gebhart/patrepeval huggingface dataset:
In multiple myeloma, t(4;14)(p16;q32) is an adverse prognostic factor irrespective of FGFR3 expression (2003)

This study analyzed the frequency and clinical significance of t(4;14)(p16;q32) in multiple myeloma (MM) among 208 patients with MM and 52 patients with monoclonal gammopathy of undetermined significance (MGUS); diagnosed between 1994 and 2001. Patients with the translocation were identified using reverse transcription-polymerase chain reaction (RT-PCR) to detect hybrid immunoglobulin heavy chain (IgH)-MMSET transcripts from the der(4) chromosome. We found 31 (14.9%) t(4;14)(+) MM patients and 1 (1.9%) t(4;14)(+) MGUS patient. IgH-MMSET hybrid transcripts were detected in bone marrow (BM) and blood. Breakpoint analysis revealed that 67.7% of t(4;14)(+) patients expressed hybrid transcripts potentially encoding full-length MMSET, whereas the remainder lacked one or more amino terminal exons. Expression of fibroblast growth factor receptor 3 (FGFR3), presumptively dysregulated on der(14), was detected by RT-PCR in only 23 of 31 (74%) patients with t(4;14)(+) MM. Patients lacking FGFR3 expression also lacked detectable der(14) products. Longitudinal analysis of 53 MM patients with multiple BM and blood samples showed that, over time, BM from t(4;14)(+) patients remained positive and that t(4;14)(-) patients did not acquire the translocation. IgH-MMSET hybrid transcripts and FGFR3 transcripts disappeared from blood during response to therapy. No correlation was observed between the occurrence of t(4;14) and known prognostic indicators. However, we find the t(4;14) translocation predicts for poor survival (P =.006; median, 644 days vs 1288 days; hazard ratio [HR], 2.0), even in FGFR3 nonexpressors (P =.003). The presence of t(4;14) is also predictive of poor response to first-line chemotherapy (P =.05). These results indicate a significant clinical impact of the t(4;14) translocation in MM that is independent of FGFR3 expression.
Biological functions of casein kinase 1 isoforms and putative roles in tumorigenesis (2014)

Isoforms of the casein kinase 1 (CK1) family have been shown to phosphorylate key regulatory molecules involved in cell cycle, transcription and translation, the structure of the cytoskeleton, cell-cell adhesion and receptor-coupled signal transduction. They regulate key signaling pathways known to be critically involved in tumor progression. Recent results point to an altered expression or activity of different CK1 isoforms in tumor cells. This review summarizes the expression and biological function of CK1 family members in normal and malignant cells and the evidence obtained so far about their role in tumorigenesis.
A Round-trip Delay Metric for IPPM (1999)

This memo defines a metric for round-trip delay of packets across Internet paths. It builds on notions introduced and discussed in the IPPM Framework document, RFC 2330 [1], and follows closely the corresponding metric for One-way Delay ("A One-way Delay Metric for IPPM") [2]; the reader is assumed to be familiar with those documents.
<title>Content-addressable polychromatic neural net using a specially doped LiNbO3 photorefractive crystal</title> (1993)

In this paper, a polychromatic neural net using a specially doped LiNbO<SUB>3</SUB> photorefractive crystal is presented. This neural net is a two-level high-content addressable memory. The first level is a polychromatic Hamming net for color image classification, and the second level is a mapping net, based on a photorefractive crystal associative memory. The major advantage of this neural net must be the large storage capacity and it requires fewer interconnection links. Experimental demonstrations are provided, in which we have shown that the proposed neural net is consistent with the theoretical model.
Chemical procedures for enzyme immobilization on porous cellulose beads (1977)

In a previous article, the method of preparation and the physical properties of porous (75 to 80% porosity) cellulose beads were described (Biotechnol. Bioeng., 18, 1057 (1976). The present article reports that the chemical procedures employed for immobilizing enzymes on ordinary cellulose can be applied to the porous cellulose beads. The results showed more enzyme loading on the beads than ordinary cellulose. The choice of the procedures might also affect the mechanical strength of the cellulose beads.
Maturation of Escherichia coli maltose-binding protein by signal peptidase I in vivo. Sequence requirements for efficient processing and demonstration of an alternate cleavage site. (1990)

