gebhart/patrepeval huggingface dataset:
Parallel Gauss Sieve Algorithm: Solving the SVP in the Ideal Lattice of 128 dimensions. (2013)

Abstract. In this paper, we report that we have solved the shortest vector problem (SVP) over a 128-dimensional lattice, which is currently the highest dimension of the SVP that has ever been solved. The security of lattice-based cryptography is based on the hardness of solving the SVP in lattices. In 2010 Micciancio et al. proposed a Gauss Sieve algorithm for heuristically solving the SVP using list L of Gauss-reduced vectors. Milde et al. proposed a parallel implementation method for the Gauss Sieve algorithm. However, the efficiency of more than 10 threads in their implementation decreases due to a large number of non-Gauss-reduced vectors appearing in the distributed list of each thread. In this paper, we propose a more practical parallelized Gauss Sieve algorithm. Our algorithm deploys an additional Gauss-reduced list V of sample vectors assigned to each thread, and all vectors in list L remain Gauss-reduced by mutually reducing them using all sample vectors in V. Therefore, our algorithm enables the Gauss Sieve algorithm to run without excessive overhead even in a large-scale parallel computation of more than 1,000 threads. Moreover, for speed-up, we use the bi-directional rotation structure of an ideal lattice that makes the generation of additional vectors in the list with almost no additional overhead. Finally, we have succeeded in solving the SVP over a 128-dimensional ideal lattice generated by cyclotomic polynomial x 128 + 1 using about 30,000 CPU hours.
Three dimensional localization of cancerous prostate tissue using backscattering scanning polarization imaging and independent component analysis (2011)

Three-dimensional (3D) localization of human cancerous prostate tissue embedded in normal prostate tissue was demonstrated and characterized using backscattering scanning polarization imaging and independent component analysis (ICA). Backscattering two-dimensional (2D) images of a tissue sample illuminated with a raster scanning laser beam were recorded using a CCD camera to obtain multiple angular views of the target embedded inside the tissue medium. The 3D location of the object was retrieved by matching the leading Independent Component(s) of intensity distribution of images to the numerical propagation of the target to the surface of the tissue medium.
Secernin-1 is a novel phosphorylated tau binding protein that accumulates in Alzheimer’s disease and not in other tauopathies (2019)

We recently identified Secernin-1 (SCRN1) as a novel amyloid plaque associated protein using localized proteomics. Immunohistochemistry studies confirmed that SCRN1 was present in plaque-associated dystrophic neurites and also revealed distinct and abundant co-localization with neurofibrillary tangles (NFTs). Little is known about the physiological function of SCRN1 and its role in Alzheimer's disease (AD) and other neurodegenerative diseases has not been studied. Therefore, we performed a comprehensive study of SCRN1 distribution in neurodegenerative diseases. Immunohistochemistry was used to map SCRN1 accumulation throughout the progression of AD in a cohort of 58 patients with a range of NFT pathology (Abundant NFT, n = 21; Moderate NFT, n = 22; Low/No NFT, n = 15), who were clinically diagnosed as having AD, mild cognitive impairment or normal cognition. SCRN1 accumulation was also examined in two cases with both Frontotemporal Lobar Degeneration (FTLD)-Tau and AD-related neuropathology, cases of Down Syndrome (DS) with AD (n = 5), one case of hereditary cerebral hemorrhage with amyloidosis - Dutch type (HCHWA-D) and other non-AD tauopathies including: primary age-related tauopathy (PART, [n = 5]), Corticobasal Degeneration (CBD, [n = 5]), Progressive Supranuclear Palsy (PSP, [n = 5]) and Pick's disease (PiD, [n = 4]). Immunohistochemistry showed that SCRN1 was a neuronal protein that abundantly accumulated in NFTs and plaque-associated dystrophic neurites throughout the progression of AD. Quantification of SCRN1 immunohistochemistry confirmed that SCRN1 preferentially accumulated in NFTs in comparison to surrounding non-tangle containing neurons at both early and late stages of AD. Similar results were observed in DS with AD and PART. However, SCRN1 did not co-localize with phosphorylated tau inclusions in CBD, PSP or PiD. Co-immunoprecipitation revealed that SCRN1 interacted with phosphorylated tau in human AD brain tissue. Together, these results suggest that SCRN1 is uniquely associated with tau pathology in AD, DS and PART. As such, SCRN1 has potential as a novel therapeutic target and could serve as a useful biomarker to distinguish AD from other tauopathies.
Improved Synthesis of MDL 73811 – A Potent AdoMetDC Inhibitor and Anti-Trypanosomal Compound (2016)

