gebhart/patrepeval huggingface dataset:
Rapid orientated cloning in a shuttle vector allowing modulated gene expression in Bacillus subtilis (2001)

An expression vector for systematic protein overproduction in Bacillus subtilis has been constructed. It derives from pDG148 and combines the main property of this vector, i.e. conditional expression of the gene in response to isopropylβ-d-thiogalactopyranoside, with (i) rapid orientated cloning by a ligation independent procedure and (ii) a ribosome binding site of high translational efficiency. When used for overproduction of several proteins in B. subtilis, this vector gave good levels of protein synthesis.
Regression in basal cell carcinoma: an immunohistochemical analysis (1994)

Spontaneous regression of some cutaneous tumours is well recognized, and is thought to result from an immunological response to the tumour. Regression has previously been noted in basal cell carcinomas, but no studies defining the role of the immune response in the regression of this malignancy have been performed. We have examined 45 primary basal cell carcinomas (BCCs) (20 nodular, 25 superficial) and identified the cellular phenotypes and activation states of the cells infiltrating primary regressing and non-regressing BCCs, by immunocytochemistry. We have found a significantly increased number of CD3+ and CD4+ T cells infiltrating regressing compared with non-regressing tumours, and the expression of interleukin-2 receptor (an early activation marker for T cells) was also increased. There were no significant differences in class II major histocompatibility complex (MHC), CD1, or macrophage antigen expression in these groups. These findings suggest that activated CD4+ cytokine-secreting cells are important in the regression of BCCs.
The effects of siRNA-mediated inhibition of E2A-PBX1 on EB-1 and Wnt16b expression in the 697 pre-B leukemia cell line. (2006)

Targeted-E2A-PBX1 inhibition leads to reduced expression of the EB-1 and Wnt16b genes; aberrant expression of these genes may be a key step in leukemogenesis in t(1;19)-positive pre-B leukemia.
Magnetic tweezers for intracellular applications (2003)

We have designed and constructed a versatile magnetic tweezer primarily for intracellular investigations. The micromanipulator uses only two coils to simultaneously magnetize to saturation micron-size superparamagnetic particles and generate high magnitude constant field gradients over cellular dimensions. The apparatus resembles a miniaturized Faraday balance, an industrial device used to measure magnetic susceptibility. The device operates in both continuous and pulse modes. Due to its compact size, the tweezers can conveniently be mounted on the stage of an inverted microscope and used for intracellular manipulations. A built-in temperature control unit maintains the sample at physiological temperatures. The operation of the tweezers was tested by moving 1.28 μm diameter magnetic beads inside macrophages with forces near 500 pN.
Genetics of Childhood Obesity (2011)

Obesity is a major health problem and an immense economic burden on the health care systems both in the United States and the rest of the world. The prevalence of obesity in children and adults in the United States has increased dramatically over the past decade. Besides environmental factors, genetic factors are known to play an important role in the pathogenesis of obesity. Genome-wide association studies (GWAS) have revealed strongly associated genomic variants associated with most common disorders; indeed there is general consensus on these findings from generally positive replication outcomes by independent groups. To date, there have been only a few GWAS-related reports for childhood obesity specifically, with studies primarily uncovering loci in the adult setting instead. It is clear that a number of loci previously reported from GWAS analyses of adult BMI and/or obesity also play a role in childhood obesity.
Future of Short-Reach Optical Interconnects based on MMF Technologies (2017)

Get PDF Email Share Share with Facebook Tweet This Post on reddit Share with LinkedIn Add to CiteULike Add to Mendeley Add to BibSonomy Get Citation Copy Citation Text J. D. Ingham, "Future of Short-Reach Optical Interconnects based on MMF Technologies," in Optical Fiber Communication Conference, OSA Technical Digest (online) (Optica Publishing Group, 2017), paper Tu2B.1. Export Citation BibTex Endnote (RIS) HTML Plain Text Citation alert Save article
Targeting TLR2 for Vaccine Development (2014)

