gebhart/patrepeval huggingface dataset:
Conversion of a Tyrosine Kinase Protein Substrate to a High Affinity Ligand by ATP Linkage (2003)

Protein kinases often show low affinity for their protein substrates, which makes it difficult to study kinase-substrate interactions. Here, we show using expressed protein ligation with the signaling protein Src that it is feasible to install a covalently linked ATP moiety into the tail of Src, generating a semisynthetic protein with a high affinity for its cognate tyrosine kinase, Csk. It is also established that this Src-ATP conjugate can be used to selectively pull down Csk from a complex protein mixture. This work outlines a general strategy for identifying an unknown kinase that is responsible for the phosphorylation of a protein substrate on a site of interest.
An endangered oasis of aquatic microbial biodiversity in the Chihuahuan desert (2006)

The Cuatro Cienegas basin in the Chihuahuan desert is a system of springs, streams, and pools. These ecosystems support >70 endemic species and abundant living stromatolites and other microbial communities, representing a desert oasis of high biodiversity. Here, we combine data from molecular microbiology and geology to document the microbial biodiversity of this unique environment. Ten water samples from locations within the Cuatro Cienegas basin and two neighboring valleys as well as three samples of wet sediments were analyzed. The phylogeny of prokaryotic populations in the samples was determined by characterizing cultured organisms and by PCR amplification and sequencing of 16S rRNA genes from total community DNA. The composition of microbial communities was also assessed by determining profiles of terminal restriction site polymorphisms of 16S rRNA genes in total community DNA. There were 250 different phylotypes among the 350 cultivated strains. Ninety-eight partial 16S rRNA gene sequences were obtained and classified. The clones represented 38 unique phylotypes from ten major lineages of Bacteria and one of Archaea. Unexpectedly, 50% of the phylotypes were most closely related to marine taxa, even though these environments have not been in contact with the ocean for tens of millions of years. Furthermore, terminal restriction site polymorphism profiles and geological data suggest that the aquatic ecosystems of Cuatro Cienegas are hydrologically interconnected with adjacent valleys recently targeted for agricultural intensification. The findings underscore the conservation value of desert aquatic ecosystems and the urgent need for study and preservation of freshwater microbial communities.
Immunomodulatory drug CC-5013 overcomes drug resistance and is well tolerated in patients with relapsed multiple myeloma (2002)

Thalidomide (Thal) can overcome drug resistance in multiple myeloma (MM) but is associated with somnolence, constipation, and neuropathy. In previous in vitro studies, we have shown that the potent immunomodulatory derivative of thalidomide (IMiD) CC-5013 induces apoptosis or growth arrest even in resistant MM cell lines and patient cells, decreases binding of MM cells to bone marrow stromal cells (BMSCs), inhibits the production in the BM milieu of cytokines (interleukin-6 [IL-6], vascular endothelial growth factor [VEGF], tumor necrosis factor-alpha [TNF-alpha]) mediating growth and survival of MM cells, blocks angiogenesis, and stimulates host anti-MM natural killer (NK) cell immunity. Moreover, CC-5013 also inhibits tumor growth, decreases angiogenesis, and prolongs host survival in a human plasmacytoma mouse model. In the present study, we carried out a phase 1 CC-5013 dose-escalation (5 mg/d, 10 mg/d, 25 mg/d, and 50 mg/d) study in 27 patients (median age 57 years; range, 40-71 years) with relapsed and refractory relapsed MM. They received a median of 3 prior regimens (range, 2-6 regimens), including autologous stem cell transplantation and Thal in 15 and 16 patients, respectively. In 24 evaluable patients, no dose-limiting toxicity (DLT) was observed in patients treated at any dose level within the first 28 days; however, grade 3 myelosuppression developed after day 28 in all 13 patients treated with 50 mg/d CC-5013. In 12 patients, dose reduction to 25 mg/d was well tolerated and therefore considered the maximal tolerated dose (MTD). Importantly, no significant somnolence, constipation, or neuropathy has been seen in any cohort. Best responses of at least 25% reduction in paraprotein occurred in 17 (71%) of 24 patients (90% confidence interval [CI], 52%-85%), including 11 (46%) patients who had received prior Thal. Stable disease (less than 25% reduction in paraprotein) was observed in an additional 2 (8%) patients. Therefore, 17 (71%) of 24 patients (90% CI, 52%-85%) demonstrated benefit from treatment. Our study therefore provides the basis for the evaluation of CC-5013, either alone or in combination, to treat patients with MM at earlier stages of disease.
Flying Under the Radar: The Immunobiology of Hepatitis C (2006)

