gebhart/patrepeval huggingface dataset:
A significant response to neoadjuvant chemotherapy in BRCA1/2 related breast cancer: Table 1 (2002)

Neoadjuvant (preoperative) chemotherapy was initially developed as a first line treatment for locally advanced breast cancer. More recently, it has been used to treat earlier stage operable disease, with the hope that not only could the treatment be used as an in vivo assessment of tumour response, but also that it might more readily eradicate occult distant micrometastases. Many studies have shown a small but significant increase in breast conservation when neoadjuvant chemotherapy was used but, overall, most randomised studies have not shown any survival advantage following this treatment.1,2 Despite this, it has been noted that women receiving neoadjuvant chemotherapy who experience either a clinical complete response (cCR) (≤40% of all those treated) or, more clearly, a pathological complete response (pCR) (≤10%) have a better long term outcome than women who achieve less than a complete response.1,2

Germline mutations in the BRCA1 and BRCA2 genes are the major genetic predisposition to breast cancer. Some of the functions of BRCA1 and BRCA2 proteins could be directly involved in response to cytotoxic agents, such as the role of BRCA1/2 in DNA repair3 or apoptosis.4,5 Distinct pathological features6 and gene expression profiles7 suggest that there are differences in hereditary breast cancer compared to sporadic cases, which might lead to differences in treatment response. In vitro data suggest that cells without functional BRCA1 or BRCA2 protein are particularly sensitive to several chemotherapeutic drugs4 or ionising radiation.8 Mouse and human cell lines deficient in BRCA1 or BRCA2 display an increased sensitivity to agents causing double strand DNA breaks.9,10 This hypersensitivity has been shown for mitoxantrone, amsacrine, etoposide, doxorubicin, and cisplatin with a subsequent increased level of apoptosis.9,11–13 Differences in drug sensitivity might be explained by interaction of BRCA1/2 proteins …
Chemotaxis for Human Monocytes by Fibrinogen‐derived Peptides (1976)

Chemotactic activity for human peripheral blood monocytes was generated by the action of thrombin on human fibrinogen, a reaction known to release low molecular fibrinopeptides. Supernatants prepared by incubating Contortrix venom with fibrinogen, which cleaves the B peptide, were also chemotactic, whereas no activity was present in supernatants from Arvin venom, which cleaves peptides A, AP and AY. Thus fibrinopeptide B was chemotactic for the monocyte in addition to the neutrophil, as previously reported. Monocyte chemotactic activity was also generated by the action of plasmin on human fibrinogen and shown to be associated with the D and E fragments but not with a mixture of fragments X and Y. When plasmin digestion was stopped at time intervals up to 24 h, monocyte chemotactic activity corresponded with the appearance of the D and E fragments. The monocyte chemotactic activity, contained in a 24 h digest, eluted from Sephadex G-75 at VO, corresponding to the expected position of the D and E fragments whereas neutrophil chemotactic activity eluted with molecules of molecular size of approximately 30 000 daltons. Thus fragments D and E derived from plasmin digestion of fibrinogen attract the monocyte whereas only the small uncharacterized peptides were chemotactic for the neutrophil. These different profiles of chemotactic activity for the neutrophil and the monocyte in terms of plasmin digestion products of fibrinogen may be of significance in the events leading to the accumulation of these cells in vivo during fibrin deposition.
High Performance Thin-Film Composite Forward Osmosis Membrane (2010)

Recent studies show that osmotically driven membrane processes may be a viable technology for desalination, water and wastewater treatment, and power generation. However, the absence of a membrane designed for such processes is a significant obstacle hindering further advancements of this technology. This work presents the development of a high performance thin-film composite membrane for forward osmosis applications. The membrane consists of a selective polyamide active layer formed by interfacial polymerization on top of a polysulfone support layer fabricated by phase separation onto a thin (40 mum) polyester nonwoven fabric. By careful selection of the polysulfone casting solution (i.e., polymer concentration and solvent composition) and tailoring the casting process, we produced a support layer with a mix of finger-like and sponge-like morphologies that give significantly enhanced membrane performance. The structure and performance of the new thin-film composite forward osmosis membrane are compared with those of commercial membranes. Using a 1.5 M NaCl draw solution and a pure water feed, the fabricated membranes produced water fluxes exceeding 18 L m(2-)h(-1), while consistently maintaining observed salt rejection greater than 97%. The high water flux of the fabricated thin-film composite forward osmosis membranes was directly related to the thickness, porosity, tortuosity, and pore structure of the polysulfone support layer. Furthermore, membrane performance did not degrade after prolonged exposure to an ammonium bicarbonate draw solution.
Thrombolysis: newer thrombolytic agents and their role in clinical medicine (2003)

