gebhart/patrepeval huggingface dataset:
The Surface Evolver (1992)

The Surface Evolver is a computer program that minimizes the energy of a surface subject to constraints. The surface is represented as a simplicial complex. The energy can include surface tension, gravity and other forms. Constraints can be geometrical constraints on vertex positions or constraints on integrated quantities such as body volumes. The minimization is done by evolving the surface down the energy gradient. This paper describes the mathematical model used and the operations available to interactively modify the surface.
Novel endophytic yeast Rhodotorula mucilaginosa strain PTD3 I: production of xylitol and ethanol (2012)

An endophytic yeast, Rhodotorula mucilaginosa strain PTD3, that was isolated from stems of hybrid poplar was found to be capable of production of xylitol from xylose, of ethanol from glucose, galactose, and mannose, and of arabitol from arabinose. The utilization of 30 g/L of each of the five sugars during fermentation by PTD3 was studied in liquid batch cultures. Glucose-acclimated PTD3 produced enhanced yields of xylitol (67% of theoretical yield) from xylose and of ethanol (84, 86, and 94% of theoretical yield, respectively) from glucose, galactose, and mannose. Additionally, this yeast was capable of metabolizing high concentrations of mixed sugars (150 g/L), with high yields of xylitol (61% of theoretical yield) and ethanol (83% of theoretical yield). A 1:1 glucose:xylose ratio with 30 g/L of each during double sugar fermentation did not affect PTD3's ability to produce high yields of xylitol (65% of theoretical yield) and ethanol (92% of theoretical yield). Surprisingly, the highest yields of xylitol (76% of theoretical yield) and ethanol (100% of theoretical yield) were observed during fermentation of sugars present in the lignocellulosic hydrolysate obtained after steam pretreatment of a mixture of hybrid poplar and Douglas fir. PTD3 demonstrated an exceptional ability to ferment the hydrolysate, overcome hexose repression of xylose utilization with a short lag period of 10 h, and tolerate sugar degradation products. In direct comparison, PTD3 had higher xylitol yields from the mixed sugar hydrolysate compared with the widely studied and used xylitol producer Candida guilliermondii.
Internet banking in the U.K.: From new distribution channel to new business models (2002)

The Internet is shaking the foundation of the banking industry. Simply deploying the Internet as a more efficient distribution channel will not bring sustainable strategic advantages. To compete effectively, banks will need to embrace a new set of strategic thinking, based on the ‘unbundling’ of banking services and processes and the ‘deconstruction’ of the integrated banking model. Based on my research of Internet banking in the personal banking area in the U.K. since the late 1990's, this paper explores a series of emerging issues, such as the adoption of various strategies and business models, channel development and coordination, and product and service offering through the Internet. As a new distribution channel for financial services, the Internet has lowered barriers to entry, allowing new players, often equipped with new technologies and business models, to enter the market. These new players are posing a serious threat to existing banks by changing the rules of competition and raising the general expectation of customers for services from all financial companies. Established banks and building societies must radically overhaul their business strategies to maintain their competitive position, and indeed, to survive in the long-term.
Hyperbaric oxygen and radiotherapy: a Medical Research Council trial in carcinoma of the cervix (1978)

In a randomized controlled clinical trial of hyperbaric oxygen in the radiotherapy of advanced carcinoma of the uterine cervix a total of 320 cases were contributed by four radiotherapy centres in the United Kingdom. The use of hyperbaric oxygen resulted in improved local control and survival. The benefit was greatest in patients under the age of 55 who presented with stage III disease. There was a slight increase in radiation morbidity but it seemed that the benefit of hyperbaric oxygen outweighed this increase in morbidity and that there was a true improvement in the therapeutic ratio.
Principles of Cancer Biotherapy (1988)

