gebhart/patrepeval huggingface dataset:
297 IDENTIFICATION OF NOVEL ALTERED PEPTIDE LIGANDS RECOGNIZED BY HUMAN TUMOR-REACTIVE T CELLS. (2006)

<h3>Background</h3> Immunotherapy offers many potential advantages to traditional chemotherapy, including high specificity and low toxicity. One of the goals of immunotherapy is to generate tumor-specific cytotoxic lymphocytes (CTLs), which have the potential to specifically kill tumors. Tumor antigens have been used to elicit CTL responses. One disadvantage of using tumor antigens is that the CTLs that recognize these antigens are often of low affinity and/or low frequency. T cell epitopes can be engineered to enhance the expansion of tumor-specific CTLs. The challenge has been to identify such altered peptide ligands (APLs). <h3>Study Design and Methods</h3> We use a positional scanning synthetic combinatorial peptide library (PS-SCL) to identify superagonist peptides of NY-ESO-1, a tumor-associated antigen expressed in melanoma, ovarian cancer, and other solid tumors. This exhaustive search method looks at all amino acid combinations of 9mer peptides (approx. 20<sup>9</sup> peptides) in a positional scanning format. T cell killing of antigen-presenting cells loaded with the library was determined by chromium release assay. Biometric analysis of the data was used to identify candidate peptide sequences. These specific peptides were then tested and compared to the parental peptide NY-ESO-1 for enhanced target sensitization to lysis and capacity to elicit CTL responses in vitro. <h3>Results</h3> Four well-characterized high affinity NY-ESO-1-specific CTL clones were used to probe the combinatorial peptide library. Potential superagonist peptides for NY-ESO-1 were identified, ranked using a scoring algorithm, and then individually tested. We identified a novel core consensus sequence within the parental epitope that yielded enhanced CTL activity. <h3>Conclusion</h3> Through these methods we have identified several novel superagonist ligands for T cell-based immunotherapy using NY-ESO-1-specific clones. Such peptides may show promise for both adoptive therapy and cancer vaccines.
Mutual injection-locked SIL sensor array for vital sign detection with random body movement cancellation (2011)

This paper presents a self-injection-locked (SIL) sensor array for cancelling the effects of random body movement on the detection of vital signs. To achieve this goal, a subject is seated between two SIL sensors to measure rates of respiration and heartbeat using the Doppler shift, and the effects of random movements by the subject are cancelled by wireless mutual injection locking (MIL) of the two sensors. In the experiments, a prototype for such a two-sensor array with a spacing of 2 m was implemented at 2.4 GHz, providing accurate and reliable cardiopulmonary monitoring of a subject who exhibited random body motions of several centimeters.
Increasing maize seed methionine by mRNA stability (2002)

The amino acid methionine is a common protein building block that is also important in other cellular processes. Plants, unlike animals, synthesize methionine de novo and are thus a dietary source of this nutrient. A new approach for using maize as a source of nutrient methionine is described. Maize seeds, a major component of animal feeds, have variable levels of protein-bound methionine. This variability is a result of post-transcriptional regulation of the Dzs10 gene, which encodes a seed-specific high-methionine storage protein. Here we eliminate methionine variability by identifying and replacing the cis-acting site for Dzs10 regulation using transgenic seeds. Interestingly, two different mechanisms affect mRNA accumulation, one dependent on and the other independent of the untranslated regions (UTRs) of Dzs10 RNA. Accumulation of chimeric Dzs10 mRNA was not reduced in hybrid crosses and was uncoupled from genomic imprinting by Dzr1, a regulator of Dzs10. Uniform high levels of Dzs10 protein were maintained over five backcross generations of the transgene. The increased level of methionine in these transgenic seeds allowed the formulation of a useful animal feed ration without the addition of synthetic methionine.
Building better passwords using probabilistic techniques (2012)