An improved synthesis of MDL 73811 - a potent AdoMetDC (S-adenosylmethionine decarboxylease) inhibitor and anti-trypanosomal compound with in vivo activity has been completed in four steps from commercially available 2',3'-<i>O</i>-isopropylideneadenosine. Utilization of Mitsunobu chemistry was crucial for the reliable and scalable introduction of the 5'-methylamine moiety, which was problematic using traditional activation/displacement chemistry as previously reported. All reactions in this synthesis were run on gram-scale resulting in a five-fold increase in yield over the original synthesis.
Highly Efficient and Broadband Wide-Angle Holography Using Patch-Dipole Nanoantenna Reflectarrays (2014)

We demonstrate wide-angle, broadband, and efficient reflection holography by utilizing coupled dipole-patch nanoantenna cells to impose an arbitrary phase profile on the reflected light. High-fidelity images were projected at angles of 45 and 20° with respect to the impinging light with efficiencies ranging between 40-50% over an optical bandwidth exceeding 180 nm. Excellent agreement with the theoretical predictions was found at a wide spectral range. The demonstration of such reflectarrays opens new avenues toward expanding the limits of large-angle holography.
Trivalent NDV-HXP-S Vaccine Protects against Phylogenetically Distant SARS-CoV-2 Variants of Concern in Mice (2022)

Equitable access to vaccines is necessary to limit the global impact of the coronavirus disease 2019 (COVID-19) pandemic and the emergence of new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants. In previous studies, we described the development of a low-cost vaccine based on a Newcastle Disease virus (NDV) expressing the prefusion-stabilized spike protein from SARS-CoV-2, named NDV-HXP-S. Here, we present the development of next-generation NDV-HXP-S variant vaccines, which express the stabilized spike protein of the Beta, Gamma, and Delta variants of concerns (VOC). Combinations of variant vaccines in bivalent, trivalent, and tetravalent formulations were tested for immunogenicity and protection in mice. We show that the trivalent preparation, composed of the ancestral Wuhan, Beta, and Delta vaccines, substantially increases the levels of protection and of cross-neutralizing antibodies against mismatched, phylogenetically distant variants, including the currently circulating Omicron variant. <b>IMPORTANCE</b> This manuscript describes an extended work on the Newcastle disease virus (NDV)-based vaccine focusing on multivalent formulations of NDV vectors expressing different prefusion-stabilized versions of the spike proteins of different SARS-CoV-2 variants of concern (VOC). We demonstrate here that this low-cost NDV platform can be easily adapted to construct vaccines against SARS-CoV-2 variants. Importantly, we show that the trivalent preparation, composed of the ancestral Wuhan, Beta, and Delta vaccines, substantially increases the levels of protection and of cross-neutralizing antibodies against mismatched, phylogenetically distant variants, including the currently circulating Omicron variant. We believe that these findings will help to guide efforts for pandemic preparedness against new variants in the future.
Expression of 8‐hydroxy‐2′‐deoxyguanosine in chronic liver disease and hepatocellular carcinoma (2003)

Reactive oxygen species may be involved in the progression of chronic liver disease and the occurrence of hepatocellular carcinoma (HCC). To clarify whether clinicopathological findings in liver diseases are related to oxidative DNA damage, hepatic expression of the 8-hydroxy-2'-deoxyguanosine (8-OHdG) was examined in 75 liver disease patients, which included 32 chronic hepatitis (CH), 13 liver cirrhosis (LC) and 30 HCC patients. The CH patients had higher 8-OHdG-positive hepatocytes than LC (P < 0.05). In CH and LC, the number of 8-OHdG-positive hepatocytes was correlated with alanine aminotransferase and asparate aminotransferase (P < 0.01 and P < 0.05, respectively). Of 30 HCC cases, 25 cases (83%) showed stronger immunoreactivity than non-cancerous counterparts. The patients with poorly differentiated HCC had a larger tumor size and higher levels of AFP, and exhibited higher labeling indices of PCNA-, TUNEL- and 8-OHdG-positive cells than those with well and moderately differentiated HCC. Our findings suggest that oxidative DNA damage is increased in association with necroinflammation in chronic liver disease and determination of 8-OHdG is useful in assessing high-grade malignancy in HCC.
Astroglia in Medullary Dorsal Horn (Trigeminal Spinal Subnucleus Caudalis) Are Involved in Trigeminal Neuropathic Pain Mechanisms (2009)