Novel and more effective immunization strategies against many animal diseases may profit from the current knowledge on the modulation of specific immunity through stimulation of innate immune receptors. Toll-like receptor (TLR)2-targeting formulations, such as synthetic lipopeptides and antigens expressed in fusion with lipoproteins, have been shown to have built-in adjuvant properties and to be effective at inducing cellular and humoral immune mechanisms in different animal species. However, contradictory data has arisen concerning the profile of the immune response elicited. The benefits of targeting TLR2 for vaccine development are thus still debatable and more studies are needed to rationally explore its characteristics. Here, we resume the main features of TLR2 and TLR2-induced immune responses, focusing on what has been reported for veterinary animals.
Human monoclonal antibodies directed against melanoma tumor-associated antigens. (1986)

To analyze the humoral immune response to melanoma, human-mouse hybridomas were generated by the fusions of regional lymph node lymphocytes of patients with the mouse myeloma cell line M5. Six stable hybridomas were cloned from six separate lymphocyte parents obtained from three patients. Ascites were obtained from nude mice after i.p. injection with cultured hybridoma cells. The monoclonal antibodies, four immunoglobulin Gs and two pentameric immunoglobulin Ms, were partially purified to remove mouse immunoglobulin and then conjugated to biotin for immunocytochemical and immunohistochemical studies. With the avidin:biotin:peroxidase complex method to detect and amplify binding by the biotin-conjugated human monoclonal antibodies, we found the six antibodies to be reactive against cytoplasmic determinants in five short-term melanoma cultures and formalin-fixed paraffin-embedded melanoma tumors from four patients. The antigenic target of the antibodies identified was not carcinoembryonic antigen. Two antibodies, 2-139-1 and 6-26-3, were studied in more detail. Each stained 25 of 25 specimens of melanomas. Little or no reactivity was detected against fixed sections of normal skin, which included tissues such as epidermis, dermis, monocytes, lymphocytes, and vascular endothelium. More striking was the absence of binding to melanocytes in the basal layer of the skin or to pigmented nevus cells. Both antibodies showed cross-reactivity against other tumors, in particular colonic and prostatic carcinomas. In the normal colon, reactivity was restricted to the surface of the columnar epithelium; no reactivity was detected against normal prostatic epithelium. Reactivity was also not observed against liver and lung. However, the epithelia of the renal tubules, pancreatic ducts, and salivary ducts were all reactive. These human monoclonal antibodies identify cytoplasmic melanoma-associated tumor antigens that appear different from the membrane antigens defined by serological approaches and by most mouse monoclonal antibodies.
Self-Assembled Monolayers Based on Chelating Aromatic Dithiols on Gold (1998)

Self-assembled monolayers (SAMs) were generated by the adsorption of xylene-α1,α2-dithiol and 1,2-bis(mercaptomethyl)-4,5-dialkylbenzene derivatives, [CH3(CH2)m]2C6H2[CH2SH]2 (m = 0, 4, 12, 13, 14, 15), on the surface of gold. These monolayers were characterized by optical ellipsometry and contact angle goniometry. Comparison of the thicknesses and wettabilities of the new SAMs to those generated from normal alkanethiols suggests that the new chelating dithiols generate densely packed and highly oriented monolayer films on gold. Furthermore, preliminary studies of film desorption in solution suggest that the new SAMs are more stable than normal SAMs on gold.
Circulating CD4+CD25+ and CD4+CD25– T Cells in Myasthenia Gravis and in Relation to Thymectomy (2004)

