gebhart/patrepeval huggingface dataset:
Prediction of peptide affinity to HLA DR molecules. (1995)

A method to quantitatively predict peptide binding to HLA DRB1*0401, B1*0101, and B1*1501 has been developed using a dataset of the relative contributions of each of the naturally occurring amino acids in the context of a simplified peptide backbone. The prediction assumed that the relative role of each of the peptide sidechains could be treated independently and could be measured by assaying each of the twenty naturally occurring amino acids at the central eleven positions of a 13 residue peptide previously shown to contain the minimal requirements for high affinity binding to HLA DR proteins. Three separate databases were generated. They were shown to have predictive value when tested on a set of 13 unrelated peptides known to bind the DR proteins with a wide range of apparent affinity. The DRB1*0401 database was tested further by analyzing myelin basic protein. All 13 amino acid peptides containing a hydrophobic amino acid at the third position were synthesized and assayed for binding purified DRB1*0401. In every case, the measured affinity correlated with the predictive values within the experimental error of the assays. Finally, the ability to predict peptide binding to MHC class II molecules was shown to help in identifying T cell determinants. The specificity of DRB1*0401 restricted T cell hybridomas against human serum albumin corresponded to two peptides, predicted, and shown to bind the class II protein with high affinity.
Long-term prophylactic treatment of attacks of vertigo in Menière's disease – comparison of a high with a low dosage of betahistine in an open trial (2008)

A total of 112 patients were included in the analysis: 50 received betahistine-dihydrochloride in a low dosage (16 mg tid, n=21, 24 mg, n=29) and 62 received 48 mg tid. Follow-up examination every 3 months showed that the number of attacks per month decreased in both groups over time. For instance, after 12 months the mean (median) number of attacks dropped from 7.6 (4.5) to 4.4 (2.0) (p<0.0001) in the low-dosage group, and from 8.8 (5.5) to 1.0 (0.0) (p<0.0001) in the high dosage group. The number of attacks after 12 months was significantly lower in the high dosage group than in the low dosage group (p(12M)=0.0002). The treatment was well tolerated in both groups.
The effects of 5-azacytidine and 5-azadeoxycytidine on chromosome structure and function: Implications for methylation-associated cellular processes (1995)

5-Azacytidine (5-aza-C) analogs demonstrate a remarkable ability to induce heritable changes in gene and phenotypic expression. These cellular processes are associated with the demethylation of specific DNA sequences. On the other hand, 5-aza-C analogs have dramatic effects on chromosomes, leading to decondensation of chromatin structure, chromosomal instability and an advance in replication timing. Condensation inhibition of genetically inactive chromatin occurs when the DNA is still hemimethylated or fully methylated. In cell cultures prolonged for several replication cycles, chromosomal rearrangements and instability affect the 5-aza-C-sensitive regions. Moreover, the normally late-replicating inactive chromatin undergoes a transient temporal shift to an earlier DNA replication, characteristic of activatable chromatin. zThe induced alterations of chromosome structure and behavior may trigger the 5-aza-C-dependent process of cellular reprogramming. Apart from their differentiating and gene-modifying effects, 5-aza-C analogs can tumorigenically transform cells and modulate their metastatic potential. High doses of 5-aza-C analogs have cytotoxic and antineoplastic activities.
Mitochondrial dysfunction in insulin insensitivity: implication of mitochondrial role in type 2 diabetes (2010)

Abundant evidence has been accumulated to suggest that mitochondrial dysfunction is associated with type 2 diabetes. Research findings from this and other laboratories have supported the notion that impaired mitochondrial function is a cause of insulin insensitivity in myocytes and adipocytes as a result of insufficient supply of energy or defects in the insulin signaling pathway. We demonstrated that inhibition of respiration and oxidative phosphorylation by respiratory inhibitors or knockdown of genes involved in mitochondrial biogenesis can impair the differentiation of preadipocytes and response of adipocytes to insulin. Moreover, defective mitochondria also cause a decrease in adiponectin secretion that leads to decline glucose utilization of other tissues. Besides, it has been elucidated that some environmental factors, pollutants, and mitochondrial toxins are involved in the pathogenesis of type 2 diabetes. Taken together, we suggest that mitochondrial dysfunction plays a role in the pathophysiology of insulin insensitivity, and that activation of mitochondrial biogenesis may be an effective strategy in the prevention or treatment of insulin resistance and type 2 diabetes.
Interaction of West Nile Virus with αvβ3 Integrin Mediates Virus Entry into Cells (2004)