The aim of this study was to investigate whether astroglia in the medullary dorsal horn (trigeminal spinal subnucleus caudalis; Vc) may be involved in orofacial neuropathic pain following trigeminal nerve injury. The effects of intrathecal administration of the astroglial aconitase inhibitor sodium fluoroacetate (FA) were tested on Vc astroglial hyperactivity [as revealed by glial fibrillary acid protein (GFAP) labeling], nocifensive behavior, Vc extracellular signal-regulated kinase phosphorylation (pERK), and Vc neuronal activity in inferior alveolar nerve-transected (IANX) rats. Compared with sham-control rats, a significant increase occurred in GFAP-positive cells in ipsilateral Vc at postoperative day 7 in IANX rats, which was prevented following FA administration. FA significantly increased the reduced head withdrawal latency to high-intensity heat stimulation of the maxillary whisker pad skin in IANX rats, although it did not significantly affect the reduced escape threshold to low-intensity mechanical stimulation of the whisker skin in IANX rats. FA also significantly reduced the increased number of pERK-like immunoreactive cells in Vc and the enhanced Vc nociceptive neuronal responses following high-intensity skin stimulation that were documented in IANX rats, and glutamine administration restored the enhanced responses. These various findings provide the first documentation that astroglia is involved in the enhanced nociceptive responses of functionally identified Vc nociceptive neurons and in the associated orofacial hyperalgesia following trigeminal nerve injury.
PRECISION AND ACCURACY PARAMETERS IN STRUCTURED LIGHT 3-D SCANNING (2016)

Abstract. Structured light systems are popular in part because they can be constructed from off-the-shelf low cost components. In this paper we quantitatively show how common design parameters affect precision and accuracy in such systems, supplying a much needed guide for practitioners. Our quantitative measure is the established VDI/VDE 2634 (Part 2) guideline using precision made calibration artifacts. Experiments are performed on our own structured light setup, consisting of two cameras and a projector. We place our focus on the influence of calibration design parameters, the calibration procedure and encoding strategy and present our findings. Finally, we compare our setup to a state of the art metrology grade commercial scanner. Our results show that comparable, and in some cases better, results can be obtained using the parameter settings determined in this study.
Estimation of the absolute shear stiffness of human lung parenchyma using 1H spin echo, echo planar MR elastography (2013)

The results indicate that stiffness variations due to respiration could be measured with the SE-EPIMRE technique and were equivalent to values generated by the previously described SE-MRE approach. Preliminary data obtained from the patient demonstrate clinical feasibility.
Cofactor Tail Length Modulates Catalysis of Bacterial F420-Dependent Oxidoreductases (2017)

F<sub>420</sub> is a microbial cofactor that mediates a wide range of physiologically important and industrially relevant redox reactions, including in methanogenesis and tetracycline biosynthesis. This deazaflavin comprises a redox-active isoalloxazine headgroup conjugated to a lactyloligoglutamyl tail. Here we studied the catalytic significance of the oligoglutamate chain, which differs in length between bacteria and archaea. We purified short-chain F<sub>420</sub> (two glutamates) from a methanogen isolate and long-chain F<sub>420</sub> (five to eight glutamates) from a recombinant mycobacterium, confirming their different chain lengths by HPLC and LC/MS analysis. F<sub>420</sub> purified from both sources was catalytically compatible with purified enzymes from the three major bacterial families of F<sub>420</sub>-dependent oxidoreductases. However, long-chain F<sub>420</sub> bound to these enzymes with a six- to ten-fold higher affinity than short-chain F<sub>420</sub>. The cofactor side chain also significantly modulated the kinetics of the enzymes, with long-chain F<sub>420</sub> increasing the substrate affinity (lower <i>K</i><sub>m</sub>) but reducing the turnover rate (lower <i>k</i><sub>cat</sub>) of the enzymes. Molecular dynamics simulations and comparative structural analysis suggest that the oligoglutamate chain of F<sub>420</sub> makes dynamic electrostatic interactions with conserved surface residues of the oxidoreductases while the headgroup binds the catalytic site. In conjunction with the kinetic data, this suggests that electrostatic interactions made by the oligoglutamate tail result in higher-affinity, lower-turnover catalysis. Physiologically, we propose that bacteria have selected for long-chain F<sub>420</sub> to better control cellular redox reactions despite tradeoffs in catalytic rate. Conversely, this suggests that industrial use of shorter-length F<sub>420</sub> will greatly increase the rates of bioremediation and biocatalysis processes relying on purified F<sub>420</sub>-dependent oxidoreductases.
Copolysiloxanes as Pyroelectric Langmuir-Blodgett Films (1993)

