gebhart/patrepeval huggingface dataset:
Repressor mutations in the marRAB operon that activate oxidative stress genes and multiple antibiotic resistance in Escherichia coli (1994)

Resistance to multiple antibiotics and certain oxidative stress compounds was conferred by three independently selected mutations (marR1, soxQ1, and cfxB1) that mapped to 34 min on the Escherichia coli chromosome. Mutations at this locus can activate the marRAB operon, in which marR encodes a putative repressor of mar transcription and marA encodes a putative transcriptional activator of defense genes against antibiotics and oxidants. Overexpression of the wild-type MarR protein reversed the phenotypes (antibiotic resistance and increased antioxidant enzyme synthesis) of all three mutants. DNA sequence analysis showed that, like marR1, the other two mutations were alterations of marR: a 285-bp deletion in cfxB1 and a GC-->AT transition at codon 70 (Ala-->Thr) in soxQ1. All three mutations cause increased amounts of mar-specific RNA, which supports the hypothesis that MarR has a repressor function in the expression of the marRAB operon. The level of mar RNA was further induced by tetracycline in both the marR1 and soxQ1 strains but not in the cfxB1 deletion mutant. In the cfxB1 strain, the level of expression of a truncated RNA, with or without tetracycline exposure, was the same as the fully induced level in the other two mutants. Overproduction of MarR in the cfxB1 strain repressed the transcription of the truncated RNA and restored transcriptional inducibility by tetracycline. Thus, induction of the marRAB operon results from the relief of the repression exerted by MarR. The marRAB operon evidently activates both antibiotic resistance and oxidative stress genes.
RHAMM and CD44 peptides-analytic tools and potential drugs (2011)

CD44 and RHAMM are two extracellar matrix receptors whose principle ligand is the polysaccharide hyaluronan (HA). Both proteins are involved in wound repair and their aberrant regulation contributes to a variety of diseases including arthritis and cancer. Over the past decade, a number of peptide-based therapeutics that block the binding of CD44 or RHAMM-specific ligands have been developed and tested in experimental models of disease. Here, we review the structure of each of these proteins, the functions they control and the mechanisms, including their interactions with each other, responsible for these functions. We also review the development of peptide mimics that block the key functions of CD44 and RHAMM and their use in experimental models of disease.
Synaptic Connections between Layer 5B Pyramidal Neurons in Mouse Somatosensory Cortex Are Independent of Apical Dendrite Bundling (2007)

Rodent somatosensory barrel cortex is organized both physiologically and anatomically in columns with a cross-sectional diameter of 100-400 microm. The underlying anatomical correlate of physiologically defined, much narrower minicolumns (20-60 microm in diameter) remains unclear. The minicolumn has been proposed to be a fundamental functional unit in the cortex, and one anatomical component of a minicolumn is thought to be a cluster of pyramidal cells in layer 5B (L5B) that contribute their apical dendrite to distinct bundles. In transgenic mice with fluorescently labeled L5B pyramidal cells, which project to the pons and thalamus, we investigated whether the pyramidal cells of a cluster also share functional properties. We found that apical dendrite bundles in the transgenic mice were anatomically similar to apical dendrite bundles previously proposed to be part of minicolumns. We made targeted whole-cell recordings in acute brain slices from pairs of fluorescently labeled L5B pyramidal cells that were located either in the same cluster or in adjacent clusters and subsequently reconstructed their dendritic arbors. Pyramids within the same cluster had larger common dendritic domains compared with pyramids in adjacent clusters but did not receive more correlated synaptic inputs. L5B pyramids within and between clusters have similar connection probabilities and unitary EPSP amplitudes. Furthermore, intrinsically bursting and regular spiking pyramidal cells were both present within the same cluster. In conclusion, intrinsic electrical excitability and the properties of synaptic connections between this subtype of L5B pyramidal cells are independent of the cell clusters defined by bundling of their apical dendrites.
A silicon MEMS structure for characterization of femto-farad-level capacitive sensors with lock-in architecture (2010)