Cancer biotherapy - general principles, R.K. Oldham the pathogenesis of cancer metastasis - relevance to biotherapy, R. Radinsky, et al developmental therapeutics and the design of clinical trials R.K. Oldham recombinant organisms as sources of cancer biotherapeutics, K. Mehta, B.B. Aggarwal current concepts in immunology, R.K. Oldham cancer-associated immune suppression - therapeutic alterations with chemical and biological agents, R.K. Oldham nonspecific immunomodulators in oncology and haematology, G. Mathe, S. Orbach cancer vaccines - tumour epitopes and gene therapy, G.C. Fareed, L.E. Spitler chemical inducers of lymphokines, R.V. Salley, R.K. Oldham lymphokines and cytokines, W. Lewko, et al interferon therapy in cancer, R.V. Smalley, et al antibody therapy, R.O. Dillman immunotoxins, L.E. Spitler drug immunoconjugates, R.K. Oldham, K.A. Foon radiolabeled monoclonal antibodies for localization and treatment of metastatic cancer, H.B. Breitz, et al stem cell/bone marrow transplantation as biotherapy, R.K. Oldham cancer adoptive cellular immunotherapy, J.R. Yannelli growth and maturation factors in cancer, R.K. Oldham G-CSF, G. Morstyn, et al GM-CSF, A. Jakubowski clinical approaches to cancer gene therapy, K.A. Whartenby, et al cancer biotherapy - 1990s disease-related activity, R.K. Oldham, et al speculations for the 1990s, R.K. Oldham.
Specific and Quantized Antigen−Antibody Interaction Measured by Atomic Force Microscopy (1999)

An atomic force microscope (AFM) has been used to directly monitor specific interactions between antigens and antibodies. By using AFM probes functionalized with the Fab fragment of an antiferritin antibody, the adhesion forces between the probe and the ferritin-coated substrates were monitored. Fourier analysis of the adhesion forces distribution data suggests quantization of the forces, with a period of approximately 63 pN. The work estimated from this unitary force and its estimated working distance was about half the free energy difference (ΔF0) relevant to the intrinsic affinity constant (K0), derived from the kinetic analysis using isothermal titration calorimetry (ITC) of the antibody−antigen interactions. This periodic force was attributed to a single unbinding event between individual antigen and antibody molecules. The probability of adhesive events was strongly influenced by the functionalization mode of the probes. Probes on which vectorially oriented Fab molecules were immobilized, without any spacers, gave much more distinct unbinding force curves than those on which the Fab molecules were randomly fixed.
Advanced glycation end products impair NLRP3 inflammasome–mediated innate immune responses in macrophages (2017)

Advanced glycation end products (AGEs) are adducts formed on proteins by glycation with reducing sugars, such as glucose, and tend to form and accumulate under hyperglycemic conditions. AGE accumulation alters protein function and has been implicated in the pathogenesis of many degenerative diseases such as diabetic complications. AGEs have also been shown to promote the production of pro-inflammatory cytokines, but the roles of AGEs in inflammasome signaling have not been explored in detail. Here, we present evidence that AGEs attenuate activation of the NLRP3 inflammasome in bone marrow-derived macrophages (BMDMs) as determined by caspase-1 processing and interleukin-1β production. AGEs also dampened the assembly of the NLRP3 inflammasome, but did not affect the NLRC4 or AIM2 inflammasome activation. Moreover, our data indicated that AGE treatment inhibited Toll-like receptor (TLR)-dependent production of pro-inflammatory cytokines in BMDMs. This immunosuppressive effect of AGE was not associated with a receptor for AGEs (RAGE)-mediated signaling. Instead, AGE treatment markedly suppressed lipopolysaccharide-induced M1 polarization of macrophages. Furthermore, AGEs significantly dampened innate immune responses including NLRP3 inflammasome activation and type-I interferon production in macrophages upon influenza virus infection. These observations collectively suggest that AGEs could impair host NLRP3 inflammasome-mediated innate immune defenses against RNA virus infection leading to an increased susceptibility to infection.
Clinical Proteomics: From Biomarker Discovery and Cell Signaling Profiles to Individualized Personal Therapy (2005)

