gebhart/patrepeval huggingface dataset:
Evaluation of MHC class I peptide binding prediction servers: Applications for vaccine research (2008)

Non-linear predictors outperform matrix-based predictors. Most predictors can be improved by non-linear transformations of their raw prediction scores. The best predictors of peptide binding are also best in prediction of T-cell epitopes. We propose a new standard for MHC-I binding prediction - a common scale for normalization of prediction scores, applicable to both experimental and predicted data. The results of this study provide assistance to researchers in selection of most adequate prediction tools and selection criteria that suit the needs of their projects.
Intraneuronal β-Amyloid Expression Downregulates the Akt Survival Pathway and Blunts the Stress Response (2005)

Early events in Alzheimer's disease (AD) pathogenesis implicate the accumulation of beta-amyloid (Abeta) peptide inside neurons in vulnerable brain regions. However, little is known about the consequences of intraneuronal Abeta on signaling mechanisms. Here, we demonstrate, using an inducible viral vector system to drive intracellular expression of Abeta42 peptide in primary neuronal cultures, that this accumulation results in the inhibition of the Akt survival signaling pathway. Induction of intraneuronal Abeta42 expression leads to a sequential decrease in levels of phospho-Akt, increase in activation of glycogen synthase kinase-3beta, and apoptosis. Downregulation of Akt also paralleled intracellular Abeta accumulation in vivo in the Tg2576 AD mouse model. Overexpression of constitutively active Akt reversed the toxic effects of Abeta through a mechanism involving the induction of heat shock proteins (Hsps). We used a small-interfering RNA approach to explore the possibility of a link between Akt activity and Hsp70 expression and concluded that neuroprotection by Akt could be mediated through downstream induction of Hsp70 expression. These results suggest that the early dysfunction associated with intraneuronal Abeta accumulation in AD involve the associated impairments of Akt signaling and suppression of the stress response.
Real-Time Polymerase Chain Reaction (RQ-PCR) for the Monitoring of Epstein-Barr Virus (EBV) Load in Peripheral Blood Mononuclear Cells (2000)

Measurement of Epstein-Barr virus (EBV) load is useful in peripheral blood for detecting primary and reactivated EBV-infections especially in immunosuppressed patients being at high risk for developing posttransplant lymphoproliferative disorder. For quantification of EBV DNA in peripheral blood of patients two real time polymerase chain reaction (RQ-PCR) assays were developed detecting sequences specific for the BAM HI-W and BAM HI-K region of EBV. In order to determine the optimal material of peripheral blood for RQ PCR analysis, DNA preparations of whole blood, peripheral blood mononuclear cells (PBMC) and B cells from 11 healthy, EBV-seropositive individuals were analysed in parallel and compared with regard to efficiency and sensitivity. While in whole blood preparations inhibitors of RQ PCR were detected influencing sensitivity, analysis of B cells being most sensitive is limited by being too labour intensive. In contrast, analysis of DNA preparations of PBMCs is sensitive enough to frequently detect EBV-specific sequences in all individuals tested and the preparation of PBMCs itself needs only a reasonable time. Thus, longitudinal monitoring of EBV load in peripheral blood of patients is possible by RQ-PCR, the optimal material for analysis being PBMCs.
Pulsed, Non-Thermal, High-Frequency Electromagnetic Energy (DIAPULSE) in the Treatment of Grade I and Grade II Ankle Sprains (1993)

Acutely sprained ankles represent a frequent and common injury among active duty troops in training, and are a significant source of morbidity with respect to days lost to training. Swelling in the form of periarticular edema limits motion, causes pain, prevents wearing of normal foot gear, and slows the healing process. Reduction of edema was attempted in acutely sprained ankles by the use of pulsed electromagnetic energy (Diapulse). In a randomized, prospective, double blind study of 50 grade I and II (no gross instability) sprained ankles, a statistically significant (p < 0.01) decrease in edema was noted following one treatment with Diapulse. The application of this modality in acutely sprained ankles could result in significant decreases in time lost to military training.
Fast coding unit size selection for HEVC based on Bayesian decision rule (2012)

