gebhart/patrepeval huggingface dataset:
Metal Recognition of Septapeptides via Polypod Molecular Architecture (2005)

The understanding of the nature of recognition of inorganic materials by proteins is one of the core elements of and has profound implications in biological materials science and engineering. Using combinatorial display methods, a considerable number of short polypeptides have recently been selected with affinity to engineering materials. During these selections, more than several polypeptides are identified with binding specificity to a chosen inorganic material. Understanding the nature of surface recognition of materials by polypeptides is essential for rational design and biomimetic engineering of these inorganic-binding polypeptides for use as linkers, catalyzers, and growth modifiers in nanotechnology and nanobiotechnology. Although there may not be direct homology among the amino acids constituting the polypeptides, their function may come from conserved molecular architecture. Here we study crystallographic surface recognition of platinum metal-binding septapeptides by conformational analysis. We find that the septapeptides conform into certain molecular architectures containing multiple protrusions (polypods) that spatially match with the crystallographic metal surfaces. While the physical recognition may originate from how well the molecular polypods spatially match a given crystallographic surface, the degree of binding may be due to the reactive groups that form the polypods, e.g., charged or polar groups (e.g., hydroxyl and amine). These results are highly consistent with the experimental binding characteristics of the Pt binders with various degrees of affinities.
mTORC1 Senses Lysosomal Amino Acids Through an Inside-Out Mechanism That Requires the Vacuolar H + -ATPase (2011)

The mTOR complex 1 (mTORC1) protein kinase is a master growth regulator that is stimulated by amino acids. Amino acids activate the Rag guanosine triphosphatases (GTPases), which promote the translocation of mTORC1 to the lysosomal surface, the site of mTORC1 activation. We found that the vacuolar H(+)-adenosine triphosphatase ATPase (v-ATPase) is necessary for amino acids to activate mTORC1. The v-ATPase engages in extensive amino acid-sensitive interactions with the Ragulator, a scaffolding complex that anchors the Rag GTPases to the lysosome. In a cell-free system, ATP hydrolysis by the v-ATPase was necessary for amino acids to regulate the v-ATPase-Ragulator interaction and promote mTORC1 translocation. Results obtained in vitro and in human cells suggest that amino acid signaling begins within the lysosomal lumen. These results identify the v-ATPase as a component of the mTOR pathway and delineate a lysosome-associated machinery for amino acid sensing.
A Hydrological Sensor Web Ontology Based on the SSN Ontology: A Case Study for a Flood (2017)

Accompanying the continuous development of sensor network technology, sensors worldwide are constantly producing observation data. However, the sensors and their data from different observation platforms are sometimes difficult to use collaboratively in response to natural disasters such as floods for the lack of semantics. In this paper, a hydrological sensor web ontology based on SSN ontology is proposed to describe the heterogeneous hydrological sensor web resources by importing the time and space ontology, instantiating the hydrological classes, and establishing reasoning rules. This work has been validated by semantic querying and knowledge acquiring experiments. The results demonstrate the feasibility and effectiveness of the proposed ontology and its potential to grow into a more comprehensive ontology for hydrological monitoring collaboratively. In addition, this method of ontology modeling is generally applicable to other applications and domains.
Physical Principles of Microbubbles for Ultrasound Imaging and Therapy (2009)

Microbubble ultrasound contrast agents have been in clinical use for more than two decades, during which time their range of applications has increased to encompass echocardiography, Doppler enhancement, perfusion studies and molecular imaging, as well as a number of therapeutic applications including drug delivery, gene therapy, high-intensity focused ultrasound treatments and sonothrombolysis. The aim of this article is to review the different types of microbubble agent, their physical behaviour and the mechanisms underlying their effectiveness in imaging and therapeutic applications.
Plasma elimination of cholyl‐lysyl‐fluorescein (CLF): a pilot study in patients with liver cirrhosis (2000)

CLF test clearly distinguished between the two analyzed groups and was more sensitive than routine liver function tests. The test appears safe, simple to perform and analyze and after validation in larger cohorts of patients may have the potential to become a useful dynamic test of liver function.
Use of a polymerase chain reaction assay and an ELISA to monitor porcine circovirus type 2 infection in pigs from farms with and without postweaning multisystemic wasting syndrome (2004)

