gebhart/patrepeval huggingface dataset:
Age and Diet Affect Genetically Separable Secondary Injuries that Cause Acute Mortality Following Traumatic Brain Injury in Drosophila (2016)

Outcomes of traumatic brain injury (TBI) vary because of differences in primary and secondary injuries. Primary injuries occur at the time of a traumatic event, whereas secondary injuries occur later as a result of cellular and molecular events activated in the brain and other tissues by primary injuries. We used a Drosophila melanogaster TBI model to investigate secondary injuries that cause acute mortality. By analyzing mortality percentage within 24 hr of primary injuries, we previously found that age at the time of primary injuries and diet afterward affect the severity of secondary injuries. Here, we show that secondary injuries peaked in activity 1-8 hr after primary injuries. Additionally, we demonstrate that age and diet activated distinct secondary injuries in a genotype-specific manner, and that concurrent activation of age- and diet-regulated secondary injuries synergistically increased mortality. To identify genes involved in secondary injuries that cause mortality, we compared genome-wide mRNA expression profiles of uninjured and injured flies under age and diet conditions that had different mortalities. During the peak period of secondary injuries, innate immune response genes were the predominant class of genes that changed expression. Furthermore, age and diet affected the magnitude of the change in expression of some innate immune response genes, suggesting roles for these genes in inhibiting secondary injuries that cause mortality. Our results indicate that the complexity of TBI outcomes is due in part to distinct, genetically controlled, age- and diet-regulated mechanisms that promote secondary injuries and that involve a subset of innate immune response genes.
Complete Cytoreductive Surgery Plus Intraperitoneal Chemohyperthermia With Oxaliplatin for Peritoneal Carcinomatosis of Colorectal Origin (2008)

Patients with isolated, resectable PC achieve a median survival of 24 months with modern chemotherapies, but only surgical cytoreduction plus HIPEC is able to prolong median survival to roughly 63 months, with a 5-year survival rate of 51%.
Post-Mississippian Paleotectonic, Stratigraphic, and Diagenetic History of the Weber Sandstone in the Rangely Field Area, Colorado: Part III: Middle Rocky Mountains (1986)

Rangely Field is situated in Rio Blanco County, Colorado, on a doubly plunging anticline of Laramide age. The Rangely structure is asymmetric with the steepest flank to the southwest. The Pennsylvanian-Permian Weber Sandstone is the primary producing formation, with cumulative production exceeding 670 million bbl. The Weber is a subarkosic arenite deposited in an eolian regime. It interfingers with the alluvial Maroon Formation in the southern and southeastern part of Rangely Field. Isopach maps of the Pennsylvanian formations suggest a paleotectonic platform in the Rangely area and a Pennsylvanian-Permian north-south-trending arch west of the Laramide Douglas Creek arch. Hydrocarbons migrated into the Rangely Field area prior to the Laramide orogeny and were stratigraphi ally trapped at the Weber-Maroon transition zone. Subsequent Laramide structure localized the hydrocarbon accumulation. Diagenetic history of the Weber Sandstone differs between the Uinta and Piceance basins. Weber diagenesis in the Uinta basin is dominated by silica precipitation, and porosity appears to be residual primary. Weber diagenesis in the Piceance basin involved dissolution of detrital material and precipitation of a complex sequence of carbonate cements. Weber porosity in the Piceance basin is both residual primary and secondary. The boundary between these two diagenetic regimes coincides with a Pennsylvanian paleoarch. The diagenetic model proposed for the Rangely area assumes a paleotectonic basin geometry consisting of a gently dipping western limb and a steeply dipping eastern limb. Silica precipitation commenced after Weber deposition throughout the Rangely area. Pre-Laramide salt tect nics may have caused sufficient faulting to permit fluid communication between the Eagle Valley Evaporites and the Weber Sandstone. Saline solutions from the Eagle Valley Evaporites migrated into the Weber in the Piceance basin halting silica precipitation and initiating precipitation of carbonate cements. Precipitation of silica continued in the Uinta basin. Development of secondary porosity in the Piceance basin occurred prior to, or simultaneously with, oil migration.
Macromodelling oscillators using Krylov-subspace methods (2006)

