gebhart/patrepeval huggingface dataset:
Towards practical application of methanotrophic metabolism in chlorinated hydrocarbon degradation, greenhouse gas removal, and immobilization of heavy metals (2010)

Methanotrophs are a group of microorganisms found in diverse environments that utilize methane for energy and biomass. These microorganisms have long been studied for their practical applications as well as for their significant contributions to the global carbon and nitrogen cycles. The scope of this study was to closely examine the physiological and genetic properties of different groups of methanotrophs to the utility of these cells for: (1) pollutant degradation by these cells and (2) removal of methane from the atmosphere. Finally, a new assay was created to screen methanotrophs for production of methanobactin, a unique copper chelating biomolecule that has significant potential industrial applications engineering practices or development of biological engineering devices and processes de novo utilizing these bacteria. Biodegradation of TCE, trans-DCE, and VC by methanotrophs was closely examined in this study. Significance of selective expression of sMMO and pMMO in biodegradation activity of Methylosinus trichosporium OB3b was examined at a realistic in situ groundwater temperature condition to support the argument that pMMO is responsible for methane-augmented bioremediation. Also Methylocystis daltona SB2 was examined for the expression of pMMO and degradation of chlorinated ethene compounds under growth on acetate in absence of methane using quantitative RT–PCR technique. Considering the significant contribution of methane emission to the greenhouse effect, the ability of methanotrophs to use methane as the electron donor has great significance in environmental perspective. In this study, a methanotrophic biotrickling filtration system was designed to actively utilize methanotrophic activity to remove atmospheric methane from local methane “hotspots”. Mathematical modeling was performed to assess the technological and economical feasibility of this biofiltration system. Methanobactin, a copper chelating biomolecule, has been hypothesized to have significant roles in methanotrophy, as well as interesting potential applications. To enable the genetic studies on methanobactin, we have adopted CAS assay for screening methanotrophs for production of methanobactin. The assay was successful in screening the methanotrophic strains for differential capability to abstract copper. Altogether, we expect the findings in this study to serve as basis for further research that will allow better understanding and more effective applications of methanotrophs.
A convex optimization approach to transistor sizing for CMOS circuits (2002)

The transistor sizing problem of minimizing the circuit area, subject to the circuit delay being less than a given specification, is formulated as a convex programming problem. An efficient convex programming algorithm is then used to obtain the exact solution. Experimental results on a variety of circuits show that, for a given delay specification this approach is able to produce circuits with significantly smaller area when compared with TILOS.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Platelet adherence to isolated rat hepatic sinusoidal endothelial cells after cold preservation1 (2002)

Background. Platelet adhesion to hepatic sinusoidal endothelial cells (SEC) is a major mechanism of cold preservation injury. This study was performed to determine whether cold preservation leads to adhesion between SEC and platelets in the absence of other cell types, whether adherent platelets become activated upon adhesion, and whether there is increased expression of the platelet receptor von Willebrand factor (vWF) on cold preserved SEC. Because we previously showed that cold causes actin disassembly and matrix metalloprotease (MMP) secretion by SEC, we also questioned whether these events are related to increased adhesion of platelets to SEC after preservation. Methods. Isolated SEC were cold preserved for 8 hr and rewarmed briefly. Biotinylated platelets were added to the plates and adhesion was assessed. Activation of platelets was determined by staining with antibody to P-selectin. Expression of vWF was assessed with a specific antibody. Results. Cold preservation induced increased adhesion of platelets to SEC in the absence of other cell types. Adherent platelets were activated. Preservation increased the expression of vWF on SEC. Pretreatment with phalloidin or treatment with MMP inhibitors partly prevented platelet adhesion and activation, as well as vWF expression. Treatment of SEC at 37°C with recombinant human MMPs for 24 hr also rendered the SEC more adherent for unactivated platelets. Conclusion. Cold preservation of SEC results in increased expression of the platelet receptor vWF, increased platelet adhesion, and platelet activation. This is at least partly mediated by actin disassembly and MMP secretion.
Profiling the Evolution of Human Metastatic Bladder Cancer (2004)