A high prevalence of PCV2 infection was found in pigs from farms with and without PMWS. Besides the presence of PCV2, unknown additional factors may be necessary to induce the full expression of PMWS.
Clinical Physiology: The Effect of Induced Arterial Hypertension upon Regional Blood Flow in Subcutaneous Tissue in Patients with Arterial Insufficiency of the Legs (1975)

In nine patients with arterial insufficiency of the legs, the effect of induced arterial hypertension upon blood flow in subcutaneous tissue was correlated to the changes of blood flow in subcutaneous tissue during dependency. Arterial pressure was increased by constant intravenous infusion of angiotensin. Blood flow in subcutaneous tissue was measured 10 cm distal to the head of fibula, at the lateral malleolus, and at the base of the first toe by means of the xenon washout technique. It was found that in areas where blood flow decreased during dependency, blood flow decreased during angiotensin infusion. An increase in blood flow during angiotensin infusion was seen in areas where blood flow increased during dependency. It is concluded that the effect of angiotensin infusion on blood flow and of therapeutically induced hypertension can be predicted from the effect of orthostatic changes on blood flow. The results obtained support the hypothesis that the vessels behave as passive channels (i.e. blood flow depends mainly upon arterial perfusion pressure) in areas where the normal vasoconstrictor response to increased transmural pressure is abolished.
Soft tissue adhesive composed of modified gelatin and polysaccharides (2000)

Although fibrin glue has been clinically used as a surgical adhesive, hemostatic agent, and sealant, it has the risk of virus infection because its components, fibrinogen and thrombin, are obtained from human blood. To circumvent this problem, we employed bioabsorbable gelatin and polysaccharides to prepare a safer hemostatic glue. Gelatin was modified with ethylenediamine using water-soluble carbodiimide to introduce additional amino groups into the original gelatin, while dextran and hydroxyethyl-starch were oxidized by sodium periodate to convert 1,2-hydroxyl groups into dialdehyde groups. Upon mixing of the two polymer components in aqueous solution, Schiff base was formed between the amino groups in the modified gelatin and the aldehyde groups in the modified polysaccharides, which thus resulted in intermolecular cross-linking and gel formation. The fastest gel formation took place within 2 s, and its bonding strength to porcine skin was about 225 gf cm(-2) when 20 wt% of an amino-gelatin (55% amino) and 10 wt% of aldehyde-HES (>84% dialdehyde) aqueous solutions were mixed. In contrast, the gelation time and bonding strength of fibrin glue was 5 s and 120 gf cm(-2), respectively.
Intravenous ketamine therapy in a patient with a treatment-resistant major depression (2007)

Ketamine not only seems to have strong antidepressant effects but also to act very swiftly. These actions were unaffected by an alcohol or benzodiazpine dependence.
Gonadotropins Activate Proteolysis and Increase Invasion through Protein Kinase A and Phosphatidylinositol 3-Kinase Pathways in Human Epithelial Ovarian Cancer Cells (2006)

Despite evidence that gonadotropins may facilitate peritoneal metastasis of ovarian cancer by increasing cell adhesion, the action and molecular mechanism of follicle-stimulating hormone (FSH) and luteinizing hormone (LH) in ovarian cancer invasion is not well characterized. In the present study, we investigated the effects of FSH and LH on the invasive activity and the expression of metastasis-related proteinases in human epithelial ovarian cancer by Western blot, zymography, reverse transcription-PCR (RT-PCR), ELISA, and Boyden chamber assay. Treatment with FSH or LH (10, 100, or 1,000 ng/mL) significantly increased the invasion of ovarian cancer cell lines, including BG-1, CaOV-3, and SKOV-3 cells but not OVCAR-3 cells. In addition, treatment of SKOV-3 cells with FSH or LH (100 or 1,000 ng/mL) enhanced the expression and activation of matrix metalloproteinases (MMP-2 and MMP-9) as shown by RT-PCR, gelatin zymography, and ELISA. Pretreatment with [(2R)-2-(hydroxamido-carbonylmethyl)-4-methylpentanoyl]-l-tryptophan methylamide (10 micromol/L), a total MMP inhibitor, and 3-(4-phenoxyphenylsulfonyl)-propylthiirane (20 micromol/L), a specific gelatinase inhibitor, neutralized the proinvasive effect of gonadotropins in SKOV-3 cells. In addition, the secretion of tissue inhibitor of metalloproteinases (TIMP-1 and TIMP-2) and plasminogen activator inhibitor-1 was significantly decreased by FSH and LH (100 or 1,000 ng/mL). We further showed that gonadotropins induced an increase in SKOV-3 invasiveness via the activation of protein kinase A (PKA) and phosphatidylinositol 3-kinase (PI3K) signaling pathways. Taken together, these results suggest that gonadotropins may contribute to ovarian cancer metastasis via activation of proteolysis and increase in invasion through the PKA and PI3K pathways.
Cigarette Smoking Increases Sympathetic Outflow in Humans (1998)

