gebhart/patrepeval huggingface dataset:
TACOMA MOVES TO ENHANCE POSITION AS A KEY CARGO HUB (2003)

The port of Tacoma, Washington, is moving to consolidate its position as a critical cargo hub and stands to become the largest container terminal on the West Coast north of Los Angeles. That distinction will come with the completion of an expansion of Taiwan-based Evergreen Marine Corp. that will cost $355 million in new facilities and locations within the port. Tacoma surpassed Seattle for the first time at the end of 2001 in container volume. To continue to expand its container business, the port is remodeling the Pierce County terminal, at a cost of $300 million, in addition to Evergreen's plan to spend $55 million on new equipment and sign a 20-year lease. The terminal work will start after completion of a new $40-million auto storage facility. Also in the works are new grade separations and improvements in rail freight facilities linked to the port. Seattle, while still committed to cargo business, is also refitting its terminal for cruise ships. It has also invested in container facilities that give it double the capacity it handles now.
MaizeRouter: Engineering an Effective Global Router (2008)

In this paper, we present the complete design and architectural details of MaizeRouter. MaizeRouter reflects a significant leap in progress over existing publicly available routing tools yet relies upon relatively simple operations, including <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">extreme</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">edge</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">shifting</i> , a technique aimed primarily at the efficient reduction of routing congestion, and <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">edge</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">retraction</i> , a counterpart to extreme edge shifting that serves to reduce unnecessary wirelength. We present enhanced variations of these operations to enable the <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">rapid</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">exploration</i> of candidate paths, along with a form of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">dynamic</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">cost</i> <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">deflation</i> that provides our various path computation procedures with progressively more accurate (and less optimistic) cost information as search continues. These algorithmic contributions are built upon a framework of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">interdependent</i> net decomposition, a representation that improves upon traditional two-pin net decomposition by preventing duplication of routing resources while enabling cheap and incremental topological reconstruction. Collectively, these operations permit a broad search space that previous algorithms have been unable to achieve, resulting in solutions of considerably higher quality than those of well-established routers.
Optical Properties of Colloidal PbSe Nanocrystals (2002)

We present the structural and optical characterization of colloidal PbSe nanocrystals. The lowest-energy exciton transitions in these structures, with diameters between 3 and 8 nm, occur at wavelengths between 1.0 and 1.85 μm. Band-edge luminescence spectra with quantum yields as high as 80% are observed. Unexpectedly long (∼300 ns) luminescence lifetimes are observed. These properties are promising for applications in optoelectronics and microscopy.
Membrane characteristics tune activities of endosomal and autophagic human VPS34 complexes (2020)

The lipid kinase VPS34 orchestrates diverse processes, including autophagy, endocytic sorting, phagocytosis, anabolic responses and cell division. VPS34 forms various complexes that help adapt it to specific pathways, with complexes I and II being the most prominent ones. We found that physicochemical properties of membranes strongly modulate VPS34 activity. Greater unsaturation of both substrate and non-substrate lipids, negative charge and curvature activate VPS34 complexes, adapting them to their cellular compartments. Hydrogen/deuterium exchange mass spectrometry (HDX-MS) of complexes I and II on membranes elucidated structural determinants that enable them to bind membranes. Among these are the Barkor/ATG14L autophagosome targeting sequence (BATS), which makes autophagy-specific complex I more active than the endocytic complex II, and the Beclin1 BARA domain. Interestingly, even though Beclin1 BARA is common to both complexes, its membrane-interacting loops are critical for complex II, but have only a minor role for complex I.
Fluorescence-enhanced optical imaging in large tissue volumes using a gain-modulated ICCD camera (2003)

A novel image-intensified charge-coupled device (ICCD) imaging system has been developed to perform 3D fluorescence tomographic imaging in the frequency-domain using near-infrared contrast agents. The imager is unique since it (i) employs a large tissue-mimicking phantom, which is shaped and sized to resemble a female breast and part of the extended chest-wall region, and (ii) enables rapid data acquisition in the frequency-domain by using a gain-modulated ICCD camera. Diffusion model predictions are compared to experimental measurements using two different referencing schemes under two different experimental conditions of perfect and imperfect uptake of fluorescent agent into a target. From these experimental measurements, three-dimensional images of fluorescent absorption were reconstructed using a computationally efficient variant of the approximate extended Kalman filter algorithm. The current work represents the first time that 3D fluorescence-enhanced optical tomographic reconstructions have been achieved from experimental measurements of the time-dependent light propagation on a clinically relevant breast-shaped tissue phantom using a gain-modulated ICCD camera.
ASPECTS OF ALCOHOLISM (1964)