This paper presents a silicon MEMS capacitive structure to investigate a test methodology for fF-level capacitive sensors' measurement. The device mimics a capacitive sensor with a changing intermediate layer between the electrodes. A single mask bulk micromachining process is used to fabricate the device, which has a nominal capacitance of 1.2 fF. A high performance measurement setup based on lock-in principle is developed to detect the capacitance variation. The maximum capacitance variation of the fabricated device is 0.31 fF, and the capacitance detection limit is 0.095 aF Hz -1/2 .
A mammalian cell line designed to test the mutagenic activity of anti‐herpes nucleosides (1987)

The herpes simplex virus (HSV) thymidine kinase (tk) gene was transfected into Chinese hamster ovary (CHO) 51-11 gly- cells to test its effect on the cytotoxic and mutagenic activity of anti-herpetic nucleoside analogues. Insertion of the viral tk was verified by Southern blot analysis, by sensitivity to acyclovir, and by elevated in vitro thymidine kinase (TK) activity. TK activity was increased by superinfection with a tk- virus and inhibited by antibody to viral TK. Acyclovir (ACV) was somewhat more cytotoxic in the 51-D3 cell line that expresses the viral TK than in the 51-11 parent line. Growth in ACV did not increase over background mutations at the hprt locus. FIAC (2'-fluoro-5-iodio-aracytosine) was slightly cytotoxic to the parent 51-11 line and the tk-containing clone 51-D3. FMAU (2'-fluoro-5-methyl-arauracil) had pronounced cytotoxicity in both cell lines: the 50% survival points were 1.0 microM for 51-11 cells and 0.2 microM for 51-D3. The clone 51-D3 was more sensitive than 51-11 to low concentrations of FIAU (2'-fluoro-5-iodo-arauracil), and when treated with FIAU 51-D3 had a mutation frequency to glycine independence 5 times greater than that of 51-11 cells. With both cell lines the mutation frequency at the hprt locus did not increase after growth in the presence of FIAC or FIAU. A 7-fold increase in mutation frequency at the hprt locus was detected after 51-D3 cells were grown with iododeoxyuridine. Trifluorothymidine was more toxic to 51-D3 than to 51-11 cells and increased the mutation frequency 2-fold. Cytosine-beta-D-arabinofuranoside showed no differential cytotoxicity on the two cell lines and did not increase the mutation frequency at the hprt locus.
In vitro synthesis of infectious poliovirus RNA. (1985)

Replication of the infectious RNA genome of poliovirus is accomplished in cells by the viral RNA polymerase through negative-strand RNA intermediates. Full-length negative-strand poliovirus RNA was synthesized in vitro by transcription of infectious poliovirus cDNA with bacteriophage SP6 DNA-dependent RNA polymerase. When provided with this negative-strand RNA as template, the poliovirus RNA-dependent RNA polymerase synthesized full-length positive-strand molecules. The positive-strand RNAs synthesized in vitro were infectious when transfected into HeLa cells. In contrast, positive-strand copies of poliovirus RNA synthesized in vitro by SP6 polymerase, using a poliovirus cDNA template, were not infectious. Production of infectious positive-strand RNA by the poliovirus polymerase was not observed when magnesium or negative-strand RNA template was omitted from the reaction mixture. Infectivity of the product RNA was not destroyed by DNase treatment. The specific infectivity in HeLa cells of in vitro-synthesized positive-strand RNA was 4 X 10(4) plaque-forming units/micrograms of RNA.
Protein Interaction Cloning by Far-Western Screening of λ-Phage cDNA Expression Libraries (2003)