Comparative analyses of a number of secretory proteins processed by eukaryotic and prokaryotic signal peptidases have identified a strongly conserved feature regarding the residues positioned -3 and -1 relative to the cleavage site. These 2 residues of the signal peptide are thought to constitute a recognition site for the processing enzyme and are usually amino acids with small, neutral side chains. It was shown previously that the substitution of aspartic acid for alanine at -3 of the Escherichia coli maltose-binding protein (MBP) signal peptide blocked maturation by signal peptidase I but had no noticeable effect or MBP translocation across the cytoplasmic membrane of its biological activity. This identified an excellent system in which to undertake a detailed investigation of the structural requirements and limitations for the cleavage site. In vitro mutagenesis was used to generate 14 different amino acid substitutions at -3 and 13 different amino acid substitutions at -1 of the MBP signal peptide. The maturation of the mutant precursor species expressed in vivo was examined. Overall, the results obtained agreed fairly well with statistically derived models of signal peptidase I specificity, except that cysteine was found to permit efficient processing when present at either -3 and -1, and threonine at -1 resulted in inefficient processing. Interestingly, it was found that substitutions at -1 which blocked processing at the normal cleavage site redirected processing, with varying efficiencies, to an alternate site in the signal peptide represented by the Ala-X-Ala sequence at positions -5 to -3. The substitution of aspartic acid for alanine at -5 blocked processing at this alternate site but not the normal site. The amino acids occupying the -5 and -3 positions in many other prokaryotic signal peptides also have the potential for constituting alternate processing sites. This appears to represent another example of redundant information contained within the signal peptide.
Development of New Benzenesulfonamides As Potent and Selective Nav1.7 Inhibitors for the Treatment of Pain (2017)

By taking advantage of certain features in piperidine 4, we developed a novel series of cyclohexylamine- and piperidine-based benzenesulfonamides as potent and selective Na<sub>v</sub>1.7 inhibitors. However, compound 24, one of the early analogs, failed to reduce phase 2 flinching in the mouse formalin test even at a dose of 100 mpk PO due to insufficient dorsal root ganglion (DRG) exposure attributed to poor membrane permeability. Two analogs with improved membrane permeability showed much increased DRG concentrations at doses of 30 mpk PO, but, confoundingly, only one of these was effective in the formalin test. More data are needed to understand the disconnect between efficacy and exposure relationships.
How to Control and Utilize Crowd‐Collected Speech (2013)

This chapter describes several efforts at collecting audio data using mechanical turk (MTurk). The authors address two overarching characteristics of speech resources that researchers may be particularly concerned with: quality and variety. The first experiments, initially presented in McGraw 
et al.
, cover the simple collection of read speech with Amazon Mechanical Turk (MTurk), using the standard mechanisms. The final set of experiments in the chapter describes an attempt to move beyond paid crowdsourcing and collect data from a large, preexisting user base. In this final set of experiments, the authors place speech data collection in the context of games with a purpose (GWAP). In doing so, the authors examine the implications of placing a speech recognizer in the loop in the game scenario. The chapter ends with a discussion of how various automated mechanisms for verification of transcription quality affected word error rate (WER).
High level expression of functional full length and truncated glucocorticoid receptor in Chinese hamster ovary cells. Demonstration of ligand-induced down-regulation of expressed receptor mRNA and protein (1991)

Full length human glucocorticoid receptor and truncated receptor derivatives lacking the major amino-terminal trans-activating domain were expressed in stably transfected Chinese hamster ovary (CHO) cells. The receptors were co-expressed together with human metallothionein IIa, and the expression levels were amplified in the presence of increasing concentrations of metal. In amplified cells, both synthesized receptor forms showed the expected molecular weights, as assayed by affinity labeling and immunoblotting. They were expressed at concentrations of about 350,000-520,000 molecules/cell which corresponds to a 10-fold increase in receptor levels as compared to rat liver cells. The hormone (agonist or antagonist) binding properties of the expressed proteins were very similar to those characteristic of authentic glucocorticoid receptors in tissues or cultured cells. Moreover, the expressed proteins specifically recognized a glucocorticoid-response element sequence motif in in vitro protein-DNA binding experiments. The activation of a glucocorticoid-responsive reporter gene by the expressed full length receptor was dramatic (about 75-fold) and strictly ligand-dependent. In contrast, the expressed amino-terminal deletion mutant exhibited considerably weaker functional activity but showed normal hormone-binding properties. Upon exposure to dexamethasone in vivo, the expressed receptor mRNAs and proteins were down-regulated about 2- to 6-fold, indicating that regulatory signals important for autoregulation may be contained within structures corresponding to the ligand and DNA-binding domains. Transcription from the expression vector was not negatively regulated from the hormone, strongly arguing that receptor down-regulation was due to a post-transcriptional mechanism. In conclusion, this expression system should be a useful tool for further structural and functional studies of the receptor, including the biochemistry of its activation from a cryptic to a functional species, and its ligand-dependent autoregulation.
A Gene Delivery System Activatable by Disease-Associated Matrix Metalloproteinases (1997)

