gebhart/patrepeval huggingface dataset:
Predicting linear B‐cell epitopes using string kernels (2008)

The identification and characterization of B-cell epitopes play an important role in vaccine design, immunodiagnostic tests, and antibody production. Therefore, computational tools for reliably predicting linear B-cell epitopes are highly desirable. We evaluated Support Vector Machine (SVM) classifiers trained utilizing five different kernel methods using fivefold cross-validation on a homology-reduced data set of 701 linear B-cell epitopes, extracted from Bcipep database, and 701 non-epitopes, randomly extracted from SwissProt sequences. Based on the results of our computational experiments, we propose BCPred, a novel method for predicting linear B-cell epitopes using the subsequence kernel. We show that the predictive performance of BCPred (AUC = 0.758) outperforms 11 SVM-based classifiers developed and evaluated in our experiments as well as our implementation of AAP (AUC = 0.7), a recently proposed method for predicting linear B-cell epitopes using amino acid pair antigenicity. Furthermore, we compared BCPred with AAP and ABCPred, a method that uses recurrent neural networks, using two data sets of unique B-cell epitopes that had been previously used to evaluate ABCPred. Analysis of the data sets used and the results of this comparison show that conclusions about the relative performance of different B-cell epitope prediction methods drawn on the basis of experiments using data sets of unique B-cell epitopes are likely to yield overly optimistic estimates of performance of evaluated methods. This argues for the use of carefully homology-reduced data sets in comparing B-cell epitope prediction methods to avoid misleading conclusions about how different methods compare to each other. Our homology-reduced data set and implementations of BCPred as well as the APP method are publicly available through our web-based server, BCPREDS, at: http://ailab.cs.iastate.edu/bcpreds/.
Control and understanding of the formation of micro/nanostructured metal surfaces using femtosecond laser pulses (2012)

An application of femtosecond lasers that has developed, in recent years, is the functionalization of surfaces. With femtosecond laser ablation micro and nano-scale features can be created in a single step without affecting the bulk material. In this dissertation micro/nanostructuring of metal surfaces, specifically nickel and SS316, was carried out using femtosecond laser pulses. By varying the fluence (between 0.01 and 3.18 J/cm2), and pulse count (between 1 and 20,000 pulses) incident on the metal surface, a number of surface morphologies were produced. It was demonstrated that a number of these morphologies can be separated in regions based on fluence and shot number. The effects of other parameters were studied in less detail, including: polarization, stationary versus rastering pulses, atmosphere during processing (processing in nitrogen and oxygen), and lens aberrations. Two morphologies from femtosecond laser ablation of metals are demonstrated for the first time: spike shaped microstructures that have peaks above the original surface, and pyramid shaped structures (with a much lower aspect ratio than commonly published morphologies) covered in thick layers of nanoparticles. Similarities and differences are shown between the commonly published relief structures, with a blunt, round top (mounds) and the protruding spikes. This work shows that the morphologies are formed through a balance between fluid flow, nanoparticle/material redeposition and preferential etching. It can be observed by watching the development of individual microstructures with increasing pulse count, what role each of these processes plays in their development. Mounds, spikes, and pyramids each have a different balance of these processes, leading to the uniqueness of each morphology. As an application of these processes, studies were completed to utilize the high surface areas of these micro/nanostructures to produce ultracapacitor electrodes. This proved to be challenging, due to the poor electrical connection between nanoparticles, and further research is needed to improve these connections.
p300 gene alterations in colorectal and gastric carcinomas. (1996)

Colorectal tumors frequently have loss of heterozygosity on chromosome 22q, suggesting that inactivation of tumor suppressor gene(s) on 22q participates in the tumor development. Neurofibromatosis 2 (NF2) gene and E1A binding protein p300 gene, recently identified on 22q, are thought to be candidates for tumor suppressor genes. In this study, mutation of the NF2 gene in 59 colorectal carcinomas, and mutation of the p300 gene in 27 colorectal and two gastric carcinomas, were analysed using PCR-SSCP, RT-PCR-SSCP and direct sequencing methods. Missense mutations of p300 gene were detected in a colorectal carcinoma, and in a gastric carcinoma, though no mutation of NF2 gene was detected. Both p300 mutations were somatic and coupled to deletion of the second allele of the gene, which suggests inactivation of the p300 gene, in these carcinomas. The mutations are located within the Cys/His-rich regions, which are assumed to play important roles in the function of p300. These are the first cases in which p300 gene has been found to be altered in both alleles, suggesting that inactivation of the p300 gene may be involved in the development of carcinomas, and that this gene may be the target of loss of 22q in carcinomas of the digestive tract.
Dendritic Cell-specific Intercellular Adhesion Molecule 3-grabbing Non-integrin (DC-SIGN)-mediated Enhancement of Dengue Virus Infection Is Independent of DC-SIGN Internalization Signals (2005)

