gebhart/patrepeval huggingface dataset:
Integrated molecular profiling of juvenile myelomonocytic leukemia (2018)

Juvenile myelomonocytic leukemia (JMML), a rare and aggressive myelodysplastic/myeloproliferative neoplasm that occurs in infants and during early childhood, is characterized by excessive myelomonocytic cell proliferation. More than 80% of patients harbor germ line and somatic mutations in RAS pathway genes (eg, <i>PTPN11</i>, <i>NF1</i>, <i>NRAS</i>, <i>KRAS</i>, and <i>CBL</i>), and previous studies have identified several biomarkers associated with poor prognosis. However, the molecular pathogenesis of 10% to 20% of patients and the relationships among these biomarkers have not been well defined. To address these issues, we performed an integrated molecular analysis of samples from 150 JMML patients. RNA-sequencing identified <i>ALK/ROS1</i> tyrosine kinase fusions (<i>DCTN1-ALK, RANBP2-ALK</i>, and <i>TBL1XR1-ROS1</i>) in 3 of 16 patients (18%) who lacked canonical RAS pathway mutations. Crizotinib, an ALK/ROS1 inhibitor, markedly suppressed <i>ALK/ROS1</i> fusion-positive JMML cell proliferation in vitro. Therefore, we administered crizotinib to a chemotherapy-resistant patient with the <i>RANBP2-ALK</i> fusion who subsequently achieved complete molecular remission. In addition, crizotinib also suppressed proliferation of JMML cells with canonical RAS pathway mutations. Genome-wide methylation analysis identified a hypermethylation profile resembling that of acute myeloid leukemia (AML), which correlated significantly with genetic markers with poor outcomes such as <i>PTPN11/NF1</i> gene mutations, 2 or more genetic mutations, an AML-type expression profile, and <i>LIN28B</i> expression. In summary, we identified recurrent activated <i>ALK/ROS1</i> fusions in JMML patients without canonical RAS pathway gene mutations and revealed the relationships among biomarkers for JMML. Crizotinib is a promising candidate drug for the treatment of JMML, particularly in patients with <i>ALK/ROS1</i> fusions.
Efficient human iPS cell derivation by a non-integrating plasmid from blood cells with unique epigenetic and gene expression signatures (2011)

To identify accessible and permissive human cell types for efficient derivation of induced pluripotent stem cells (iPSCs), we investigated epigenetic and gene expression signatures of multiple postnatal cell types such as fibroblasts and blood cells. Our analysis suggested that newborn cord blood (CB) and adult peripheral blood (PB) mononuclear cells (MNCs) display unique signatures that are closer to iPSCs and human embryonic stem cells (ESCs) than age-matched fibroblasts to iPSCs/ESCs, thus making blood MNCs an attractive cell choice for the generation of integration-free iPSCs. Using an improved EBNA1/OriP plasmid expressing 5 reprogramming factors, we demonstrated highly efficient reprogramming of briefly cultured blood MNCs. Within 14 days of one-time transfection by one plasmid, up to 1000 iPSC-like colonies per 2 million transfected CB MNCs were generated. The efficiency of deriving iPSCs from adult PB MNCs was approximately 50-fold lower, but could be enhanced by inclusion of a second EBNA1/OriP plasmid for transient expression of additional genes such as SV40 T antigen. The duration of obtaining bona fide iPSC colonies from adult PB MNCs was reduced to half (∼14 days) as compared to adult fibroblastic cells (28-30 days). More than 9 human iPSC lines derived from PB or CB blood cells are extensively characterized, including those from PB MNCs of an adult patient with sickle cell disease. They lack V(D)J DNA rearrangements and vector DNA after expansion for 10-12 passages. This facile method of generating integration-free human iPSCs from blood MNCs will accelerate their use in both research and future clinical applications.
ANTI-BACTERIAL SILVER COATINGS ON ORTHOPAEDIC METALS – AN IN VITRO AND ANIMAL STUDY (2003)