Password creation policies attempt to help users generate strong passwords but are generally not very effective and tend to frustrate users. The most popular policies are rule based which have been shown to have clear limitations. In this paper we consider a new approach that we term analyze-modify that ensures strong user passwords while maintaining usability. In our approach we develop a software system called AMP that first analyzes whether a user proposed password is weak or strong by estimating the probability of the password being cracked. AMP then modifies the password slightly (to maintain usability) if it is weak to create a strengthened password. We are able to estimate the strength of the password appropriately since we use a probabilistic password cracking system and associated probabilistic context-free grammar to model a realistic distribution of user passwords. In our experiments we were able to distinguish strong passwords from weak ones with an error rate of 1.43%. In one of a series of experiments, our analyze-modify system was able to strengthen a set of weak passwords, of which 53% could be easily cracked to a set of strong passwords of which only 0.27% could be cracked with only a slight modification to the passwords. In our work, we also show how to compute and use various entropy measures from the grammar and show that our system remains effective with continued use through a dynamic updating capability.
S3C: An architecture for space-efficient semantic search over encrypted data in the cloud (2016)

The recent rapid growth in Internet speeds and file storage requirements has made cloud storage an appealing option on both a personal and enterprise level. Despite the many benefits offered by cloud storage, many potential users with sensitive data refrain from fully utilizing this service due to valid concerns about information privacy. An established solution to this concern is to perform encryption on the user side with the key stored on a local machine, meaning the cloud will never see the user's plaintext data. However, by encrypting data on the user side data processing capabilities (e.g., searching) are lost. In particular, the ability to semantically search is of the user's interest in large datasets. In this paper, we present S3C, a system that provides a semantic search functionality over encrypted data in the cloud. S3C combines approaches from traditional keyword-based searchable encryption and semantic web searching. It offers a user transparent experience that accepts a simple multi-phrase query and returns a list of documents ranked by semantic relevance to the query. Our proposed approach is space-efficient, which makes it suitable for large scale datasets. Our minimal processing also allows the system to be run on thin clients such as smart-phones or tablets. We evaluate the performance of our system against various real-world datasets, and our results show that it produces accurate search results while maintaining minimal storage overhead (~0.3% of the dataset size).
C-Arm Image-Based Surgical Path Planning Method for Distal Locking of Intramedullary Nails (2018)

Due to the curvature of the bone marrow cavity, the intramedullary nail used in long bone fracture fixation can be deformed, causing displacement of the locking holes. In this study, an algorithm using only one C-arm image to determine the center positions and axial directions of locking holes was developed for drilling guidance. Based on conventional method that the axial direction of locking hole would be identified when locking hole contour is presented as a circle, the proposed method can locate the circle contour centroid by using one C-arm image including two elliptical contours. Then the two distal locking holes' axial direction and centers would be determined. Three experiments were conducted to verify the performance of the proposed algorithm, which are (1) computer simulation, (2) use of real intramedullary nails, and (3) actual drilling test with the bone model. The experimental results showed that the average error of the axial direction and center position were 0.62 ± 0.6°, 0.73 ± 0.53 mm (simulation) and 3.16 ± 1.36°, 1.10 ± 0.50 mm (actual nail), respectively. The last ten drilling test sets were completed successfully (with an average duration of 48 seconds). Based on the experimental results, the proposed algorithm was feasible for clinic applications.
choros: correction of sequence-based biases for accurate quantification of ribosome profiling data (2023)