The discovery of new highly sensitive and specific biomarkers for early disease detection and risk stratification coupled with the development of personalized "designer" therapies holds the key to future treatment of complex diseases such as cancer. Mounting evidence confirms that the low molecular weight (LMW) range of the circulatory proteome contains a rich source of information that may be able to detect early stage disease and stratify risk. Current mass spectrometry (MS) platforms can generate a rapid and high resolution portrait of the LMW proteome. Emerging novel nanotechnology strategies to amplify and harvest these LMW biomarkers in vivo or ex vivo will greatly enhance our ability to discover and characterize molecules for early disease detection, subclassification and prognostic capability of current proteomics modalities. Ultimately genetic mutations giving rise to disease are played out and manifested on a protein level, involving derangements in protein function and information flow within diseased cells and the interconnected tissue microenvironment. Newly developed highly sensitive, specific and linearly dynamic reverse phase protein microarray systems are now able to generate circuit maps of information flow through phosphoprotein networks of pure populations of microdissected tumor cells obtained from patient biopsies. We postulate that this type of enabling technology will provide the foundation for the development of individualized combinatorial therapies of molecular inhibitors to target tumor-specific deranged pathways regulating key biologic processes including proliferation, differentiation, apoptosis, immunity and metastasis. Hence future therapies will be tailored to the specific deranged molecular circuitry of an individual patient's disease. The successful transition of these groundbreaking proteomic technologies from research tools to integrated clinical diagnostic platforms will require ongoing continued development, and optimization with rigorous standardization development and quality control procedures.
Cloning and Expression of a Plasma Membrane Cystine/Glutamate Exchange Transporter Composed of Two Distinct Proteins (1999)

Transport system xc- found in plasma membrane of cultured mammalian cells is an exchange agency for anionic amino acids with high specificity for anionic form of cystine and glutamate. We have isolated cDNA encoding the transporter for system xc- from mouse activated macrophages by expression in Xenopus oocytes. The expression of system xc- activity in oocytes required two cDNA transcripts, and the sequence analysis revealed that one is identical with the heavy chain of 4F2 cell surface antigen (4F2hc) and the other is a novel protein of 502 amino acids with 12 putative transmembrane domains. The latter protein, named xCT, showed a significant homology with those recently reported to mediate cationic or zwitterionic amino acid transport when co-expressed with 4F2hc. Thus xCT is a new member of a family of amino acid transporters that form heteromultimeric complex with 4F2hc, with a striking difference in substrate specificity. The expression of system xc- was highly regulated, and Northern blot analysis demonstrated that the expression of both 4F2hc and xCT was enhanced in macrophages stimulated by lipopolysaccharide or an electrophilic agent. However, the expression of xCT was more directly correlated with the system xc- activity.
High electron mobility transistor based on a GaN-AlxGa1−xN heterojunction (1993)

In this letter we report the fabrication and dc characterization of a high electron mobility transistor (HEMT) based on a n-GaN-Al0.14Ga0.86N heterojunction. The conduction in our low pressure metalorganic chemical vapor deposited heterostructure is dominated by two-dimensional electron gas at the heterostructure interface. HEMT devices were fabricated on ion-implant isolated mesas using Ti/Au for the source drain ohmic and TiW for the gate Schottky. For a device with a 4 μm gate length (10 μm channel opening, i.e., source-drain separation), a transconductance of 28 mS/mm at 300 K and 46 mS/mm at 77 K was obtained at +0.5 V gate bias. Complete pinchoff was observed for a −6 V gate bias.
Histidase and histidinemia. Clinical and molecular considerations. (1991)

Histidase (histidine ammonia-lyase, EC 4.3.1.3) catalyzes the deamination of L-histidine to trans-urocanic acid in the liver and skin of mammals. Histidase deficiency results in increased histidine and histamine in blood, and decreased urocanic acid in blood and skin. In this review we discuss current research on: (1) the mechanism of formation of an unusual residue, dehydroalanine, at the active site of histidase; and (2) the role of urocanic acid as an ultraviolet light-induced immunoregulator in the skin, and the implications of urocanic acid deficiency for human histidinemia. Genetic mechanisms that may account for the 1% of histidinemic patients with neurological impairments are considered briefly.
Frequency of B cells committed to the production of antibodies to insulin in newly diagnosed patients with insulin-dependent diabetes mellitus and generation of high affinity human monoclonal IgG to insulin. (1990)