Studies in experimental animal models of human autoimmune diseases have revealed that CD4(+)CD25(+) T regulatory (Tr) cells are of thymic origin and have potentials in preventing auto-aggressive immunity. Myasthenia gravis (MG) is the best-characterized autoimmune disease. Changes in the thymus are found in a majority of patients with MG. Thymectomy has beneficial effects on the disease severity and course in a substantial proportion of MG patients. But the occurrence and characteristics of Tr cells have not yet been defined in MG. We determined the frequencies and properties of circulating CD4(+)CD25(+) versus CD4(+)CD25(-) cells in MG patients and healthy controls (HCs), with special focus on the effect of thymectomy on CD4(+)CD25(+) cells. CD4(+)CD25(high) cells comprise only about 2% of blood lymphocytes in both MG patients and HCs. Frequencies of CD4(+)CD25(high) cells were similar in MG patients irrespective of treatment with thymectomy. CD4(+)CD25(+) cells in both MG patients and HCs are mainly memory T cells and are activated to a greater extent than CD4(+)CD25(-) cells, as reflected by high levels of CD45RO and human leucocyte antigen (HLA)-DR-positive cells. In both MG patients and HCs, CD4(+)CD25(+) cells also contained a high proportion of CD95-expressing cells as possible evidence of apoptosis-proneness. Upon stimulation with anti-CD3/CD28 monoclonal antibodies, CD4(+)CD25(+) cells responded more vigorously than CD4(+)CD25(-) cells in MG, irrespective of treatment with thymectomy, as well as in HCs. Although CD4(+)CD25(-) cells are mainly naïve T cells, in non-thymectomized MG patients, they are activated to a greater extent as reflected by higher expression of HLA-DR and CD95 on the surface compared to HCs. The data thus show that there is no deficiency of CD4(+)CD25(+) cells in MG, nor is the proportion of CD4(+)CD25(+) cells influenced by thymectomy.
Functional similarity between HPV16E7, SV40 large T and adenovirus E1a proteins. (1989)

We have analysed the immortalizing function of Human Papillomavirus type 16 (HPV16) in a rat cell line which has been derived by immortalizing rat embryo fibroblasts with a thermolabile SV40 large T antigen and is temperature sensitive for growth. Introduction of wild type SV40 large T antigen or the adenovirus E1a 12s gene product has previously been shown to readily overcome the inability of these cells to divide at the non-permissive temperature. In contrast, the introduction of myc, another known immortalizing gene, cannot complement the growth defect of these cells. This cell line therefore provides a novel assay system which can distinguish two groups of immortalizing oncogenes. We have shown here that expression of HPV16 can readily complement the growth defect in this rat cell line and that this function can be genetically localised to E7. Cells expressing HPV16 E6 sequences are also weakly rescued from growth arrest at the non-permissive temperature. These results demonstrate a functional similarity between HPV16 E7, SV40 large T and adenovirus E1a and suggest that these genes may immortalize cells by a common mechanism. Interestingly, the limited sequence homology between these three gene products is restricted to the domain which has recently been implicated in binding the retinoblastoma gene product.
Silica‐Coated InP/ZnS Nanocrystals as Converter Material in White LEDs (2008)

White-LEDs are produced with the addition of a silicone-composite layer containing light-emitting converter material on top of a high-performance blue-LED chip. The color reproduction was significantly improved in comparison with commercially available white-LEDs. Detailed facts of importance to specialist readers are published as "Supporting Information". Such documents are peer-reviewed, but not copy-edited or typeset. They are made available as submitted by the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Aerosolized antigen dose-response studies in asthmatic monkeys. (1978)

This study used rhesus monkeys which had consistent respiratory responses to a standard (single dose) aerosolized concentration of A. Beginning at lower concentrations of A which did not produce an airway response, fourfold increases in concentrations of A were aerosolized until an airway response occurred. Compared with the single-dose SAC after the TAC, some consistently reactive animals did not respond to the SAC, the maximal concentration of A used for testing. Thus the TAC may result in an acute form of airway desensitization. Animals vary in the threshold concentrations of A required to produce an airway response. A repeat challenge with the threshold antigen concentration during the same experiment resulted in a second response generally greater than the initial response at the same concentration. When the SAC system was similarly evaluated by repeat challenges with the same A concentration, the second response was generally less than the first. Different methods for evaluation of pharmacologic inhibitors of IgE-mediated airway responses may be developed from this rhesus model of asthma.
Pathogen Reduction in Human Plasma Using an Ultrashort Pulsed Laser (2014)

Pathogen reduction is a viable approach to ensure the continued safety of the blood supply against emerging pathogens. However, the currently licensed pathogen reduction techniques are ineffective against non-enveloped viruses such as hepatitis A virus, and they introduce chemicals with concerns of side effects which prevent their widespread use. In this report, we demonstrate the inactivation of both enveloped and non-enveloped viruses in human plasma using a novel chemical-free method, a visible ultrashort pulsed laser. We found that laser treatment resulted in 2-log, 1-log, and 3-log reductions in human immunodeficiency virus, hepatitis A virus, and murine cytomegalovirus in human plasma, respectively. Laser-treated plasma showed ≥70% retention for most coagulation factors tested. Furthermore, laser treatment did not alter the structure of a model coagulation factor, fibrinogen. Ultrashort pulsed lasers are a promising new method for chemical-free, broad-spectrum pathogen reduction in human plasma.
Use of mutation profiles to refine the classification of endometrial carcinomas (2012)