Ribosome profiling quantifies translation genome-wide by sequencing ribosome-protected fragments, or footprints. Its single-codon resolution allows identification of translation regulation, such as ribosome stalls or pauses, on individual genes. However, enzyme preferences during library preparation lead to pervasive sequence artifacts that obscure translation dynamics. Widespread over- and under-representation of ribosome footprints can dominate local footprint densities and skew estimates of elongation rates by up to five fold. To address these biases and uncover true patterns of translation, we present choros, a computational method that models ribosome footprint distributions to provide bias-corrected footprint counts. choros uses negative binomial regression to accurately estimate two sets of parameters: (i) biological contributions from codon-specific translation elongation rates; and (ii) technical contributions from nuclease digestion and ligation efficiencies. We use these parameter estimates to generate bias correction factors that eliminate sequence artifacts. Applying choros to multiple ribosome profiling datasets, we are able to accurately quantify and attenuate ligation biases to provide more faithful measurements of ribosome distribution. We show that a pattern interpreted as pervasive ribosome pausing near the beginning of coding regions is likely to arise from technical biases. Incorporating choros into standard analysis pipelines will improve biological discovery from measurements of translation.
Inhibition of the acute‐phase response <i>in vivo</i> by anti‐gp130 monoclonal antibodies (1996)

The acute‐phase response is believed to be an important systemic defence reaction to inflammation during infection, trauma, injury or neoplasia. Although the interleukin‐6 (IL‐6) family of cytokines appear to be the major regulators of the acute‐phase reaction, the exact biological significance of this process remains unknown. In this study, a panel of monoclonal antibodies (Mabs) was raised against the extracellular domain of human gp130 (the common signal transducing chain of the IL‐6 cytokine family) in order to inhibit the biological activity of IL‐6‐like cytokines in vivo . Mabs designated 4B11 and 2H4 were most effective in the inhibition of the in vitro acute‐phase response on hepatoma cells and prevented the IL‐6‐induced growth inhibition of A375 cells. Administration of the antibodies to dogs at a dosage of 8 mg/kg/d showed that 2H4 was a potent inhibitor of the IL‐6‐induced (40 μg/kg/d) acute‐phase response, abrogating IL‐6‐mediated increments in fibrinogen, C‐reactive protein and the platelet count. This antibody, the first described to abrogate the acute‐phase response in vivo , may not only permit development of a new anti‐inflammatory strategy, but provides an excellent tool for defining the function of acute‐phase proteins in inflammation and infection.
On‐line handwritten signature verification using stroke direction coding (1996)

A method for the automatic verification of handwritten signatures
is described. The method relies on global and local features that
summarize aspects of signature shape and dynamics of signature production.
We demonstrate that with the addition of our local feature based
on stroke direction coding, the performance of signature verification improves
significantly. The improvement is comparable with that of more
sophisticated algorithms, which require much more computer resources.
The current version of the program needs about 150 bytes to store a
signature model and has 3% equal error rate. At the 1% false rejection
point, the addition of the stroke direction information to the algorithm with
only global features reduces the false acceptance rate from 13 to 7.5%.
Prior to extraction of stroke direction information, signatures are normalized
for position, size, and orientation using their Fourier transform. Such
a scheme can also be useful in signature smoothing and compression.
Convolutional self doubly orthogonal codes for iterative decoding without interleaving (2002)

We present a novel turbo error control technique which circumvents both the complexity and latency shortcomings of the usual turbo codes. It differs from usual turbo coding techniques as if uses single encoder and a single decoder. The technique is based on a novel class of orthogonal threshold decodable codes called convolutional self doubly orthogonal codes (CSO/sup 2/C) which do not require interleaving.
Ultrafast mode-locked optical frequency Kerr comb oscillators (2014)

Recently, continuous-wave pumped monolithic microresonators have been examined as an alternative platform for frequency comb and ultrashort pulse generation. With a delicate balance of anomalous group velocity dispersion (GVD) and self-phase modulation, optical solitons can be formed in these microresonators and remarkable broad optical bandwidths and RF-optical stability have been demonstrated. Here we report the first observations of coherent broadband frequency combs and ultrashort pulse generation from on-chip normal group-velocity dispersion microresonators. The observation is supported by phase noise characterization, direct frequency-resolved optical gating pulse measurement, and first-principles nonlinear coupled-mode modeling. All comb spectral lines are collected in our frequency-resolved optical gating pulse measurement and the phase-retrieved pulses demonstrate mode-locking down to 74 fs, one of the shortest frequency comb pulses on-chip to date. Nonlinear coupled-mode modeling of the comb growth and dynamics, with the measured normal group velocity dispersion and quality factor, confirms the feasibility of frequency comb and ultrashort pulse generation. We show, through measurements and theory, the physical mechanisms and basis for ultrafast mode-locking in Kerr comb oscillators.
Suppression of even-order photodiode distortions via predistortion linearization with a bias-shifted Mach-Zehnder modulator (2013)

