gebhart/patrepeval huggingface dataset:
Engineering unnatural nucleotide specificity for Rous sarcoma virus tyrosine kinase to uniquely label its direct substrates (1997)

Protein phosphorylation plays a central role in controlling many diverse signal transduction pathways in all cells. Novel protein kinases are identified at a rapid rate using homology cloning methods and genetic screens or selections; however identification of the direct substrates of kinases has proven elusive to genetic methods because of the tremendous redundancy and overlapping of substrate specificities among protein kinases. We describe the development of a protein engineering-based method to identify the direct substrates of the prototypical protein tyrosine kinase v-Src, which controls fibroblast transformation by the Rous sarcoma virus. To differentiate the substrates of v-Src from all other kinase substrates, we mutated the ATP binding site of v-Src such that the engineered v-Src uniquely accepted an ATP analog. We show that the engineered v-Src kinase displayed catalytic efficiency with the ATP analog, N(6)-(cyclopentyl) ATP, which is similar to the wild-type kinase catalytic efficiency with ATP itself. However, the N(6)-(cyclopentyl) ATP analog was not accepted by the wild-type kinase. Furthermore, the engineered v-Src exhibited the same protein target specificity as wild-type v-Src despite the proximity of the reengineered nucleotide binding site to the phosphoacceptor binding site. The successful engineering of v-Src's active site to accept a unique nucleotide analog provides a unique handle by which the direct substrates of one kinase (v-Src) can be traced in the presence of any number of cellular kinases.
Synthesis and radiocarbon evidence of terephthalate polyesters completely prepared from renewable resources (2011)

Monomers used for the synthesis of terephthalate polyesters have been prepared starting from renewable resources. In particular, dimethyl terephthalate was synthesised starting from bio-limonene while butanediol was synthesised starting from bio-succinic acid. Using these bio-monomers it was possible to synthesise polyesters with the same chemical structure and molecular weight of commercially available polymers. Moreover, the polymers obtained from bio-based monomers, present the same thermal properties of the polyesters obtained using petrol-derived monomers. A poly(butylene terephthalate) completely obtained from renewable resources was also synthesised. The radiocarbon and isotope mass spectroscopy analysis confirmed that this polyester contains 94 ± 3% of bio-based material.
Chloroform mineralization by toluene-oxidizing bacteria (1996)

Seven toluene-oxidizing bacterial strains (Pseudomonas mendocina KR1, Burkholderia cepacia G4, Pseudomonas putida F1, Pseudomonas pickettii PKO1, and Pseudomonas sp. strains ENVPC5, ENVBF1, and ENV113) were tested for their ability to degrade chloroform (CF). The greatest rate of CF oxidation was achieved with strain ENVBF1 (1.9 nmol/min/mg of cell protein). CF also was oxidized by P. mendocina KR1 (0.48 nmol/min/mg of cell protein), strain ENVPC5 (0.49 nmol/min/mg of cell protein), and Escherichia coli DH510B(pRS202), which contained cloned toluene 4-monooxygenase genes from P. mendocina KR1 (0.16 nmol/min/mg of cell protein). Degradation of [14C]CF and ion analysis of culture extracts revealed that CF was mineralized to CO2 (approximately 30 to 57% of the total products), soluble metabolites (approximately 15%), a total carbon fraction irreversibly bound to particulate cellular constituents (approximately 30%), and chloride ions (approximately 75% of the expected yield). CF oxidation by each strain was inhibited in the presence of trichloroethylene, and acetylene significantly inhibited trichloroethylene oxidation by P. mendocina KR1. Differences in the abilities of the CF-oxidizing strains to degrade other halogenated compounds were also identified. CF was not degraded by B. cepacia G4, P. putida F1, P. pickettii PKO1, Pseudomonas sp. strain ENV113, or P. mendocina KRMT, which contains a tmo mutation.
NetCTLpan: pan-specific MHC class I pathway epitope predictions (2010)