Metallic implants are used frequently in the operative repair of joints and fractures in orthopaedic surgery. Orthopaedic implant infection is chronic and biofilm based. Present treatment focuses on removing the infective substratum and implant surgically as well as prolonged anti-microbial therapy. Biofilms are up to 500 times more resistant than planktonic strains of bacterial flora to antibiotics. Silver coatings on polymers and nylon (catheters, heart valve cuffs, burn dressings) have shown inhibition of this biofilm formation in its adhesion stage. Our aim was to deposit effective, minute, antibacterial layers of silver on orthopaedic stainless steel and titanium K-wires and to investigate the effect of these coatings when exposed to Staphylococcus Aureus biofilms in an in vitro and in vivo environment. Combining magnetron sputtering with a neutral atom beam (Saddle Field) plasma source at 10 −4 mbar in argon gas at temperatures of 60°C, a silver coating of 99.9% purity was deposited onto stainless steel and titanium orthopaedic K-wires. Coating thickness measurements were obtained using glancing angle x-ray diffraction of glass slides coated adjacent to wires. Magnetron parameters were modified to produce varying thickness of silver. Adhesiveness was examined using Rockwell punch tests. Silver leaching experiments were carried out in phosphate buffered saline at 37°C for 48 hours and using inductive coupled plasma spectrometry to assess leached silver ions. Surface microscopy visualised physical changes in the coatings. Biofilm adhesion was determined by exposing wires to Staphylococcus Aureus ATCC 29213 – NCTC 12973 for 15 minutes to allow biofilm initiation and adhesion. Wires were then culturing for 24 hours at 37°C in RPMI. Subsequently, wires were sonicated at 50Hz in ringer’s solution and gently vortexed to dislodge biofilm. Sonicate was plated out by log dilution method on Columbia blood agar plates. Bacterial colonies were then counted and changes expressed in log factors. K-wires were coated with 1 to 50 nm of silver by running the magnetron sputtering at low currents. These coatings showed excellent adhesive properties within the 48 hours exposed with only 3.7% of silver leaching in buffered saline. The silver coated stainless steel wires showed a log 2.31 fold reduction in biofilm formation as compared to control wires (p We have perfected a method of depositing tiny layers of anti-bacterial silver onto stainless steel and titanium, which is anti-infective in vitro but not in vivo. Further studies involving other metal coatings such as platinum and copper are warranted.
The N-terminal end of the CH2 domain of chimeric human IgG1 anti-HLA-DR is necessary for C1q, Fc gamma RI and Fc gamma RIII binding. (1995)

We have found that amino acid residues necessary for C1q and Fc gamma R binding of human IgG1 are located in the N-terminal region of the CH2 domain, residues 231-238, using a matched set of engineered antibodies based on the anti-HLA-DR antibody L243. Changing the leucine 235 in the CH2 region of IgG3 and IgG4 to glutamic acid was already known to abolish Fc gamma RI binding. We have confirmed this for IgG1 and also found a concomitant abolition of human complement lysis with retention of Fc gamma RIII-mediated function. Changing the glycine at 237 to alanine of IgG1 also abolished Fc gamma RI binding and reduced human complement lysis and Fc gamma RIII-mediated function. Exchanging the whole region 233-236 with the sequence found in human IgG2, abolished Fc gamma RI binding and human complement lysis and reduced Fc gamma RIII-mediated function of IgG1. In contrast, a change in the previously described C1q-binding motif, from lysine at 320 to alanine, had no effect on IgG1-mediated complement lysis.
Atomic layer deposition of insulating nitride interfacial layers for germanium metal oxide semiconductor field effect transistors with high-κ oxide/tungsten nitride gate stacks (2007)

Atomic layer deposition (ALD) was used to deposit passivating interfacial nitride layers between Ge and high-κ oxides. High-κ oxides on Ge surfaces passivated by ultrathin (1–2nm) ALD Hf3N4 or AlN layers exhibited well-behaved C-V characteristics with an equivalent oxide thickness as low as 0.8nm, no significant flatband voltage shifts, and midgap density of interface states values of 2×1012cm−1eV−1. Functional n-channel and p-channel Ge field effect transistors with nitride interlayer/high-κ oxide/metal gate stacks are demonstrated.
Specificity of proliferative response of human CD8 clones to mycobacterial antigens (1988)