Abstract A series of aliphatic acid side-chain copolysiloxanes based on a poly(hydrogenmethyldimethylsiloxane) backbone have been synthesised and evaluated. The length of the aliphatic acid side-chain of each compound has been varied in order to examine the effect on the Langmuir film properties. The surface pressure - area isotherms have indicated that each copolysiloxane forms a stable monomolecular layer on a pure watersubphase. Alternate layer structures, in which each siloxane copolymer is co-deposited with a monomeric eicosylamine, have been prepared in order to measure their static pyroelectric coefficients. The magnitude of the coefficient increases as the length of the aliphatic acid side-chain is reduced. The thickness dependence of the coefficient has also been characterised for one of the copolysiloxane derivatives and shows that the pyroelectric effect is greatest for a 25 layer sample (13 layers of copolysiloxane 8/12 layers of eicosylamine).
Cumulative Quality Modeling for HTTP Adaptive Streaming (2021)

HTTP Adaptive Streaming has become the de facto choice for multimedia delivery. However, the quality of adaptive video streaming may fluctuate strongly during a session due to throughput fluctuations. So, it is important to evaluate the quality of a streaming session over time. In this article, we propose a model to estimate the cumulative quality for HTTP Adaptive Streaming. In the model, a sliding window of video segments is employed as the basic building block. Through statistical analysis using a subjective dataset, we identify four important components of the cumulative quality model, namely the minimum window quality, the last window quality, the maximum window quality, and the average window quality. Experiment results show that the proposed model achieves high prediction performance and outperforms related quality models. In addition, another advantage of the proposed model is its simplicity and effectiveness for deployment in real-time estimation. Our subjective dataset as well as the source code of the proposed model have been made publicly available at https://sites.google.com/site/huyenthithanhtran1191/cqmdatabase .
Scaling of the interfacial tension of microemulsions: A phenomenological description (1996)

Recent experiments revealed a striking scaling behavior of the low and ultralow interfacial tension of microemulsions. A description of this behavior based on the Helfrich elastic free energy, which is symmetric in the principal curvatures c1 and c2, appears to be inconsistent. We show that, within the phenomenological theory of membrane bending elasticity, symmetry breaking between the two principal curvatures seems to be required in order to explain the low, but nonzero, values of the interfacial tension and its temperature dependence. We propose two simple generalizations of the Helfrich free energy which describe the experimental results. The first considers a quadratic elastic free energy and anisotropy in the membrane which breaks the symmetry between the two principal curvatures. In the second, which is applicable to systems with positive saddle-splay rigidities, the symmetry between the two principal curvatures is spontaneously broken by inclusion of higher-order terms in the curvatures in order to stabilize the free energy of the system. This analysis provides a straightforward method to obtain estimates of the bending elastic constants from interfacial tension measurements. Experiments confirming the theoretical picture are presented and values for κ and κ̄, for a variety of systems, are obtained.
Importance of the Extracellular Loop 4 in the Human Serotonin Transporter for Inhibitor Binding and Substrate Translocation (2015)