Reliable predictions of immunogenic peptides are essential in rational vaccine design and can minimize the experimental effort needed to identify epitopes. In this work, we describe a pan-specific major histocompatibility complex (MHC) class I epitope predictor, NetCTLpan. The method integrates predictions of proteasomal cleavage, transporter associated with antigen processing (TAP) transport efficiency, and MHC class I binding affinity into a MHC class I pathway likelihood score and is an improved and extended version of NetCTL. The NetCTLpan method performs predictions for all MHC class I molecules with known protein sequence and allows predictions for 8-, 9-, 10-, and 11-mer peptides. In order to meet the need for a low false positive rate, the method is optimized to achieve high specificity. The method was trained and validated on large datasets of experimentally identified MHC class I ligands and cytotoxic T lymphocyte (CTL) epitopes. It has been reported that MHC molecules are differentially dependent on TAP transport and proteasomal cleavage. Here, we did not find any consistent signs of such MHC dependencies, and the NetCTLpan method is implemented with fixed weights for proteasomal cleavage and TAP transport for all MHC molecules. The predictive performance of the NetCTLpan method was shown to outperform other state-of-the-art CTL epitope prediction methods. Our results further confirm the importance of using full-type human leukocyte antigen restriction information when identifying MHC class I epitopes. Using the NetCTLpan method, the experimental effort to identify 90% of new epitopes can be reduced by 15% and 40%, respectively, when compared to the NetMHCpan and NetCTL methods. The method and benchmark datasets are available at http://www.cbs.dtu.dk/services/NetCTLpan/.
Phase I Dose Escalation Study To Evaluate the Safety and Pharmacokinetic Profile of Tefibazumab in Subjects with End-Stage Renal Disease Requiring Hemodialysis (2006)

Two cohorts of four subjects requiring hemodialysis received tefibazumab (10 or 20 mg/kg). The mean elimination half-life was between 17 and 18 days, the average volume of distribution was 7.3 liters, and the average clearance was 12 ml/h for both dose groups. At a dose of 20 mg/kg of body weight, plasma levels were 88 microg/ml at 21 days.
Selective inhibition of growth factor-dependent human B cell proliferation by monoclonal antibody AB1 to an antigen expressed by activated B cells. (1984)

A monoclonal antibody, AB1, was established with activated human B cells as immunogen. AB1 stained activated B cells but not activated T cells. Its selective reactivity to activated B cells was further documented by its nonreactivity to activated T cells, resting T and B cells, monocytes, granulocytes, bone marrow cells, leukemic cells, and cells from cell lines of T, B, and myeloid lineages. Upon activation, the antigen appeared on B cells as early as 3-4 h after stimulation and was fully expressed by 38 h. The expression of this antigen was not dependent on the presence of B cell stimulatory factor(s). Anti-IgM antibodies by themselves induced its expression. AB1 inhibited B cell proliferation that was induced by a low dose anti-IgM antibody and conditioned medium containing B cell stimulatory factor. It did not inhibit B cell proliferation induced by either high doses of anti-IgM antibodies or by formalinized Staphylococcus aureus. It also failed to inhibit T cell mitogenesis. The possibility exists that this antigen is related to the receptor for B cell stimulatory factor.
Interleukin‐1 up‐regulates transcription of its own receptor in a human fibroblast cell line TIG‐1: role of endogenous PGE2 and cAMP (1992)

The regulation of interleukin-1 receptor (IL-1R) mRNA expression by IL-1 in a human lung fibroblast cell line (TIG-1) was investigated. After 2 h of stimulation with human recombinant IL-1 alpha or IL-1 beta, the levels of T cell/fibroblast-type IL-1R mRNA increased, and the elevation was sustained for at least 72 h. IL-1 also stimulated synthesis of prostaglandin E2 (PGE2) and secondary cAMP accumulation. Exogenously added PGE2 increased the levels of both IL-1R mRNA and intracellular cAMP. Forskolin, cholera toxin and 8-Bromo adenosine (8-Br-cAMP) all increased IL-1R mRNA levels. Indomethacin blocked IL-1 stimulation of IL-1R mRNA expression, PGE2 production and cAMP. 125I-labeled IL-1 alpha-binding studies showed that this cell line expresses 2.6 x 10(4) IL-1R per cell with a Kd of 5.1 x 10(-10) M. After treatment of the cells with IL-1, the level of IL-1R increased over that of control cells. PGE2 also increased IL-1R without alteration in its affinity. Cross-linking experiments indicate that this cell line expresses the 80-kDa receptor molecule before and after treatment with PGE2; the molecular mass corresponds to the T cell/fibroblast type I IL-1R. These results indicate that IL-1 does not directly stimulate expression of IL-1R mRNA or cell surface IL-1R, but only indirectly by stimulation of endogenous PGE2.
Hierarchical hidden Markov models for information extraction (2003)