The classification of endometrial carcinomas is based on pathological assessment of tumour cell type; the different cell types (endometrioid, serous, carcinosarcoma, mixed, undifferentiated, and clear cell) are associated with distinct molecular alterations. This current classification system for high-grade subtypes, in particular the distinction between high-grade endometrioid (EEC-3) and serous carcinomas (ESC), is limited in its reproducibility and prognostic abilities. Therefore, a search for specific molecular classifiers to improve endometrial carcinoma subclassification is warranted. We performed target enrichment sequencing on 393 endometrial carcinomas from two large cohorts, sequencing exons from the following nine genes: ARID1A, PPP2R1A, PTEN, PIK3CA, KRAS, CTNNB1, TP53, BRAF, and PPP2R5C. Based on this gene panel, each endometrial carcinoma subtype shows a distinct mutation profile. EEC-3s have significantly different frequencies of PTEN and TP53 mutations when compared to low-grade endometrioid carcinomas. ESCs and EEC-3s are distinct subtypes with significantly different frequencies of mutations in PTEN, ARID1A, PPP2R1A, TP53, and CTNNB1. From the mutation profiles, we were able to identify subtype outliers, ie cases diagnosed morphologically as one subtype but with a mutation profile suggestive of a different subtype. Careful review of these diagnostically challenging cases suggested that the original morphological classification was incorrect in most instances. The molecular profile of carcinosarcomas suggests two distinct mutation profiles for these tumours: endometrioid-type (PTEN, PIK3CA, ARID1A, KRAS mutations) and serous-type (TP53 and PPP2R1A mutations). While this nine-gene panel does not allow for a purely molecularly based classification of endometrial carcinoma, it may prove useful as an adjunct to morphological classification and serve as an aid in the classification of problematic cases. If used in practice, it may lead to improved diagnostic reproducibility and may also serve to stratify patients for targeted therapeutics.
Review of Acute Treatment of Migraine Trial Results With the New FDA Endpoints: Design Implications for Future Trials (2019)

The observed range of placebo response and treatment effect sizes suggests that use of the newly recommended 2 co-primary endpoints could reduce the sample sizes required to achieve significance compared with past trials using 4 primary endpoints (in which mean and median group sizes for recent trials were 375 and 362, respectively). However, the initial trials using the newly recommended co-primary endpoints tended to treat more participants than would have been minimally required. We anticipate that with the growing body of information regarding the use of these new endpoints, samples sizes may be more aligned with treatment efficacy, enabling faster and more cost-effective trials for acute migraine treatment.
Distributed algorithms for optimal power flow problem (2012)

Optimal power flow (OPF) is an important problem for power generation and it is in general non-convex. With the employment of renewable energy, it will be desirable if OPF can be solved very efficiently so that its solution can be used in real time. With some special network structure, e.g. trees, the problem has been shown to have a zero duality gap and the convex dual problem yields the optimal solution. In this paper, we propose a primal and a dual algorithm to coordinate the smaller subproblems decomposed from the convexified OPF. We can arrange the subproblems to be solved sequentially and cumulatively in a central node or solved in parallel in distributed nodes. We test the algorithms on IEEE radial distribution test feeders, some random tree-structured networks, and the IEEE transmission system benchmarks. Simulation results show that the computation time can be improved dramatically with our algorithms over the centralized approach of solving the problem without decomposition, especially in tree-structured problems. The computation time grows linearly with the problem size with the cumulative approach while the distributed one can have size-independent computation time.
Evaluation of Islet Cell Antigen (ICA) 512/IA-2 Autoantibody Radioassays Using Overlapping ICA512/IA-2 Constructs1 (1997)