These data provide the first direct evidence that cigarette smoking increases sympathetic outflow.
Therapy of chemotherapy‐induced peripheral neuropathy (2009)

Chemotherapy-induced peripheral neuropathy (CIPN) is still a common and disabling side effect of many chemotherapy agents in use today. Unfortunately, neither prophylactic strategies nor symptomatic treatments have proven useful yet. This review will discuss the diagnosis and evaluation of neuropathy in cancer patients, as well as reviewing the various prophylactic and symptomatic treatments that have been proposed or tried. However, sufficient evidence is lacking to recommend any of these treatments to patients suffering with CIPN. Therefore, the best approach is to treat symptomatically, and to start with broad-spectrum analgesic medications such as non-steroidal anti-inflammatory drugs (NSAIDs). If NSAIDs fail, a reasonable second-line agent in properly selected patients may be an opioid. Unfortunately, even when effective in other types of neuropathic pain, anti-depressants and anticonvulsants have not yet proven effective for treating the symptoms of CIPN.
Upregulation of OX40 ligand on monocytes contributes to early virological control in patients with chronic hepatitis C (2013)

Dysfunctional hepatitis C virus (HCV) specific CD4(+) T cells are known to contribute to inadequate adaptive immunity in chronic hepatitis C (CHC), although the underlying mechanisms remain largely undefined. In this study, OX40 ligand (OX40L) expression was investigated in 41 treatment-naïve CHC patients, 20 sustained virological responders and 36 healthy subjects. We observed that OX40L expression was significantly upregulated in peripheral monocytes in CHC patients compared with sustained virological responders and healthy subjects. OX40L upregulation correlated significantly with plasma viral load rather than serum alanine aminotransaminase levels. Furthermore, longitudinal analyses indicated that upregulated OX40L expression on monocytes is closely associated with rapid or early virological responses in patients receiving pegylated IFN-α/ribavirin treatment. In vitro, HCV core antigen strongly stimulated monocyte expression of OX40L and blockade of TLR2 signaling significantly downregulated OX40L expression. More importantly, elevated OX40L expression was also shown to be closely associated with elevation of the HCV-specific CD4(+) T-cell response and in vitro blockade of OX40L expressed on monocytes led to impaired CD4(+) T-cell function. These findings, therefore, implicate OX40L expression can be used as a marker to evaluate antiviral treatment efficacy and extend the notion that enhancement of OX40L expression could be a good way for immunotherapy in CHC patients.
Characterization of Adenosine Diphosphate Glucose Pyrophosphorylases from Developing Maize Seeds (1975)

Electrophoretic examination of 22-day-old, normal maize (Zea mays L.) endosperm extracts revealed two zones of adenosine diphosphate glucose pyrophosphorylase activity. The enzymes are identical in terms of Km for glucose 1-phosphate and the effect of 3-phosphoglyceric acid on apparent Km for glucose 1-phosphate. Both enzymatic activities increase with increasing doses of the functional alleles at the shrunken-2 and brittle-2 loci. Molecular weight differences between the two electrophoretic species were inferred from sucrose gradient centrifugation. It is suggested that the two bands of activity represent different aggregation states of the same enzyme because under different extraction conditions, only one enzyme is found. Molecular weight estimates of 237,000 and 253,000 were obtained for the smaller enzyme. It is suggested that this enzyme is an aggregate of several subunits. Comparison of the embryo and endosperm pyrophosphorylases showed the embryo activity to be more heat stable and probably independent of direct shrunken-2 or brittle-2 control.
Label-free biosensing with functionalized nanopipette probes (2009)