Information extraction can be defined as the task of automatically extracting instances of specified classes or relations from text. We consider the case of using machine learning methods to induce models for extracting relation instances from biomedical articles. We propose and evaluate an approach that is based on using hierarchical hidden Markov models to represent the grammatical structure of the sentences being processed. Our approach first uses a shallow parser to construct a multi-level representation of each sentence being processed. Then we train hierarchical HMMs to capture the regularities of the parses for both positive and negative sentences. We evaluate our method by inducing models to extract binary relations in three biomedical domains. Our experiments indicate that our approach results in more accurate models than several baseline HMM approaches. 1
Call admission in power controlled CDMA systems (2002)

In power controlled CDMA systems, the number of users that each cell can support is limited by the total interference received at each base station and will vary with time. When a system is congested, admitting a new call can only make the link quality worse for ongoing calls and may result in call dropping. Thus, a system needs a call admission policy for new call requests to maintain acceptable connections for existing users. We use a weighted combination of call blocking and call dropping probabilities as a system performance measure. We study a transmitted power based call admission control (TPCAC) scheme that protects ongoing calls and a received power based call admission control (RPCAC) scheme that blocks new calls when the total received at a base station exceeds a threshold. The proposed schemes are evaluated by simulation of a one dimensional system and the RPCAC scheme is found to offer significant performance improvements.
Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery (2012)

Genome-wide disease association studies contrast genetic variation between disease cohorts and healthy populations to discover single nucleotide polymorphisms (SNPs) and other genetic markers revealing underlying genetic architectures of human diseases. Despite scores of efforts over the past decade, many reproducible genetic variants that explain substantial proportions of the heritable risk of common human diseases remain undiscovered. We have conducted a multispecies genomic analysis of 5,831 putative human risk variants for more than 230 disease phenotypes reported in 2,021 studies. We find that the current approaches show a propensity for discovering disease-associated SNPs (dSNPs) at conserved genomic positions because the effect size (odds ratio) and allelic P value of genetic association of an SNP relates strongly to the evolutionary conservation of their genomic position. We propose a new measure for ranking SNPs that integrates evolutionary conservation scores and the P value (E-rank). Using published data from a large case-control study, we demonstrate that E-rank method prioritizes SNPs with a greater likelihood of bona fide and reproducible genetic disease associations, many of which may explain greater proportions of genetic variance. Therefore, long-term evolutionary histories of genomic positions offer key practical utility in reassessing data from existing disease association studies, and in the design and analysis of future studies aimed at revealing the genetic basis of common human diseases.
Tenwen: The Reengineering of a Computing Environment (1994)

In the summer of 1992, the computing environment at the College of Computer Science of Northeastern University was completely dysfunctional. Among other things, the network was down over 25 percent of the time, the computers and software were badly misconfigured, the users were confused, and it was nearly impossible to administer. It was on the verge of collapse.

Now, two years later, the situation is entirely reversed. The network is up well over 99 percent of the time, the computers and software are easily managed, and the users are (for the most part) satisfied. Many people have stated that it is the nicest and most functional computing environment they've ever used.