The hepatitis C virus (HCV) is a remarkably successful pathogen, establishing persistent infection in more than two-thirds of those who contract it. Its success is related to its abilities to blunt innate antiviral pathways and to evade adaptive immune responses. These two themes may be related. We propose that HCV takes advantage of the impaired innate response to delay the organization of an effective adaptive immune attack. The tolerogenic liver environment may provide cover, prolonging this delay. HCV's error-prone replication strategy permits rapid evolution under immune pressure. Persistent high levels of viral antigens may contribute to immune exhaustion. Finally, the virus may benefit from the efficient enlistment of memory T and B cells in the pursuit of a moving target.
An evaluation of the cost‐effectiveness of omalizumab for the treatment of severe allergic asthma (2008)

Omalizumab is the first licensed anti-immunoglobulin (Ig) E antibody shown to be effective for treatment of allergic (IgE-mediated) asthma. Recent international guidelines recommend omalizumab as add-on treatment to fixed dose inhaled corticosteroid (ICS) and long-acting beta(2)-agonist (LABA) combination therapy. However, omalizumab is more expensive than other current asthma treatments and health and reimbursement authorities are increasingly demanding evidence of economic benefit to support pricing and formulary listing. The aims of this article are to (i) summarize data on the human and economic burden of severe asthma, (ii) summarize the efficacy data obtained for omalizumab in clinical trials in patients with inadequately controlled severe persistent allergic asthma despite high-dose ICS plus a LABA, and (iii) discuss the cost-effectiveness evidence published for omalizumab in this patient population. A wealth of evidence exists highlighting that the health, economic and societal burden of asthma is considerable and is highly skewed towards patients with severe asthma, particularly when asthma is inadequately controlled. Omalizumab is clinically beneficial in patients with severe persistent allergic asthma despite high-dose ICS plus a LABA, particularly in a subgroup of patients who respond to therapy. In patients who respond to therapy, the cost-effectiveness of omalizumab compares well with other biologic treatments for chronic illness.
S1P3-mediated cardiac fibrosis in sphingosine kinase 1 transgenic mice involves reactive oxygen species (2009)

These results suggest that chronic activation of SPHK1-S1P signalling results in both pathological cardiac remodelling through ROS mediated by S1P3 and favourable cardioprotective effects.
The complement system in ischemic heart disease. (1990)

The mechanisms by which tissue injury after acute myocardial infarction (AMI) occurs has not been fully elucidated. Recent evidence in experimental models has suggested involvement of the complement system in microvascular and macrovascular injury subsequent to AMI. With respect to angina pectoris, whether or not the complement system is activated is not clear. The present study assessed the role of complement as a mediator of myocardial inflammation by quantifying products of complement activation, including C3d, C4d, Bb, and SC5b-9 complexes, in 31 patients with AMI, 17 patients with unstable angina pectoris, 19 patients with stable angina pectoris, and 20 normal volunteers. The plasma C3d levels increased in patients with AMI and in those with unstable angina pectoris (p less than 0.01). The plasma levels of C4d, Bb, and SC5b-9 increased only in patients with AMI (p less than 0.01). The plasma SC5b-9 level was related to peak creatine phosphokinase (r = 0.71) and inversely related to the ejection fraction (r = -0.71). The plasma SC5b-9 level of patients with congestive heart failure was higher than that of patients without congestive heart failure in AMI. These results show that activation of complement system occurs after AMI and show an association of myocardial damage with complement activation. With respect to angina pectoris, the complement system is mildly activated in patients with unstable angina pectoris; however, the cardiac function of patients with unstable angina pectoris is not damaged. The complement system of patients with stable angina pectoris is not activated.
Evidence for hydrophobic region within heavy chains of mouse B lymphocyte membrane-bound IgM (1979)