We present an efficient method for automatically extracting unified amplitude/phase macromodels of arbitrary oscillators from their SPICE-level circuit descriptions. Such comprehensive oscillator macromodels are necessary for accuracy when speeding up simulation of higher-level circuits/systems, such as PLLs, in which oscillators are embedded. Standard MOR techniques for linear time invariant (LTI) and varying (LTV) systems are not applicable to oscillators on account of their fundamentally nonlinear phase behavior. By employing a cancellation technique to deflate out the phase component, we restore the validity and efficacy of Krylov-subspace-based LTV MOR techniques for macromodelling oscillator amplitude responses. The nonlinear phase response is re-incorporated into the macromodel after the amplitude components have been reduced. The resulting unified macromodels predict oscillator waveforms, in the presence of any kind of input or interference, at far lower computational cost than full SPICE-level simulation, and with far greater accuracy compared to existing macromodels. We demonstrate the proposed techniques on LC and ring oscillators, obtaining speedups of 30-120 x with no appreciable loss of accuracy, even for small circuits.
A note on an infeasible linearization of some block ciphers (2018)

A block cipher can be easily broken if its encryption functions can be seen as linear maps on a small vector space. Even more so, if its round functions can be seen as linear maps on a small vector space. We show that this cannot happen for the AES. More precisely, we prove that if the AES round transformations can be embedded into a linear cipher acting on a vector space, then this space is huge-dimensional and so this embedding is infeasible in practice. We present two elementary proofs.
<title>Simple method to segment motion field for video coding</title> (1992)

ABSTRACT This paper describes a motion compensated video coding method that employs a simple segmentationscheme to achieve sub-block resolution of the motion field. This increased accuracy of the motion esti-mation reduces the energy of the residue or displaced frame difference by as much as 30%. Including theoverhead to send the side information, the average bit rate is reduced by approximately 10%. 1. INTRODUCTION In block based motion compensated video coding, a frame is divided into non-overlapping blocks ofN * N pixels. For each block, a best match is determined in the previously transmitted frames. The criterion is usually the mean absolute difference (MAD) between the two blocks. The match is subtractedfrom the block to form the displaced frame difference (DFD) or residue which is then compressed by transform coding. The relative position from the block to the matched block in the previous frame is called motion vector. The collection of all the motion vectors forms a motion field.Block based motion estimation assumes that all pixels in a block move by the same amount. When twoor more objects in a block move at different velocities, the motion vector obtained by the conventional blockmatching method may correspond to only one of the objects, or in the worst case, to none of the objects.This can result in large DFD energy. The DFD can be reduced by using smaller block sizes, incurring thecost of sending more motion vectors. Orchard [1] applied segmentation to the previously reconstructedframe by dividing each block into regions corresponding to objects moving at different velocities. Motionestimate of each region is chosen from one of its nearest neighbors, so no extra motion vector needs to besent. However, segmentation adds a nontrivial amount of computation, must be done at both the encoderand decoder, and may not be easy to implement in hardware.In this paper, we present a simple motion field segmentation scheme that achieves sub-block resolution.Simulations show that the DFD energy can be reduced by as much as 30% and the overall bit rate byapproximately 10%.
Haploinsufficiency of RPS14 in 5q− syndrome is associated with deregulation of ribosomal‐ and translation‐related genes (2008)

We have previously demonstrated haploinsufficiency of the ribosomal gene RPS14, which is required for the maturation of 40S ribosomal subunits and maps to the commonly deleted region, in the 5q- syndrome. Patients with Diamond-Blackfan anaemia (DBA) show haploinsufficiency of the closely related ribosomal protein RPS19, and show a consequent downregulation of multiple ribosomal- and translation-related genes. By analogy with DBA, we have investigated the expression profiles of a large group of ribosomal- and translation-related genes in the CD34(+) cells of 15 myelodysplastic syndrome (MDS) patients with 5q- syndrome, 18 MDS patients with refractory anaemia (RA) and a normal karyotype, and 17 healthy controls. In this three-way comparison, 55 of 579 ribosomal- and translation-related probe sets were found to be significantly differentially expressed, with approximately 90% of these showing lower expression levels in the 5q- syndrome patient group. Using hierarchical clustering, patients with the 5q- syndrome could be separated both from other patients with RA and healthy controls solely on the basis of the deregulated expression of ribosomal- and translation-related genes. Patients with the 5q- syndrome have a defect in the expression of genes involved in ribosome biogenesis and in the control of translation, suggesting that the 5q- syndrome represents a disorder of aberrant ribosome biogenesis.
Mechanical response of porous scaffolds for cartilage engineering (2007)