Reperfusion treatment in acute myocardial infarction represents the main indication for thrombolytic therapy. The most common thrombolytic agents have been streptokinase (first generation thrombolytic agent) and alteplase (tissue type plasminogen activator, t-PA, second generation thrombolytic agent). In the meantime third generation thrombolytic agents have reached clinical practice. Many of them are derivatives of alteplase, the current gold standard for thombolytic therapy in acute coronary syndromes with ST segment elevation. The most prominent among them are reteplase, tenecteplase, and lanoteplase.

Reteplase (recombinant plasminogen activator, r-PA) is a single chain deletion mutant of alteplase that is expressed in Escherichia coli and, therefore, is expressed as an unglycosylated protein (table 1, figs 1 and 2). Reteplase includes 355 amino acids with a total molecular weight of 39 kDa. The molecule consists of cringle 2 and the protease domain of the alteplase molecule. Because of the deletion of the fibronectin finger region, the binding of reteplase to fibrin is significantly reduced in comparison with that of alteplase. Although kringle 2 (known to stimulate protease in the presence of fibrin) is part of the reteplase molecule, reteplase is stimulated in the presence of fibrin to a lower extent than alteplase, suggesting that the fibronectin finger is involved in the stimulation of the protease as well. Reteplase, in comparison with alteplase, is characterised by reduced fibrin selectivity. In the abscence of fibrin, reteplase and alteplase do not differ with respect to their activity as plasminogen activators, nor do they differ with respect to their inhibition by the plasminogen activator inhibitor type 1 (PAI-1).

View this table:

 Table 1 
Alteplase: structure of the molecule and function of its components





 Figure 1 
Alteplase.





 Figure 2 
Reteplase.



The elimination of reteplase from the circulating plasma predominantly occurs in the liver. Because of the deletion of the fibronectin finger region, the epidermal growth factor domain and kringle 1, as …
Degradation Behaviour of Metallic Biomaterials for Degradable Stents (2006)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
Complex Metabolic Phenotypes Caused by a Mutation in yjgF , Encoding a Member of the Highly Conserved YER057c/YjgF Family of Proteins (1998)

The oxidative pentose phosphate pathway is required for function of the alternative pyrimidine biosynthetic pathway, a pathway that allows thiamine synthesis in the absence of the PurF enzyme in Salmonella typhimurium. Mutants that no longer required function of the oxidative pentose phosphate pathway for thiamine synthesis were isolated. Further phenotypic analyses of these mutants demonstrated that they were also sensitive to the presence of serine in the medium, suggesting a partial defect in isoleucine biosynthesis. Genetic characterization showed that these pleiotropic phenotypes were caused by null mutations in yjgF, a previously uncharacterized open reading frame encoding a hypothetical 13.5-kDa protein. The YjgF protein belongs to a class of proteins of unknown function that exhibit striking conservation across a wide range of organisms, from bacteria to humans. This work represents the first detailed phenotypic characterization of yjgF mutants in any organism and provides important clues as to the function of this highly conserved class of proteins. Results also suggest a connection between function of the isoleucine biosynthetic pathway and the requirement for the pentose phosphate pathway in thiamine synthesis.
Chemical Synthesis and Folding Pathways of Large Cyclic Polypeptides:  Studies of the Cystine Knot Polypeptide Kalata B1 (1999)