We are developing protease-activatable gene delivery vehicles for selective gene delivery to protease-expressing cells. Angiogenesis, inflammation, and cancer invasion are linked to the overexpression of matrix metalloproteinases (MMPs), which destroy the extracellular matrix. Therefore, the MMPs are promising targets for therapy. We have displayed epidermal growth factor (EGF) on retroviral vector particles as an MMP-cleavable amino-terminal extension of the 4070A murine leukemia virus (MLV) envelope glycoprotein. This was achieved by engineering an MMP-cleavage signal (PLGLWA) into the linker between the EGF domain and the 4070A SU. The chimeric envelope was expressed and incorporated into viral particles, and the EGF domain could be cleaved from the surface of the viral particles by gelatinase A (MMP-2). The MMP-sensitive vector and control MMP-insensitive vectors could bind, via their displayed EGF domains, to EGF receptors on A431 cells but were unable to infect them because the EGF receptor (EGFR) does not support postbinding steps required for retroviral entry. In the presence of exogenous MMPs, the infectivity of the MMP-sensitive vector, but not of the MMP-insensitive vectors, was restored on A431 cells, and this cleavage activation could be partially blocked by MMP inhibitors. Endogenous MMPs produced by EGFR-positive HT 1080 cells could selectively activate the MMP-sensitive vector giving rise to a titer that was 1,000-fold higher on HT 1080 cells than on MMP-negative A431 cells. Inhibitor studies and gelatin zymograms indicated that the membrane-associated MT-MMP expressed on the HT 1080 cells played an important role in cleavage activation of the vector. When presented simultaneously with both EGFR-positive cell lines A431 and HT 1080, the vector could efficiently discriminate between the two different cell types, infecting the MMP-positive HT 1080 cells in preference over the A431 cells.
Pyridazines. Part 26: Efficient and Regioselective Pd-Catalysed Arylation of 4-Bromo-6-chloro-3-phenylpyridazine (2002)

The regioselective arylation at position 4 of 4-bromo-6-chloro-3-phenylpyridazine has been performed using a Suzuki cross-coupling reaction. This route allows access to a wide-ranging series of pharmacologically useful pyridazine derivatives and confirms the usefulness of chloropyridazines as a masking group for the carbonyl moiety in cross-coupling reactions involving 5-bromo-3(2H)-pyridazinones.
Gene expression profiling of porokeratosis (2008)

Here, we report that keratinocytes (KCs)-harboring lesions have activated and overexpressed wound-induced keratin genes, which appear to be coregulated with other genes involved in mediating epidermal differentiation, intercellular communication and immunity. This study, from the perspective of gene profiling, supports that gene misregulation in PK mimics that of psoriasis. Our data indicate that the genes implicated in the T-cell-mediated immune response pathway and activation of KCs play a key role in the pathogenesis of PK.
FcRn: an IgG receptor on phagocytes with a novel role in phagocytosis (2006)

Here, we report that the MHC class I-related neonatal Fc receptor (FcRn) is expressed within azurophilic and specific granules of neutrophils and relocates to phagolysosomes on phagocytosis of IgG-opsonized bacteria. We found FcRn to enhance phagocytosis in a pH-dependent manner which was independent of IgG recycling. IgG-opsonized bacteria were inefficiently phagocytosed by neutrophils from beta2M knock-out or FcRn alpha-chain knock-out mice, which both lack expression of FcRn. Similarly, low phagocytic activity was also observed with mutated IgG (H435A), which is incapable of binding to FcRn, while retaining normal binding to classical leukocyte Fcgamma receptors. Finally, a TAT peptide representing intracellular endocytosis and transport motifs within FcRn strongly inhibited IgG-mediated phagocytosis. These findings support a novel concept in which FcRn fulfills a major role in IgG-mediated phagocytosis.
miR-634 Activates the Mitochondrial Apoptosis Pathway and Enhances Chemotherapy-Induced Cytotoxicity (2015)