Dengue virus (DV) is a mosquito-borne flavivirus that causes hemorrhagic fever in humans. In the natural infection, DV is introduced into human skin by an infected mosquito vector where it is believed to target immature dendritic cells (DCs) and Langerhans cells (LCs). We found that DV productively infects DCs but not LCs. We show here that the interactions between DV E protein, the sole mannosylated glycoprotein present on DV particles, and the C-type lectin dendritic cell-specific intercellular adhesion molecule 3-grabbing non-integrin (DC-SIGN) are essential for DV infection of DCs. Binding of mannosylated N-glycans on DV E protein to DC-SIGN triggers a rapid and efficient internalization of the viral glycoprotein. However, we observed that endocytosis-defective DC-SIGN molecules allow efficient DV replication, indicating that DC-SIGN endocytosis is dispensable for the internalization step in DV entry. Together, these results argue in favor of a mechanism by which DC-SIGN enhances DV entry and infection in cis. We propose that DC-SIGN concentrates mosquito-derived DV particles at the cell surface to allow efficient interaction with an as yet unidentified entry factor that is ultimately responsible for DV internalization and pH-dependent fusion into DCs.
Biochemical safety profiles of gadolinium‐based extracellular contrast agents and nephrogenic systemic fibrosis (2007)

Gadolinium (Gd)-based paramagnetic contrast agents are relatively safe when used in clinically recommended doses. However, with the rapidly expanding body of literature linking Gd-based paramagnetic contrast agents and nephrogenic systemic fibrosis (NSF), awareness of the potential side effects and adverse reactions from Gd is now an important requirement for practicing radiologists. In addition to the ongoing accumulation and analyses of clinical NSF data, it is also essential for the practicing radiologist to understand the biochemical characteristics of the extracellular Gd-chelates. The purpose of this review is to consolidate and update the available information on known side effects, adverse reactions, and toxicity of the Gd chelates, with particular emphasis on the potential mechanisms of NSF.
Association of hepatic veno-occlusive disease with interstitial pneumonitis in bone marrow transplant recipients. (1989)

MR disinsertion can be considered in patients with chronic complete sixth nerve palsy and refractory diplopia when the conventional methods have failed.
mHDA1/HDAC5 Histone Deacetylase Interacts with and Represses MEF2A Transcriptional Activity (2000)

Recently we identified a new family of histone deacetylases in higher eukaryotes related to yeast HDA1 and showed their differentiation-dependent expression. Data presented here indicate that HDAC5 (previously named mHDA1), one member of this family, might be a potent regulator of cell differentiation by interacting specifically with determinant transcription factors. We found that HDAC5 was able to interact in vivo and in vitro with MEF2A, a MADS box transcription factor, and to strongly inhibit its transcriptional activity. Surprisingly, this repression was independent of HDAC5 deacetylase domain. The N-terminal non-deacetylase domain of HDAC5 was able to ensure an efficient repression of MEF2A-dependent transcription. We then mapped protein domains involved in the HDAC5-MEF2A interaction and showed that MADS box/MEF2-domain region of MEF2A interacts specifically with a limited region in the N-terminal part of HDAC5 which also possesses a distinct repressor domain. These data show that two independent class II histone deacetylases HDAC4 and HDAC5 are able to interact with members of the MEF2 transcription factor family and regulate their transcriptional activity, thus suggesting a critical role for these deacetylases in the control of cell proliferation/differentiation.
Temperature-Sensitive Replication-Competent Adenovirus shRNA Vectors to Study Cellular Genes in Virus-Induced Apoptosis (2007)