Human CD8 T lymphocyte clones (TLC) were generated from the pleural effusion of patients with tuberculosis using a protocol that required, in addition to antigen, coculture of purified CD8+ T cells, accessory cells, interleukin 2 (IL2) and anti-CD3-Sepharose. The TLC obtained were stimulated by mycobacterial soluble extracts in an IL2-dependent and MHC class I-restricted manner. When antigen-responsive TLC were screened with extracts from the recombinant mycobacterial library they were found to respond to either the Y3125 (100-kDa) or the Y3111 (71-kDa) lambda gt11 clones. Polyacrylamide gel immunoblot analysis demonstrated that the CD8 TLC responded to fractions with the molecular mass range 27-45 kDa in the Y3125 lysogen and 60-90 kDa in the mycobacterial soluble extract. The specificity of TLC reactive with the Y3111 clone was confirmed using the 71-kDa antigen purified from the same lysogen. These TLC recognized sequences common to the 71-kDa protein derived from mycobacteria, E. coli or a human cell line. Studies of three TLC using antigen-presenting cells of known genetic haplotype indicated that stimulation with both the Y3125 and the 71-kDa antigens were restricted by determinants encoded by HLA-B8.
Intracellular Signaling by Hydrolysis of Phospholipids and Activation of Protein Kinase C (1992)

Hydrolysis of inositol phospholipids by phospholipase C is initiated by either receptor stimulation or opening of Ca2+ channels. This was once thought to be the sole mechanism to produce the diacylglycerol that links extracellular signals to intracellular events through activation of protein kinase C. It is becoming clear that agonist-induced hydrolysis of other membrane phospholipids, particularly choline phospholipids, by phospholipase D and phospholipase A2 may also take part in cell signaling. The products of hydrolysis of these phospholipids may enhance and prolong the activation of protein kinase C. Such prolonged activation of protein kinase C is essential for long-term cellular responses such as cell proliferation and differentiation.
Engineering Egress with Edge Fabric (2017)

Large content providers build points of presence around the world, each connected to tens or hundreds of networks. Ideally, this connectivity lets providers better serve users, but providers cannot obtain enough capacity on some preferred peering paths to handle peak traffic demands. These capacity constraints, coupled with volatile traffic and performance and the limitations of the 20 year old BGP protocol, make it difficult to best use this connectivity.
Biosynthesis of a major lipofuscin fluorophore in mice and humans with ABCR -mediated retinal and macular degeneration (2000)

Increased accumulation of lipofuscin in cells of the retinal pigment epithelium (RPE) is seen in several forms of macular degeneration, a common cause of blindness in humans. A major fluorophore of lipofuscin is the toxic bis-retinoid, N-retinylidene-N-retinylethanolamine (A2E). Previously, we generated mice with a knockout mutation in the abcr gene. This gene encodes rim protein (RmP), an ATP-binding cassette transporter in rod outer segments. Mice lacking RmP accumulate A2E in RPE cells at a greatly increased rate over controls. Here, we identify three precursors of A2E in ocular tissues from abcr-/- mice and humans with ABCR-mediated recessive macular degenerations. Our results corroborate the scheme proposed by C. A. Parish, M. Hashimoto, K. Nakanishi, J. Dillon & J. Sparrow [Proc. Natl. Acad. Sci. USA (1998) 95, 14609-14613], for the biosynthesis of A2E: (i) condensation of all-trans-retinaldehyde (all-trans-RAL) with phosphatidylethanolamine to form a Schiff base; (ii) condensation of the amine product with a second all-trans-RAL to form a bis-retinoid; (iii) oxidation to yield a pyridinium salt; and (iv) hydrolysis of the phosphate ester to yield A2E. The latter two reactions probably occur within RPE phagolysosomes. As predicted by this model, formation of A2E was completely inhibited when abcr-/- mice were raised in total darkness. Also, once formed, A2E was not eliminated by the RPE. These data suggest that humans with retinal or macular degeneration caused by loss of RmP function may slow progression of their disease by limiting exposure to light. The precursors of A2E identified in this study may represent pharmacological targets for the treatment of ABCR-mediated macular degeneration.
Millimeter Wave Mobile Communications for 5G Cellular: It Will Work! (2013)