Kalata B1 is a member of a new family of polypeptides, isolated from plants, which have a cystine knot structure embedded within an amide-cyclized backbone. This family of molecules are the largest known cyclic peptides, and thus, the mechanism of synthesis and folding is of great interest. To provide information about both these phenomena, we have synthesized kalata B1 using two distinct strategies. In the first, oxidation of the cysteine residues of a linear precursor peptide to form the correct disulfide bonds results in folding of the three-dimensional structure and preorganization of the termini in close proximity for subsequent cyclization. The second approach involved cyclization prior to oxidation. In the first method, the correctly folded peptide was produced only in the presence of partially hydrophobic solvent conditions. These conditions are presumably required to stabilize the surface-exposed hydrophobic residues. However, in the synthesis involving cyclization prior to oxidation, the cyclic reduced peptide folded to a significant degree in the absence of hydrophobic solvents and even more efficiently in the presence of hydrophobic solvents. Cyclization clearly has a major effect on the folding pathway and facilitates formation of the correctly disulfide-bonded form in aqueous solution. In addition to facilitating folding to a compact stable structure, cyclization has an important effect on biological activity as assessed by hemolytic activity.
A new method for constructing linker scanning mutants (1987)

A new procedure for the construction of linker scanning mutants is described. A plasmid containing the target DNA is randomly linearized and slightly shortened by a novel combination of established methods. After partial apurination with formic acid a specific nick or small gap is introduced at the apurinic site by exonuclease III, followed by nuclease S1 cleavage of the strand opposite the nick/gap. Synthetic linkers are ligated to the ends and plasmids having the linker inserted in the target DNA are enriched. Putative linker scanning mutants are identified by their topoisomer patterns after relaxation with topoisomerase I. This technique allows the distinction of plasmids differing in length by a single basepair. We have used this rapid and efficient strategy to generate a set of 32 linker scanning mutants covering the chicken lysozyme promoter from -208 to +15.
Characterization of TEM1/endosialinin human and murine brain tumors (2009)

TEM1/endosialin was induced in the vasculature of high-grade brain tumors where its expression was inversely correlated with patient age. Although lack of TEM1/endosialin did not suppress growth of intracranial GBM xenografts, it did increase tumor vascularity. The cellular localization of TEM1/endosialin and its expression profile in primary and metastatic brain tumors support efforts to therapeutically target this protein, potentially via antibody mediated drug delivery strategies.
Neuronal Pathway from the Liver Modulates Energy Expenditure and Systemic Insulin Sensitivity (2006)

Coordinated control of energy metabolism and glucose homeostasis requires communication between organs and tissues. We identified a neuronal pathway that participates in the cross talk between the liver and adipose tissue. By studying a mouse model, we showed that adenovirus-mediated expression of peroxisome proliferator-activated receptor (PPAR)-g2 in the liver induces acute hepatic steatosis while markedly decreasing peripheral adiposity. These changes were accompanied by increased energy expenditure and improved systemic insulin sensitivity. Hepatic vagotomy and selective afferent blockage of the hepatic vagus revealed that the effects on peripheral tissues involve the afferent vagal nerve. Furthermore, an antidiabetic thiazolidinedione, a PPARg agonist, enhanced this pathway. This neuronal pathway from the liver may function to protect against metabolic perturbation induced by excessive energy storage.
NOX3, a Superoxide-generating NADPH Oxidase of the Inner Ear (2004)

Reactive oxygen species (ROS) play a major role in drug-, noise-, and age-dependent hearing loss, but the source of ROS in the inner ear remains largely unknown. Herein, we demonstrate that NADPH oxidase (NOX) 3, a member of the NOX/dual domain oxidase family of NADPH oxidases, is highly expressed in specific portions of the inner ear. As assessed by real-time PCR, NOX3 mRNA expression in the inner ear is at least 50-fold higher than in any other tissues where its expression has been observed (e.g. fetal kidney, brain, skull). Microdissection and in situ hybridization studies demonstrated that NOX3 is localized to the vestibular and cochlear sensory epithelia and to the spiral ganglions. Transfection of human embryonic kidney 293 cells with NOX3 revealed that it generates low levels of ROS on its own but produces high levels of ROS upon co-expression with cytoplasmic NOX subunits. NOX3-dependent superoxide production required a stimulus in the absence of subunits and upon co-expression with phagocyte NADPH oxidase subunits p47(phox) and p67(phox), but it was stimulus-independent upon co-expression with colon NADPH oxidase subunits NOX organizer 1 and NOX activator 1. Pre-incubation of NOX3-transfected human embryonic kidney 293 cells with the ototoxic drug cisplatin markedly enhanced superoxide production, in both the presence and the absence of subunits. Our data suggest that NOX3 is a relevant source of ROS generation in the cochlear and vestibular systems and that NOX3-dependent ROS generation might contribute to hearing loss and balance problems in response to ototoxic drugs.
Comparison of Computed Density and Microscopic Morphometry in Pulmonary Emphysema (1996)