The use of shRNA for knockdown of gene expression is a powerful method. In addition to transient transfection of RNA oligonucleotides, various DNA-based vectors that express short hairpin RNAs have been successfully used for efficient depletion of gene products. Replication-defective retrovirus and adenovirus (Ad) vectors have also gained wide usage. The extension of shRNA technology to replication-competent Ad would be desirable to investigate the role of various cellular genes in Ad replication. This approach is hampered because the effect of shRNA is neutralized by the Ad VA-RNA that is expressed at late stages after infection, and the infected cells are killed prior to significant depletion of some long-lived target gene products. We have constructed replication-competent Ad vectors for the depletion of the pro-apoptotic proteins BAX and BAK. We have modified a replication-defective Ad multivalent shRNA expression vector developed by Welgen, Inc. In our vector design, the multivalent shRNA expression cassette is contained in the E1B region. Additionally, we have incorporated a temperature-sensitive mutation in the viral DBP gene (ts125). The use of this vector has resulted in efficient depletion of critical cellular apoptotic modulators, BAX and BAK. This vector may be useful to study the role of various cellular genes in Ad-induced apoptosis and viral replication.
Expression of Novel Molecules, MICAL2-PV (MICAL2 Prostate Cancer Variants), Increases with High Gleason Score and Prostate Cancer Progression (2006)

Our findings suggest that MICAL2-PV is likely to be involved in cancer progression of prostate cancer and could be a candidate as a novel molecular marker and/or target for treatment of prostate cancers with high Gleason score.
Interfacial role in room-temperature diffusion of Au into Si substrates (2007)

X-ray reflectivity is used in tracking the diffusion of Au into Si(001) substrates with time at room temperature. It has been observed that the diffusion of Au into Si substrates strongly depends on the initial pretreatment conditions of Si surface. In particular, there is very little diffusion for the untreated Si surface, while the Si surface pretreated with HF seems to be prone to strong diffusion and the surface further pretreated with Br shows diffusion in between. Such different diffusion and apparent non-Fickian-type time dependence in the diffusion can be quantitatively explained by Fickian diffusion of Au through changing unblocked interfacial layer. The growth of the blocking (oxide) layer with time essentially prevents further diffusion through those areas, and the growth of that layer is directly related to the surface stability due to the surface pretreatment and/or passivation conditions, which gives a control in the formation of diffusion-induced Au-Si nanolayer of different widths and compositions. The morphology and evolution of the top surface, mapped with atomic force microscopy and scanning electron microscopy, further helped to verify and understand such differences.
Long-Term Survival after Out-of-Hospital Cardiac Arrest (1982)

EFFORTS to resuscitate the dead are as old as recorded history, and many techniques, including magic, ritual, and shamanism, have been employed.1 , 2 It is only in recent years that measures that regularly resuscitate patients from out-of-hospital cardiac arrest have been developed. Special emergency-service programs, known as paramedic programs and numbering over 300 in the United States, provide advanced cardiac life support after cardiac arrest.3 Well-documented studies demonstrate hospital discharge rates of up to 30 per cent for patients with out-of-hospital ventricular fibrillation.4 5 6 7 Despite numerous descriptions of paramedic programs and documentation of hospital admission and discharge rates after out-of-hospital cardiac arrest, . . .
Acute systemic erythropoietin therapy to reduce delayed ischemic deficits following aneurysmal subarachnoid hemorrhage: a Phase II randomized, double-blind, placebo-controlled trial (2009)

This preliminary study showed that EPO seemed to reduce delayed cerebral ischemia following aSAH via decreasing severity of vasospasm and shortening impaired autoregulation.
GROWTH OF DUCK INFLUENZA VIRUS A/DUCK/HOKKAIDO/5/77 (HAV7N2) AND HUMAN INFLUENZA VIRUS A/KUMAMOTO/22/76 (H3N2) IN DUCK AND CHICKEN COLON ORGAN CULTURES (1981)

All test products showed a recovery of the Knoop Hardness Number (KHN) after remineralization cycling treatment. The recovery of enamel KHN for Colgate Sensitive Pro-Relief, GC Mousse, Crest toothpasteand NaF groups were 44.53 +/- 6.72%, 35.00 +/- 7.83%, 24.56 +/- 5.95% and 42.51 +/- 6.74% respectively, while the recovery of negative control group was 18.99 +/- 4.98%. PLM results indicated the lesion depth recovery of 49.63 +/- 8.06%, 35.08 +/- 2.19%, 22.60 +/- 7.30% and 53.20 +/- 1.48% respectively, which were also significantly greater than that of the negative group (20.51 +/- 4.80%). CLSM analysis showed a reduction of average area, and total and average dye fluorescence of the lesions after treatment. The Colgate Sensitive Pro-Relief group presented significantly greater remineralization than the other toothpaste groups, while the Crest toothpaste group showed the lowest remineralization ability.
Germ Warfare in a Microbial Mat Community: CRISPRs Provide Insights into the Co-Evolution of Host and Viral Genomes (2009)