A new technique to cancel photodiode-induced even-order distortion in microwave photonic links is demonstrated. A single Mach-Zehnder modulator, biased slightly away from the quadrature point, is shown to suppress photodiode second-order intermodulation distortion in excess of 40 dB without affecting the fundamental power. The technique is theoretically described with supporting experimental results.
Thermal conductivity reduction by nanophononic metamaterials (2014)

Engineered manipulation of phonons can yield beneficial thermal properties in semiconducting materials. One pivotal application relates to thermoelectric materials, or the concept of conversion of a temperature difference into an electric voltage and vice-versa. The ability to use nanostructuring to reduce the thermal conductivity without negatively impacting the power factor provides a promising avenue for achieving high values of the thermoelectric energy conversion figure-of-merit, ZT. In this work, we propose a novel nanostructured material configuration that seeks to achieve this goal. Termed "nanophononic metamaterial," the configuration is based on a silicon thin-film with a periodic array of pillars erected on one or two of the free surfaces. The pillars qualitatively alter the base thin-film phonon spectrum due to a hybridization mechanism between their local resonances and the underlying atomic lattice dispersion. Using an experimentally-fitted lattice dynamics- based model, we conservatively predict a drop in the thermal conductivity to as low as 50% of the corresponding uniform thin-film value despite the fact that the pillars add more phonon modes to the spectrum.
Large, identical, tandem repeating units in the C protein alpha antigen gene, bca, of group B streptococci. (1992)

Group B Streptococcus (GBS) is the leading cause of neonatal sepsis and meningitis in the United States. The surface-associated C protein alpha antigen of GBS is thought to have a role in both virulence and immunity. We previously cloned the C protein alpha antigen structural gene (named bca for group B, C protein, alpha) into Escherichia coli. Western blots of both the native alpha antigen and the cloned gene product demonstrate a regularly laddered pattern of heterogeneous polypeptides. The nucleotide sequence of the bca locus reveals an open reading frame of 3060 nucleotides encoding a precursor protein of 108,705 Da. Cleavage of a putative signal sequence of 41 amino acids yields a mature protein of 104,106 Da. The 20,417-Da N-terminal region of the alpha antigen shows no homology to previously described protein sequences and is followed by a series of nine tandem repeating units that make up 74% of the mature protein. Each repeating unit is identical and consists of 82 amino acids with a molecular mass of 8665 Da, which is encoded by 246 nucleotides. The size of the repeating units corresponds to the observed size differences in the heterogeneous ladder of alpha C proteins expressed by GBS. The C-terminal region of the alpha antigen contains a membrane anchor domain motif that is shared by a number of Gram-positive surface proteins. The large region of identical repeating units in bca defines protective epitopes and may play a role in generating phenotypic and genotypic diversity of the alpha antigen.
Dual work function metal gate CMOS transistors by Ni-Ti interdiffusion (2002)

In this letter, we present dual work function metal gate complementary metal-oxide semiconductor (CMOS) transistors with thin SiO/sub 2/ gate dielectric fabricated through the interdiffusion of nickel and titanium. The threshold voltage of the n-MOS devices is determined solely by Ti, while the threshold voltage of the p-MOS devices is determined by the Ni-rich alloy of Ti and Ni. The advantage of this new approach is that low threshold voltages for surface-channel n-MOS and p-MOS transistors can be achieved simultaneously. At the same time, the integrity of the gate dielectric is preserved since no metal has to be etched from the surface of the gate dielectric. With gate depletion eliminated, these transistors exhibit high inversion charge and drive current.
Sensing and metrological applications of holography (2011)