The gel filtration behavior, in the presence of detergents, of membrane-bound IgM from normal mouse spleen B lymphocytes was compared to that of secretory IgM from mouse plasma cells. The proteins were labeled either by surface radioiodination or biosynthetically with radioactive amino acids. Cell lysates were fractionated on calibrated Sepharose 6B columns in the presence of the detergents Nonidet P-40 or deoxycholate. Eluted fractions were immunoprecipitated and the reduced or unreduced precipitates were analyzed by sodium dodecyl sulfate gel electrophoresis followed by radioautography. Surface (125)I-labeled 8S IgM exhibited a gel filtration pattern in Nonidet P-40 corresponding to much higher apparent molecular weight than that of secretory 8S IgM, a difference that almost disappeared when gel filtration was performed in the presence of deoxycholate, which forms much smaller micelles than does Nonidet P-40. Biosynthetically labeled lymphocytes contain two types of IgM molecules differing in their gel filtration behavior and fate: one identical to secretory 8S IgM of plasma cells and secreted in the medium during chase periods, and the other identical to surface (125)I-labeled IgM and remaining cell-associated. Because the surface-bound 8S IgM was not found to be associated with other labeled molecules, it is likely that the detergent-binding behavior of surface IgM is due to a hydrophobic segment carried by these Ig molecules. That lymphocytes synthesize two types of mu chains was also shown by the use of tunicamycin, an inhibitor of glycosylation. In its presence, two unglycosylated mu chains were observed: one identical in size to that made by tunicamycin-treated plasma cells, and the second slightly larger. Gel filtration in Nonidet P-40 of the cell lysates of tunicamycin-treated lymphocytes showed that the nonsecretory 8S IgM contains this second type of mu chains, whereas the IgM molecules of the secretory type contain plasma cell-like mu chains. It is suggested that membrane IgM mu chains contain a hydrophobic segment which is responsible for its association to the membrane.
Cardiovascular Status of Carriers of the Apolipoprotein A-I Milano Mutant (2001)

Despite severe HA, carriers of the apoA-I(M) mutant do not show structural changes in the arteries and heart, in contrast to HA subjects, who are characterized by a marked increase in carotid IMT and increased prevalence of atherosclerotic plaques.
A Selection of Recent Advances in C1 Chemistry (2016)

This review presents a selection of recent publications related to the chemistry and catalysis of C1 molecules, including methane, methanol, carbon monoxide, and carbon dioxide. These molecules play an important role in the current supply of energy and chemicals and will likely become even more relevant because of the need to decarbonize fuels (shift from coal to natural gas) in line with CO2 capture and use to mitigate global warming, as well as a gradual shift on the supply side from crude oil to natural gas. This review includes both recent industrial developments, such as the huge increase in methanol-to-olefins-capacity build in China and the demonstration of oxidative coupling of methane, and scientific developments in these chemistries facilitated by improved capabilities in, for example, analytical tools and computational modeling.
Hepatocyte Growth Factor in Ascites from Patients with Cirrhosis1 (1991)

Hepatocyte growth factor (HGF) stimulating DNA synthesis of adult rat hepatocytes in primary culture was found in the ascites and plasma from patients with liver cirrhosis, but not in those from patients without cirrhosis. HGF was purified about 400-fold in 10% yield from cirrhotic ascites by ultrafiltration, cation-exchange chromatography on a S-Sepharose column, and affinity chromatography on a heparin-Sepharose CL-6B column. The partially purified factor was a heat- and acid-labile cationic protein with a molecular weight of 100,000-150,000. Its effect was half-maximal at 3.8 micrograms/ml, and was additive with those of insulin and epidermal growth factor. HGF in ascites from patients with cirrhosis had the same properties as HGF purified and characterized from rat platelets. These findings suggest that HGF is secreted into the ascites from the plasma or liver of patients with cirrhosis and may increase in the plasma with the development of hepatic impairment and act in repair of the damaged liver of patients with chronic liver disease.
Structure−Property Relationships in Porous 3D Nanostructures as a Function of Preparation Conditions:  Isocyanate Cross-Linked Silica Aerogels (2007)

