gebhart/patrepeval huggingface dataset:
Human Placenta-Derived Adherent Cells Prevent Bone loss, Stimulate Bone formation, and Suppress Growth of Multiple Myeloma in Bone (2010)

Human placenta has emerged as a valuable source of transplantable cells of mesenchymal and hematopoietic origin for multiple cytotherapeutic purposes, including enhanced engraftment of hematopoietic stem cells, modulation of inflammation, bone repair, and cancer. Placenta-derived adherent cells (PDACs) are mesenchymal-like stem cells isolated from postpartum human placenta. Multiple myeloma is closely associated with induction of bone disease and large lytic lesions, which are often not repaired and are usually the sites of relapses. We evaluated the antimyeloma therapeutic potential, in vivo survival, and trafficking of PDACs in the severe combined immunodeficiency (SCID)-rab model of medullary myeloma-associated bone loss. Intrabone injection of PDACs into nonmyelomatous and myelomatous implanted bone in SCID-rab mice promoted bone formation by stimulating endogenous osteoblastogenesis, and most PDACs disappeared from bone within 4 weeks. PDACs inhibitory effects on myeloma bone disease and tumor growth were dose-dependent and comparable with those of fetal human mesenchymal stem cells (MSCs). Intrabone, but not subcutaneous, engraftment of PDACs inhibited bone disease and tumor growth in SCID-rab mice. Intratumor injection of PDACs had no effect on subcutaneous growth of myeloma cells. A small number of intravenously injected PDACs trafficked into myelomatous bone. Myeloma cell growth rate in vitro was lower in coculture with PDACs than with MSCs from human fetal bone or myeloma patients. PDACs also promoted apoptosis in osteoclast precursors and inhibited their differentiation. This study suggests that altering the bone marrow microenvironment with PDAC cytotherapy attenuates growth of myeloma and that PDAC cytotherapy is a promising therapeutic approach for myeloma osteolysis.
Can Network Coding Help in P2P Networks? (2006)

In this paper, we compare the maximum achieveable throughput using network coding with routing in P2P networks. Our analysis is based on a simple star network where there is no multicast and network coding can only be applied at the peers. Under the idealized assumption that there is perfect information to realize optimal routing, this model captures the essential elements of a P2P network, yet allows simple analysis for what can be achieved by network coding and by routing respectively. The conclusion is that there is no coding advantage. We then discuss the applicability of this result to a real P2P content distribution system which may operate at lower throughput due to various other factors. Finally, in addition to yielding insights to the present case of P2P networks, we believe this type of non-multicast network models can lead to other new results for network coding in general.
State of the art and the dark side of amyotrophic lateral sclerosis (2010)

Amyotrophic lateral sclerosis (ALS) is a disorder that involves the degeneration of motor neurons, muscle atrophy, and paralysis. In a few familiar forms of ALS, mutations in the superoxide dismutase-1 (SOD1) gene have been held responsible for the degeneration of motor neurons. Nevertheless, after the discovery of the SOD1 mutations no consensus has emerged as to which cells, tissues and pathways are primarily implicated in the pathogenic events that lead to ALS. Ubiquitous overexpression of mutant SOD1 in transgenic animals recapitulates the pathological features of ALS. However, the toxicity of mutant SOD1 is not necessarily limited to the central nervous system. Views about ALS pathogenesis are now enriched by the recent discovery of mutations in a pair of DNA/RNA-binding proteins called TDP-43 and FUS/TLS as causes of familial and sporadic forms of ALS. Although the steps that lead to the pathological state are well defined, several fundamental issues are still controversial: are the motor neurons the first direct targets of ALS; and what is the contribution of non-neuronal cells, if any, to the pathogenesis of ALS? The state of the art of ALS pathogenesis and the open questions are discussed in this review.
An implantable electrical stimulator used for peripheral nerve rehabilitation in rats (2013)

