved ATP binding site or docking sites and thus show only moderate selectivity. To target novel binding epitopes, we used designed ankyrin repeat proteins (DARPins) to generate alternative intracellular JNK inhibitors that discriminate two very similar isoforms, JNK1 and JNK2. DARPins are small binding proteins that are well expressed, stable, and cysteine-free, which makes them ideal candidates for applications in the reducing intracellular environment. We performed ribosome display selections against JNK1α1 and JNK2α1 using highly diverse combinatorial libraries of DARPins. The selected binders specifically recognize either JNK1 or JNK2 or both isoforms in vitro and in mammalian cells. All analyzed DARPins show affinities in the low nanomolar range and isoform-specific inhibition of JNK activation in vitro at physiological ATP concentrations. Importantly, DARPins that selectively inhibit JNK activation in human cells were also identified. These results emphasize the great potential of DARPins as a novel class of highly specific intracellular inhibitors of distinct enzyme isoforms for use in biological studies and as possible therapeutic leads.
Constitution of the twin polymerase of DNA polymerase III holoenzyme. (1991)

It is speculated that DNA polymerases which duplicate chromosomes are dimeric to provide concurrent replication of both leading and lagging strands. DNA polymerase III holoenzyme (holoenzyme), is the 10-subunit replicase of the Escherichia coli chromosome. A complex of the alpha (DNA polymerase) and epsilon (3'-5' exonuclease) subunits of the holoenzyme contains only one of each protein. Presumably, one of the eight other subunit(s) functions to dimerize the alpha epsilon polymerase within the holoenzyme. Based on dimeric subassemblies of the holoenzyme, two subunits have been elected as possible agents of polymerase dimerization, one of which is the tau subunit (McHenry, C. S. (1982) J. Biol. Chem. 257, 2657-2663). Here, we have used pure alpha, epsilon, and tau subunits in binding studies to determine whether tau can dimerize the polymerase. We find tau binds directly to alpha. Whereas alpha is monomeric, tau is a dimer in its native state and thereby serves as an efficient scaffold to dimerize the polymerase. The epsilon subunit does not associate directly with tau but becomes dimerized in the alpha epsilon tau complex by virtue of its interaction with alpha. We have analyzed the dimeric alpha epsilon tau complex by different physical methods to increase the confidence that this complex truly contains a dimeric polymerase. The tau subunit is comprised of the NH2-terminal two-thirds of tau but does not bind to alpha epsilon, identifying the COOH-terminal region of tau as essential to its polymerase dimerization function. The significance of these results with respect to the organization of subunits within the holoenzyme is discussed.
Building bridges for web query classification (2006)

Web query classification (QC) aims to classify Web users' queries, which are often short and ambiguous, into a set of target categories. QC has many applications including page ranking in Web search, targeted advertisement in response to queries, and personalization. In this paper, we present a novel approach for QC that outperforms the winning solution of the ACM KDDCUP 2005 competition, whose objective is to classify 800,000 real user queries. In our approach, we first build a bridging classifier on an intermediate taxonomy in an offline mode. This classifier is then used in an online mode to map user queries to the target categories via the above intermediate taxonomy. A major innovation is that by leveraging the similarity distribution over the intermediate taxonomy, we do not need to retrain a new classifier for each new set of target categories, and therefore the bridging classifier needs to be trained only once. In addition, we introduce category selection as a new method for narrowing down the scope of the intermediate taxonomy based on which we classify the queries. Category selection can improve both efficiency and effectiveness of the online classification. By combining our algorithm with the winning solution of KDDCUP 2005, we made an improvement by 9.7% and 3.8% in terms of precision and F1 respectively compared with the best results of KDDCUP 2005.
Halftone QR codes (2013)