The serotonin transporter (SERT) terminates serotonergic neurotransmission by performing reuptake of released serotonin, and SERT is the primary target for antidepressants. SERT mediates the reuptake of serotonin through an alternating access mechanism, implying that a central substrate site is connected to both sides of the membrane by permeation pathways, of which only one is accessible at a time. The coordinated conformational changes in SERT associated with substrate translocation are not fully understood. Here, we have identified a Leu to Glu mutation at position 406 (L406E) in the extracellular loop 4 (EL4) of human SERT, which induced a remarkable gain-of-potency (up to >40-fold) for a range of SERT inhibitors. The effects were highly specific for L406E relative to six other mutations in the same position, including the closely related L406D mutation, showing that the effects induced by L406E are not simply charge-related effects. Leu(406) is located >10 Å from the central inhibitor binding site indicating that the mutation affects inhibitor binding in an indirect manner. We found that L406E decreased accessibility to a residue in the cytoplasmic pathway. The shift in equilibrium to favor a more outward-facing conformation of SERT can explain the reduced turnover rate and increased association rate of inhibitor binding we found for L406E. Together, our findings show that EL4 allosterically can modulate inhibitor binding within the central binding site, and substantiates that EL4 has an important role in controlling the conformational equilibrium of human SERT.
Myocardial Gd-DTPA Kinetics Determine MRI Contrast Enhancement and Reflect the Extent and Severity of Myocardial Injury After Acute Reperfused Infarction (1996)

In contrast-enhanced magnetic resonance images of acute, reperfused rabbit infarcts, differential image intensity is primarily due to regional differences in contrast agent wash-in and washout time constants. These regional differences in time constants also indicate the extent and severity of myocardial injury.
Neuroimaging in Dementia: In Vivo Amyloid Imaging (2008)

Dementia, a progressive cognitive decline, leads to a gradually increasing restriction of daily activities. Alzheimer's disease (AD) is the most common form of dementia. The pathological features of AD include plaques and tangles which are constituted by amyloid beta peptide (A beta) and tau protein. These amyloidogenic molecules have been mechanistically implicated in the pathogenesis of AD and related neurodegenerative dementias. The key strategy for establishment of diagnostic and therapeutic approaches to AD is sensitive and specific detection of the incipient neuropathology characteristics of AD, combined with emerging treatments that counteract molecular processes in AD pathogenesis. Recent advances in molecular imaging research have enabled visualization of brain amyloidosis. The rapid development of different compounds suitable for visualizing amyloid would permit pathology-specific diagnosis of AD at an asymptomatic stage in a noninvasive manner, and could also allow early immunotherapeutic intervention without causing an excessive neuroinflammatory response.
Noninvasive determination of respiratory ozone absorption: the bolus-response method. (1994)

Morphometric studies in animals exposed to ozone (O3), and mathematical simulations of O3 transport in human lungs indicate that O3 toxicity is focal in nature, causing tissue damage that is more pronounced in the proximal alveolar region (the proximal end of the respiratory airspaces in our compartment models) than in other airways. These findings suggest that the internal distribution of O3 uptake must be known in order to assess health risk reliably. In previous work (Ultman and Ben-Jebria 1990), we developed a fast-responding chemiluminescent O3 analyzer and a small-scale O3 generator, both of which are suitable for respiratory measurements. The objective of the current research was to integrate these instruments into a bolus inhalation system capable of noninvasively measuring the longitudinal distribution of O3 absorption in intact human lungs. With this system we aimed to carry out baseline experiments in healthy men during quiet oral breathing at a respiratory flow rate of 250 mL/sec, determine the effect of alternative respiratory flow rates between 150 and 1,000 mL/sec, compare the absorption distribution during quiet oral breathing with that during quiet nasal breathing, and ascertain the influence of a peak inspired concentration between 0.3 and 4.0 parts per million (ppm). Ozone uptake (lambda) was expressed as the amount of O3 absorbed during a single breath relative to the amount in the inhaled bolus. Measurements of lambda were correlated with the penetration volume (VP) of the bolus into the respiratory tract. Values of VP less than 70 mL were considered to be associated with the upper airways, values between 70 and 180 mL were associated with the lower conducting airways, and values greater than 180 mL were associated with the respiratory airspaces. During quiet oral breathing, lambda increased smoothly with VP, with 50% of the inhaled O3 absorbed in the upper airways and the balance absorbed within the lower conducting airways. This compares favorably with the results of direct-sampling methods, which have indicated that 40.4% of continuously inhaled O3 is removed by the extrathoracic airways (Gerrity et al. 1988). The effect of increasing the respiratory flow, which occurs when people exercise, was to shift the lambda-VP distribution distally so that significantly less O3 was absorbed in the upper airways and more reached the respiratory airspaces. Compared with oral breathing, nasal breathing caused a proximal shift in the lambda-VP distribution to the extent that absorption in the upper airways increased from 50% to 80%.(ABSTRACT TRUNCATED AT 400 WORDS)