gebhart/patrepeval huggingface dataset:
Trellis-based R-D optimal quantization in H.263+ (2000)

We describe a trellis-based algorithm which enables R-D optimum quantization decisions in the H.263+ video coding standard. The use of the trellis allows the quantization decisions for all coefficients in a block to be made jointly, and contrasts with more commonly used R-D optimizations which operate on one coefficient at a time. Experiments conducted using H.263+ for video coding rates of 40-50 kbps show an average improvement of 3.5% in bit rate, or equivalently 0.17 dB in PSNR, relative to implementations which follow the International Telecommunications Union (ITU) Test Model specifications in making quantization decisions.
Photoaffinity Labeling Analysis of the Interaction of Pituitary Adenylate‐Cyclase‐Activating Polypeptide (PACAP) with the PACAP Type I Receptor (1997)

To identify residues and domains of the peptide hormone pituitary adenylate-cyclase-activating polypeptide (PACAP) that interact with the type I receptor, two photoreactive analogues of PACAP-(1-27)-peptide were synthesized using solid-phase peptide synthesis. Phe6 or Tyr22 within the PACAP sequence were replaced by p-benzoyl-L-phenylalanine (Bz-Phe) thus creating two PACAP derivatives with a photoreactive amino acid in either the disordered N-terminal or the helical C-terminal part of the peptide. The ligand-binding properties and the efficiencies of these peptide analogues as photolabels were tested for pig brain PACAP receptors. [Bz-Phe6]-PACAP-(1-27)-peptide (Kd 1.3 nM) retained the high binding affinity of PACAP-(1-27)-peptide (Kd 0.5 nM), wheras Bz-Phe substitution of Tyr22 reduced the affinity about tenfold (Kd 4.4 nM) thus demonstrating the importance of Tyr22 for receptor binding. Monoiodination of the photoreactive analogues did not change the binding affinity of the photoreactive analogues. Photoaffinity labeling using pig brain membrane demonstrated that the 125I-labeled photoreactive analogues specifically label a 66000-Mr protein band. Photoaffinity labeling of the rat brain PACAP receptor expressed in COS cells resulted in two specifically photolabeled proteins: a major band of Mr 58000 and a minor band of Mr 78000. By treatment of photolabeled membranes with N-glycosidase F, both of the polypeptide bands were converted to a single polypeptide band of Mr 54000, which corresponds to the deglycosylated PACAP receptor. Despite its lower receptor affinity, [Bz-Phe22]-PACAP-(1-27)-peptide labeled the PACAP type I receptor in pig brain membranes and the rat receptor expressed in COS cells with much higher efficiency (20-fold for the pig receptor) than [Bz-Phe6]-PACAP-(1-27)-peptide. These findings suggest that Tyr22 in PACAP-(1-27)-peptide is located in or close to the hormone-binding site of the PACAP type I receptor. The results provide evidence that the alpha-helical C-terminal region of PACAP is directly involved in receptor binding.
Single-shot ultrafast optical imaging (2018)

Single-shot ultrafast optical imaging can capture two-dimensional transient scenes in the optical spectral range at ≥100 million frames per second. This rapidly evolving field surpasses conventional pump-probe methods by possessing the real-time imaging capability, which is indispensable for recording non-repeatable and difficult-to-reproduce events and for understanding physical, chemical, and biological mechanisms. In this mini-review, we survey comprehensively the state-of-the-art single-shot ultrafast optical imaging. Based on the illumination requirement, we categorized the field into active-detection and passive-detection domains. Depending on the specific image acquisition and reconstruction strategies, these two categories are further divided into a total of six sub-categories. Under each sub-category, we describe operating principles, present representative cutting-edge techniques with a particular emphasis on their methodology and applications, and discuss their advantages and challenges. Finally, we envision prospects of technical advancement in this field.
Amino‐ and carboxyl‐terminal mutants of presenilin 1 cause neuronal cell death through distinct toxic mechanisms: Study of 27 different presenilin 1 mutants (2003)