This paper is an overview of the key changes that we made and the methodology that we used in bringing about this transformation. I examine the lessons we learned as well as the mistakes we made, and offer advice to others starting with a similar predicament.
Expression of CD27 and its ligand, CD70, on chronic lymphocytic leukemia B cells (1995)

Crosslinking the CD27 antigen on T cells provides a costimulatory signal that, in concert with T-cell receptor crosslinking, can induce T-cell proliferation and cellular immune activation. We find that chronic lymphocytic leukemia (CLL) B cells from most patients coexpress both membrane-bound and soluble CD27, along with its newly identified ligand, CD70. The expression of soluble CD27 may preclude leukemic B cells from stimulating T cells via CD70, thereby potentially impairing their ability to function as effective antigen-presenting cells. We find that leukemic B-cell expression of soluble and membrane-bound CD27 can be downmodulated through a CD40-dependent signal. This signal also induces enhanced expression of CD70 on both normal and leukemic B cells. We find that tumor necrosis factor (TNF)-alpha, or the Th1 cytokine interferon (IFN)-gamma, also can induce downmodulation of CD27, whereas Th2-associated cytokines interleukin-4 (IL-4) or IL-10 can enhance leukemic B-cell expression of this accessory molecule. The modulation of CD27 induced by these conditions is accompanied by reciprocal changes in the expression levels of CD70, suggesting that these accessory molecules may be engaged in reciprocal receptor-ligand downmodulation. Consistent with this, we observe that co-culture of CLL B cells with transfected murine plasmacytoma cells that express human CD70 affects downmodulation of CD27 and enhanced expression of CD70 on leukemic B cells, but does not affect expression of CD27 mRNA. However, we find that CD40-crosslinking, in addition to reducing the level of CD27 protein, also reduces leukemic B-cell expression of CD27 mRNA. This argues that the changes in the expression levels of CD27 following CD40-signaling are not simply due to induced increases in the expression levels of CD70. Finally, we demonstrate that reciprocal changes in expression of CD27 and CD70 may contribute to the enhanced antigen-presenting capacity of CLL B cells after CD40-dependent leukemic B-cell activation. These findings expand the understanding of the regulation of costimulatory molecules important in antigen presentation and also have implications for the immunobiology of and therapy for CLL.
Carbon Nanofibers Prepared via Electrospinning (2012)

Carbon nanofibers prepared via electrospinning and following carbonization are summarized by focusing on the structure and properties in relation to their applications, after a brief review of electrospinning of some polymers. Carbon precursors, pore structure control, improvement in electrical conductivity,and metal loading into carbon nanofibers via electrospinning are discussed from the viewpoint of structure and texture control of carbon.
Eradication of Helicobacter pylori Infection Reduces the Incidence of Peptic Ulcer Disease in Patients using Nonsteroidal Anti‐Inflammatory Drugs: A Meta‐Analysis (2012)

NSAID use is not associated with H. pylori infection in patients with PUD. PUD is more common in H. pylori positive than in negative NSAID users. Moreover, H. pylori eradication therapy reduces PUD incidence in NSAID users, especially in naive users and in the Asian population.
Material Challenges for Terawatt Level Deployment of Photovoltaics (2006)

In this work several photovoltaic technologies, ranging from silicon to thin films, multi-junction and solar concentrator systems are analyzed. The estimates of the energy production limits are established for each technology, based on available global material reserves. It is shown that many existing technologies, albeit playing an important in the present sub-GW energy production levels, are affected by severe material shortages, preventing their scale-up to the terawatt range. This is the case for thin film solar cells technologies based on CdTe and CIGS where the showstopper is the scarcity of tellurium and indium respectively. Despite the abundance of silicon, crystalline Si solar cells will hardly surpass the few terawatt range as further scale-up will be impeded by the global reserves of silver, commonly used as electrode material. For amorphous silicon and dye sensitized thin film technologies, avoiding the use of ITO transparent conductive oxides (ZnO for a-Si and SnO <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> for dye sensitized cells) should favor access to terawatt levels. For existing III-V concentrator cells, operating under moderate concentration (<200X), one to two terawatt year level can be afforded by simply substituting Ge substrates by more abundant GaAs wafer. The development of reliable epitaxial solar cell lift-off techniques should enable the attainment of multi-Terawatt levels
Acoustic Emission Based Monitoring of the Microdamage Evolution During Fatigue of Human Cortical Bone (2013)