Abstract The purpose of this prospective study was to verify whether the percentage area of lung occupied by lowest attenuation values on high-resolution computed tomography (HRCT) scans reflects microscopic emphysema and to compare this quantification with the information yielded by the most widely used pulmonary function tests (PFT). Preoperative HRCT scans were obtained with 1-cm intervals in 38 subjects. With a semiautomatic evaluation procedure, the percentage areas occupied by attenuation values inferior to thresholds ranging from -900 Hounsfield units (HU) to -970 HU were calculated for the lobe or lung to be resected. Emphysema was microscopically quantified by using a computer-based method, measuring the perimeters and interwall distances of alveoli and alveolar ducts. The strongest correlation was found for -950 HU. As a second step, we evaluated possible correlations between PFT and microscopic measurements. Finally, considering the microscopic measurements as a standard, we tried to investigate their relationships with each of the PFT and with the relative area occupied by attenuation values lower than -950 HU for both lungs. This revealed that the diffusing capacity for carbon monoxide associated with HRCT quantification is sufficient to predict microscopic measurements. We concluded that the percentage area of lung occupied by attenuation values lower than -950 HU is a valid index of pulmonary emphysema.
Rationale and design of the allogeneiC human mesenchymal stem cells (hMSC) in patients with aging fRAilTy via intravenoUS delivery (CRATUS) study: A phase I/II, randomized, blinded and placebo controlled trial to evaluate the safety and potential efficacy of allogeneic human mesenchymal stem cell infusion in patients with aging frailty (2016)

Frailty is a syndrome associated with reduced physiological reserves that increases an individual's vulnerability for developing increased morbidity and/or mortality. While most clinical trials have focused on exercise, nutrition, pharmacologic agents, or a multifactorial approach for the prevention and attenuation of frailty, none have studied the use of cell-based therapies. We hypothesize that the application of allogeneic human mesenchymal stem cells (allo-hMSCs) as a therapeutic agent for individuals with frailty is safe and efficacious. The CRATUS trial comprises an initial non-blinded phase I study, followed by a blinded, randomized phase I/II study (with an optional follow-up phase) that will address the safety and pre-specified beneficial effects in patients with the aging frailty syndrome. In the initial phase I protocol, allo-hMSCs will be administered in escalating doses via peripheral intravenous infusion (n=15) to patients allocated to three treatment groups: Group 1 (n=5, 20 million allo-hMSCs), Group 2 (n=5, 100 million allo-hMSCs), and Group 3 (n=5, 200 million allo-hMSCs). Subsequently, in the randomized phase, allo-hMSCs or matched placebo will be administered to patients (n=30) randomly allocated in a 1:1:1 ratio to one of two doses of MSCs versus placebo: Group A (n=10, 100 million allo-hMSCs), Group B (n=10, 200 million allo-hMSCs), and Group C (n=10, placebo). Primary and secondary objectives are, respectively, to demonstrate the safety and efficacy of allo-hMSCs administered in frail older individuals. This study will determine the safety of intravenous infusion of stem cells and compare phenotypic outcomes in patients with aging frailty.
Purification and properties of ornithine decarboxylase from Lactobacillus sp. 30a. (1980)