Mechanical properties of scaffolds seeded with mesenchymal stem cells used for cartilage repair seem to be one of the critical factors in possible joint resurfacing. In this paper, the effect of adding hyaluronic acid, hydroxyapatite nanoparticles or chitosan nanofibers into the cross-linked collagen I on the mechanical response of the lyophilized porous scaffold has been investigated in the dry state at 37 oC under tensile loading. Statistical significance of the results was evaluated using ANOVA analysis. The results showed that the addition of hyaluronic acid significantly (p<<0.05) reduced the tensile elastic modulus and enhanced the strength and deformation to failure of the modified cross-linked collagen I under the used test conditions. On the other hand, addition of hydroxyapatite nanoparticles and chitosan nanofibers, respectively, increased the elastic modulus of the modified collagen ten-fold and four-fold, respectively. Hydroxyapatite caused significant reduction in the ultimate deformation at break while chitosan nanofibers enhanced the ultimate deformation under tensile loading substantially (p<<0.05). The ultimate tensile deformation was significantly (p<<0.05) increased by addition of the chitosan nanofibers. The enhanced elastic modulus of the scaffold was translated into enhanced resistance of the porous scaffolds against mechanical load compared to scaffolds based on cross-linked neat collagen or collagen with hyaluronic acid with similar porosity. It can be concluded that enhancing the rigidity of the compact scaffold material by adding rigid chitosan nanofibers can improve the resistance of the porous scaffolds against compressive loading, which can provide more structural protection to the seeded mesenchymal stem cells when the construct is implanted into a lesion. Moreover, scaffolds with chitosan nanofibers seemed to enhance cell growth compared to the neat collagen I when tested in vitro as well as the scaffold stability, extending its resorption to more than 10 weeks.
Prying Apart Ruddlesden−Popper Phases:  Exfoliation into Sheets and Nanotubes for Assembly of Perovskite Thin Films (2000)

Protonated Ruddlesden−Popper tantalates and titanotantalates H2[An-1BnO3n+1] (A = Na, Ca, Sr, La; B = Ta, Ti) that have acidic interlayer protons were exfoliated using tetra(n-butyl)ammonium hydroxide (TBA+OH-). H2CaNaTa3O10 forms both single sheets and tubular "scrolls" when reacted to make TBAxH2-xCaNaTa3O10 colloids. In contrast, TBAxH2-xA2Ta2TiO10 and TBAxH2-xALaTi2TaO10 (A = Ca, Sr) form sheets exclusively. The n = 2 tantalate TBAxH2-xSrTa2O7 forms high aspect ratio scrolls, as well as smaller amounts of sheets. In contrast to the analogous tantalates, the Ruddlesden−Popper titanates and titanoniobates have weakly acidic interlayer protons and exfoliate only to a limited extent. TBAxH2-xSrNb2O7 forms sheets exclusively, whereas TBAxH2-xCa2Nb2TiO10 forms both sheets and scrolls. The n = 3 titanate H2La2Ti3O10 exfoliates into sheets using n-butylamine, and Na2La2Ti3O10·xH2O forms sheets when exfoliated with TBA+OH-. When reacted with O-(2-aminopropyl)-O'-(2-methoxyethyl) polypropylene glycol 500, H2La2Ti3O10 exfoliates into monodisperse 20 × 100 nm scrolls. The exfoliated tantalates and titanotantalates can be electrostatically adsorbed to a Si/SiO2/PDDA [PDDA = poly(diallyldimethylammonium chloride)] surface, forming perovskite monolayers. Above pH 9.5, TBAxH2-xSrLaTi2TaO10 sheets tile to densely cover a Si/SiO2 surface derivatized with 4-aminobutyldimethylmethoxysilane (4-ABDMMS) and two bilayers of poly(sodium styrenesulfonate) (PSS) and poly(allylamine hydrochloride) (PAH). The exfoliated titanates and titanoniobates generally do not adhere to polycationic surfaces.
Production of Hydrogen Using Nanocrystalline Protein-Templated Catalysts on M13 Phage (2010)