ASPECTS OF ALCOHOLISM Jay N. Cross CopyRight https://doi.org/10.2105/AJPH.54.3.544-b Published Online: August 29, 2011
Capsular Penetration in Prostate Cancer. Significance for Natural History and Treatment (1990)

We established the location and extent of complete capsule penetration by prostate cancer in 176 radical prostatectomy specimens and related these findings to cancer volume, location of positive surgical margins, and presence of nodal metastases or seminal vesicle (SV) invasion. Extent of capsule penetration, cancer volume, and positive nodes/SV were strongly intercorrelated. It could not be shown that capsule penetration was related to prognosis independently of its correlation with cancer volume. Twelve cubic centimeters was a critical cancer volume; above that, combinations of extensive capsule penetration, positive surgical margins, and positive nodes/SV were almost universal. In cancers under 12 cc, positive surgical margins were only moderately correlated with cancer volume; they often represented surgical resection into the capsule rather than a complication of capsule penetration by tumor and were most common at the apex, where dissection is most difficult. In non-transition zone cancers (148 cases), capsule penetration was most common posterolaterally, where nerves penetrate the capsule. In transition zone cancers (28 cases), capsule penetration was much less common and was located more anteriorly. Apical positive margins were also relatively common in transition zone cancers, but seminal vesicle invasion was never seen.
Expression of crossreactive idiotypes by human antibodies specific for the capsular polysaccharide of Hemophilus influenzae B. (1988)

Human antibodies specific, for polyribosyl-ribitol-phosphate (PRP), the capsular polysaccharide of Hemophilus influenzae b, were studied using idiotypic analysis. Antisera were prepared against purified F(ab')2 anti-PRP from two unrelated adults, H.H. and P.T. After repeated absorption with IgG myeloma proteins and with PRP-absorbed normal human Ig and donor Ig, anti-idiotypic (anti-Id) sera were obtained that specifically reacted with anti-PRP antibodies. Anti-IdHH and anti-IdPT reciprocally crossreacted with H.H. and P.T. anti-PRP antibodies and F(ab')2 fragments, and also reacted with the serum anti-PRP antibodies from three additional adults unrelated to P.T. and H.H. Both anti-Id sera partially inhibited anti-PRP paratopes but not anti-tetanus toxoid paratopes. PRP did not inhibit anti-Id recognition of shared or crossreactive idiotypic (CRI) determinants. Naturally occurring and PRP immunization-induced anti-PRP antibodies expressed CRI. While CRI titer increased after immunization, the increase was usually less than the rise in total anti-PRP antibody. Quantitative differences in CRI expression were also apparent between natural and immunization-induced H.H. and P.T. anti-PRP antibodies as shown by their differential inhibitability by anti-Id. Our data demonstrate that anti-PRP antibodies from five unrelated adults express CRI determinants that are probably distant from the PRP combining site. Naturally occurring and immunization-induced anti-PRP antibodies share CRI and therefore appear to be clonally related, although immunization apparently induces the expression CRI-negative antibodies as well. These results, taken with previous studies showing restricted and identical anti-PRP isoelectric focusing spectrotypes in unrelated adults, suggest that some PRP-specific V domains are structurally conserved and probably germ-line encoded.
Tiling Nussinov’s RNA folding loop nest with a space-time approach (2019)