The functional receptor for the flavivirus West Nile (WNV) infection has been characterized in this study with a combination of biochemical and molecular approaches. A 105-kDa protease-sensitive glycoprotein that binds WNV was isolated from the plasma membrane of cells permissive to WNV infection. The protein was subjected to peptide sequencing, and this glycoprotein was identified as a member of the integrin superfamily. Infection of WNV was shown to be markedly inhibited in Vero cells pretreated with blocking antibodies against alpha(v)beta(3) integrin and its subunits by receptor competition assay. It was also noted that cells pretreated with antibodies against alpha(v)beta(3) integrin can effectively inhibit flavivirus Japanese encephalitis but to a lesser extent flavivirus dengue infections. West Nile virus entry is independent of divalent cations and is not highly blocked by arginine-glycine-aspartic acid (RGD) peptides, suggesting that the interaction between the virus and alpha(v)beta(3) integrin is not highly dependent on the classical RGD binding motif. In addition, gene silencing of the beta(3) integrin subunit in cells has resulted in cells largely resistant to WNV infection. In contrast, expression of recombinant human beta(3) integrin substantially increased the permissiveness of CS-1 melanoma cells for WNV infection. Soluble alpha(v)beta(3) integrin can also effectively block WNV infection in a dose-dependent manner. Furthermore, WNV infection also triggered the outside-in signaling pathway via the activation of integrin-associated focal adhesion kinase. The identification of alpha(v)beta(3) integrin as a receptor for WNV provides insight into virus-receptor interaction, hence creating opportunities in the development of anti-viral strategies against WNV infection.
Die Alanatreduktion von β‐Carbonyl‐oxalylsäure‐estern (1959)

Abstract β‐Carbonyl‐oxalylsäure‐ester sind Vinyloge der Carbonsäureester, die bei der Alanatreduktion, neben den erwarteten 1.2.4‐Triolen, durch Hydrogenolyse der Oxogruppe auch 1.2‐Diole liefern. Die Ausbeuten an 1.2‐Diolen steigen mit dem Enolisierungsgrad der Carbonyloxalylsäure‐ester an.
Olig2 expression, GFAP, p53 and 1p loss analysis contribute to glioma subclassification (2004)

The expression of Olig2, a basic helix-loop-helix (bHLH) transcription factor involved in oligodendroglial specification, was investigated by immunohistochemistry in a series of 146 tumours and control samples. Olig2 expression was restricted to glial tumours and nontumoral oligodendrocytes. It was higher in oligodendrogliomas as compared to astrocytomas and oligoastrocytomas, and in grade III as compared to grade II tumours. Olig 2 was absent or weakly expressed in glioblastoma (GBM), whereas strong expression was found in the oligodendroglial foci of GBM with oligodendroglial component (GBMO). Double labelling was performed on a subset of the most typical tumours, according to the WHO classification. It showed a mutual exclusion, at cell level, of Olig2 and GFAP expression. In pure oligodendrogliomas, tumour cells were Olig2+/GFAP-. In contrast, two main tumour populations, Olig2+/GFAP- and Olig2-/GFAP+, were found in both oligoastrocytomas and astrocytomas. Based on these data from selected samples, two separate entities can be established, corresponding to 'pure oligodendrogliomas' and 'astrocytomas and oligoastrocytomas'. The relevance of this subdivision is further supported by the association with 1p loss and a trend to better survival for pure oligodendrogliomas and with p53 expression and a trend to shorter survival for astrocytomas and oligoastrocytomas. Combined testing of Olig2, 1p status, GFAP and p53 expression may therefore be helpful in refining current classification and providing more homogeneous sets of gliomas for clinical studies.
Extracting relations with integrated information using kernel methods (2005)