Nanopipette technology can uniquely identify biomolecules such as proteins based on differences in size, shape, and electrical charge. These differences are determined by the detection of changes in ionic current as the proteins interact with the nanopipette tip coated with probe molecules. Here we show that electrostatic, biotin-streptavidin, and antibody-antigen interactions on the nanopipette tip surface affect ionic current flowing through a 50-nm pore. Highly charged polymers interacting with the glass surface modulated the rectification property of the nanopipette electrode. Affinity-based binding between the probes tethered to the surface and their target proteins caused a change in the ionic current due to a partial blockade or an altered surface charge. These findings suggest that nanopipettes functionalized with appropriate molecular recognition elements can be used as nanosensors in biomedical and biological research.
Aspirin Dosage and Thromboxane Synthesis in Patients with Vascular Disease (2003)

Different aspirin dosages significantly affect serum and urinary markers of thromboxane synthesis.
Large duplications at reciprocal translocation breakpoints that might be the counterpart of large deletions and could arise from stalled replication bubbles (2011)

Reciprocal chromosome translocations are often not exactly reciprocal. Most familiar are deletions at the breakpoints, up to megabases in extent. We describe here the opposite phenomenon-duplication of tens or hundreds of kilobases at the breakpoint junction, so that the same sequence is present on both products of a translocation. When the products of the translocation are mapped on the genome, they overlap. We report several of these "overlapping-breakpoint" duplications in breast cancer cell lines HCC1187, HCC1806, and DU4475. These lines also had deletions and essentially balanced translocations. In HCC1187 and HCC1806, we identified five cases of duplication ranging between 46 kb and 200 kb, with the partner chromosome showing deletions between 29 bp and 31 Mb. DU4475 had a duplication of at least 200 kb. Breakpoints were mapped using array painting, i.e., hybridization of chromosomes isolated by flow cytometry to custom oligonucleotide microarrays. Duplications were verified by fluorescent in situ hybridization (FISH), PCR on isolated chromosomes, and cloning of breakpoints. We propose that these duplications are the counterpart of deletions and that they are produced at a replication bubble, comprising two replication forks with the duplicated sequence in between. Both copies of the duplicated sequence would go to one daughter cell, on different products of the translocation, while the other daughter cell would show deletion. These duplications may have been overlooked because they may be missed by FISH and array-CGH and may be interpreted as insertions by paired-end sequencing. Such duplications may therefore be quite frequent.
Hydrolysis of the soft amphiphilic antimicrobial agent tetradecyl betainate is retarded after binding to and killing Salmonella typhimurium (1998)

Hydrolysis of tetradecyl betainate (B14), a fast-acting microbicidal amphiphilic quaternary ammonium compound (QAC) being an ester of betaine and tetradecanol, occurred after binding to Salmonella typhimurium, resulting in release of the water-soluble betaine portion and retention of the lipophilic tetradecanol. The rate of the hydrolysis was significant but retarded in comparison to B14 in solution. As in free solution, the hydrolysis of substance bound to S. typhimurium was increased in an alkaline environment and by heat. At pH 6.0 and 20 degrees C the hydrolysis of bound ester was about 10% after 180 min, whereas at pH 9.0 and 50 degrees C it was about 50% after 60 min. These results are consistent with a model where amphiphilic QACs are inserted into the bacterial outer membrane (OM) with the quaternary ammonium head group facing outwards and the lipophilic portion, including the ester bond, being in the membrane lipid environment enough for retarding the hydrolysis. However, calculation of the mean concentration of B14 in the bacteria at MBC99 (minimum bactericidal concentration required to kill 99% of cells) showed a 7000-8000 times greater concentration than in the medium. At this concentration, when most B14 is considered to be bound to the OM, the available surface area for each molecule was only 2 A2. This is only 6-7% of that required for close packing of the quaternary ammonium head group (30 A2), indicating that a three-dimensional, presumably continuous arrangement was formed. Since B14 is hydrolysed after its binding to bacteria with microbicidal effect, it may be used under conditions where stable QACs might be harmful to the close or the common environment.
Liver-Directed Gene Therapy: A Retroviral Vector with a Complete LTR and the ApoE Enhancer- α 1 -Antitrypsin Promoter Dramatically Increases Expression of Human α 1 -Antitrypsin In Vivo (1996)