Presenilin (PS)1 and its mutants, which consist of the N-terminal and C-terminal fragments, cause certain familial forms of Alzheimer's disease (FAD). Our earlier studies found that FAD-linked M146L-PS1 causes neuronal cell death through nitrogen oxide synthase (NOS) and that FAD-linked N141I-PS2, another member of the PS family, causes neuronal cell death through NADPH oxidase. In this study, we examined 27 different FAD-linked mutants of PS1, and found that PS1 mutants with mutations in the N-terminal fragment caused NOS inhibitor (NOSI)-sensitive neuronal cell death; in contrast, the PS1 mutants with mutations in the C-terminal fragment caused NOSI-resistant neuronal cell death. The former toxicity was resistant to the specific NADPH oxidase inhibitor apocynin and was inhibited by Humanin (HN), a newly identified neuroprotective factor against Alzheimer's disease (AD)-relevant insults, but not by insulin-like growth factor-I (IGF-I). In contrast, the latter toxicity was sensitive to apocynin and inhibited by both IGF-I and HN. This study indicates for the first time that N- and C-terminal fragment PS1 mutants can generate distinct neurotoxic signals, which will provide an important clue to the understanding of the entire array of neurotoxic signals generated by FAD-causative mutations of PS1.
MR imaging of articular cartilage using driven equilibrium (1999)

The high incidence of osteoarthritis and the recent advent of several new surgical and non-surgical treatment approaches have motivated the development of quantitative techniques to assess cartilage loss. Although magnetic resonance (MR) imaging is the most accurate non-invasive diagnostic modality for evaluating articular cartilage, improvements in spatial resolution, signal-to-noise ratio (SNR), and contrast-to-noise ratio (CNR) would be valuable. Cartilage presents an imaging challenge due to its short T(2) relaxation time and its low water content compared with surrounding materials. Current methods sacrifice cartilage signal brightness for contrast between cartilage and surrounding tissue such as bone, bone marrow, and joint fluid. A new technique for imaging articular cartilage uses driven equilibrium Fourier transform (DEFT), a method of enhancing signal strength without waiting for full T(1) recovery. Compared with other methods, DEFT imaging provides a good combination of bright cartilage and high contrast between cartilage and surrounding tissue. Both theoretical predictions and images show that DEFT is a valuable method for imaging articular cartilage when compared with spoiled gradient-recalled acquisition in the steady state (SPGR) or fast spin echo (FSE). The cartilage SNR for DEFT is as high as that of either FSE or SPGR, while the cartilage-synovial fluid CNR of DEFT is as much as four times greater than that of FSE or SPGR. Implemented as a three-dimensional sequence, DEFT can achieve coverage comparable to that of other sequences in a similar scan time. Magn Reson Med 42:695-703, 1999.
Secretion and autoproteolytic maturation of subtilisin. (1986)

The sequence of the cloned Bacillus amyloliquefaciens subtilisin gene suggested that this secreted serine protease is produced as a larger precursor, designated preprosubtilisin [Wells, J. A., Ferrari, E., Henner, D. J., Estell, D. A. & Chen, E. Y. (1983) Nucleic Acids Res. 11, 7911-7925]. Biochemical evidence presented here shows that a subtilisin precursor is produced in Bacillus subtilis hosts. The precursor is first localized in the cell membrane, reaching a steady-state level of approximately equal to 1000 sites per cell. Mutations in the subtilisin gene that alter a catalytically critical residue (i.e., aspartate +32----asparagine), or delete the carboxyl-terminal portion of the enzyme that contains catalytically critical residues, block the maturation of this precursor. This block occurs when these mutant genes are expressed in B. subtilis hosts where the chromosomal subtilisin gene has been deleted. When the mutant B. amyloliquefaciens subtilisins are expressed in B. subtilis hosts that contain an intact chromosomal subtilisin gene, the mutant precursors are processed to a mature form and released to the medium. Such processing, in trans, of the precursor is also demonstrated in vitro by addition of active subtilisin. Thus, the release of subtilisin from the cell membrane is dependent on an autoproteolytic process that appears to be novel among secreted proteins.
Crystallization and preliminary X-ray analysis of B-domain fragments of a Staphylococcus aureus collagen-binding protein (1999)

Recombinant proteins of monomeric and dimeric B-domain repeats of a Staphylococcus aureus FDA 574 collagen-binding adhesin have been crystallized. The single repeat unit (B1) was crystallized in a body-centered orthorhombic lattice with a = 96.9, b = 101.3, c = 120. 8 A in either the I222 or I212121 space group. These crystals diffracted to 2.5 A resolution and the calculated Vm values of 3.2 and 2.2 A3 Da-1 suggest the possibility of a dimer or a trimer in the asymmetric unit. The two-repeat fragment (B1B2) crystallized in the orthorhombic space group P212121 with cell dimensions a = 42.4, b = 79.4, c = 130.4 A and diffracted to 2.3 A resolution. For this species, the calculated Vm value of 2.2 A3 Da-1 indicates the presence of a monomer in the asymmetric unit.
Dkk1 Stabilizes Wnt Co-Receptor LRP6: Implication for Wnt Ligand-Induced LRP6 Down-Regulation (2010)