One of the most powerful ways to gain novel insights into a particular protein’s cellular functions is to identify other proteins with which it specifically interacts. Traditionally, this problem has been approached by use of protein biochemistry, involving purification of interacting proteins and determination of at least a portion of their amino acid sequences by microsequencing techniques, so that degenerate oligonucleotides can be prepared and cDNAs obtained by conventional hybridization screening of cDNA libraries. This biochemical approach, however, is an enormously laborious task, and in the vast majority of cases, the yields of protein are simply inadequate to make it feasible. As an alternative, cDNAs encoding interacting proteins can be obtained by direct screening of λ-phage cDNA expression libraries using recombinant proteins and methods similar to those developed for antibody-based screening. This expression cloning approach is based on the “far-western” method (also known as ligand blotting or West-Western) in which proteins immobilized on nitrocellulose or other suitable membranes can be detected by their ability to bind to soluble recombinant proteins of interest (, , , , , ). These protein-protein interactions are conceptually similar to traditional antigen-antibody interactions involved in Western blotting, but typically occur with lower affinity.
The maternal and neonatal effects of adding tramadol to 2% lidocaine in epidural anesthesia for Cesarean section (2011)

Background: Opioid analgesics are commonly added to epidural local anesthetics to improve analgesia during surgery. Objectives: The goal of this study was to evaluate the maternal and neonatal effects of adding different doses of tramadol to 2% lidocaine in the epidural anesthesia for cesarean section. Patients and Methods: Ninety pregnant patients who were candidates for cesarean section under epidural anesthesia were randomly categorized into three groups. Group L received 2% lidocaine. In the LT50 and LT100 groups, 50 and 100 mg of tramadol were added to epidural 2% lidocaine. For additional analgesia during surgery, 2% lidocaine through epidural catheter or IV sufentanil were administered. Analgesia after surgery was provided by IV injection of meperidine. Onset and duration of sensory and motor blockades, total drug consumption, neonatal Apgar score, and complications were recorded. Results: In the LT100 group, onset of complete sensory and motor blockade at T6 was less than in the two other groups, but the highest level of sensory blockade and two segment regression and duration of motor blockades between the LT50 and LT100 groups were not significantly different, although they were higher and more prolonged than in the L group. Average lidocaine and sufentanil consumption during surgery between the LT50 and LT100 groups were not significantly different but were lower than in the L group. The incidence of maternal complications and neonatal Apgar scores were not significantly different between the three groups. In the LT50 and LT100 groups, the time until the first request for analgesics after surgery was prolonged, and average meperidine consumption was less than in the L group. Conclusions: The addition of tramadol to epidural 2% lidocaine offers advantages in cesarean section.
QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials (2009)

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, and projector-augmented wave). The acronym ESPRESSO stands for opEn Source Package for Research in Electronic Structure, Simulation, and Optimization. It is freely available to researchers around the world under the terms of the GNU General Public License. QUANTUM ESPRESSO builds upon newly-restructured electronic-structure codes that have been developed and tested by some of the original authors of novel electronic-structure algorithms and applied in the last twenty years by some of the leading materials modeling groups worldwide. Innovation and efficiency are still its main focus, with special attention paid to massively parallel architectures, and a great effort being devoted to user friendliness. QUANTUM ESPRESSO is evolving towards a distribution of independent and interoperable codes in the spirit of an open-source project, where researchers active in the field of electronic-structure calculations are encouraged to participate in the project by contributing their own codes or by implementing their own ideas into existing codes.
Evaluation of the in vivo biodistribution of yttrium-labeled isomers of CHX-DTPA-conjugated monoclonal antibodies. (1998)

Although the CHX-B" and CHX-B' were not acceptable for labeling with yttrium, the CHX-A' and CHX-A" were suitable, indicating that differences in stereochemistry can greatly influence stability of radionuclide in the chelate.
A Remote Attestation Approach for a Secure Virtual Machine Migration in Federated Cloud Environments (2011)

Nowadays, cloud computing is considered as a new charming technology, where new opportunities in ICT world are becoming real. Cloud is appealing many IT companies, but the largest business is in hand of big cloud operators. In the near future the scenario could change, and becoming much more complex even involving small and medium providers. Cloud operators could collaborate to satisfy the increasing cloud customer demand. The security is one of the main aspects that might limit such a collaboration. This paper deals with the opportunity to leverage the Trusted Computing technology for encouraging the federation in trustiness among heterogeneous clouds. In this work, we describe how Trusted Computing may increase the security in clouds, in particular when VM migration takes place between federated providers.
Technetium-99m-Ethylenedicysteine in the Diagnosis and Follow-Up of Renovascular Hypertension (1996)