Some tumor-suppressing miRNAs target multiple oncogenes concurrently and therefore may be useful as cancer therapeutic agents. Further, such miRNAs may be useful to address chemotherapeutic resistance in cancer, which remains a primary clinical challenge in need of solutions. Thus, cytoprotective processes upregulated in cancer cells that are resistant to chemotherapy are a logical target for investigation. Here, we report that overexpression of miR-634 activates the mitochondrial apoptotic pathway by direct concurrent targeting of genes associated with mitochondrial homeostasis, antiapoptosis, antioxidant ability, and autophagy. In particular, we show how enforced expression of miR-634 enhanced chemotherapy-induced cytotoxicity in a model of esophageal squamous cell carcinoma, where resistance to chemotherapy remains clinically problematic. Our findings illustrate how reversing miR-634-mediated cytoprotective processes may offer a broadly useful approach to improving cancer therapy.
Risk Algorithm Using Serial Biomarker Measurements Doubles the Number of Screen-Detected Cancers Compared With a Single-Threshold Rule in the United Kingdom Collaborative Trial of Ovarian Cancer Screening (2015)

Screening by using ROCA doubled the number of screen-detected iEOCs compared with a fixed cutoff. In the context of cancer screening, reliance on predefined single-threshold rules may result in biomarkers of value being discarded.
Late sodium current in the pathophysiology of cardiovascular disease: consequences of sodium–calcium overload (2006)

Late sodium current in cardiac cells is very small compared with the fast component, but as it flows throughout the action potential it may make a substantial contribution to sodium loading during each cardiac cycle. Late sodium current may contribute to triggering arrhythmia in two ways: by causing repolarisation failure (early after depolarisations); and by triggering late after depolarisations attributable to calcium oscillations in sodium-calcium overload conditions. Reduction of late sodium current would therefore be expected to have therapeutic benefits, particularly in disease states such as ischaemia in which sodium-calcium overload is a major feature.
The Uptake and Cellular Distribution of Zinc in Saccharomyces cerevisiae (1987)

Zn2+ uptake by Saccharomyces cerevisiae was biphasic. The first phase was independent of metabolic energy, consisting of adsorption to the cell surface, and followed a Freundlich isotherm. The second phase was dependent on metabolic energy, ATPase activity and the transmembrane proton gradient, and consisted of uptake into the cell. Energy-dependent uptake showed Michaelis-Menten kinetics with a K m of 3·7μm-Zn2+ and a V max of 1·6 nmol min-1 per 107 cells at Zn2+ concentrations below 80 μm but deviated at higher concentrations. K+ and Mg2+ inhibited energy-dependent Zn2+ uptake while Na+ and Ca2+ did not. The effect of heavy metals was complex and included both inhibition and stimulation of Zn2+ uptake. K+ efflux accompanied Zn2+ uptake at all Zn2+ concentrations but there was no simple stoichiometric relationship between the two. Toxic effects of Zn2+ such as inhibition of H+ efflux and K+ uptake and reduction of viability were observed at all Zn2+ concentrations and toxicity appeared to be a major factor in K+ efflux. Toxicity also affected the kinetics of Zn2+ uptake, being a major cause of deviation from Michaelis-Menten kinetics. Zn2+ was compartmented within the cell: 56 % of the total intracellular pool was in the soluble vacuolar fraction, 39 % was bound to insoluble components and only 5 % was found in the cytosol. Isolated yeast vacuoles possessed an ATP-dependent Zn2+ uptake system whose properties were consistent with a Zn2+/H+ antiport.
CpG Motifs in Bacterial DNA Activate Leukocytes Through the pH-Dependent Generation of Reactive Oxygen Species (1998)