CRISPR arrays and associated cas genes are widespread in bacteria and archaea and confer acquired resistance to viruses. To examine viral immunity in the context of naturally evolving microbial populations we analyzed genomic data from two thermophilic Synechococcus isolates (Syn OS-A and Syn OS-B') as well as a prokaryotic metagenome and viral metagenome derived from microbial mats in hotsprings at Yellowstone National Park. Two distinct CRISPR types, distinguished by the repeat sequence, are found in both the Syn OS-A and Syn OS-B' genomes. The genome of Syn OS-A contains a third CRISPR type with a distinct repeat sequence, which is not found in Syn OS-B', but appears to be shared with other microorganisms that inhabit the mat. The CRISPR repeats identified in the microbial metagenome are highly conserved, while the spacer sequences (hereafter referred to as "viritopes" to emphasize their critical role in viral immunity) were mostly unique and had no high identity matches when searched against GenBank. Searching the viritopes against the viral metagenome, however, yielded several matches with high similarity some of which were within a gene identified as a likely viral lysozyme/lysin protein. Analysis of viral metagenome sequences corresponding to this lysozyme/lysin protein revealed several mutations all of which translate into silent or conservative mutations which are unlikely to affect protein function, but may help the virus evade the host CRISPR resistance mechanism. These results demonstrate the varied challenges presented by a natural virus population, and support the notion that the CRISPR/viritope system must be able to adapt quickly to provide host immunity. The ability of metagenomics to track population-level variation in viritope sequences allows for a culture-independent method for evaluating the fast co-evolution of host and viral genomes and its consequence on the structuring of complex microbial communities.
Rehabilitation of walking with electromyographic biofeedback in foot-drop after stroke. (1994)

Our data confirm that the electromyographic biofeedback technique increases muscle strength and improves recovery of functional locomotion in patients with hemiparesis and foot-drop after cerebral ischemia.
<title>Compact ultrahigh-power laser systems</title> (1995)

Compact sources of high energy ultrashort pulses are described. Femtosecond and picosecond optical pulses with microjoule energies are obtained using chirped-pulse fiber amplifiers. Mode-locked fiber lasers and fast-tuned laser diodes are used to generate initial pulses for amplification. Efficient frequency conversion of amplified pulses is demonstrated and microjoule second-harmonic pulses are produced. The first all-fiber chirped pulse amplification circuit is demonstrated. It uses in-fiber chirped Bragg gratings, which replaces conventional diffraction-grating compressors and stretchers.
Light‐Induced Click Reactions (2013)

Spatial and temporal control over chemical and biological processes, both in terms of "tuning" products and providing site-specific control, is one of the most exciting and rapidly developing areas of modern science. For synthetic chemists, the challenge is to discover and develop selective and efficient reactions capable of generating useful molecules in a variety of matrices. In recent studies, light has been recognized as a valuable method for determining where, when, and to what extent a process is started or stopped. Accordingly, this Minireview will present the fundamental aspects of light-induced click reactions, highlight the applications of these reactions to diverse fields of study, and discuss the potential for this methodology to be applied to the study of biomolecular systems.
Comparison of different polymerase chain reaction-based approaches for clonality assessment of immunoglobulin heavy-chain gene rearrangements in B-cell neoplasia. (1999)