Abstract Pulmonary metastases frequently develop in patients with aggressive bladder cancer, yet investigation of this process at the molecular level suffers from the poor availability of human metastatic tumor tissue and the absence of suitable animal models. To address this, we developed progressively more metastatic human bladder cancer cell lines and an in vivo bladder-cancer lung-metastasis model, and we successfully used these to identify genes of which the expression levels change according to the degree of pulmonary metastatic potential. By initially intravenously injecting the poorly metastatic T24T human urothelial cancer cells into nude mice, and then serially reintroducing and reisolating the human tumor cells from the resultant mouse lung tumors, three derivative human lines with increasingly metastatic phenotypes, designated FL1, FL2, and FL3, were sequentially isolated. To identify the genes associated with the most lung-metastatic phenotype, the RNA complement from the parental and derivative cells was evaluated with oligonucleotide microarrays. In doing so, we found 121 genes to be progressively up-regulated during the transition from T24T to FL3, whereas 43 genes were progressively down-regulated. As expected, many of the genes identified in these groups could, according to the ascribed functions of their protein product, theoretically participate in tissue invasion and metastasis. In addition, the magnitude of gene expression changes observed during the metastatic transition correlated with the in vivo propensity for earlier lung colonization and decreased host survival. To additionally define which genes found in the experimental system were of relevance to human bladder cancer lung metastasis, we evaluated gene expression profiles of 23 primary human bladder tumors of various stages and grades, and then we compared these gene expression profiles to the altered profiles in our model cell lines. Here we found that the expression of epiregulin, urokinase-type plasminogen activator (uPA), matrix metalloproteinase (MMP)14, and tissue inhibitor of metalloproteinase (TIMP-2) were consistently and progressively up-regulated when viewed as a function of tumor stage in tissues of patients versus the metastatic potential seen in the mouse lung model. The strong correlation of these four markers between the experimental and clinical situations helps validate this system as a useful tool for the study of lung metastasis and defines targets of therapy that may reduce the incidence of this process in patients.
Phase III Trial Evaluating the Addition of Paclitaxel to Doxorubicin Followed by Cyclophosphamide, Methotrexate, and Fluorouracil, As Adjuvant or Primary Systemic Therapy: European Cooperative Trial in Operable Breast Cancer (2009)

Incorporating paclitaxel into anthracycline-based adjuvant therapy resulted in a significant improvement in RFS and distant RFS. When given as primary systemic therapy, the paclitaxel-containing regimen allowed breast-sparing surgery in a significant percentage of patients.
Discovery of Pyrazolo[1,5-a]pyrimidine TTK Inhibitors: CFI-402257 is a Potent, Selective, Bioavailable Anticancer Agent (2016)

This work describes a scaffold hopping exercise that begins with known imidazo[1,2-a]pyrazines, briefly explores pyrazolo[1,5-a][1,3,5]triazines, and ultimately yields pyrazolo[1,5-a]pyrimidines as a novel class of potent TTK inhibitors. An X-ray structure of a representative compound is consistent with 1(1)/2 type inhibition and provides structural insight to aid subsequent optimization of in vitro activity and physicochemical and pharmacokinetic properties. Incorporation of polar moieties in the hydrophobic and solvent accessible regions modulates physicochemical properties while maintaining potency. Compounds with enhanced oral exposure were identified for xenograft studies. The work culminates in the identification of a potent (TTK K i = 0.1 nM), highly selective, orally bioavailable anticancer agent (CFI-402257) for IND enabling studies.
The antifungal activity of secondary metabolic products from Xenorhabdus nematophilus YL001 (2006)

This study investigated the antifungal activity of secondary metabolic products from Xenorhabdus nematophilus YL001 in vitro and in vivo. The results indicated that the supernatant of the bacteria broth inhibited mycelial growth of 15-species plant-pathogenic fungal in vitro. It especially could markedly inhibited the mycelial growth to Botrytis cinerea and Phytophthora capsici. Their EC_ 50 value against Botrytis cinerea and Phytophthora capsici were 53.54 mg·L~ -1 and 90.39mg·L~ -1 , respectively. The spore germination EC_ 50 value against Botrytis cinerea and Alternaria alternata were 16.97mg·L~ -1 and 21.87 mg·L~ -1 , respectively. In addition,protective effect and therapeutic effect of the fermentation products diluted 10 times against the Botrytis cinerea were 74.98% and 63.50% on tomato, respectively. Finally protective effect and therapeutic effect of the fermentation products against the Botrytis cinerea were 65.11% and 54.64% on cucumber in potted, respectively. The decrease of spore germination rate and the abnormal hyphal growth was observed under microscope.
Collagen mediates adhesion of Streptococcus mutans to human dentin (1993)