Our results reveal a novel role for Dkk1 in preventing Wnt ligand-induced LRP6 down-regulation and contribute significantly to our understanding of Dkk1 function in Wnt/LRP6 signaling.
Cloning, sequencing and expression of subtilisin Carlsberg fromBacillus licheniformis (1985)

The gene encoding subtilisin Carlsberg from Bacillus licheniformis has been isolated by molecular cloning using a mixture of synthetic oligonucleotides. The entire nucleotide sequence of the coding sequence as well as 5' and 3' flanking sequences have been determined. The deduced amino acid sequence reveals an N-terminal signal peptide consisting of 29 residues, a pro-peptide of 76 residues followed by the mature protein comprising 274 residues. The ATG initiator codon is preceded by two putative overlapping ribosomal binding sequences. A palindromic sequence typical for transcription termination is found downstream from the TAA stop codon. Structural comparisons between different known subtilisin genes reveal extensive homology, particularly in the parts coding for the pro-region and the mature protein. Expression studies in Bacillus subtilis show that the cloned fragment produces a functional enzyme when inserted after a B. subtilis promoter.
Intravascular Adenovirus-Mediated VEGF-C Gene Transfer Reduces Neointima Formation in Balloon-Denuded Rabbit Aorta (2000)

Adenovirus-mediated VEGF-C gene transfer may be useful for the treatment of postangioplasty restenosis and vessel wall thickening after vascular manipulations.
Wideband acoustic wave resonators composed of hetero acoustic layer structure (2018)

"Hetero acoustic layer (HAL) surface acoustic wave (SAW) device" is a new type of SAW device using a single crystal piezoelectric thin plate supported by a substrate. In this study, a HAL SAW resonator using a LiNbO3 (LN) thin plate and a multi-layer acoustic film was designed by finite element method (FEM) and fabricated. The thickness of LN is 3.6 µm and the pitch of an interdigital transducer (IDT) (λ) is 5.24 µm for a resonance frequency of 600 MHz. The multi-layer acoustic film is composed of 3 layers of SiO2 and AlN for each, i.e., 6 layers in total, alternately deposited on a glass substrate. The HAL SAW resonator achieved a wide bandwidth of 20.3% and a high impedance ratio of 83 dB. Compared with a 0th shear horizontal (SH0) mode plate wave resonator, the performance is better and the thickness of LN is 7 times larger. The HAL SAW without a cavity is advantageous in terms of mechanical stability, thickness controllability and fabrication yield.
Local lung responses following local lung challenge with recombinant lungworm antigen in systemically sensitized sheep (2001)

Mast cell phenotypic events occurring as a consequence of antigen challenge were limited to segments in which changes in BALF were characterized by neutrophil influx and increased local antibody production.
An effective hash-based algorithm for mining association rules (1995)

In this paper, we examine the issue of mining association rules among items in a large database of sales transactions. The mining of association rules can be mapped into the problem of discovering large itemsets where a large itemset is a group of items which appear in a sufficient number of transactions. The problem of discovering large itemsets can be solved by constructing a candidate set of itemsets first and then, identifying, within this candidate set, those itemsets that meet the large itemset requirement. Generally this is done iteratively for each large k -itemset in increasing order of k where a large k -itemset is a large itemset with k items. To determine large itemsets from a huge number of candidate large itemsets in early iterations is usually the dominating factor for the overall data mining performance. To address this issue, we propose an effective hash-based algorithm for the candidate set generation. Explicitly, the number of candidate 2-itemsets generated by the proposed algorithm is, in orders of magnitude, smaller than that by previous methods, thus resolving the performance bottleneck. Note that the generation of smaller candidate sets enables us to effectively trim the transaction database size at a much earlier stage of the iterations, thereby reducing the computational cost for later iterations significantly. Extensive simulation study is conducted to evaluate performance of the proposed algorithm.
Diversity of Human αβ T Cell Receptors (2000)