Stress fractures are frequently observed in physically active populations, and they are believed to be associated with microcrack accumulation. There are not many tools for real-time monitoring of microdamage formation during fatigue of bone, in vivo or in vitro. Acoustic emission (AE) based detection of stress waves resulting from microdamage formation is a promising method to assess the rate and energetics of microdamage formation during fatigue. The current study aims to assess the time history of the occurrence of AE events during fatigue loading of human tibial cortical bone and to determine the associations between AE variables (energy content of waves, number of AE waveforms, etc.), fatigue life, and bone ash content. Fatigue test specimens were prepared from the distal diaphysis of human tibial cortical bone (N = 32, 22 to 52 years old, male and female). The initiation of acoustic emissions was concomitant with the nonlinear increase in sample compliance and the cumulative number of AE events increased asymptotically in the prefailure period. The results demonstrated that AE method was able to predict the onset of failure by 95% of the fatigue life for the majority of the samples. The variation in the number of emissions until failure ranged from 6 to 1861 implying a large variation in crack activity between different samples. The results also revealed that microdamage evolution was a function of the level of tissue mineralization such that more mineralized bone matrix failed with fewer crack events with higher energy whereas less mineralized tissue generated more emissions with lower energy. In conclusion, acoustic emission based surveillance during fatigue of cortical bone demonstrates a large scatter, where some bones fail with substantial crack activity and a minority of samples fail without significant amount of crack formation.
A Java-based wireless network management system (2002)

To support the high quality services with wireless networks, the wireless network management module is indispensable. Based on the Java facility, CORBA engine, and SNMP management protocol, a universal browser-based wireless network management system (WNMS) is designed and reported. We use the CORBA engine for communication between the manager and agent (managed system). The SNMP protocol and Java facility are utilized for the design of the management applications to take the advantage of the platform independence. In the WNMS, two new features, agent discovery and binding operation, are also implemented. From the prototype system, it is observed that with the new features and traditional management functions the WNMS can achieve a high quality in wireless-wireline network management.
Translocator Protein (18 kD) as Target for Anxiolytics Without Benzodiazepine-Like Side Effects (2009)

Most antianxiety drugs (anxiolytics) work by modulating neurotransmitters in the brain. Benzodiazepines are fast and effective anxiolytic drugs; however, their long-term use is limited by the development of tolerance and withdrawal symptoms. Ligands of the translocator protein [18 kilodaltons (kD)] may promote the synthesis of endogenous neurosteroids, which also exert anxiolytic effects in animal models. Here, we found that the translocator protein (18 kD) ligand XBD173 enhanced gamma-aminobutyric acid-mediated neurotransmission and counteracted induced panic attacks in rodents in the absence of sedation and tolerance development. XBD173 also exerted antipanic activity in humans and, in contrast to benzodiazepines, did not cause sedation or withdrawal symptoms. Thus, translocator protein (18 kD) ligands are promising candidates for fast-acting anxiolytic drugs with less severe side effects than benzodiazepines.
Revision anual del Banco Mundial sobre la importancia del medio ambiente (2004)

This Annual Review of Environment Matters, dedicated to Economic Growth and the Environment, brings together a wide variety of external and internal viewpoints on the challenges ahead, and the progress that is taking place. In this issue, three major partner countries-China, India and Mexico-present their perspectives. Among other topics, this edition features the Bank's recent research on what happens to environment during growth, and the different tools available to promote environmentally, and socially sustainable economic growth. It also includes reviews of the Bank's environmental programs in developing countries and its global engagement. The review includes viewpoints on the environment and competitiveness; on harmonizing environmental concerns and economic growth from the Indian perspective; integrating rapid growth and environmental protection as a challenge for China; mainstreaming and infrastructure; and, health-driven environmental issues. Moreover, the review features articles such as the environment during growth - accounting for governance and vulnerability, on sustainable development and policy reform, on energy, climate change, and development, and, on the elements of sustainable infrastructure. Other subjects include regional articles, and institutional perspectives by the International Development Association (IFC) and the World Bank Institute (WBI).
Mapping of local renal blood flow with PET and H(2)(15)O. (2002)

Parametric mapping of RBF with PET and H(2)(15)O provides a straightforward, noninvasive method for quantitative mapping of RBF, which may prove useful in research applications and in the management of patients whose therapy alters renal tubular transport.