Some strains of Streptococcus mutans were found to recognize and bind collagen type I. Binding of 125I-labeled collagen type I was specific in that collagen types I and II, but not unrelated proteins, were able to inhibit binding of the labeled ligand to bacteria. Collagen binding to S. mutans was partially reversible and involved a limited number of bacterial binding sites per cell. S. mutans UA 140 cells bound collagen type I with high affinity (Kd = 8 x 10(-8) M). The number of binding sites per cell was 4 x 10(4). Collagen-binding strains of S. mutans were found to adhere to collagen-coated surfaces as well as to pulverized root tissue. S. mutans strains that did not bind the soluble ligand were unable to adhere to these substrata. Adherence to collagen-coated surfaces could be inhibited with collagen or clostridial collagenase-derived collagen peptides. Adherence of S. mutans to dentin was enhanced by collagen types I and II but inhibited by collagen peptides. S. mutans UA 140 bound significantly less 125I-collagen type I following treatment with peptidoglycan-degrading enzymes. These enzymes released a collagen-binding protein (collagen receptor) with a relative molecular size of 16 kDa. The results of this study suggest that collagen mediates adhesion of S. mutans to dentin. This interaction may target collagen-binding strains of S. mutans to dentin in the oral cavity and may play a role in the pathogenesis of root surface caries.
Angiotensin II in Septic Shock (2014)

Angiotensin II reversed sepsis-induced hypotension with systemic and regional hemodynamic effects similar to those of norepinephrine. Inhibition of angiotensin-converting enzyme before sepsis worsened the hypotension but enhanced skeletal muscle adenosine triphosphate. Modifying the renin-angiotensin system in sepsis should be further evaluated.
<p>Safety and sedative effect of intranasal dexmedetomidine in mandibular third molar surgery: a systematic review and meta-analysis</p> (2019)

Intranasal inhalation of Dex 30 minutes before third molar extraction can provide a good sedative effect, and large-sample multicenter RCTs are needed to evaluate the analgesic effect of Dex.
Induction of MAGE Genes in Lymphoid Cells by the Demethylating Agent 5‐Aza‐2′‐deoxycytidine (1996)

MAGE genes encoding tumor antigens recognized by cytotoxic T lymphocytes are appropriate target molecules for specific immunotherapy of cancer. We have investigated whether the demethylating agent 5-aza-2'-deoxycytidine (DAC) induces MAGE-1, -2, -3, and -6 in normal and malignant lymphoid cells. DAC induced these MAGE genes in both PHA/interleukin-2 (IL-2)-activated T cells from healthy donors and MAGE-negative T and B cell leukemias in most cases. It also induced MAGE-1 in IL-2-dependent T cell clones and all MAGE genes tested in Epstein-Barr virus-transformed B cell lines. Expression of MAGE-1 protein in the cells was confirmed by western blot analysis with anti-MAGE-1 polyclonal antibody. Therefore, demethylation is a potent stimulus to induce MAGE genes in both normal and malignant lymphoid cells.
Recent Advances in Viscoelastic Surfactants for Improved Production From Hydrocarbon Reservoirs (2016)