High Efficiency Video Coding (HEVC) is being developed by Joint Collaborative Team on Video Coding (JCT-VC). The new standard aims at a significant improvement on Rate Distortion (RD) performance over state-of-the-art video coding standards. Some new efficient coding tools are adopted, such as flexible data structure representation: Coding Unit (CU), Prediction Unit (PU), and Transform Unit (TU). Meanwhile, these new tools impose lots of complexity. We propose a CU size decision algorithm that greatly reduces the complexity of HEVC. The proposed algorithm collects relevant and computational-friendly features to assist decisions on CU splitting. To minimize the RD loss of the fast algorithm, a Bayesian decision rule is defined, based on which the encoder can save 41.4% encoding time on average (up to 66%) whilst suffers from negligible loss (1.88%) on RD performance.
State of the art and future directions of scaffold-based bone engineering from a biomaterials perspective (2007)

Scaffold-based bone tissue engineering aims to repair/regenerate bone defects. Such a treatment concept involves seeding autologous osteogenic cells throughout a biodegradable scaffold to create a scaffold-cell hybrid that may be called a tissue-engineered construct (TEC). A variety of materials and scaffolding fabrication techniques for bone tissue engineering have been investigated over the past two decades. This review aims to discuss the advances in bone engineering from a scaffold material point of view. In the first part the reader is introduced to the basic principles of bone engineering. The important properties of the biomaterials and the scaffold design in the making of tissue engineered bone constructs are discussed in detail, with special emphasis placed on the new material developments, namely composites made of synthetic polymers and calcium phosphates. Advantages and limitations of these materials are analysed along with various architectural parameters of scaffolds important for bone tissue engineering, e.g. porosity, pore size, interconnectivity and pore-wall microstructures.
Short-term intermittent hypoxia enhances sympathetic responses to continuous hypoxia in humans (2007)

Short-term intermittent hypoxia leads to sustained sympathetic activation and a small increase in blood pressure in healthy humans. Because obstructive sleep apnea, a condition associated with intermittent hypoxia, is accompanied by elevated sympathetic activity and enhanced sympathetic chemoreflex responses to acute hypoxia, we sought to determine whether intermittent hypoxia also enhances chemoreflex activity in healthy humans. To this end, we measured the responses of muscle sympathetic nerve activity (MSNA, peroneal microneurography) to arterial chemoreflex stimulation and deactivation before and following exposure to a paradigm of repetitive hypoxic apnea (20 s/min for 30 min; O(2) saturation nadir 81.4 +/- 0.9%). Compared with baseline, repetitive hypoxic apnea increased MSNA from 113 +/- 11 to 159 +/- 21 units/min (P = 0.001) and mean blood pressure from 92.1 +/- 2.9 to 95.5 +/- 2.9 mmHg (P = 0.01; n = 19). Furthermore, compared with before, following intermittent hypoxia the MSNA (units/min) responses to acute hypoxia [fraction of inspired O(2) (Fi(O(2))) 0.1, for 5 min] were enhanced (pre- vs. post-intermittent hypoxia: +16 +/- 4 vs. +49 +/- 10%; P = 0.02; n = 11), whereas the responses to hyperoxia (Fi(O(2)) 0.5, for 5 min) were not changed significantly (P = NS; n = 8). Thus 30 min of intermittent hypoxia is capable of increasing sympathetic activity and sensitizing the sympathetic reflex responses to hypoxia in normal humans. Enhanced sympathetic chemoreflex activity induced by intermittent hypoxia may contribute to altered neurocirculatory control and adverse cardiovascular consequences in sleep apnea.
Lipid-tagged antibodies: bacterial expression and characterization of a lipoprotein—single-chain antibody fusion protein (1993)