Circulating autoantibodies to insulin can be detected in patients with insulin-dependent (type I) diabetes mellitus (IDDM) at the onset of the clinical disease. To characterize the autoantibody response in IDDM patients, we determined the frequency of circulating B cells committed to the production of IgM, IgG, and IgA to insulin in 12 newly diagnosed IDDM patients and, for comparison, in 9 healthy subjects and 17 insulin-treated IDDM patients. We found that B cells committed to the production of anti-insulin IgG, but not IgM, autoantibodies are present at much higher frequency in the circulation of newly diagnosed IDDM patients before insulin treatment (0.209 +/- 0.142%, mean value +/- SD of total IgG-producing cell precursors) as compared with age-matched healthy controls (0.032 +/- 0.030% of total IgG-producing cell precursors). In IDDM patients who had been treated with insulin, cells producing IgG antibody to insulin were 0.177 +/- 0.139% of total IgG-producing cell precursors. Generation of IgG mAb from B cells of IDDM patients revealed that they were monoreactive, i.e., they bound to insulin, but to none of the other Ag tested, and displayed a high affinity for insulin (Kd approximately 10(-7) moles/liter). In contrast, the IgG mAb derived from healthy subjects were polyreactive, i.e., they bound to all Ag tested, and displayed a low to moderate affinity for insulin (Kd approximately 10(-5) to 10(-6) moles/liter). These findings show that lymphocytes committed to the production of high affinity IgG autoantibodies to insulin are common in the B cell repertoire at the onset of IDDM.
Modeling of the Growth Kinetics of Occult Breast Tumors: Role in Interpretation of Studies of Prevention and Menopausal Hormone Therapy (2012)

Our OGTG model suggests that occult, undiagnosed tumors are prevalent, grow slowly, and are the biologic targets of anti-estrogen therapy for prevention and hormone therapy for menopausal women.
Catalytically active centres in porous oxides: design and performance of highly selective new catalysts (2001)

Active centres have been designed on high-area, molecular sieve catalysts which, inter alia, can convert n-alkanes to n-alkanols and n-alkanoic acids, cyclohexane to cyclohexanol, cyclohexanone and adipic acid, and n-hexane to adipic acid all using either oxygen or air as oxidants. A number of one-step processes and solvent-free chemical conversions, of paramount importance in the development of clean technology, are also described with catalysts designed (i) to oxidise p-xylene to terephthalic acid aerobically, (ii) to effect Baeyer–Villiger reactions with oxygen, and (iii) for the conversion of cyclohexanone to ε-caprolactam under mild conditions. The inner surfaces of mesoporous silicas may also be atomically engineered so as to yield high-performance epoxidation of alkenes at TiIV-centred active sites, as well as enantioselective hydrogenations of organic species using constrained chiral catalysts.
Blood Biomarkers in the Diagnosis of Ischemic Stroke (2008)

We make recommendations for the design and reporting of studies of diagnostic blood biomarkers in stroke.
Characterization of humoral immune responses against p16, p53, HPV16 E6 and HPV16 E7 in patients with HPV‐associated cancers (2008)

The cellular tumor suppressor p16 is strongly overexpressed in cervical cancers and precancers. We have previously demonstrated that infiltrating T lymphocytes reactive against p16 can be found in cervical cancer patients. Here, we analyzed whether p16 induces humoral immune responses. Sera of patients with cervical cancer, oropharyngeal cancer, colorectal cancer and autoimmune disease were included. A total of 919 sera were analyzed, including 486 matched sera from a cervical cancer case control study. p16 antibodies were analyzed in Western blot and a newly developed peptide ELISA covering the complete p16 protein. In addition, a Luminex-based multiplex assay was used for simultaneous detection of antibodies directed against p16, p53, HPV16 E6 and HPV16 E7. In all entities, only low p16 antibody reactivity was observed. Epitope mapping revealed 2 predominant epitope regions of the p16 protein. No significant difference in p16 antibody frequency (OR = 0.9; 95% CI = 0.6-1.3) and p53 antibody frequency (OR = 0.6; 95% CI = 0.3-1.2) was found between patients and healthy controls in the cervical cancer case control study. Antibodies against the HPV16 oncoproteins E6 and E7 were detected more frequently in cervical cancer patients when compared with healthy controls (E6 OR = 27.8; 95% CI = 11.1-69.7, E7 OR = 5.7; 95% CI = 2.9-11.1). In conclusion, despite the strong expression of p16 and the observed induction of cellular immune responses, antibody reactivity against p16 was observed only at very low levels independent of the disease background.
Stimulation of TLR9 with CpG ODN enhances apoptosis of glioma and prolongs the survival of mice with experimental brain tumors (2006)