Sol−gel-derived silica aerogels are attractive candidates for many unique thermal, optical, catalytic, and chemical applications because of their low density and high mesoporosity. However, their inherent fragility has restricted use of aerogel monoliths to applications in which they are not subject to any load. We have previously reported cross-linking of the mesoporous silica structure of aerogels with di-isocyanates, styrenes, or epoxies reacting with amine-decorated silica surfaces. These approaches have been shown to significantly increase the strength of aerogels with only a small effect on density or porosity. Though density is a prime predictor of properties such as strength and thermal conductivity for aerogels, it is becoming clear from previous studies that varying the silica backbone and size of the polymer cross-link independently can give rise to combinations of properties that cannot be predicted from density alone. Herein, we examine the effects of four processing parameters for producing this type of polymer cross-linked aerogel on properties of the resulting monoliths. We focus on the results of 13C CP-MAS NMR, which gives insight to the size and structure of polymer cross-link present in the monoliths and relates the size of the cross-links to microstructure, mechanical properties, and other characteristics of the materials obtained.
Fundamental Limits of Pooled-DNA Sequencing (2016)

In this paper, fundamental limits in sequencing of a set of closely related DNA molecules are addressed. This problem is called pooled-DNA sequencing which encompasses many interesting problems such as haplotype phasing, metageomics, and conventional pooled-DNA sequencing in the absence of tagging. From an information theoretic point of view, we have proposed fundamental limits on the number and length of DNA reads in order to achieve a reliable assembly of all the pooled DNA sequences. In particular, pooled-DNA sequencing from both noiseless and noisy reads are investigated in this paper. In the noiseless case, necessary and sufficient conditions on perfect assembly are derived. Moreover, asymptotically tight lower and upper bounds on the error probability of correct assembly are obtained under a biologically plausible probabilistic model. For the noisy case, we have proposed two novel DNA read denoising methods, as well as corresponding upper bounds on assembly error probabilities. It has been shown that, under mild circumstances, the performance of the reliable assembly converges to that of the noiseless regime when, for a given read length, the number of DNA reads is sufficiently large. Interestingly, the emergence of long DNA read technologies in recent years envisions the applicability of our results in real-world applications.
Why Do We Not Yet Have a Human Immunodeficiency Virus Vaccine? (2008)

A 2-day meeting to explore why we do not yet have a human immunodeficiency virus (HIV) vaccine was held under the joint sponsorship of the Simons Center for Systems Biology at the Institute for Advanced Study and the International AIDS Vaccine Initiative, with additional support from Merck & Co., at
Mechanism of Apoptosis Induced by the Inhibition of Fatty Acid Synthase in Breast Cancer Cells (2006)

Fatty acid synthase (FAS) has been found to be overexpressed in a wide range of epithelial tumors, including breast cancer. Pharmacologic inhibitors of FAS cause apoptosis of breast cancer cells and result in decreased tumor size in vivo. However, how the inhibition of FAS induces apoptosis in tumor cells remains largely unknown. To understand the apoptotic pathway resulting from direct inhibition of FAS, we treated breast tumor cells with or without FAS small interfering RNA (siRNA) followed by a microarray analysis. Our results indicated that the proapoptotic genes BNIP3, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), and death-associated protein kinase 2 (DAPK2) were significantly up-regulated on direct inhibition of the FAS gene. We also found that the knockdown of FAS expression significantly increased ceramide level in the tumor cells, and this increase was abrogated by acetyl-CoA carboxylase inhibitor. In addition, carnitine palmitoyltransferase-1 (CPT-1) inhibitor up-regulated the ceramide and BNIP3 levels in these cells, whereas treatment of tumor cells with FAS siRNA in the presence of a ceramide synthase inhibitor abrogated the up-regulation of BNIP3 and inhibited apoptosis. Furthermore, we found that treatment of cells with BNIP3 siRNA significantly counteracted the effect of FAS siRNA-mediated apoptosis. Consistent with these results, a significant inverse correlation was observed in the expression of FAS and BNIP3 in clinical samples of human breast cancer. Collectively, our results indicate that inhibition of FAS in breast cancer cells causes accumulation of malonyl-CoA, which leads to inhibition of CPT-1 and up-regulation of ceramide and induction of the proapoptotic genes BNIP3, TRAIL, and DAPK2, resulting in apoptosis.
Stand-by current in PD-SOI pseudo-nMOS circuits (2003)