Hepatic gene therapy could improve the treatment of many inherited disorders. Although retroviral vectors result in long-term expression in hepatocytes in vivo, their low level of expression currently precludes most clinical applications. Four copies of the liver-specific apolipoprotein E (ApoE) enhancer were placed upstream of the human alpha 1-antitrypsin (hAAT) promoter in either orientation into a retroviral vector with a complete long terminal repeat (LTR) and the hAAT cDNA to generate ApoE(+)hAAT-LTR and ApoE(-)hAAT-LTR. In addition, the ApoAI promoter was placed upstream of the hAAT cDNA in a similar retroviral vector backbone. Amphotropic retroviral vectors were transferred into regenerating rat liver cells in vivo by intraportal injection. ApoE(-)hAAT-LTR and ApoE(+)hAAT-LTR led to average hAAT levels of 5 micrograms/ml (0.5% of normal levels of a very abundant protein), and 2.5 micrograms/ml, respectively, which was stable for at least 10 months after transduction. This level of serum hAAT was > 25-fold higher than what was observed from the ApoAI promoter used in this study. Serum levels of hAAT were > 15-fold higher than what was observed from retroviral vectors containing the hAAT cDNA that were analyzed previously by this lab. In some cases, improved expression was due to the promoter chosen. In other cases, the increase in expression was primarily due to the higher titers obtained by using a retroviral backbone with an intact LTR as opposed to a vector with a deletion in the LTR. The increased expression levels observed from this enhancer/promoter combination in an intact retroviral backbone may enable one to achieve therapeutic levels of clinically important genes from a retroviral vector in liver cells of animals.
The Thiol-Michael Addition Click Reaction: A Powerful and Widely Used Tool in Materials Chemistry (2013)

The key attribute of the thiol-Michael addition reaction that makes it a prized tool in materials science is its modular “click” nature, which allows for the implementation of this highly efficient, “green” reaction in applications that vary from small molecule synthesis to in situ polymer modifications in biological systems to the surface functionalization of material coatings. Over the past few decades, interest in the thiol-Michael addition reaction has increased dramatically, as is evidenced by the number of studies that have been dedicated to elucidating different aspects of the reaction that range from an in-depth analysis aimed at understanding the mechanistic pathways of the reaction to synthetic studies that have examined modifying molecular structures with the aim of yielding highly efficient thiol-Michael reaction monomers. This review examines the reaction mechanisms, the substrates and catalysts used in the reaction, and the subsequent implementation of the thiol-Michael reaction in materials science over the years, with particular emphasis on the recent developments in the arena over the past decade.
Halogen bonding to a divalent sulfur atom: an experimental study of the interactions of CF3X (X = Cl, Br, I) with dimethyl sulfide (2011)

Using FTIR and Raman spectroscopy, the formation of halogen bonded complexes of the trifluorohalomethanes CF(3)Cl, CF(3)Br and CF(3)I with dimethyl sulfide (DMS) dissolved in liquid krypton has been investigated. For CF(3)Br and CF(3)I, evidence was found for the formation of C-XS halogen bonded 1:1 complexes. At higher concentrations of CF(3)I weak absorptions due to a 2:1 complex were also observed. Using spectra recorded at temperatures between 118 and 163 K, the complexation enthalpies for the complexes were determined to be -9.5(5) kJ mol(-1) for CF(3)Br·DMS, -17.4(1) kJ mol(-1) for CF(3)I·DMS and -30.8(16) kJ mol(-1) for (CF(3)I·)(2)DMS. The results from the cryospectroscopic study are compared with ab initio calculations at the MP2/aug-cc-pVDZ(-PP) level. Apart from vibrational modes localized in the trifluorohalomethanes and the DMS moieties, for both CF(3)Br and CF(3)I, an additional band, which we assign as the intermolecular stretching mode in the complex, was identified in the infrared and Raman spectra.
A novel approach to temporary stenting: degradable cardiovascular stents produced from corrodible metal—results 6–18 months after implantation into New Zealand white rabbits (2001)

This initial in vivo experience suggests that degradable iron stents can be safely implanted without significant obstruction of the stented vessel caused by inflammation, neointimal proliferation, or thrombotic events.