An analyte or measurand may change the diffraction efficiency of a hologram or the colour of a reflection hologram. The formation of a holographic grating can itself be a sensing action. Holographic optical elements (HOEs) can provide the reference and object beams in an unbalanced, out-of-plane sensitive, electronic speckle pattern interferometer for metrology, with wavelength modulation enabling the fringe analysis.
Double-Jet Film-Cooling for Highly Efficient Film-Cooling With Low Blowing Ratios (2008)

Further improvement of the thermal efficiency of modern gas turbines can be achieved by a further reduction of the cooling air amount. Therefore, it is necessary to increase the cooling effectiveness so that the available cooling air fulfils the cooling task even if the amount has been reduced. In particular, the cooling effort for the vanes and blades of the first stage in a modern gas turbine is very high. The task of the film-cooling is to protect the blade material from the hot gas attack to the surface. Unfortunately, aerodynamic mixing processes are enhanced by secondary vortices in the cooling jets and, thus, the film-cooling effectiveness is reduced shortly behind the cooling air ejection through the holes. By improvement of the hole positioning the negative interaction effects can be reduced. The Double-jet Film-cooling (DJFC) Technology invented by the authors is one method to reach a significant increase in film-cooling effectiveness by establishing an anti-kidney vortex pair in a combined jet from the two jets starting from cylindrical ejection holes. This has been shown by numerical investigations and application to an industrial gas turbine as reported in recent publications. Whereas the original design application has been for moderate and high blowing ratios, the present numerical investigation shows that the DJFC is also applicable for lower blowing ratios (0.5&lt;M&lt;1.0) with only slight modification of the geometry of the configuration. The anti-kidney vortex concept can also be established for the lower blowing ratios and, as a result, a very high film-cooling effectiveness is reached not only behind the ejection holes but also for a very long distance downstream (&gt; 30 hole diameters).
Active glass nanoparticles by ultrafast laser pulses (2008)

The authors have successfully demonstrated a method employing pulsed-laser ablation of active glass to produce nanoparticles exhibiting upconversion, pumped by near-infrared wavelengths and emitting visible light. A high repetition rate ultrashort pulsed laser was used to ablate glass under atmospheric conditions. Ejected particles collected were analysed by electron microscopy to determine particle size and characterise the morphology. The measured mean particle diameter was ∼17 nm. A bright upconversion green emission was observed from the nanoparticles almost in a similar fashion as from the bulk specimen. The upconversion photoluminescence characteristics have been investigated to explore potential applications for efficient bioimaging and light-emitting devices.
A Thermophilic Phage Endolysin Fusion to a Clostridium perfringens-Specific Cell Wall Binding Domain Creates an Anti-Clostridium Antimicrobial with Improved Thermostability (2015)

Clostridium perfringens is the third leading cause of human foodborne bacterial disease and is the presumptive etiologic agent of necrotic enteritis among chickens. Treatment of poultry with antibiotics is becoming less acceptable. Endolysin enzymes are potential replacements for antibiotics. Many enzymes are added to animal feed during production and are subjected to high-heat stress during feed processing. To produce a thermostabile endolysin for treating poultry, an E. coli codon-optimized gene was synthesized that fused the N-acetylmuramoyl-L-alanine amidase domain from the endolysin of the thermophilic bacteriophage ɸGVE2 to the cell-wall binding domain (CWB) from the endolysin of the C. perfringens-specific bacteriophage ɸCP26F. The resulting protein, PlyGVE2CpCWB, lysed C. perfringens in liquid and solid cultures. PlyGVE2CpCWB was most active at pH 8, had peak activity at 10 mM NaCl, 40% activity at 150 mM NaCl and was still 16% active at 600 mM NaCl. The protein was able to withstand temperatures up to 50° C and still lyse C. perfringens. Herein, we report the construction and characterization of a thermostable chimeric endolysin that could potentially be utilized as a feed additive to control the bacterium during poultry production.