An RNA primary structure, or sequence, is a single strand considered as a chain of nucleotides from the alphabet AUGC (adenine, uracil, guanine, cytosine). The strand can be folded onto itself, i.e., one segment of an RNA sequence might be paired with another segment of the same RNA sequence into a two-dimensional structure composed by a list of complementary base pairs, which are close together with the minimum energy. That list is called RNA’s secondary structure and is predicted by an RNA folding algorithm. RNA secondary structure prediction is a computing-intensive task that lies at the core of search applications in bioinformatics. We suggest a space-time tiling approach and apply it to generate parallel cache effective tiled code for RNA folding using Nussinov’s algorithm. Parallel tiled code generated with a suggested space-time loop tiling approach outperforms known related codes generated automatically by means of optimizing compilers and codes produced manually. The presented approach enables us to tile all the three loops of Nussinov’s recurrence that is not possible with commonly known tiling techniques. Generated parallel tiled code is scalable regarding to the number of parallel threads – increasing the number of threads reduces code execution time. Defining speed up as the ratio of the time taken to run the original serial program on one thread to the time taken to run the tiled program on P threads, we achieve super-linear speed up (a value of speed up is greater than the number of threads used) for parallel tiled code against the original serial code up to 32 threads and super-linear speed up scalability (increasing speed up with increasing the thread number) up to 8 threads. For one thread used, speed up is about 4.2 achieved on an Intel Xeon machine used for carrying out experiments.
SsrA-Mediated Tagging in <i>Bacillus subtilis</i> (2001)

A general mechanism in bacteria to rescue stalled ribosomes involves a stable RNA encoded by the ssrA gene. This RNA, termed tmRNA, encodes a proteolytic peptide tag which is cotranslationally added to truncated polypeptides, thereby targeting them for rapid proteolysis. To study this ssrA-mediated mechanism in Bacillus subtilis, a bipartite detection system was constructed that was composed of the HrcA transcriptional repressor and the bgaB reporter gene coding for a heat-stable beta-galactosidase fused to an HrcA-controlled promoter. After the predicted proteolysis tag was fused to HrcA, the reporter beta-galactosidase was expressed constitutively at a high level due to the instability of the tagged HrcA. Replacement of the two C-terminal alanine residues of the tag by aspartate rendered the repressor stable. Replacement of the hrcA stop codon by a transcriptional terminator sequence rendered the protein unstable; this was caused by trans translational addition of the proteolytic tag. Inactivating the B. subtilis ssrA or smpB (yvaI) gene prevented the trans translational tagging reaction. Various protease-deficient strains of B. subtilis were tested for proteolysis of tagged HrcA. HrcA remained stable only in clpX or clpP knockouts, which suggests that this ATP-dependent protease is primarily responsible for the degradation of SsrA-tagged proteins in B. subtilis.
Perfusion magnetic resonance imaging of the liver (2010)

Perfusion magnetic resonance imaging (MRI) studies quantify the microcirculatory status of liver parenchyma and liver lesions, and can be used for the detection of liver metastases, assessing the effectiveness of anti-angiogenic therapy, evaluating tumor viability after anti-cancer therapy or ablation, and diagnosis of liver cirrhosis and its severity. In this review, we discuss the basic concepts of perfusion MRI using tracer kinetic modeling, the common kinetic models applied for analyses, the MR scanning techniques, methods of data processing, and evidence that supports its use from published clinical and research studies. Technical standardization and further studies will help to establish and validate perfusion MRI as a clinical imaging modality.
The <i>Cre1</i> and <i>Cre3</i> Nematode Resistance Genes Are Located at Homeologous Loci in the Wheat Genome (2003)

Differential responses in host-nematode pathotype interactions occur in wheat lines carrying different cereal cyst nematode resistance (Cre) genes. Cre1, located on chromosome 2B, confers resistance to most European nematodes and the sole Australian pathotype, while Cre3, present on chromosome 2D, is highly resistant to the Australian pathotype and susceptible to a number of European pathotypes. Genes encoding nucleotide binding site-leucine rich repeat (NBS-LRR) proteins that cosegregate with the Cre3 locus cross hybridize to homologues whose restriction fragment length polymorphism (RFLP) patterns distinguish near-isogenic Cre1 nematode-resistant wheat lines. Genetic mapping showed that the NBS-LRR gene members that distinguished the Cre1 near-isogenic lines were located on chromosome 2BL at a locus, designated Xcsl107, that cosegregates with the Cre1 locus. A haplotype of NBS-LRR genes from the Xcsl107 locus provides a diagnostic marker for the presence of Cre1 nematode resistance in a wide collection of wheat lines and segregating families. Genetic analysis of NBS-LRR haplotypes that cosegregate with Cre1 and Cre3 resistance, together with flanking cDNA markers and other markers from homoeologous group 2 chromosomes, revealed a conserved gene order that suggests Cre1 and Cre3 are homeoloci.
Computation of the head-related transfer function via the fast multipole accelerated boundary element method and its spherical harmonic representation (2010)