Several frequently applied polymerase chain reaction strategies for analysis of immunoglobulin heavy-chain gene rearrangements were compared by analyzing 70 B-cell lymphoproliferative disorders and 24 reactive lymphoid lesions. Southern blot analysis was used as the "gold standard" for clonality assessment. For polymerase chain reaction analysis, primers directed against framework (FR) 3 (FR3-A and FR3-B), FR2, and FR1 of the variable gene segments and against joining gene segments of the immunoglobulin heavy-chain gene were used. Polymerase chain reaction products were analyzed by high-resolution fingerprinting analysis using radiolabeled nucleotides, gene scanning using fluorochrome-labeled primers, and heteroduplex analysis. All of the assays generated polyclonal patterns in the reactive tissues. The sensitivity in detecting monoclonality as defined by Southern blotting varied between 60% (heteroduplex analysis with FR3 primers) and 77% (high-resolution fingerprinting analysis with FR2 primers). Comparison of the three FR3 assays revealed that gene scanning had the highest sensitivity (69%), probably because it could detect small aberrant monoclonal amplicons. False-negative results were especially frequent in follicular center lymphoma (n = 20), but also in diffuse large B-cell lymphoma (n = 18), both renowned for having mutated variable gene segments, potentially leading to primer mismatching. For example, in follicular center lymphoma, the FR3, FR2, and FR1 region primer sets detected clonality in only 35 to 40, 65, and 50%, respectively. Combining these techniques, 17 (85%) of 20 follicular center lymphoma samples showed monoclonality. Therefore, especially in follicular center lymphoma, diffuse large B-cell lymphoma, and, to a lesser extent, in other lymphomas, multiple variable gene segment primer sets must be used for a reliable assessment of clonality. Our results also suggest that gene scanning is somewhat more sensitive than other read-out systems. Heteroduplex analysis, however, is a reliable alternative within a diagnostic setting, avoiding the use of radioactivity or expensive automated sequencing equipment and fluorochrome-labeled (oligo)nucleotides.
Evolution of substrate recognition sites (SRSs) in cytochromes P450 from Apiaceae exemplified by the CYP71AJ subfamily (2015)

Two subclades functionally assigned to the biosynthesis of furanocoumarins and four other subclades were identified and shown to be part of two distinct clades within the CYP71AJ subfamily. The subclades show significant variability within their substrate recognition sites between the clades, suggesting different biochemical functions and providing insights into the evolution of cytochrome P450 'blooms' in response to environmental pressures.
Spiral Spin Order of Self-Assembled Co Nanodisk Arrays (2006)

Spin order in hexagonal close packed cobalt nanodisk rows is quantitatively determined by off-axis electron holography. Periodic variation in the density of the local magnetic flux shows features of a spiral spin arrangement along the row axis, resulting from a tilted magnetic moment of nanoparticles with respect to the nanodisk axis.
Expression of the 5.1 H11 antigen, a fetal muscle surface antigen, in normal and neoplastic tissue. (1990)

The monoclonal antibody 5.1 H11 recognizes an antigen on human fetal muscle and on rhabdomyosarcoma cell lines and xenografts that has been shown to be homologous to the neural cell adhesion molecule. To evaluate its range of expression, we used immunoperoxidase staining of fresh frozen-tissue sections to determine monoclonal antibody 5.1 H11 reactivity in normal and neoplastic tissue. Among normal tissue specimens, intense antibody staining was seen in brain and peripheral nerve, and weaker staining in ganglionic elements of colon. In addition to 26 of 29 rhabdomyosarcoma specimens, 5.1 H11 antibody showed reactivity to 9 of 10 Wilms' tumors, 6 of 6 neural tumors, and 4 of 4 gliomas, and with single specimens of ectomesenchymoma, clear-cell sarcoma of kidney, undifferentiated sarcoma of liver, ovarian fibroma, and neurofibroma. We conclude that the monoclonal antibody 5.1 H11 recognizes an antigen present not only on fetal muscle but on normal brain and nerve as well. In addition to rhabdomyosarcoma, a variety of other tumors, most of which have been previously shown to express neural cell adhesion molecule, also appear to express the antigen recognized by 5.1 H11. Our results thus offer additional confirmatory evidence that an epitope of neural cell adhesion molecule is the antigen for 5.1 H11.
Association of multiple copies of the c-erbB-2 oncogene with spread of breast cancer. (1987)

Amplification of c-erbB-2 was at least three times more frequent in breast cancer than in most other types of carcinoma, and was not found in sarcomas or hematological malignancies. Amplification of c-erbB-2 was found in 15 of 86 primary breast cancers and in 3 of 12 secondary breast cancers. Amplification was more common in breast tumors of advanced stage, and in tumors which had metastasized to regional lymph nodes sites. Gene amplification was observed in 21% (4 of 19) of primary tumors which recurred within 3 years of mastectomy and in 6% (2 of 32) of nonrecurrent tumors.