Entity relation detection is a form of information extraction that finds predefined relations between pairs of entities in text. This paper describes a relation detection approach that combines clues from different levels of syntactic processing using kernel methods. Information from three different levels of processing is considered: tokenization, sentence parsing and deep dependency analysis. Each source of information is represented by kernel functions. Then composite kernels are developed to integrate and extend individual kernels so that processing errors occurring at one level can be overcome by information from other levels. We present an evaluation of these methods on the 2004 ACE relation detection task, using Support Vector Machines, and show that each level of syntactic processing contributes useful information for this task. When evaluated on the official test data, our approach produced very competitive ACE value scores. We also compare the SVM with KNN on different kernels.
Tyrosine phosphorylation of specific proteins after mitogen stimulation of chicken embryo fibroblasts. (1983)

We found that stimulation of density-inhibited chicken embryo fibroblasts with serum, epidermal growth factor (EGF), platelet-derived growth factor, (PDGF), or multiplication-stimulating activity (MSA) leads to an increase in tyrosine phosphorylation of proteins in the region of Mr 40,000 (40K) to 42K. The increase in tyrosine phosphorylation after serum or EGF stimulation was transient, reaching a maximum at about 5 min and then declining. By fine-resolution analysis of proteins separated on sodium dodecyl sulfate-polyacrylamide gels, we found that after EGF stimulation, the major increase in phosphotyrosine content was in a 42K Mr protein, with a smaller increase in a 40K Mr protein. The increased phosphorylation in the 40K to 42K Mr region accounted for almost all of the increase in phosphotyrosine observed in these cells. These phosphotyrosine-containing proteins were different from the major phosphotyrosine-containing protein of Rous sarcoma virus-transformed chicken embryo fibroblasts, which migrates at an approximate Mr of 36K. Increased tyrosine phosphorylation of proteins of similar Mr was found in 3T3 cells treated with EGF, but not in NR-6 cells, which lack detectable EGF receptors. It is possible that the 40K to 42K Mr phosphotyrosine-containing proteins are involved in the integration of the biological response to a number of different growth factors.
Solvent-induced collapse of α-synuclein and acid-denatured cytochrome c (2020)

The effects of solution conditions on protein collapse were studied by measuring the hydrodynamic radii of two unfolded proteins, α-synuclein and acid-denatured ferricytochrome c, in dilute solution and in 1 M glucose. The radius of α-synuclein in dilute solution is less than that predicted for a highly denatured state, and adding 1 M glucose causes further collapse. Circular dichroic data show that α-synuclein lacks organized structure in both dilute solution and 1 M glucose. On the other hand, the radius of acid-denatured cytochrome c in dilute solution is consistent with that of a highly denatured state, and 1 M glucose induces collapse to the size and structure of native cytochrome c. Taken together, these data show that α-synuclein, a natively unfolded protein, is collapsed even in dilute solution, but lacks structure.
Gaze-awareness for Videoconferencing: A Software Approach (2000)

Many desktop videoconferencing systems are ineffective due to deficiencies in gaze awareness and sense of spatial relationship. Previous works employ special hardware to address these problems. Here, we describe a software-only approach. Heads and eyes in the video are tracked using computer-vision techniques, and the tracking information is transmitted along with the video stream. Receivers take the tracking information corresponding to the video and graphically place the head and eyes in a virtual 3D space such that gaze awareness and a sense of space are provided.
Immunological responses in a patient with glioblastoma multiforme treated with sequential courses of temozolomide and immunotherapy: Case study (2007)

Cytotoxic chemotherapy that induces lymphopenia is predicted to ablate the benefits of active antitumor immunization. Temozolomide is an effective chemotherapeutic agent for patients with glioblastoma multiforme, but it induces significant lymphopenia. Although there is monthly fluctuation of the white blood cell count, specifically the CD4 and CD8 counts, there was no cumulative decline in the patient described in this case report. Depriving patients of this agent, in order to treat with immunotherapy, is controversial. Despite conventional dogma, we demonstrated that chemotherapy and immunotherapy can be delivered concurrently without negating the effects of immunotherapy. In fact, the temozolomide-induced lymphopenia may prove to be synergistic with a peptide vaccine secondary to inhibition of regulatory T cells or their delayed recovery.
A simple and reliable 5'-RACE approach (2000)