The global bandwidth shortage facing wireless carriers has motivated the exploration of the underutilized millimeter wave (mm-wave) frequency spectrum for future broadband cellular communication networks. There is, however, little knowledge about cellular mm-wave propagation in densely populated indoor and outdoor environments. Obtaining this information is vital for the design and operation of future fifth generation cellular networks that use the mm-wave spectrum. In this paper, we present the motivation for new mm-wave cellular systems, methodology, and hardware for measurements and offer a variety of measurement results that show 28 and 38 GHz frequencies can be used when employing steerable directional antennas at base stations and mobile devices.
COMBINING LOCATION AND EXPRESSION DATA FOR PRINCIPLED DISCOVERY OF GENETIC REGULATORY NETWORK MODELS (2001)

We develop principled methods for the automatic induction (discovery) of genetic regulatory network models from multiple data sources and data modalities. Models of regulatory networks are represented as Bayesian networks, allowing the models to compactly and robustly capture probabilistic multivariate statistical dependencies between the various cellular factors in these networks. We build on previous Bayesian network validation results by extending the validation framework to the context of model induction, leveraging heuristic simulated annealing search algorithms and posterior model averaging. Using expression data in isolation yields results inconsistent with location data so we incorporate genomic location data to guide the model induction process. We combine these two data modalities by allowing location data to influence the model prior and expression data to influence the model likelihood. We demonstrate the utility of this approach by discovering genetic regulatory models of thirty-three variables involved in S. cerevisiae pheromone response. The models we automatically generate are consistent with the current understanding regarding this regulatory network, but also suggest new directions for future experimental investigation.
Visualization of coupled protein folding and binding in bacteria and purification of the heterodimeric complex (2003)

During overexpression of recombinant proteins in Escherichia coli , misfolded proteins often aggregate and form inclusion bodies. If an aggregation-prone recombinant protein is fused upstream (as an N-terminal fusion) to GFP, aggregation of the recombinant protein domain also leads to misfolding of the downstream GFP domain, resulting in a decrease or loss of fluorescence. We investigated whether the GFP domain could fold correctly if aggregation of the upstream protein domain was prevented in vivo by a coupled protein folding and binding interaction. Such interaction has been previously shown to occur between the E. coli integration host factors α and β, and between the domains of the general transcriptional coactivator cAMP response element binding protein (CREB)-binding protein and the activator for thyroid hormone and retinoid receptors. In this study, fusion of integration host factor β or the CREB-binding protein domain upstream to GFP resulted in aggregation of the fusion protein. Coexpression of their respective partners, on the other hand, allowed soluble expression of the fusion protein and a dramatic increase in fluorescence. The study demonstrated that coupled protein folding and binding could be correlated to GFP fluorescence. A modified miniintein containing an affinity tag was inserted between the upstream protein domain and GFP to allow rapid purification and identification of the heterodimeric complex. The GFP coexpression fusion system may be used to identify novel protein–protein interactions that involve coupled folding and binding or protein partners that can solubilize aggregation-prone recombinant proteins.
Chaperone‐mediated autophagy is defective in mucolipidosis type IV (2008)

Mucolipidosis type IV (MLIV) is a lysosomal storage disorder caused by mutations in the MCOLN1 gene, a member of the transient receptor potential (TRP) cation channel gene family. The encoded protein, transient receptor potential mucolipin-1 (TRPML1), has been localized to lysosomes and late endosomes but the pathogenic mechanism by which loss of TRPML1 leads to abnormal cellular storage and neuronal cell death is still poorly understood. Yeast two-hybrid and co-immunoprecipitation (coIP) experiments identified interactions between TRPML1 and Hsc70 as well as TRPML1 and Hsp40. Hsc70 and Hsp40 are members of a molecular chaperone complex required for protein transport into the lysosome during chaperone-mediated autophagy (CMA). To determine the functional relevance of this interaction, we compared fibroblasts from MLIV patients to those from sex- and age-matched controls and show a defect in CMA in response to serum withdrawal. This defect in CMA was subsequently confirmed in purified lysosomes isolated from control and MLIV fibroblasts. We further show that the amount of lysosomal-associated membrane protein type 2A (LAMP-2A) is reduced in lysosomal membranes of MLIV fibroblasts. As a result of decreased CMA, MLIV fibroblasts have increased levels of oxidized proteins compared to control fibroblasts. We hypothesize that TRPML1 may act as a docking site for intralysosomal Hsc70 (ly-Hsc70) allowing it to more efficiently pull in substrates for CMA. It is also possible that TRPML1 channel activity may be required for CMA. Understanding the role of TRPML1 in CMA will undoubtedly help to characterize the pathogenesis of MLIV.
Acceleration of Cardiovascular Disease by a Dysfunctional Prostacyclin Receptor Mutation (2008)