Summary Viscoelastic surfactants (VES) are used in upstream oil and gas applications, particularly hydraulic fracturing and matrix acidizing. A description of surfactant types is introduced along with a description of how they assemble into micelles, what sizes and shapes of micelles can be formed under different conditions, and finally how specific structures can lead to bulk viscoelastic-solution properties. This theoretical discussion leads into a description of the specific VES systems that have been used over the last 20 years in improved oil recovery for upstream applications. VES-based fluids have been used most extensively for hydraulic fracturing. They are preferred over conventional polymer-based fracturing-fluid systems because they are essentially solids-free systems that have demonstrated less damage to the reservoir-rock formation. In fact, approximately 10% of the fracturing treatments use VES-based fluids. Important advancements in VESs have been made by introducing “pseudocrosslinking agents,” such as nanoparticles, to enhance the viscosity. Fracturing-fluid systems modeled after VES have also been improved recently by developing internal breakers to lower their viscosity to flow back the well. The flexibility of VES-based fluids has been demonstrated by their application as foamed fluids, as well as their incorporation with brine systems such as produced water. A second key area that has benefited from VES-based systems is matrix acidizing of carbonate-based reservoirs. The viscosity of these VES-based fluids is mostly controlled by pH; at low pH (low viscosity), the acid system flows easily and invades pore spaces in the formation. During acidizing, the acid is spent, and the pH and viscosity increase. Because the spent acid has higher viscosity, fresh acid is diverted to low-permeability, uncontacted zones and penetrates the rocks to form wormholes. A number of experimental studies and field applications to these effects have been performed and will be described in this study. In order for VES-based fluids to play a more-prominent role in the field, inherent limitations such as cost, applicable temperature range, and leakoff characteristics will need to continue to be addressed. If we can efficiently and economically overcome these issues, VES-based fluids offer the industry an excellent clean and nondamaging alternative to conventional polymer-based fluids.
CLINICAL DEVELOPMENT OF HISTONE DEACETYLASE INHIBITORS AS ANTICANCER AGENTS (2004)

Acetylation is a key posttranslational modification of many proteins responsible for regulating critical intracellular pathways. Although histones are the most thoroughly studied of acetylated protein substrates, histone acetyltransferases (HATs) and deacetylases (HDACs) are also responsible for modifying the activity of diverse types of nonhistone proteins, including transcription factors and signal transduction mediators. HDACs have emerged as uncredentialed molecular targets for the development of enzymatic inhibitors to treat human cancer, and six structurally distinct drug classes have been identified with in vivo bioavailability and intracellular capability to inhibit many of the known mammalian members representing the two general types of NAD+-independent yeast HDACs, Rpd3 (HDACs 1, 2, 3, 8) and Hda1 (HDACs 4, 5, 6, 7, 9a, 9b, 10). Initial clinical trials indicate that HDAC inhibitors from several different structural classes are very well tolerated and exhibit clinical activity against a variety of human malignancies; however, the molecular basis for their anticancer selectivity remains largely unknown. HDAC inhibitors have also shown preclinical promise when combined with other therapeutic agents, and innovative drug delivery strategies, including liposome encapsulation, may further enhance their clinical development and anticancer potential. An improved understanding of the mechanistic role of specific HDACs in human tumorigenesis, as well as the identification of more specific HDAC inhibitors, will likely accelerate the clinical development and broaden the future scope and utility of HDAC inhibitors for cancer treatment.
Relevance of nucleic acid amplification techniques for diagnosis of respiratory tract infections in the clinical laboratory (1997)

Clinical laboratories are increasingly receiving requests to perform nucleic acid amplification tests for the detection of a wide variety of infectious agents. In this paper, the efficiency of nucleic acid amplification techniques for the diagnosis of respiratory tract infections is reviewed. In general, these techniques should be applied only for the detection of microorganisms for which available diagnostic techniques are markedly insensitive or nonexistent or when turnaround times for existing tests (e.g., viral culture) are much longer than those expected with amplification. This is the case for rhinoviruses, coronaviruses, and hantaviruses causing a pulmonary syndrome, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Coxiella burnetii. For Legionella spp. and fungi, contamination originating from the environment is a limiting factor in interpretation of results, as is the difficulty in differentiating colonization and infection. Detection of these agents in urine or blood by amplification techniques remains to be evaluated. In the clinical setting, there is no need for molecular diagnostic tests for the diagnosis of Pneumocystis carinii. At present, amplification methods for Mycobacterium tuberculosis cannot replace the classical diagnostic techniques, due to their lack of sensitivity and the absence of specific internal controls for the detection of inhibitors of the reaction. Also, the results of interlaboratory comparisons are unsatisfactory. Furthermore, isolates are needed for susceptibility studies. Additional work remains to be done on sample preparation methods, comparison between different amplification methods, and analysis of results. The techniques can be useful for the rapid identification of M. tuberculosis in particular circumstances, as well as the rapid detection of most rifampin-resistant isolates. The introduction of diagnostic amplification techniques into a clinical laboratory implies a level of proficiency for excluding false-positive and false-negative results.
Clinical Presentation, Investigation, and Management of Pulmonary Vein Stenosis Complicating Ablation for Atrial Fibrillation (2005)