This study evaluated an implantable electrical stimulator using a sciatic nerve injury animal model, and ethological, electrophysiological and histological assessments. Forty Sprague-Dawley rats were used in the study, and were subjected to crushing of the right sciatic nerve with a micro-vessel clamp. Electrical stimulators were implanted in twenty of the rats (the implantation group), while the remaining twenty rats were assigned to the control group. At three and six weeks following the surgery, the sciatic nerve function index (SFI) and the motor nerve conduction velocity (MCV) were demonstrated to be significantly higher in the implantation group compared with the control group (P<0.05). Histological analysis, using hematoxylin and eosin (H&E) staining, showed the typical pathological atrophy, and an assessment of the nerve that had been crushed revealed distal axonal breakdown in the control group. These results suggest that the implantable electrical stimulator was effective, and was suitable for implantation in a Sprague-Dawley rat model.
Androgen Receptor Signaling in Prostate Cancer: New Twists for an Old (2011)

Secretory leukocyte protease inhibitor is a multifunctional protein with a variety of activities attributed to it. A significant increase in the expression of Secretory leukocyte protease inhibitor was noticed in syncytiotrophoblasts following differentiation of cytotrophoblasts in to syncytiotrophoblasts by addition of Forskolin. Using the BeWo cells which are derived from choriocarcinoma, the effect of addition of progesterone and estradiol on the expression of Secretory leukocyte protease inhibitor by Reverse Transcription Polymerase Chain Reaction was assessed. It was found that while addition of low concentration of progesterone resulted in a significant increase in expression of Secretory leukocyte protease inhibitor, addition of estradiol even at high concentration had no effect. The specificity of effect of progesterone was established by the observation that addition of Progesterone along with progesterone receptor antagonist (RU484) resulted in decrease in the level of expression of Secretory leukocyte protease inhibitor. These results suggest that Secretory protease leukocyte protease inhibitor is a progesterone regulated gene.
Developing Basic and Clinical Research on von Willebrand Factor and von Willebrand Disease (2000)

Studies on von Willebrand factor (vWF) and von Willebrand disease have been conceptually linked since the latter was identified as a distinct bleeding disorder (see relevant reviews and articles in the current issue of Thromb Haemost). Obvious genetic and clinical differences indicated from the beginning that the pathogenesis of the newly recognized “angiohemophilia” was distinct from that of classic hemophilia, and implied the existence of a hitherto unknown protein important for hemostasis. Eventually, the identification and characterization of vWF facilitated the efforts to categorize the heterogeneous manifestations of von Willebrand disease. Then, the demonstration of unique molecular abnormalities in variant forms of the disease greatly aided the elucidation of how vWF participates in platelet adhesion and aggregation at sites of vascular injury. The cross-fertilization between clinical studies and basic research continues, and is now leading to a clearer structural and functional understanding of vWF. Such advances should benefit patients with congenital and acquired von Willebrand disease through improved diagnosis, classification and treatment. Moreover, a better explanation of how vWF contributes to platelet function should shed light on the pathogenetic mechanisms that cause arterial thrombosis.
Radial parallel plate flow with mechanical agitation (2013)

Thesis (S.B.)--Massachusetts Institute of Technology, Department of Mechanical Engineering, 2013.
Distribution patterns of HP1, a heterochromatin-associated nonhistone chromosomal protein of Drosophila. (1989)

We have previously reported the identification of a nonhistone chromosomal protein (nhcp-19; now called HP1) preferentially associated with the heterochromatin of Drosophila melanogaster. A detailed study of the HP1 distribution pattern on polytene chromosomes by immunofluorescent staining, using monoclonal antibody C1A9, has been carried out. The results indicate that this protein is found within the centric beta-heterochromatin, in cytological regions 31, 41 and 80, and throughout polytene chromosome 4. Staining of telomeres is frequently observed, those of chromosome arms 2R and 3R and the X chromosome being the most conspicuous. Analysis of a fourth chromosome insertional translocation T(3;4)f/In(3L)P confirms an autonomous interaction with chromosome 4 material. Similarly, the beta-heterochromatin distal to light on chromosome arm 2L, moved to position 97D2 on chromosome arm 3R in the rearrangement ltx13, is prominently stained using the C1A9 antibody. Staining of intact salivary glands indicates that this rearranged segment of beta-heterochromatin is not associated with the polytene chromocenter, but provides an independent structural reference point. HP1 is not observed in the nuclei of the early syncytial embryo, but becomes concentrated in the nuclei at the syncytial blastoderm stage (ca. nuclear division cycle 10). This suggests that heterochromatin formation occurs at approximately the same stage at which nuclei first become transcriptionally competent. Thus, the C1A9 antibody may serve as a useful marker for both structural and functional studies of the Drosophila nucleus.
Anti‐α/β T cell receptor monoclonal antibody provides an efficient therapy for autoimmune diabetes in nonobese diabetic (NOD) mice (1991)