In order to achieve a stable and functional immobilization of antibodies, we investigated the possibility of adding hydrophobic membrane anchors to antibody fragments expressed in Escherichia coli. The DNA sequence encoding the signal peptide and the nine N-terminal amino acid residues of the major lipoprotein of E.coli was fused to the sequence of an anti-2-phenyloxazolone single-chain Fv antibody fragment [Takkinen et al. (1991) Protein Engng, 4,837-841]. The expression of the fusion construct in E.coli resulted in specific accumulation of an immunoreactive 28 kDa polypeptide. Unlike the unmodified single-chain Fv fragment, the fusion protein was cell-associated, labelled by [3H]palmitate which is indicative of the presence of N-terminal lipid modification, partitioned into the detergent phase upon Triton X-114 phase separation and was localized predominantly in the bacterial outer membrane. The fusion antibody displayed specific 2-phenyloxazolone-binding activity in the membrane-bound form and after solubilization with non-ionic detergents. Furthermore, upon removal of detergent the fusion antibody was incorporated into proteoliposomes which displayed specific hapten-binding activity. Our results show that antibodies can be converted to membrane-bound proteins with retention of antigen-binding properties by introduction of lipid anchors during biosynthesis. This approach may prove useful in the design of immunoliposomes and immunosensors.
Cell Infectivity in Relation to Bovine Leukemia Virus gp51 and p24 in Bovine Milk Exosomes (2013)

Exosomes are small membranous microvesicles (40-100 nm in diameter) and are extracellularly released from a wide variety of cells. Exosomes contain microRNA, mRNA, and cellular proteins, which are delivered into recipient cells via these exosomes, and play a role in intercellular communication. In bovine leukemia virus (BLV) infection of cattle, although it is thought to be a minor route of infection, BLV can be transmitted to calves via milk. Here, we investigated the association between exosomes and BLV in bovine milk. BLV structural proteins, gp51 (Env) and p24 (Gag), were detected in bovine milk exosomes from BLV-infected cattle by Western blot analysis. In cells inoculated with these milk exosomes, BLV DNA was not detected during three serial passages by nested PCR. Purification of exosomes from persistently BLV-infected cells was achieved by immuno-magnetic separation using an antibody against exosomes coupled to magnetic beads. Consistently, BLV gp51 and p24 proteins were detected in purified exosomes. Moreover, reverse transcriptase activity was observed in purified exosomes, meaning that exosomes also contain viral enzyme. However, BLV DNA was not detected in serially passaged cells after inoculation of purified exosomes, indicating that exosomes carrying BLV proteins appeared to be not infectious. These results suggest that BLV proteins are released with milk exosomes and could be transferred into recipient cells of calves via milk exosomes as an alternative route not requiring virus infection. Moreover it is also possible that bovine milk exosomes play a role in clearance of BLV proteins from infected cells.
Next‐generation technologies for spatial proteomics: Integrating ultra‐high speed MALDI‐TOF and high mass resolution MALDI FTICR imaging mass spectrometry for protein analysis (2016)

MALDI imaging mass spectrometry is a powerful analytical tool enabling the visualization of biomolecules in tissue. However, there are unique challenges associated with protein imaging experiments including the need for higher spatial resolution capabilities, improved image acquisition rates, and better molecular specificity. Here we demonstrate the capabilities of ultra-high speed MALDI-TOF and high mass resolution MALDI FTICR IMS platforms as they relate to these challenges. High spatial resolution MALDI-TOF protein images of rat brain tissue and cystic fibrosis lung tissue were acquired at image acquisition rates >25 pixels/s. Structures as small as 50 μm were spatially resolved and proteins associated with host immune response were observed in cystic fibrosis lung tissue. Ultra-high speed MALDI-TOF enables unique applications including megapixel molecular imaging as demonstrated for lipid analysis of cystic fibrosis lung tissue. Additionally, imaging experiments using MALDI FTICR IMS were shown to produce data with high mass accuracy (<5 ppm) and resolving power (∼75 000 at m/z 5000) for proteins up to ∼20 kDa. Analysis of clear cell renal cell carcinoma using MALDI FTICR IMS identified specific proteins localized to healthy tissue regions, within the tumor, and also in areas of increased vascularization around the tumor.
ChemInform Abstract: Combinatorial and High‐Throughput Screening of Materials Libraries: Review of State of the Art (2012)

Abstract Review: 516 refs.
Application of Erbium: YAG Laser in Ocular Ablation (1990)