QR code is a popular form of barcode pattern that is ubiquitously used to tag information to products or for linking advertisements. While, on one hand, it is essential to keep the patterns machine-readable; on the other hand, even small changes to the patterns can easily render them unreadable. Hence, in absence of any computational support, such QR codes appear as random collections of black/white modules, and are often visually unpleasant. We propose an approach to produce high quality visual QR codes, which we call halftone QR codes , that are still machine-readable. First, we build a pattern readability function wherein we learn a probability distribution of what modules can be replaced by which other modules. Then, given a text tag, we express the input image in terms of the learned dictionary to encode the source text. We demonstrate that our approach produces high quality results on a range of inputs and under different distortion effects.
Migalastat improves diarrhea in patients with Fabry disease: clinical-biomarker correlations from the phase 3 FACETS trial (2018)

NCT00925301 ; June 19, 2009.
Sanofi-aventis and Regeneron Extend Therapeutic Antibody Agreement (2009)

Pharmaceutical strategic business consultancy involved in partnering, licensing, acquisitions, divestments and new business start-ups. We assist in due diligence and write expert reports for investors. We are experts in business intelligence and markets
A major human lacrimal gland mRNA encodes a new proline-rich protein family member. (1995)

The human lacrimal gland produces a previously unknown member of the proline-rich protein family. By analogy with other proline-rich proteins, this LPRP most likely mediates protective functions in the eye, such as modulation of the microflora. In contrast to other proline-rich protein genes, LPRP is expressed in the lacrimal acinar cells, and other anterior exocrine glands. LPRP should be a useful marker for human lacrimal gland acinar cell function in vitro.
Mature natural killer cells with phenotypic and functional alterations accumulate upon sustained stimulation with IL-15/IL-15Rα complexes (2010)

Cytotoxic lymphocytes such as natural killer (NK) and CD8 T cells play important roles in immunosurveillance by killing virally infected or malignant cells. The homeostatic cytokine, IL-15, promotes the development, function, and survival of NK and CD8 T cells. IL-15 is normally presented in trans as a surface complex with IL-15 receptor-alpha-chain (IL-15Rα) by dendritic cells (DCs) and monocytes. Signaling by IL-15 occurs via the IL-2/IL-15 receptor β-chain (CD122) which is expressed primarily by NK1.1(+) cells and CD8 T cells. The use of preformed complexes of IL-15 with soluble IL-15Rα complexes to boost the effector function of CD122(+) cytolytic lymphocytes such as NK and CD8 T cells has recently gained considerable attention. Here we describe the impact of transient and prolonged in vivo stimulation by IL-15/IL-15Rα complexes on NK and CD8 T cells. Whereas transitory stimulation increased the number of activated NK cells and significantly enhanced their effector function, prolonged stimulation by IL-15/IL-15Rα complexes led to a marked accumulation of mature NK cells with considerably impaired activation, cytotoxicity, and proliferative activity, and an altered balance of activating and inhibitory receptors. In contrast to NK cells, CD8 T cells exhibited an activated phenotype and robust T cell receptor stimulation and effector function upon chronic stimulation with IL-15/IL-15Rα complexes. Thus, prolonged stimulation with the strong activating signal leads to a preferential accrual of mature NK cells with altered activation and diminished functional capacity. These findings point to a negative feedback mechanism to preferentially counterbalance excessive NK cell activity and may have important implications for cytokine immunotherapy.
Symbolic Model Checking for Sequential Circuit Verification (1994)

The temporal logic model checking algorithm of Clarke, Emerson, and Sistla (1986) is modified to represent state graphs using binary decision diagrams (BDD's) and partitioned transition relations. Because this representation captures some of the regularity in the state space of circuits with data path logic, we are able to verify circuits with an extremely large number of states. We demonstrate this new technique on a synchronous pipelined design with approximately 5×10120 states. Our model checking algorithm handles full CTL with fairness constraints. Consequently, we are able to express a number of important liveness and fairness properties, which would otherwise not be expressible in CTL. We give empirical results on the performance of the algorithm applied to both synchronous and asynchronous circuits with data path logic