A novel approach for the amplification of cDNA ends is described. It requires only minimal amounts of material, a simple cDNA synthesis reaction and a single PCR reaction to amplify the desired 5'- or 3'-ends of a certain cDNA of interest. It combines the so called CapFinder approach with solid phase cDNA synthesis, thus almost eliminating background problems usually associated with 5'-RACE protocols. This approach could be used to generate complete 5'-ends of numerous cDNAs using only one cDNA synthesis reaction. In combination with LA PCR, several kilobases of unknown 5'-ends could be amplified. It is easy to perform, quick, inexpensive and reliable, which should enable it to replace most currently used 5'-RACE protocols.
A Fast Caption Detection Method for Low Quality Video Images (2012)

Captions in videos are important and accurate clues for video retrieval. In this paper, we propose a fast and robust video caption detection and localization algorithm to handle low quality video images. First, the stroke response maps from complex background are extracted by a stoke filter. Then, two localization algorithms are used to locate thin stroke and thick stroke caption regions respectively. Finally, a HOG based SVM classifier is carried out on the detected results to further remove noises. Experimental results show the superior performance of our proposed method compared with existing work in terms of accuracy and speed.
K-ras Asp12 mutant neither interacts with Raf, nor signals through Erk and is less tumorigenic than K-ras Val12 (2006)

Different mutant amino acids in the Ras proteins lead to distinct transforming capacities and different aggressiveness in human tumors. K-Ras Asp12 (K12D) is more prevalent in benign than in malignant human colorectal tumors, whereas K-Ras Val12 (K12V) associates with more advanced and metastatic carcinomas, higher recurrence and decreased survival. Here, we tested, in a nude mouse xenograft model, whether different human K-Ras oncogenes mutated at codon 12 to Val, Asp or Cys would confer NIH3T3 fibroblasts distinct oncogenic phenotypes. We studied tumor histology and growth, apoptotic and mitotic rates, activation of signal transduction pathways downstream of Ras and regulation of the cell cycle and apoptotic proteins in tumors derived from the implanted transformants. We found that the K12V oncogene induces a more aggressive tumorigenic phenotype than the K12D oncogene, whereas K12C does not induce tumors in this model. Thus, K12V mutant tumors proliferate about seven times faster, and have higher cellularity and mitotic rates than the K12D mutant tumors. A molecular analysis of the induced tumors shows that the K12V mutant protein interacts with Raf-1 and transduces signals mainly through the Erk pathway. Unexpectedly, in tumors induced by the K12D oncogene, the K-Ras mutant protein does not interact with Raf-1 nor activates the Erk canonical pathway. Instead, it transduces signals through the PI3K/Akt, JNK, p38 and FAK pathways. Finally, the higher growth rate of the K12V tumors associates with enhanced Rb phosphorylation, and PCNA and cyclin B upregulation, consistent with faster G1/S and G2/M transitions, without alteration of apoptotic regulation.
Effective edge-corner detection method for defected images (2002)

The locations of junctions, parallelism of lines and inclined angles of lines are difficult to be ascertained but essential in the geometrical transformation into objects from images. A fast and effective edge-corner detection method, named the cellular vectorization method (CVM), is proposed. This method is particularly effective in hand line drawings containing imperfections, such as unattached edges, misaligned junctions, overshoot junctions, and roughly parallel lines. All such defects can be detected and corrected. When in use, the CVM interprets hand line drawings directly and does away with filtering and thinning processes. Thus, the CVM is both a time-saving and versatile method for image detection based on edges and corners data. Experimental results are given to show the correctness and effectiveness of the proposed method.
GPU Activity Prediction using Representation Learning (2017)

GPU activity prediction is an important and complex problem. This is due to the high level of contention among thousands of parallel threads. This problem was mostly addressed using heuristics. We propose a representation learning approach to address this problem. We model any performance metric as a temporal function of the executed instructions with the intuition that the flow of instructions can be identified as distinct activities of the code. Our experiments show high accuracy and non-trivial predictive power of representation learning on a benchmark.
Insertion of an articulated human into a networked virtual environment (2002)