The nonobese diabetic (NOD) mouse is a relevant model for studying human insulin-dependent diabetes mellitus (IDDM). The selective destruction of insulin-secreting cells in this model is subsequent to an autoimmune reaction directed towards the beta cells inside the islets of Langerhans of the pancreas. Given the key role played by T cells in the development of IDDM, we investigated a model of IDDM prevention in NOD mice by administration of a monoclonal antibody to the alpha/beta dimer of the T cell receptor for antigen. Our data provide evidence that aiming at the T cell receptor protects against both spontaneous and cyclophosphamide-induced diabetes in the NOD mouse. Interestingly, potential clinical application is suggested by the efficient and durable reversal of recent onset diabetes in mice treated with anti-alpha/beta monoclonal antibody within 1 week following the clinical discovery of IDDM.
Poly(ethylene glycol)-Grafted Liposomes with Oligopeptide or Oligosaccharide Ligands Appended to the Termini of the Polymer Chains (1997)

Novel conjugates tailor-made for inclusion in liposomal formulations, containing distearoylphosphatidylethanolamine (DSPE) as a lipid anchor, heterobifunctional polyethylene glycol (PEG) with a molecular weight of 2000 as a linking moiety, and a biological cell adhesive ligand [YIGSR peptide or Sialyl Lewis(X) oligosaccharide (SLX)], were synthesized. They were characterized by NMR, chromatography, and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOFMS). Inclusion of either of the ligand-PEG-lipid conjugates (2 mol %) in a lecithin/cholesterol/ methoxy-PEG2000-DSPE (55:40:3 mole ratio) lipid mixture followed by preparation of unilamellar vesicles (100 nm) resulted in positioning of 55% of the YIGSR and 63% of the SLX ligands on the periphery of the outer surface-grafted polymeric "brush", as determined by a combination of specific enzymatic alterations of each ligand and HPLC. Similar densities of ligand-bearing PEG chains were incorporated into liposomes by simply incubating (37 degrees C, 5 h) either one of the ligand-PEG-lipid conjugates with preformed lipid vesicles. This conjugate insertion process was aggregation free. Using enzymatic derivatization-HPLC, it was demonstrated that all the ligands incorporated into lipid membranes by this new approach were positioned exclusively on the outer leaflet of the liposomal bilayers. Since liposomes of this type are intended for in vivo use as long-circulating, ligand-presenting platforms, the insertion approach is preferable because of the more efficient utilization of ligand-PEG-lipid conjugates.
The smcL gene of Listeria ivanovii encodes a sphingomyelinase C that mediates bacterial escape from the phagocytic vacuole (1999)

The ruminant pathogen Listeria ivanovii differs from Listeria monocytogenes in that it causes strong, bizonal haemolysis and a characteristic shovel-shaped co-operative haemolytic ('CAMP-like') reaction with Rhodococcus equi. We cloned the gene responsible for the differential haemolytic properties of L. ivanovii, smcL. It encodes a sphingomyelinase C (SMase) highly similar (> 50% identity) to the SMases from Staphylococcus aureus (beta-toxin), Bacillus cereus and Leptospira interrogans. smcL was transcribed monocistronically and was expressed independently of PrfA. Low-stringency Southern blots demonstrated that, within the genus Listeria, smcL was present only in L. ivanovii. We constructed an smcL knock-out mutant. Its phenotype on blood agar was identical to that of L. monocytogenes (i.e. weak haemolysis and no shovel-shaped CAMP-like reaction with R. equi ). This mutant was less virulent for mice, and its intracellular proliferation was impaired in the bovine epithelial-like cell line MDBK. The role of SmcL in intracellular survival was investigated using an L. monocytogenes mutant lacking the membrane-damaging determinants hly, plcA and plcB, being thus unable to grow intracellularly. Complementation of this mutant with smcL on a plasmid was sufficient to promote bacterial intracellular proliferation in MDBK cells. Transmission electron microscopy showed that SmcL mediates the disruption of the phagocytic vacuole and the release of bacteria into the cytosol. Therefore, L. ivanovii possesses a third phospholipase with membrane-damaging activity that, together with PlcA and PlcB, may act in concert with the pore-forming toxin Hly to mediate efficient escape from the vacuolar compartment. The 5' end of smcL is contiguous with the internalin locus i-inlFE, which is also specific to L. ivanovii and is required for full virulence in mice. Thus, smcL forms part of a novel virulence gene cluster in Listeria that is species specific.
Compatibility of gas turbine materials with steam cooling (2009)