The head-related transfer function (HRTF) is computed using the fast multipole accelerated boundary element method. For efficiency, the HRTF is computed using the reciprocity principle by placing a source at the ear and computing its field. Analysis is presented to modify the boundary value problem accordingly. To compute the HRTF corresponding to different ranges via a single computation, a compact and accurate representation of the HRTF, termed the spherical spectrum, is developed. Computations are reduced to a two stage process, the computation of the spherical spectrum and a subsequent evaluation of the HRTF. This representation allows easy interpolation and range extrapolation of HRTFs. HRTF computations are performed for the range of audible frequencies up to 20 kHz for several models including a sphere, human head models [the Neumann KU-100 ("Fritz") and the Knowles KEMAR ("Kemar") manikins], and head-and-torso model (the Kemar manikin). Comparisons between the different cases are provided. Comparisons with the computational data of other authors and available experimental data are conducted and show satisfactory agreement for the frequencies for which reliable experimental data are available. Results show that, given a good mesh, it is feasible to compute the HRTF over the full audible range on a regular personal computer.
Biological Stability Evaluation of the α2β1 Receptor Imaging Agents: Diamsar and DOTA Conjugated DGEA Peptide (2011)

Robust chelating stability under biological condi-tions is critical for the design of copper-based radiopharmaceuticals. In this study, the stabilities of (64)Cu-DOTA and diamsar (two bifunctional Cu-64 chelators (BFCs)) conjugated DGEA peptides were evaluated. The in vitro stabilities of (64)Cu-DOTA-DGEA, (64)Cu-DOTA-Ahx-DGEA, and (64)Cu-Z-E(diamsar)-Ahx-DGEA were evaluated in PBS. A carboxyl-protected DOTA-DGEA was also synthesized to study the potential inter- and intramolecular interactions between DOTA and the carboxylate groups of DGEA peptide. microPET imaging of (64)Cu-DOTA-DGEA and (64)Cu-Z-E(diamsar)-Ahx-DGEA were performed in PC-3 prostate tumor model to further investigate the in vivo behavior of the tracers. DOTA-DGEA, DOTA-Ahx-DGEA, Z-E(diamsar)-Ahx-DGEA, and protected DOTA-DGEA peptides were readily obtained, and their identities were confirmed by MS. (64)Cu(2+) labeling was performed with high radiochemical yields (>98%) for all tracers after 1 h incubation. Stability experiments revealed that (64)Cu-DOTA-DGEA had unexpectedly high (64)Cu(2+) dissociation when incubated in PBS (>55% free (64)Cu(2+) was observed at 48 h time point). The (64)Cu(2+) dissociation was significantly reduced in the carboxyl-protected (64)Cu-DOTA-DGEA complex but not in the (64)Cu-DOTA-Ahx-DGEA complex, which suggests the presence of competitive binding for (64)Cu(2+) between DOTA and the carboxyl groups of the DGEA peptide. In contrast, no significant (64)Cu(2+) dissociation was observed for (64)Cu-Z-E(diamsar)-Ahx-DGEA in PBS. For microPET imaging, the PC-3 tumors were clearly visualized with both (64)Cu-DOTA-DGEA and (64)Cu-Z-E(diamsar)-Ahx-DGEA tracers. However, (64)Cu-DOTA-DGEA demonstrated 5× higher liver uptake than (64)Cu-Z-E(diamsar)-Ahx-DGEA. This biodistribution variance could be attributed to the chelating stability difference between these two tracers, which correlated well with the PBS stability experiments. In summary, the in vitro and in vivo evaluations of (64)Cu-Z-E(diamsar)-Ahx-DGEA and (64)Cu-DOTA-DGEA have demonstrated the significantly superior Cu-chelation stability for the diamsar derivative compared with the established DOTA chelator. The results also suggest that diamsar may be preferred for Cu chelation especially when multiple carboxylic acid groups are present. Free carboxyl groups may naturally compete with DOTA for (64)Cu(2+) binding and therefore reduce the complex stability.
Caspase-8 activation by TRAIL monotherapy predicts responses to IAPi and TRAIL combination treatment in breast cancer cell lines (2015)