Technetium-99m-ethylenedicysteine (99mTc-EC) captopril scintigraphy performed in a patient with severe hypertension revealed increased parenchymal retention in the left kidney, suggesting renal artery stenosis. After angiographic confirmation of renal artery stenosis, percutaneous transluminal angioplasty (PTA) was performed on the left renal artery. Captopril scintigraphy after PTA showed normal findings with no evidence of parenchymal retention, consistent with reversal to normal kidney functions. In light of this case of renal artery stenosis, it was concluded that 99mTc-EC can be used successfully as a potential renal agent in the diagnosis and follow-up of renovascular hypertension.
Crystal Structure of the Catalytic Domains of Adenylyl Cyclase in a Complex with G sα ·GTPγS (1997)

The crystal structure of a soluble, catalytically active form of adenylyl cyclase in a complex with its stimulatory heterotrimeric G protein alpha subunit (Gsalpha) and forskolin was determined to a resolution of 2.3 angstroms. When P-site inhibitors were soaked into native crystals of the complex, the active site of adenylyl cyclase was located and structural elements important for substrate recognition and catalysis were identified. On the basis of these and other structures, a molecular mechanism is proposed for the activation of adenylyl cyclase by Gsalpha.
An NFS Configuration Management System and its Underlying Object-Oriented Model (1998)

This paper describes an NFS configuration and management system for large and heterogeneous computer environments. It also shows how this system can be extended to address other services in the network. The solution is composed of a process that describes service configuration and management life-cycle, a modular architecture and an objected oriented model. The system supports multiple features, including: automatic host and service installation, service dependency inference and analysis, performance analysis, configuration optimization as well as service functioning monitoring and problem correction.
DELAYED GRAFT FUNCTION: RISK FACTORS AND IMPLICATIONS FOR RENAL ALLOGRAFT SURVIVAL1 (1997)

Delayed graft function (DGF) may be associated with diminished kidney allograft survival. We studied the risk factors that lead to nonimmediate function of a renal allograft and the consequences of DGF on short- and long-term renal transplant survival. Data from the U.S. Renal Data System were used to measure the relationships among cold ischemia time, delayed graft function, acute rejection, and graft survival in 37,216 primary cadaveric renal transplants (1985-1992). These relationships were investigated using the unconditional logistic and Cox multivariate regression methods. Cold ischemia time was strongly associated with DGF, with a 23% increase in the risk of DGF for every 6 hr of cold ischemia (P<0.001). Acute transplant rejection occurred more frequently in grafts with delayed function (37% vs. 20%; odds ratio=2.25, P=0.001). DGF was independently predictive of 5-year graft loss (relative risk=1.53, P<0.001). The presence of both early acute rejection and DGF portended a dismal 5-year graft survival rate of 35%. Zero-HLA mismatch conferred a 10-15% improvement in 1- and 5-year graft survival regardless of early functional status of the allograft. However, the 5-year graft survival rate in HLA-mismatched kidneys without DGF was significantly higher than that of zero-mismatched kidneys with DGF (63% vs. 51%; P<0.001). DGF independently portends a significant reduction in short- and long-term graft survival. Delayed function and early rejection episodes exerted an additive adverse effect on allograft survival. The deleterious impact of delayed function is comparatively more severe than that of poor HLA matching.
Magnetic cell separation using nano‐sized bacterial magnetic particles with reconstructed magnetosome membrane (2008)