Recent increased adverse cardiovascular events observed with selective cyclooxygenase-2 inhibition led to the withdrawal of rofecoxib (Vioxx) and valdecoxib (Bextra), but the mechanisms underlying these atherothrombotic events remain unclear. Prostacyclin is the major end product of cyclooxygenase-2 in vascular endothelium. Using a naturally occurring mutation in the prostacyclin receptor, we report for the first time that a deficiency in prostacyclin signaling through its G protein-coupled receptor contributes to atherothrombosis in human patients. We report that a prostacyclin receptor variant (R212C) is defective in adenylyl cyclase activation in both patient blood and in an in vitro COS-1 overexpression system. This promotes increased platelet aggregation, a hallmark of atherothrombosis. Our analysis of patients in 3 separate white cohorts reveals that this dysfunctional receptor is not likely an initiating factor in cardiovascular disease but that it accelerates the course of disease in those patients with the greatest risk factors. R212C was associated with cardiovascular disease only in the high cardiovascular risk cohort (n=980), with no association in the low-risk cohort (n=2293). In those at highest cardiovascular risk, both disease severity and adverse cardiovascular events were significantly increased with R212C when compared with age- and risk factor-matched normal allele patients. We conclude that for haploinsufficient mutants, such as the R212C, the enhanced atherothrombotic phenotype is likely dependent on the presence of existing atherosclerosis or injury (high risk factors), analogous to what has been observed in the cyclooxygenase-2 inhibition studies or prostacyclin receptor knockout mice studies. Combining both biochemical and clinical approaches, we conclude that diminished prostacyclin receptor signaling may contribute, in part, to the underlying adverse cardiovascular outcomes observed with cyclooxygenase-2 inhibition.
Type II membrane protein CD69 regulates the formation of resting T-helper memory (2012)

Memory T-helper (Th) lymphocytes are crucial for the maintenance of acquired immunity to eliminate infectious pathogens. We have previously demonstrated that most memory Th lymphocytes reside and rest on stromal niches of the bone marrow (BM). Little is known, however, regarding the molecular basis for the generation and maintenance of BM memory Th lymphocytes. Here we show that CD69-deficient effector CD4 T lymphocytes fail to relocate into and persist in the BM and therefore to differentiate into memory cells. Consequently, CD69-deficient CD4 T cells fail to facilitate the production of high-affinity antibodies and the generation of BM long-lived plasma cells in the late phase of immune responses. Thus, CD69 is critical for the generation and maintenance of professional memory Th lymphocytes, which can efficiently help humoral immunity in the late phase. The deficit of immunological memory in CD69-deficient mice also highlights the essential role of BM for the establishment of Th memory.
Gene expression profile changes in NB4 cells induced by realgar. (2003)

PSMC2 and PSMD1 genes may play an important role in the apoptosis and partial differentiation of NB(4) cells.
Resource Contention in Multiagent Systems (1995)

The dynamics of resource contention in multiagent systems with imperfect information can be extremely complex, ranging from nonlinear oscillations to chaotic behavior. It was shown by Hogg and Huberman that it is possible to stabilize such systems by allowing agents to follow different strategies. We now show that there is a wide range of possible strategies consistent with the existing equilibrium. As time progresses, agents explore different strategy mixes, resulting in bursts of momentary instability. These bursts eventually relax into a stable equilibrium. This mechanism of stability punctuated by bursts of erratic activity appears to be quite general in systems where agents explore strategies in search of local improvements.