Gas turbines had been traditionally used for peak load plants and remote locations as they offer advantage of low installation costs and quick start up time. Their use as a base load generator had not been feasible owing to their poor efficiency. However, with the advent of gas turbines based combined cycle plants (CCPs), continued advances in efficiency are being made. Coupled with ultra low NO{sub x} emissions, coal compatibility and higher unit output, gas turbines are now competing with conventional power plants for base load power generation. Currently, the turbines are designed with TIT of 2300{degrees}F and metal temperatures are maintained around 1700{degrees}F by using air cooling. New higher efficiency ATS turbines will have TIT as high as 2700{degrees}F. To withstand this high temperature improved materials, coatings, and advances in cooling system and design are warranted. Development of advanced materials with better capabilities specifically for land base applications are time consuming and may not be available by ATS time frame or may prove costly for the first generation ATS gas turbines. Therefore improvement in the cooling system of hot components, which can take place in a relatively shorter time frame, is important. One way to improve cooling efficiency is to use better cooling agent. Steam as an alternate cooling agent offers attractive advantages because of its higher specific heat (almost twice that of air) and lower viscosity.
Slr1293 in Synechocystis sp. Strain PCC 6803 Is the C-3′,4′ Desaturase (CrtD) Involved in Myxoxanthophyll Biosynthesis (2004)

When grown at high light intensity, more than a quarter of the total carotenoids in the unicellular cyanobacterium Synechocystis consists of myxoxanthophyll, a polar carotenoid glycoside. The biosynthetic pathway of myxoxanthophyll is unknown but is presumed to involve a number of enzymes, including a C-3',4' desaturase required to add one double bond to generate 11 conjugated double bonds in the monocyclic myxoxanthophyll. A candidate for this desaturase is Slr1293, which was identified by genome similarity searching. To determine whether Slr1293 is a desaturase recognizing neurosporene and lycopene, slr1293 was expressed in Escherichia coli strains accumulating neurosporene or lycopene. Confirming such a desaturase function for Slr1293, these E. coli strains accumulated 3',4'-didehydroneurosporene and 3',4'-didehydrolycopene, respectively. Indeed, deletion of slr1293 in Synechocystis provides further evidence that Slr1293 is a desaturase recognizing neurosporene: In the slr1293 deletion mutant, neurosporene was found to accumulate and was further processed to produce neurosporene glycoside. Neurosporene hereby becomes a primary candidate to be the branch point molecule between carotene and myxoxanthophyll biosynthesis in this cyanobacterium. The slr1293 gene was concluded to encode a C-3',4' desaturase that is essential for myxoxanthophyll biosynthesis, and thus it was designated as crtD. Furthermore, as Slr1293 appears to recognize neurosporene and to catalyze the first committed step on the myxoxanthophyll biosynthesis pathway, Slr1293 plays a pivotal role in directing a portion of the precursor pool for carotenoid biosynthesis toward myxoxanthophyll biosynthesis in Synechocystis sp. strain PCC 6803.
Tandem extraction strategy for separation of metallic and semiconducting SWCNTs using condensed benzenoid molecules: effects of molecular morphology and solvent (2009)

Separation of metallic and semiconducting single-walled carbon nanotubes (SWCNTs) is of great importance for SWCNT-based nano-electronics. We propose a tandem extraction strategy for efficient separation of different types of SWCNTs. This strategy is based on chiral angle discriminated adsorption of soluble condensed benzenoid aromatic molecules on SWCNTs, which induce different dispersibility of SWCNTs in various organic solvents. The proposed tandem extraction strategy involves two extraction steps, in which the first step extracts metallic SWCNTs with large chiral angles and the subsequent step enriches large chiral angle semiconducting SWCNTs. This separation strategy is tested on a series of condensed benzenoid aromatic molecules. Both experimental and theoretical results show that the separation efficiency is strongly dependent on the molecular morphology, i.e. higher aspect ratio gives better separation results. The separation efficiency is also dependent on the SWCNT diameter and the solvent properties. This tandem extraction strategy may also be applied to other available noncovalent separation reagents to improve their separation efficiency.
Winter Flounder “Antifreeze” Proteins:  Synthesis and Ice Growth Inhibition of Analogues that Probe the Relative Importance of Hydrophobic and Hydrogen-Bonding Interactions (1999)