Magnetic nanoparticles produced by magnetotactic bacterium, bacterial magnetic particles (BacMPs), covered with a lipid bilayer membrane (magnetosome membrane) can be used to separate specific target cells from heterogeneous mixtures because they are easily manipulated by magnets and it is easy to display functional proteins on their surface via genetic engineering. Despite possessing unique and valuable characteristics, the potential toxicity of BacMPs to the separated cells has not been characterized in detail. Here, a novel technique was developed for the reconstruction of magnetosome membrane of BacMPs expressing protein A (protein A-BacMPs) to reduce cytotoxicity and the newly developed nanomaterial was then used for magnetic cell separation. The development of the magnetosome membrane-reconstructed protein A-BacMP was based on the characteristics of the Mms13 anchor protein, which strongly binds to the magnetite surface of BacMPs. Treatment of protein A-BacMPs with detergents removed contaminating proteins but did not affect retention of Mms13-protein A fusion proteins. The particle surfaces were then reconstructed with phosphatidylcholine. The protein A-BacMPs containing reconstructed magnetosome membranes remained dispersible and retained the ability to immobilize antibody. In addition, they contained few membrane surface proteins and endotoxins, which were observed on non-treated protein A-BacMPs. Magnetic separation of monocytes and B-lymphocytes from the peripheral blood was achieved with high purity using magnetosome membrane-reconstructed protein A-BacMPs.
Polypharmacy in chronic heart failure: practical issues regarding the use of angiotensin-converting enzyme inhibitors, beta-blockers and other drugs (2002)

Angiotensin-converting enzyme (ACE) inhibitors and beta-blockers are the cornerstone for treatment of patients with chronic heart failure (CHF), and are usually combined with diuretics, with or without digoxin. With the development of new, additional treatments, the problem of polypharmacy becomes relevant, and strategies to individualize treatment are warranted. This review considers optimal drug treatment in patients with CHF, focusing on the possible problems that can occur when combining drugs. A hierarchy of drugs is suggested, starting from the assumption of a central role for early and widespread use of ACE inhibitors and beta-blockers. A model of drug therapy is proposed that is based on each patient's individual clinical and genetic considerations, which might serve to further optimize treatment.
GRP78 Upregulation by Atheroprone Shear Stress Via p38-, α2β1-Dependent Mechanism in Endothelial Cells (2008)

This study supports a role of the hemodynamic environment in preferentially inducing GRP78 and the UPR in atheroprone regions, before lesion development, and suggests a potential atheroprotective (ie, prosurvival), compensatory effect in response to ER stress within atherosclerotic lesions.
Effects of enalapril maleate on survival of dogs with naturally acquired heart failure. The Long-Term Investigation of Veterinary Enalapril (LIVE) Study Group. (1998)

Use of enalapril in combination with standard treatment (diuretics with or without digoxin) appears to be beneficial over an extended period, compared with standard treatment alone.
Enjoy the Silence: The Story of let-7 MicroRNA and Cancer (2007)

Cancer is a multi-step disease involving dynamic changes in the genome. However, studies on cancer genome so far have focused most heavily on protein-coding genes, and our knowledge on alterations of the functional noncoding sequences in cancer is largely absent. MicroRNAs (miRNAs) are endogenous small noncoding RNAs weighing 20 to 23 nucleotides that negatively regulate gene expression at the posttranscriptional level by base pairing to the 3' untranslated region of target messenger RNAs. Hundreds of miRNAs have been identified in humans and are evolutionarily conserved from plants to animals. These tiny but potent molecules regulate various physiological and pathological pathways such as cell differentiation and cell proliferation. Recently, miRNA alterations have been linked to the initiation and the progression of human cancer. As a consequence, MiRNA-expression profiling of human tumors has identified signatures associated with diagnosis, staging, progression, prognosis and response to treatment. In addition, profiling has been exploited to identify miRNA genes that might represent downstream targets of activated oncogenic pathways, or that target proteincoding genes involved in cancer. Of importance, pioneering studies described let-7 miRNA as a negative regulator of the oncogenic family of Ras guanosine triphosphatases in both Caenorhabditis elegans and human tumor cell lines. Later, let-7 expression deregulation was reported in several cancers, suggesting that let-7 may act as a tumor suppressor. This review will discuss the late insights in let-7 function, the elationship between let-7 and tumorigenesis, and the potential for modulating let-7 expression for the treatment of cancer.