Islet cell antigen (ICA) 512 also termed IA-2 is a novel autoantigen of type 1 diabetes, which has a tyrosine phosphatase-like domain. We have assessed autoantibody RIAs using a series of ICA512/IA-2 constructs to produce in vitro synthesized 35S-methionine-labeled proteins. Levels of ICA512/IA-2 (256-979, truncated aminoterminus) autoantibodies were strongly correlated with those of the full-length ICA512/IA-2 (1-979) autoantibodies (r = 0.96, P < 0.0001) and ICA512/IA-2 (687-979) autoantibodies (r = 0.98, P < 0.0001). RIAs using these 3 constructs had increased sensitivity relative to our initially reported ICA512 autoantibody RIA (amino acids 389-948, truncated carboxy- and aminoterminus). Only 2 of 38 sera examined in this study reacted with an aminoterminus ICA512/IA-2 (1-577) construct. The mean SD score (SD score = (index of unknown sample-mean index of controls)/SD of controls) using the ICA512/IA-2 (256-979) construct was significantly higher than the SD score obtained with other ICA512/IA-2 constructs (P < 0.001). Amongst patients with new-onset diabetes and prediabetic relatives, using RIAs for autoantibodies reacting with ICA512/IA-2 (256-979), insulin, and glutamic acid decarboxylase 65, 98% expressed one or more of these autoantibodies and 78% expressed two or more, whereas no control (n = 208) expressed more than a single autoantibody. A combined ICA512/IA-2 (256-979), glutamic acid decarboxylase 65 autoantibody RIA with differential autoantigen labeling (35S-methionine, 3H-leucine) has been developed that uses 96-well plate membrane filtration and Top Counter beta counting. Concordance between results of dual and single RIAs was greater than 90%. This simple combined autoantibody assay should facilitate large-scale autoantibody screening.
Neutralization of Transthyretin Reverses the Neuroprotective Effects of Secreted Amyloid Precursor Protein (APP) in APPSwMice Resulting in Tau Phosphorylation and Loss of Hippocampal Neurons: Support for the Amyloid Hypothesis (2004)

Alzheimer's disease (AD) may be caused by the abnormal processing of the amyloid precursor protein (APP) and the accumulation of beta-amyloid (Abeta). The amyloid precursor protein can be proteolytically cleaved into multiple fragments, many of which have distinct biological actions. Although a high level of Abeta can be toxic, the alpha-secretase cleaved APP (sAPPalpha) is neuroprotective. However, the mechanism of sAPPalpha protection is unknown. Here, we show that sAPPalpha increases the expression levels of several neuroprotective genes and protects organotypic hippocampal cultures from Abeta-induced tau phosphorylation and neuronal death. Antibody interference and small interfering RNA knock-down demonstrate that the sAPPalpha-driven expression of transthyretin and insulin-like growth factor 2 is necessary for protection against Abeta-induced neuronal death. Mice overexpressing mutant APP possess high levels of sAPPalpha and transthyretin and do not develop the tau phosphorylation or neuronal loss characteristic of human AD. Chronic infusion of an antibody against transthyretin into the hippocampus of mice overexpressing APP with the Swedish mutation (APP(Sw)) leads to increased Abeta, tau phosphorylation, and neuronal loss and apoptosis within the CA1 neuronal field. Therefore, the elevated expression of transthyretin is mediated by sAPPalpha and protects APP(Sw) mice from developing many of the neuropathologies observed in AD.
Chronic painful peripheral neuropathy in an urban community: a controlled comparison of people with and without diabetes (2004)

CPPN is common, often severe but frequently unreported and inadequately treated.
Active Learning with Support Vector Machines in the Drug Discovery Process (2003)

We investigate the following data mining problem from computer-aided drug design: From a large collection of compounds, find those that bind to a target molecule in as few iterations of biochemical testing as possible. In each iteration a comparatively small batch of compounds is screened for binding activity toward this target. We employed the so-called "active learning paradigm" from Machine Learning for selecting the successive batches. Our main selection strategy is based on the maximum margin hyperplane-generated by "Support Vector Machines". This hyperplane separates the current set of active from the inactive compounds and has the largest possible distance from any labeled compound. We perform a thorough comparative study of various other selection strategies on data sets provided by DuPont Pharmaceuticals and show that the strategies based on the maximum margin hyperplane clearly outperform the simpler ones.