Abstract Toll‐like receptors (TLRs) recognize a set of conserved molecular structures, so called pathogen‐associated molecular patterns, which allow them to sense and initiate innate and adaptive immune responses. In this study, we examined the expression of TLRs in both human and murine glioma. We then analyzed the change in TLR expression after treatment with synthetic phosphorothioate oligodeoxynucleotides (ODNs) containing unmethylated CpG dinucleotides (CpG ODNs), strong activators of both innate and adaptive immunity. In addition, we investigated the in vivo effect of CpG injection into C57BL/6 mice implanted with syngeneic GL261 glioma. Our results indicate that TLR9 is overexpressed in human and murine glioma cell lines and CpG stimulation prolongs the survival of mice with experimental brain tumors. CpGs induce TLR9 down‐regulation, followed by apoptosis of GL261 cells in vitro as well as in vivo. Furthermore, the effects of CpG stimulation appear to enhance the antigen presenting capacity of microglia, shift the immune response toward CD8 + T cells, and decrease the number of CD4 + CD25 + regulatory T cells. Taken together, our data support the role of CpG in glioma immunotherapy and provide a rationale for further clinical development of CpG therapy in patients with malignant glioma. © 2006 Wiley‐Liss, Inc.
Efficient solution of systems of Boolean equations (1996)

This paper describes an algorithm for the efficient solution of large systems of Boolean equations. The algorithm exploits the fact that, in some cases, the composition operation of Boolean functions represented by BDD's can be performed in a very efficient manner. Thus, the algorithm tries to eliminate as many variables and equations as possible through function composition. When the system can no longer be reduced in this way, the elimination process is continued through the use of Shannon decomposition. Numerical results show that the performance of this algorithm is significantly superior to that of a previous algorithm proposed by the authors.
Photolithography with transparent reflective photomasks (1998)

A new type of photomask was fabricated by casting a prepolymer of a transparent, elastomeric polymer (polydimethylsiloxane, PDMS) against a Si(100) master whose surface has been patterned with V-shaped trenches or pyramidal pits using anisotropic etching. The PDMS replica, when placed in contact with a film of photoresist and illuminated, acts as a photomask. The sidewalls of the trenches and pits in the silicon master meet with the plateaus in dihedral angles of 54°; as a result, the PDMS replica selectively blocks the incident light in regions where it has sloping features by total internal reflection, and acts as a reflective contact mask for photolithography. The feasibility of this new type of photomask has been demonstrated by the fabrication of micropatterns in photoresist (and in an underlying silicon substrate) with smaller feature sizes and higher complexities than those present on the original chrome mask used in patterning the silicon master. The patterns produced using these elastomeric photomasks can be changed by varying the pressure applied in contacting them.
Short-term and long-term variability of plasma homocysteine measurement (1997)

Within-person and methodological variability of a given analyte are important elements in determining whether an individual has altered concentrations of that analyte. We report the short-term (1 month) within-person, between-person, and methodological variability of plasma homocysteine in 20 healthy participants from whom samples were drawn weekly for 4 weeks. The short-term between-person variance was high, whereas within-person and methodological variances were relatively very low, giving a high reliability coefficient (R) for homocysteine (R = 0.94). The long-term (30 months) reliability coefficient was 0.65, but was greatly influenced by an outlier (R = 0.82 with the outlier excluded). The data suggest that an individual's plasma homocysteine concentration is relatively constant over at least 1 month, and a single measurement characterizes the average concentration reasonably well.
Room-temperature bonding of lithium niobate and silicon wafers by argon-beam surface activation (1999)

The residual stress originating form the thermal expansion mismatch has been a serious problem in the bonding of piezoelectric crystals onto silicon wafers. The room-temperature bonding method using argon-beam surface activation is applied to the bonding of lithium niobate and silicon. In this method, the surfaces of the specimens are etched by fast argon atom beam and bonded to each other in vacuum. Bonding strength equivalent to that of the bulk material is achieved without any heat treatment. Transmission electron microscope observations show intimate contact at the interface. This method is quite suitable for bonding dissimilar materials with thermal expansion mismatch, because the bonding is performed at room temperature throughout the whole process and no thermal stress is generated.