Inducible ornithine decarboxylase from Lactobacillus sp. 30a has been purified to homogeneity as judged by ultracentrifugation and gel electrophoresis. Unlike histidine decarboxylase from the same species (a pyruvoyl enzyme), ornithine decarboxylase is a pyridoxal phosphate enzyme. The purified enzyme is specific for L-pornithine (Km 1.7 mM; specific activity, 150 to 200 mumol min-1 mg-1 at 37 degrees C) and is inhibited by various homologous omega-amino acids, amines, and polyamines. The native enzyme has an isoelectric point of 4.55 and a molecular weight of 1.04 X 10(6). At pH 7.3 and above, it dissociates reversibly to a species of Mr = 184,000, and on gel electrophoresis in the presence of sodium dodecyl sulfate shows a single band of Mr = 85,000. We ascribe these species to the dodecamer, dimer, and monomer, respectively, of a single peptide subunit; electron micrographs show a hexagonal array of apparently dimeric subunits in the native enzyme. Highest enzymatic activity is present in the dodecamer. The holoenzyme is resolved by dialysis against cysteine; spectrophotoemetric titration of the apoenzyme with pyridoxal 5'-phosphate indicates the presence of 1 coenzyme-binding site/monomeric subunit.
Interactions between the bone matrix proteins osteopontin and bone sialoprotein and the osteoclast integrin alpha v beta 3 potentiate bone resorption (1993)

We have investigated the mechanism by which osteoclasts adhere to and resorb bone. We show that these cells express beta 1 and beta 3 integrins which are involved in attachment to purified bone matrix proteins. Binding to osteopontin and bone sialoprotein is mediated by alpha v beta 3, while a beta 1 integrin is responsible for attachment to fibronectin. Both the rapid attachment by osteoclasts to intact bone particles and their subsequent resorption are blocked by a monoclonal antibody directed to the alpha v beta 3 complex but not by an antibody against beta 1 integrins. Attachment of osteoclasts to bone is also inhibited with soluble osteopontin, Arg-Gly-Asp-containing peptides derived from both osteopontin and bone sialoprotein, or a monospecific polyclonal antibody against osteopontin. We conclude that both osteoclast adherence to bone and subsequent resorption of its matrix are dependent on interactions between the bone matrix proteins osteopontin and/or bone sialoprotein and the integrin alpha v beta 3. Moreover, collagen, which constitutes 90% of its organic matrix, is minimally involved in binding of chicken osteoclasts to bone.
Oral magnesium supplementation as prophylaxis for noise-induced hearing loss: results of a double blind field study. (1993)

The effect of oral Mg-supplementation as prophylaxis against noise-induced hearing loss was tested in a placebo-controlled double blind study involving 320 voluntary subjects during a 2-month period of military training. The hearing thresholds of all subjects were checked and only persons with normal hearing were accepted. Before and after the 2-month training, blood samples were collected and Mg was analysed in serum, erythrocytes and lymphocytes. Seven days after the last exposure to firearm noise, the audiograms of all test subjects were checked and permanent threshold shifts (PTS) were determined. The total group received a drink containing either 4g Mg granulate verum (6.7 mmol Mg aspartate) or placebo every working day during the 2-month training period. The primary source of noise exposure were firearms: 420 shots per person, mean peak level 164 dB(A). The recruits used ear plugs with a mean insertion loss of 25 dB. In both groups Mg-concentration in serum and in erythrocytes increased with time. Lymphocyte Mg increased in the Mg group only. In the placebo group the percentages of ears with PTS > 25 dB at 4 kHz/6 kHz and/or 8 kHz after exposure to firearm noise were twice as high as in the Mg group.
Interactive Tools for Virtual X-Ray Vision in Mobile Augmented Reality (2005)

This paper presents a set of interactive tools designed to give users virtual x-ray vision. These tools address a common problem in depicting occluded infrastructure: either too much information is displayed, confusing users, or too little information is displayed, depriving users of important depth cues. Four tools are presented: the tunnel tool and room selector tool directly augment the user's view of the environment, allowing them to explore the scene in direct, first person view. The room in miniature tool allows the user to select and interact with a room from a third person perspective, allowing users to view the contents of the room from points of view that would normally be difficult or impossible to achieve. The room slicer tool aids users in exploring volumetric data displayed within the room in miniature tool. Used together, the tools presented in this paper can be used to achieve the virtual x-ray vision effect. We test our prototype system in a far-field mobile augmented reality setup, visualizing the interiors of a small set of buildings on the UCSB campus.