Recent developments in lasers have provided us the possibility of laser ocular surgery. The xenon, argon, neodymium:YAG and dye lasers have been successfully used in out-patient clinics. The excimer laser has been attracting researchers' interest in the new application of laser to cornea and lens. The erbium:YAG laser emits a 2.94-microns beam that can ablate the transparent ocular tissues such as lenses and corneas. The author has applied this laser to the cornea, lens, vitreous and other ocular tissues. The erbium:YAG laser beam was directed through a 1.5-meter-long, 200-microns-diameter fiberoptic guide. The radiant energy measured about 50 mJ at the end of the probe. The laser was emitted as a 400-microsecond pulse. Freshly enucleated rabbit eyes were used in this study. Laser burns were applied to the tissue surface at various energy settings. At minimal power, the tissues were coagulated by the erbium:YAG laser application. At a power of more than 636-954 mJ/mm2, tissue began to evaporate; the tissue loss was observed under a surgical light microscope. Corneal photoablation, lens ablation, iridotomy, trabeculotomy, cutting of the vitreous and retinal ablation were easily performed. Like the excimer laser, the erbium:YAG laser is a potential tool for ocular surgery.
The CTAB-DNA precipitation method: a common mini-scale preparation of template DNA from phagemids, phages or plasmids suitable for sequencing. (1989)

This report describes a common method of obtaining template DNA from phagemids, phages and plasmids. The strategy is based on the use of the cationic detergent cetyl-trimethylammonium bromide (CTAB) for DNA precipitation. By avoiding phase separation, many manipulation steps are reduced. A time-saving modification to perform double-stranded DNA sequencing directly after alkaline-denaturation is also introduced. The protocols described here allow the researcher to obtain template DNA from a variety of initial sources, thus giving reproducible sequencing results when using T7 DNA polymerase.
Phase modulation of stretched optical pulses forsuppression of third-order dispersion effects in fibre transmission (1998)

Transmission of short pulses with suppressed third-order fibre dispersion effects is demonstrated by sinusoidal phase modulation of stretched optical pulses. Numerical simulation results show significantly less pulse distortion for transmission of 530 fs pulses over a 10 km fibre link achieved by applying 2.56 GHz phase modulation with a peak phase shift of 3π.
RNA transcripts, miRNA-sized fragments and proteins produced from D4Z4 units: new candidates for the pathophysiology of facioscapulohumeral dystrophy (2009)

Deletion of a subset of the D4Z4 macrosatellite repeats in the subtelomeric region of chromosome 4q causes facioscapulohumeral muscular dystrophy (FSHD) when occurring on a specific haplotype of 4qter (4qA161). Several genes have been examined as candidates for causing FSHD, including the DUX4 homeobox gene in the D4Z4 repeat, but none have been definitively shown to cause the disease, nor has the full extent of transcripts from the D4Z4 region been carefully characterized. Using strand-specific RT-PCR, we have identified several sense and antisense transcripts originating from the 4q D4Z4 units in wild-type and FSHD muscle cells. Consistent with prior reports, we find that the DUX4 transcript from the last (most telomeric) D4Z4 unit is polyadenylated and has two introns in its 3-prime untranslated region. In addition, we show that this transcript generates (i) small si/miRNA-sized fragments, (ii) uncapped, polyadenylated 3-prime fragments that encode the conserved C-terminal portion of DUX4 and (iii) capped and polyadenylated mRNAs that contain the double-homeobox domain of DUX4 but splice-out the C-terminal portion. Transfection studies demonstrate that translation initiation at an internal methionine can produce the C-terminal polypeptide and developmental studies show that this peptide inhibits myogenesis at a step between MyoD transcription and the activation of MyoD target genes. Together, we have identified new sense and anti-sense RNA transcripts, novel mRNAs and mi/siRNA-sized RNA fragments generated from the D4Z4 units that are new candidates for the pathophysiology of FSHD.
Association of Plasma Phospholipid Long-Chain Omega-3 Fatty Acids With Incident Atrial Fibrillation in Older Adults (2012)

In older adults, higher circulating total long-chain n-3 PUFA and docosahexaenoic acid levels were associated with lower risk of incident AF. These results highlight the need to evaluate whether increased dietary intake of these fatty acids could be effective for the primary prevention of AF.
Novel methods for estimating the ballistocardiogram signal using a simultaneously acquired electrocardiogram (2009)