Percutaneous intervention produces rapid and dramatic symptom relief in patients with highly symptomatic PV stenosis after radiofrequency ablation for AF. Nevertheless, alternative treatment methods will be required to decrease recurrent in-stent or in-segment restenosis.
Disease-modifying activity of SB 273005, an orally active, nonpeptide ?v?3 (vitronectin receptor) antagonist, in rat adjuvant-induced arthritis (2001)

Symptoms of AIA in rats were significantly reduced by either prophylactic or therapeutic treatment with the alphavbeta3 antagonist, SB 273005. Measurements of paw inflammation and of bone, cartilage, and soft tissue structure indicated that this compound exerts a protective effect on joint integrity and thus appears to have disease-modifying properties.
High quality time-scale modification for speech (2005)

We present a new and simple method for speech rate modification that yields high quality rate-modified speech. Earlier algorithms either required a significant amount of computation for good quality output speech or resulted in poor quality rate-modified speech. The algorithm we describe allows arbitrary linear or nonlinear scaling of the time axis. The algorithm operates in the time domain using a modified overlap-and-add (OLA) procedure on the waveform. It requires moderate computation and could be easily implemented in real time on currently available hardware. The algorithm works equally well on single voice speech, multiple-voice speech, and speech in noise. In this paper, we discuss an earlier algorithm for time-scale modification (TSM), and present both objective and informal subjective results for the new and previous TSM methods.
Memory management for user-level network interfaces (1998)

Presents an extension to the U-Net user-level network architecture allows messages to be transferred directly to and from any part of an application's address space without operating system intervention.
Ionic Conductivity of β-Fe2(SO4)3 Type Li3Cr2(PO4)3 Based Electrolyte (1993)

Abstract The electrical properties were studied for the (1-y)Li3Cr2(PO4)3-yLi5Mg2(PO4)3 system. The Mg2+ ion can not replace the Cr3+ site. The crystal structure for Li3Cr2(PO4)3 in this system is the β-Fe2(SO4)3 type monoclinic phase. The conductivity and the sinterability improve with the increase in y for the phosphate system. The maximum conductivity was 4.6 × 10−5 S·cm−1 at 298 K for y = 0.2. The activation energy for a Li+ ion migration at the bulk component was ca. 0.43 eV for all the samples.
TRUNDD, a new member of the TRAIL receptor family that antagonizes TRAIL signalling (1998)

TRAIL/Apo-2L induces rapid apoptosis of a variety of tumor cell lines. A family of tumor necrosis factor receptor-related molecules have been identified as receptors for TRAIL. Herein, we report the identification of another member of the TRAIL receptor family, TRUNDD (TRAIL receptor with a truncated death domain). The TRUNDD transcript was detected in multiple human tissues. TRUNDD is highly homologous to all known TRAIL receptors and has an extracellular TRAIL-binding domain but lacks a functional intracellular death domain and does not induce apoptosis. Consistent with an inhibitory role, ectopic expression of TRUNDD attenuated TRAIL-induced apoptosis in mammalian cells.
Analyzing interaction between distributed denial of service attacks and mitigation technologies (2004)

Under sponsorship of the Defense Advanced Research Projects Agency's (DARPA) Fault Tolerant Networks (FTN) program, The Johns Hopkins University Applied Physics Laboratory (JHU/APL) has been conducting the Distributed Denial of Service Defense Attack Tradeoff Analysis (DDOS-DATA). DDOS-DATA's goal is to analyze Distributed Denial of Service (DDOS) attacks and mitigation technologies to develop an understanding of how well mitigation technologies perform and how they can be combined to limit the potential attack space. This paper provides an overview of the DDOS-DATA project and discusses analysis results for the proof of work, rate limiting, and active monitor mitigation technologies considered both individually and when deployed in combinations.