Two series of mutant polypeptides of the type I, 37-residue winter flounder “antifreeze” protein have been synthesized and analyzed by nanoliter osmometry, the “ice hemisphere” test, measurement of ice growth hysteresis and circular dichroism (CD) spectroscopy. In series 1 peptides the central two threonines and all four threonines of the native protein were mutated to serine. In series 2 peptides two additional salt bridges (K7, E11 and K29, E33) were incorporated, and all four threonine residues in this sequence were mutated simultaneously to each of serine, valine, alanine, and glycine, respectively. The CD studies showed that all mutants are 100% helical in structure at low temperature, except for the glycine derivative which was estimated to be 70% α-helical. Dilute solutions of serine-substituted series 1 peptides showed no detectable, nonbasal faceting, or hysteresis behavior, indicating either no or extremely weak interaction with ice. The analogous serine-substituted mutant in series 2, as well as the glycine derivative, displayed unfaceted growth and showed no hysteresis. Hysteresis values, ice growth patterns, and the helicity measurements showed that the additional salt bridges present in series 2 peptides do not alter significantly the properties of the protein. The valine-substituted mutant gave a distinct etching pattern in which polypeptide accumulates on the {2 0 2̄ 1}plane of ice 1h, and exhibited thermal hysteresis comparable to that of the native protein. In the case of the alanine-substituted mutant, reduced hysteresis behavior was measured, together with a distinct etch pattern in the ice hemisphere test. These combined results show that existing hypotheses for the action of native winter flounder peptide are incorrect; these hypotheses include models in which the -OH groups on four threonine side chains, equally spaced 11 residues apart on the 37-residue native polypeptide, are responsible for “binding” of the molecule to the ice/water interface. The antifreeze activity of the valine- and alanine-substituted mutants indicate a significant contribution to the mechanism of ice growth inhibition by type I antifreeze proteins from the hydrophobic methyl group in threonine and valine. Arguments against the importance of the role of hydrogen-bonding are summarized, and alternate ice growth inhibition mechanisms that include hydrophobic interactions are discussed.
Evolutionarily emerged G tracts between the polypyrimidine tract and 3′ AG are splicing silencers enriched in genes involved in cancer (2014)

The 3′ splice site (SS) at the end of pre-mRNA introns has a consensus sequence (Y)nNYAG for constitutive splicing of mammalian genes. Deviation from this consensus could change or interrupt the usage of the splice site leading to alternative or aberrant splicing, which could affect normal cell function or even the development of diseases. We have shown that the position “N” can be replaced by a CA-rich RNA element called CaRRE1 to regulate the alternative splicing of a group of genes. Taking it a step further, we searched the human genome for purine-rich elements between the -3 and -10 positions of the 3′ splice sites of annotated introns. This identified several thousand such 3′SS; more than a thousand of them contain at least one copy of G tract. These sites deviate significantly from the consensus of constitutive splice sites and are highly associated with alterative splicing events, particularly alternative 3′ splice and intron retention. We show by mutagenesis analysis and RNA interference that the G tracts are splicing silencers and a group of the associated exons are controlled by the G tract binding proteins hnRNP H/F. Species comparison of a group of the 3′SS among vertebrates suggests that most (~87%) of the G tracts emerged in ancestors of mammals during evolution. Moreover, the host genes are most significantly associated with cancer. We call these elements together with CaRRE1 regulatory RNA elements between the Py and 3′AG (REPA). The emergence of REPA in this highly constrained region indicates that this location has been remarkably permissive for the emergence of de novo regulatory RNA elements, even purine-rich motifs, in a large group of mammalian genes during evolution. This evolutionary change controls alternative splicing, likely to diversify proteomes for particular cellular functions.