The ballistocardiogram (BCG) signal represents the movements of the body in response to cardiac ejection of blood. Recently, many groups have developed low-cost instrumentation for facilitating BCG measurement in the home. The standard method used in the literature for estimating the BCG pulse response has generally been ensemble averaging over several beats. Unfortunately, since the BCG pulse response is likely longer than a typical heartbeat interval, this standard approach does not yield a full-length estimate of the response. This paper describes a simple, novel algorithm for estimating the full-length BCG pulse response using the R-wave timing of a simultaneously acquired electrocardiogram (ECG). With this pulse response, the full signal can be reconstructed, enabling the analysis of slow transient effects in the BCG signal, and of the measurement noise. Additionally, while this paper focuses only on the BCG signal, the same algorithm could be applied to other biomedical signals such as the phonocardiogram or impedance cardiogram, particularly when the heartbeat interval is shorter than the duration of the pulse response.
Antisense TR3 Orphan Receptor Can Increase Prostate Cancer Cell Viability with Etoposide Treatment (1998)

In androgen-responsive LNCaP human prostatic cancer cells, human TR3 orphan receptor, a member of the steroid receptor superfamily, can be rapidly induced by androgen. In contrast, ablation of androgen by castration can induce the expression of the TR3 orphan receptor gene in rat ventral prostate that has undergone apoptosis. This phenomenon prompted us to further analyze the potential role of human TR3 orphan receptor in prostate cancer cells in which apoptosis had been induced. Northern blot analysis shows that human TR3 orphan receptor expression can be induced rapidly after treatment of LNCaP and PC-3 prostate cancer cells with calcium ionophore or etoposide. Our data further demonstrate that a much higher concentration of etoposide was needed to kill the same number of cells in LNCaP and PC-3 cells transfected stably with antisense TR3 orphan receptor compared with that in control vector transfectants. Together, our data suggest that the human TR3 orphan receptor may play an important role in modulating drug-induced prostate apoptosis.
Optimal Dose of Hypertonic Saline/Dextran in Hemorrhaged Swine (2003)

In terms of survival time, the 11.5- and 4-mL/kg doses were not significantly different. Therefore, optimum resuscitative effectiveness of HSD is achieved within the dose range of 4 to 11.5 mL/kg.
Role of Micro-organisms in Caries Etiology (1994)

The microbial etiology of dental caries is discussed in terms of the dynamic relationship among the dental plaque microbiota, dietary carbohydrate, saliva, and the pH-lowering and cariogenic potential of dental plaque. The evidence supports a concept of caries as a dietary carbohydrate-modified bacterial infectious disease. Its key feature is a dietary carbohydrate-induced enrichment of the plaque microbiota with organisms such as the mutans streptococci and lactobacilli which causes an increase of plaque's pH-lowering and cariogenic potential. The shift in the plaque proportions of these organisms appears to be related to their relatively high acid tolerance. A large body of evidence also supports a major effect of saliva on caries development. Integration of salivary effects with the concept of caries as a dietary carbohydrate-modified bacterial infectious disease suggests a broader concept which includes a major role of saliva in the regulation of the exposure of tooth surfaces to carbohydrate and of plaque acidity and, hence, the microbial composition and the pH-lowering and cariogenic potential of dental plaque. It is proposed that caries occurs preferentially in dentition sites characterized by a relatively high exposure to carbohydrate and diminished salivary effects. Some implications of this concept are discussed.
Fabrication of microscale medical devices by two-photon polymerization with multiple foci via a spatial light modulator (2011)

Two-photon polymerization is an appealing technique for producing microscale devices due to its flexibility in producing structures with a wide range of geometries as well as its compatibility with materials suitable for biomedical applications. The greatest limiting factor in widespread use of two-photon polymerization is the slow fabrication times associated with line-by-line, high-resolution structuring. In this study, a recently developed technology was used to produce microstructures by two-photon polymerization with multiple foci, which significantly reduces the production time. Computer generated hologram pattern technology was used to generate multiple laser beams in controlled positions from a single laser. These multiple beams were then used to simultaneously produce multiple microstructures by two-photon polymerization. Arrays of micro-Venus structures, tissue engineering scaffolds, and microneedle arrays were produced by multifocus two-photon polymerization. To our knowledge, this work is the first demonstration of multifocus two-photon polymerization technology for production of a functional medical device. Multibeam fabrication has the potential to greatly improve the efficiency of two-photon polymerization production of microscale devices such as tissue engineering scaffolds and microneedle arrays.