Most distributed interactive simulation (DIS) technology demonstrated in recent years has focused on vehicle interaction. The dismounted infantryman-the individual soldier-has been largely ignored or represented by static models. In six weeks of development, the Naval Postgraduate School, SARCOS Inc., and University of Pennsylvania, under Army Research Laboratory sponsorship, demonstrated the insertion of a fully articulated human figure into a DIS environment. This paper describes the system architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Structure of the cel-3 gene from Fibrobacter succinogenes S85 and characteristics of the encoded gene product, endoglucanase 3 (1989)

The cel-3 gene cloned from Fibrobacter succinogenes into Escherichia coli coded for the enzyme EG3, which exhibited both endoglucanase and cellobiosidase activities. The gene had an open reading frame of 1,974 base pairs, coding for a protein of 73.4 kilodaltons (kDa). However, the enzyme purified from the osmotic shock fluid of E. coli was 43 kDa. The amino terminus of the 43-kDa protein matched amino acid residue 266 of the protein coded for by the open reading frame, indicating proteolysis in E. coli. In addition to the 43-kDa protein, Western immunoblotting revealed a 94-kDa membranous form of the enzyme in E. coli and a single protein of 118 kDa in F. succinogenes. Thus, the purified protein appears to be a proteolytic degradation product of a native protein which was 94 kDa in E. coli and 118 kDa in F. succinogenes. The discrepancy between the molecular weight expected on the basis of the DNA sequence and the in vivo form may be due to anomalous migration during electrophoresis, to glycosylation of the native enzyme, or to fatty acyl substitution at the N terminus. One of two putative signal peptide cleavage sites bore a strong resemblance to known lipoprotein leader sequences. The purified 43-kDa peptide exhibited a high Km (53 mg/ml) for carboxymethyl cellulose but a low Km (3 to 4 mg/ml) for lichenan and barley beta-glucan. The enzyme hydrolyzed amorphous cellulose, and cellobiose and cellotriose were the major products of hydrolysis. Cellotriose, but not cellobiose, was cleaved by the enzyme. EG3 exhibited significant amino acid sequence homology with endoglucanase CelC from Clostridium thermocellum, and as with both CelA and CelC of C. thermocellum, it had a putative active site which could be aligned with the active site of hen egg white lysozyme at the highly conserved amino acid residues Asn-44 and Asp-52.
Fractionation of Recombinant Tumor Necrosis Factor Using Hydrophobic and Hydrophilic Membranes (1990)

Recombinant tumor necrosis factor (TNF) is expressed in Escherichia coli as a soluble intracellular protein. A purification process is described that incorporates a hydrophilic membrane (cellulosic) separation followed by a hydrophobic one (PTFE). The hydrophilic step is a traditional one in that species are separated primarily on the basis of size. The hydrophobic step separates species on the basis of parameters apparently not related to size. By combining these two steps, an increase in TNF purity of 7-10-fold can be achieved with a yield of 50%. The effects of cellular debris and pH on selectivity and recovery of the hydrophobic filtration step are discussed.
Results of a prospective, multicenter study evaluating quality of life, safety, and efficacy of sacral neuromodulation at twelve months in subjects with symptoms of overactive bladder (2014)

This multicenter study shows SNM is safe and effective and results in improved outcomes through 12 months in subjects with OAB symptoms, without requiring failure of all medications.
High-resolution restriction maps of bacterial artificial chromosomes constructed by optical mapping (1998)

Large insert clone libraries have been the primary resource used for the physical mapping of the human genome. Research directions in the genome community now are shifting direction from purely mapping to large-scale sequencing, which in turn, require new standards to be met by physical maps and large insert libraries. Bacterial artificial chromosome libraries offer enormous potential as the chosen substrate for both mapping and sequencing studies. Physical mapping, however, has come under some scrutiny as being "redundant" in the age of large-scale automated sequencing. We report the development and applications of nonelectrophoretic, optical approaches for high-resolution mapping of bacterial artificial chromosome that offer the potential to complement and thereby advance large-scale sequencing projects.