(a = alpha)&#13;\nArstila et al. (1) estimated an average diversity&#13;\nof 9 * 10^5 different b chains and 4.5 *&#13;\n10^5 different a chains in the human nai¨ve T&#13;\ncell repertoire. To calculate the total T cell&#13;\nrepertoire diversity, the b-chain diversity was&#13;\nestimated within a certain variable (V) gene&#13;\nfamily, Va12^+, comprising 2.5% of the total&#13;\na-chain repertoire. Finding in this particular&#13;\nfamily an estimated total of 6 * 105 different&#13;\nß chains (i.e., two-thirds of the total ß-chain&#13;\nrepertoire), Arstila et al. suggested that the&#13;\ntotal T cell receptor (TCR) diversity comprises&#13;\nat least (6 * 105) * 40 = 2.4 * 10^7&#13;\ndifferent aß combinations (1). The authors&#13;\nacknowledge that this is only a lower bound,&#13;\nbecause the calculation assumes that the ß&#13;\nchains that do bind at least one Va12 chain&#13;\nbind only one of the 4.5 * 10^5 different a&#13;\nchains in the Va12^+ family. If each ß chain&#13;\nfound within the Va12^+ family were to bind&#13;\nan average of n different Va12 chains instead,&#13;\nthe total estimated TCR diversity would be&#13;\nn-fold higher than this lower bound.
Histone Deacetylase Inhibitors for Purging HIV-1 from the Latent Reservoir (2011)

A reservoir of latently infected memory CD4(+) T cells is believed to be the source of HIV-1 reemergence after discontinuation of antiretroviral therapy. HIV-1 eradication may depend on depletion of this reservoir. Integrated HIV-1 is inaccessible for expression, in part because of histone deacetylases (HDACs). One approach is to exploit the ability of HDAC inhibitors to induce HIV-1 expression from an integrated virus. With effective antiretroviral therapy, newly expressed HIV-1 is incapable of reinfecting naive cells. With HIV-1 expression, one assumes the infected cell dies and there is a progressive reduction in the size of the reservoir. The concept was tested using the HDAC inhibitor valproic acid. However, valproic acid is weak in inducing HIV-1 from latency in vitro. As such, clinical trials revealed a small or no effect on reducing the number of latently infected T cells in the peripheral blood. However, the new HDAC inhibitors vorinostat, belinostat and givinostat are more effective at targeting specific HDACs for HIV-1 expression than valproic acid. Here, we review studies on HDAC inhibitor-induced expression of latent HIV-1, with an emphasis on new and specific HDAC inhibitors. With increased potency for HIV-1 expression as well as safety and ease of oral administration, new HDAC inhibitors offer a unique opportunity to deplete the latent reservoir. An additional benefit is the antiinflammatory properties of HDAC inhibitors, including downregulation of HIV-1 coreceptor expression.
A new twist on plasma membrane repair (2011)

Cells in multicellular organisms are under constant mechanical stress, and often the plasma membrane (PM) is compromised. Fortunately, there is a vigorous repair mechanism that rapidly (within seconds) reseals the wound site by fusion with an internal membrane patch. Downstream events, remodeling of the injury site and forming replacement PM, must be carried out quickly (within minutes) if a cell is to survive multiple sequential injuries. The repertoire of proteins required to repair breaks (the PM repairome) is one of the major unknowns in this area of research. As an initial approach to defining the PM repairome, a cell surface biotinylation protocol was developed to identify intracellular proteins that become exposed at the site of reversible PM injury. It is likely that at least some of these proteins are important mediators of repair. These initial studies led to a surprising finding, namely the identification of some nuclear and endoplasmic reticulum resident proteins transiently exposed at the surface of cells that ultimately recovered from PM damage. Thus, in reversible mechanical damage to the PM, underlying cellular structures may also be injured, and will also require mechanisms for repair. Other proteins at wound sites were previously identified docking partners for pathogenic bacteria and viruses (vimentin and nucleolin), or found to be upregulated and exposed on the surface of cancer cells (nucleolin and nucleophosmin-1). The new information from these studies may lead to development of novel antimicrobial and antineoplastic drugs.
Ultra Temperature-Stable Bulk-Acoustic-Wave Resonators with SiO 2 Compensation Layer (2007)

This paper describes temperature compensated bulk acoustic-wave resonators (BAR) with temperature coefficient of frequency (TCF) less than 1 ppm/degrees C at above 3 GHz. The temperature compensation is produced from the unique physical property of silicon dioxide's positive TCF, unlike most other materials that have negative TCF. Two types of resonators have been explored: film bulk acoustic resonator (FBAR) composed of Al/ZnO/Al/SiO2 on a surface micromachined cantilever that is released by XeF2 vapor etching and high-overtone acoustic resonator (HBAR) composed of an Al/ZnO/Al resonator on a bulk micromachined SiO2/Si/SiO2 supporting substrate.
The prevalence and characteristics of chronic ocular itch: a cross-sectional survey (2017)