In this paper, we compare the stand-by leakage power of controlled-load pseudo-nMOS circuits to that of conventional CMOS and MTCMOS in a 0.13/spl mu/m dual V/sub T/partially-depleted SOI tehnology.
The novel chemokine receptor CXCR7 regulates trans-endothelial migration of cancer cells (2011)

Exposure of CXCR4⁺CXCR7⁺ cancer cells to CXCL12 greatly potentiated their TEM towards the chemokines CCL19 and CXCL13. This CXCL12-potentiated TEM was inhibited by the second CXCR7 chemokine ligand, CXCL11, as well as CXCR7-specific small molecule antagonists and antibodies. In contrast, the CXCR4 antagonist AMD3100 was less effective at inhibiting CXCL12-potentiated TEM. Thus, CXCR7 antagonists may be effective therapeutic agents for blocking CXCL12-mediated migration of CXCR4⁺CXCR7⁺ tumor cells into lymph nodes, regardless of whether the cancer cells follow a CXCL12 gradient or whether serum CXCL12 stimulates their migration towards CCR7 and CXCR5 chemokines in the lymph nodes.
Niemann‐Pick type C disease: molecular mechanisms and potential therapeutic approaches (2010)

Cholesterol is an important lipid of mammalian cells. Its unique physicochemical properties modulate membrane behavior and it serves as the precursor for steroid hormones, oxysterols and vitamin D. Cholesterol is effluxed from the late endosomes/lysosomes via the concerted action of at least two distinct proteins: Niemann-Pick C (NPC)1 and NPC2. Mutations in these two proteins manifest as NPC disease - a very rare, usually fatal, autosomal, recessive, neurovisceral, lysosomal storage disorder. In this review, we discuss the possible mechanisms of action for NPC1 and NPC2 in mediating cholesterol efflux, as well as the different therapeutic approaches being pursued for the treatment of this lipid storage disorder.
Implementation of MPEG transport demultiplexer with a RISC-based microcontroller (1996)

An MPEG transport demultiplexer (demux) has been implemented by the use of a RISC-based microcontroller as the core of the system in order to provide flexible data processing and a possibly cost-effective solution for an IRD (integrated receiver decoder) application. The hardware part filters out the packets necessary for one program and the microcontroller receives the packet, parses the headers and contents, and transfers the elementary stream data to the MPEG video/audio decoders. The implemented system shows that it still has approximately 60% of the CPU cycles, 16 Mcycles/sec, left with a video input of 15 Mbps.
Viscosity and elasticity during collagen assembly in vitro: Relevance to matrix-driven translocation (1997)

In order to better understand the gelation process associated with collagen assembly, and the mechanism of the in vitro morphogenetic phenomenon of "matrix-driven translocation" [S.A. Newman et al. (1985) Science, 228, 885-889], the viscosity and elastic modulus of assembling collagen matrices in the presence and absence of polystyrene latex beads was investigated. Viscosity measurements at very low shear rates (0.016-0.0549 s(-1)) were performed over a range of temperatures (6.9-11.5 degrees C) in a Couette viscometer. A magnetic levitation sphere rheometer was used to measure the shear elastic modulus of the assembling matrices during the late phase of the gelation process. Gelation was detected by the rapid increase in viscosity that occurred after a lag time tL that varied between O and approximately 500 s. After a rise in viscosity that occurred over an additional approximately 500 s, the collagen matrix was characterized by an elastic modulus of the order of several Pa. The lag time of the assembly process was relatively insensitive to differences in shear rate within the variability of the sample preparation, but was inversely proportional to the time the sample spent on ice before being raised to the test temperature, for test temperatures > 9 degrees C. This suggests that structures important for fibrillogenesis are capable of forming at 0 degrees C. The time dependence of the gelation process is well-described by an exponential law with a rate constant K approximately 0.1 s(-1). Significantly, K was consistently larger in collagen preparations that contained cell-sized polystyrene beads. From these results, along with prior information on effective surface tension differences of bead-containing and bead-lacking collagen matrices, we conclude that changes in matrix organization contributing to matrix-driven translocation are initiated during the lag phase of fibrillogenesis when the viscosity is < or = 0.1 Poise. The phenomenon may make use of small differentials in viscosity and/or elasticity, resulting from the interaction of the beads with the assembling matrix. These properties are well described by standard models of concentrated solutions.