The discovery of cancer cell-selective tumour necrosis factor-related apoptosis inducing ligand (TRAIL)-induced apoptosis generated broad excitement and development of TRAIL receptor agonists (TRA) as potential cancer therapy. Studies demonstrating the synergistic combination effect of SMAC mimetics and TRA further suggested potentially effective treatment in multiple tumour settings. However, predictive biomarkers allowing identification of patients that could respond to treatment are lacking. Here, we described a high throughput combination screen conducted across a panel of 31 breast cancer cell lines in which we observed highly synergistic activity between TRAIL and the inhibitors of apoptosis proteins (IAP) inhibitor (IAPi) AZD5582 in ~30% of cell lines. We detected no difference in the expression levels of the IAPi or TRAIL-targeted proteins or common modulators of the apoptotic pathway between the sensitive and resistant cell lines. Synergistic combination effect of AZD5582 and TRAIL correlated with sensitivity to TRAIL, but not to AZD5582 as a single agent. TRAIL treatment led to significantly greater activity of Caspase-8 in sensitive than in resistant cell lines (P=0.002). The majority (12/14) of AZD5582+TRAIL-resistant cell lines retained a functional cell death pathway, as they were sensitive to AZD5582+TNFα combination treatment. This suggested that failure of the TRAIL receptor complex to transduce the death signal to Caspase-8 underlies AZD5582+TRAIL resistance. We developed a 3D spheroid assay and demonstrated its suitability for the ex vivo analysis of the Caspase-8 activity as a predictive biomarker. Altogether, our study demonstrated a link between the functionality of the TRAIL receptor pathway and the synergistic activity of the IAPi+TRA combination treatment. It also provided a rationale for development of the Caspase-8 activity assay as a functional predictive biomarker that could allow better prediction of the response to IAPi+TRA-based therapies than the analysis of expression levels of protein biomarkers.
Reducing the TCP acknowledgment frequency (2007)

Delayed acknowledgments were introduced to conserve network and host resources. Further reduction of the acknowledgment frequency can be motivated in the same way. However, reducing the dependency on frequent acknowledgments in TCP is difficult because acknowledgments support reliable delivery, loss recovery, clock out new segments, and serve as input when determining an appropriate sending rate. Our results show that in scenarios where there are no obvious advantages of reducing the acknowledgment frequency, performance can be maintained although fewer acknowledgments are sent. Hence, there is a potential for reducing the acknowledgment frequency more than is done through delayed acknowledgments today. Advancements in TCP loss recovery is one of the key reasons that the dependence on frequent acknowledgments has decreased. We propose and evaluate an end-to-end solution, where four acknowledgments per send window are sent. The sender compensates for the reduced acknowledgment frequency using a form of Appropriate Byte Counting. The proposal also includes a modification of fast loss recovery to avoid frequent timeouts.
A 12.8-Gb/s/link Tri-Modal Single-Ended Memory Interface (2012)

This paper presents a tri-modal asymmetric memory controller interface that achieves 12.8-Gbps single-ended (SE) signaling over 3" stripline FR4 traces. The controller can be configured to communicate with commercially available GDDR5 and DDR3 memories at 6.4 and 1.6 Gbps, respectively, with no package change. The interface is equipped with a compact voltage-mode driver with 1-tap pre-emphasis, in the WRITE direction, and a linear equalizer (LEQ) and 1-tap decision feedback equalizer (DFE), in the READ direction, to compensate for channel inter-symbol interference (ISI). The receiver front-end contains a supply noise tracking scheme to mitigate reference voltage (VREF) noise. A tri-VCO PLL and an efficient global clock distribution scheme support a wide range of operating frequencies at low power consumption. Finally, the interface also incorporates two overhead links per byte for data-bus encoding (DBE) experiments to mitigate simultaneous switching noise (SSN). Implemented in a 40-nm CMOS process, the × 16 tri-modal interface achieves an energy efficiency of better than 5.0 mW/Gbps per data link at 12.8 Gbps.