Chronic ocular itch is common and may be related to ophthalmologic or dermatologic pathologies. The present findings highlight the importance of identifying and managing this uncomfortable symptom that may negatively impact the quality of life and sleep of affected patients.
Structure and function of declarative and nondeclarative memory systems (1996)

This article reviews recent studies of memory systems in humans and nonhuman primates. Three major conclusions from recent work are that (i) the capacity for nondeclarative (nonconscious) learning can now be studied in a broad array of tasks that assess classification learning, perceptuomotor skill learning, artificial grammar learning, and prototype abstraction; (ii) cortical areas adjacent to the hippocampal formation, including entorhinal, perirhinal, and parahippocampal cortices, are an essential part of the medial temporal lobe memory system that supports declarative (conscious) memory; and (iii) in humans, bilateral damage limited to the hippocampal formation is nevertheless sufficient to produce severe anterograde amnesia and temporally graded retrograde amnesia covering as much as 25 years.
Evidence for metalloproteinase and metalloproteinase inhibitor imbalance in human osteoarthritic cartilage. (1989)

Cartilage specimens from tibial plateaus, obtained from 13 osteoarthritic (OA) patients and seven controls, were selected from three regions: zone A, center of fibrillated area; zone B, area adjacent to fibrillation, and zone C, remote region of plateau. Acid and neutral metalloproteinases and tissue inhibitor of metalloproteinase (TIMP) were extracted with 2 M guanidine. Methods were developed to selectively destroy either proteinases or TIMP to prevent cross-reaction during assay. Acid and neutral proteinases were elevated approximately 150% in OA; TIMP was elevated approximately 50%. A positive correlation (r = 0.50) was found between acid and neutral proteinase activities in OA, but not in controls. Both proteinases were elevated two-to threefold in zones A, B, and C. However, the self-active form of the acid metalloproteinase was elevated only in zones A and B (200%); it correlated well with the Mankin scores, whereas the total activities did not. TIMP was elevated (50%) only in zones A and B. Both the proteinase levels and the Mankin score were elevated to a greater extent in the medial, than in the lateral, compartment. Titration of TIMP against the two metalloproteinases indicates that there is a small excess of inhibitor over enzymes in normal cartilage. In OA, TIMP does not increase to the same extent as the proteinases; the resultant excess of proteinases over TIMP may contribute to cartilage breakdown.
Neuropilin-1 promotes Hedgehog signaling through a novel cytoplasmic motif (2017)

Hedgehog (HH) signaling critically regulates embryonic and postnatal development as well as adult tissue homeostasis, and its perturbation can lead to developmental disorders, birth defects, and cancers. Neuropilins (NRPs), which have well-defined roles in Semaphorin and VEGF signaling, positively regulate HH pathway function, although their mechanism of action in HH signaling remains unclear. Here, using luciferase-based reporter assays, we provide evidence that NRP1 regulates HH signaling specifically at the level of GLI transcriptional activator function. Moreover, we show that NRP1 localization to the primary cilium, a key platform for HH signal transduction, does not correlate with HH signal promotion. Rather, a structure-function analysis suggests that the NRP1 cytoplasmic and transmembrane domains are necessary and sufficient to regulate HH pathway activity. Furthermore, we identify a previously uncharacterized, 12-amino acid region within the NRP1 cytoplasmic domain that mediates HH signal promotion. Overall, our results provide mechanistic insight into NRP1 function within and potentially beyond the HH signaling pathway. These insights have implications for the development of novel modulators of HH-driven developmental disorders and diseases.
Resting frontal brain asymmetry predicts affective responses to films. (1990)

This article assessed whether resting electroencephalographic (EEG) asymmetry in anterior regions of the brain can predict affective responses to emotion elicitors. Baseline EEG was recorded from 32 female adults, after which Ss viewed film clips preselected to elicit positive or negative affect. Resting alpha power asymmetry in the frontal region significantly predicted self-reported global negative affect in response to clips and predicted the difference between global positive and negative affect. Analyses of discrete emotions revealed a strong relation between frontal asymmetry and fear responses to films. Effects were independent of Ss mood ratings at the time at which baseline EEG was measured. Resting anterior asymmetry may be a state-independent index of the individual's predisposition to respond affectively.