B cells and monocytes endocytose DNA into an acidified intracellular compartment. If this DNA contains unmethylated CpG dinucleotides in particular base contexts (CpG motifs), these leukocytes are rapidly activated. We now show that both B cell and monocyte-like cell line responses to DNA containing CpG motifs (CpG DNA) are sensitive to endosomal acidification inhibitors; they are completely blocked by bafilomycin A, chloroquine, and monensin. The specificity of these inhibitors is demonstrated by their failure to prevent responses to LPS, PMA, or ligation of CD40 or IgM. Acidification of endosomal CpG DNA is coupled to the rapid generation of intracellular reactive oxygen species. The CpG DNA-induced reactive oxygen species burst is linked to the degradation of IkappaB and the activation of NFkappaB, which induces leukocyte gene transcription and cytokine secretion. These studies demonstrate a novel pathway of leukocyte activation triggered by CpG motifs.
Continuous Delivery of Stromal Cell-Derived Factor-1 from Alginate Scaffolds Accelerates Wound Healing (2010)

Proper wound diagnosis and management is an increasingly important clinical challenge and is a large and growing unmet need. Pressure ulcers, hard-to-heal wounds, and problematic surgical incisions are emerging at increasing frequencies. At present, the wound-healing industry is experiencing a paradigm shift towards innovative treatments that exploit nanotechnology, biomaterials, and biologics. Our study utilized an alginate hydrogel patch to deliver stromal cell-derived factor-1 (SDF-1), a naturally occurring chemokine that is rapidly overexpressed in response to tissue injury, to assess the potential effects SDF-1 therapy on wound closure rates and scar formation. Alginate patches were loaded with either purified recombinant human SDF-1 protein or plasmid expressing SDF-1 and the kinetics of SDF-1 release were measured both in vitro and in vivo in mice. Our studies demonstrate that although SDF-1 plasmid- and protein-loaded patches were able to release therapeutic product over hours to days, SDF-1 protein was released faster (in vivo K(d) 0.55 days) than SDF-1 plasmid (in vivo K(d) 3.67 days). We hypothesized that chronic SDF-1 delivery would be more effective in accelerating the rate of dermal wound closure in Yorkshire pigs with acute surgical wounds, a model that closely mimics human wound healing. Wounds treated with SDF-1 protein (n = 10) and plasmid (n = 6) loaded patches healed faster than sham (n = 4) or control (n = 4). At day 9, SDF-1-treated wounds significantly accelerated wound closure (55.0 +/- 14.3% healed) compared to nontreated controls (8.2 +/- 6.0%, p < 0.05). Furthermore, 38% of SDF-1-treated wounds were fully healed at day 9 (vs. none in controls) with very little evidence of scarring. These data suggest that patch-mediated SDF-1 delivery may ultimately provide a novel therapy for accelerating healing and reducing scarring in clinical wounds.
A region of the 5' noncoding region of foot-and-mouth disease virus RNA directs efficient internal initiation of protein synthesis within cells: involvement with the role of L protease in translational control (1990)

Plasmids encoding bicistronic mRNAs have been constructed and used to identify a region from the 5' noncoding region of foot-and-mouth disease virus (FMDV) which directs efficient internal initiation of protein synthesis within cells. The loss of about 30 nucleotides (nt) from the 5' terminus or about 50 nt from the 3' terminus of the 435-nt region completely abolished the activity of this region. The expression of the FMDV L protease severely inhibited the expression of other genes unless they were preceded by this element. The regulation of protein synthesis mediated by FMDV is discussed.
Screening and Characterization of Squalene-Producing Thraustochytrids from Hong Kong Mangroves (2009)

Eighteen strains of thraustochytrids were newly isolated from Hong Kong mangroves, and their fatty acid and squalene contents were analyzed. All strains could grow well heterotrophically with glucose as the sole carbon source. All of them had the typical fatty acid profile of thraustchytrids and could produce a large amount of docosahexaenoic acid. The cell dry weight ranged from 5.49 to 15.62 g/L and squalene content from 0.02 to 0.18 mg/g at 72 h. The highest squalene-producing strain, BR-MP4-A1 was identified as a new strain of Aurantiochytrium species through sequence comparison of the 18S rRNA gene. The highest biomass of Aurantiochytrium sp. BR-MP4-A1 was achieved at 72 h, whereas its squalene content reached the maximum of 0.567 mg/g at 36 h but decreased rapidly thereafter. The production of squalene by thraustochytrids might be highly influenced by culture conditions.