For decades, ethanol has been in use as a fuel for the storage of solar energy in an energy-dense, liquid form. Over the past decade, the ability to reform ethanol into hydrogen gas suitable for a fuel cell has drawn interest as a way to increase the efficiency of both vehicles and stand-alone power generators. Here we report the use of extremely small nanocrystalline materials to enhance the performance of 1% Rh/10% Ni@CeO(2) catalysts in the oxidative steam reforming of ethanol with a ratio of 1.7:1:10:11 (air/EtOH/water/argon) into hydrogen gas, achieving 100% conversion of ethanol at only 300 degrees C with 60% H(2) in the product stream and less than 0.5% CO. Additionally, nanocrystalline 10% Ni@CeO(2) was shown to achieve 100% conversion of ethanol at 400 degrees C with 73% H(2), 2% CO, and 2% CH(4) in the product stream. Finally, we demonstrate the use of biological templating on M13 to improve the resistance of this catalyst to deactivation over 52 h tests at high flow rates (120 000 h(-1) GHSV) at 450 degrees C. This study suggests that the use of highly nanocrystalline, biotemplated catalysts to improve activity and stability is a promising route to significant gains over traditional catalyst manufacture methods.
Application of CT‐Processing to Neutron Radiography Imaging of a Fluidized‐Bed (2006)

Abstract CT‐processing is very effective in obtaining 3‐dimensional information for industrial instruments, and several trials have also been applied to fluidized‐beds. In the CT‐processing of fluidized‐beds, X‐rays are used mainly because they are readily availability. Similar processing can be performed by neutron‐rays which penetrate most metals, but not some chemical substances, such as hydrogen, boron, gadolinium, which are opaque to the neutrons. Due to these unique characteristics, neutron radiography can be considered as a suitable visualization method of actual industrial instruments made of metal. Thus, neutron radiography also has significant advantages for the visualization of fluidized‐beds. However, neutron radiography requires a nuclear reactor or an accelerator as the neutron source in order to obtain high quality images, which means that the real time CT‐processing of multiphase flows by neutron radiography is quite difficult. Consequently, CT‐images in this investigation were reconstructed by using time‐averaged visualization images. Although time averaging makes the understanding of the void movement difficult, 3‐dimensional characteristics of the void fraction propagation in fluidized‐beds could be clearly visualized by using test sections with significant non‐uniformity of the fluidized‐gas distribution.
Pepsinogens to Distinguish Patients With Gastric Intestinal Metaplasia and Helicobacter pylori Infection Among Populations at Risk for Gastric Cancer (2016)

This study demonstrated an important increase in gastrin G17 serum level in autoimmune gastritis. PG1 serum level corrected by patient age can be used in the management of patients at risk for GC with a high predicted probability of having an OLGIM stage ≥2. Using a cutoff of 47.9 ng/ml, PG1 testing in FDR-GC and ACAG patients had a sensitivity of 95.83% and a specificity of 93.37. Although these results could be validated in a prospective study, the known importance of higher OLGIM stages in increasing the risk of GC development supports the rationale of proposing PG1 algorithm as a diagnostic tool for the selection of high-risk FDR-GC and ACAG patients at high-risk stages for subsequent detailed endoscopic examination to detect dysplasia and asymptomatic GC. In addition, serum PG1 and PG2 levels could stratify patients based on both H. pylori infection and OLGIM risk in consideration of the increased acknowledge regarding the role of H. pylori in the progression of gastritis to GC.
Goldnanopartikel in Biologie und Medizin (2010)

Abstract Goldkolloide werden in Chemie, Biologie, Technik und Medizin häufig eingesetzt. Heute kann man diese Materialien reproduzierbar herstellen, mit einer scheinbar unbegrenzten Zahl an funktionellen Gruppen chemisch modifizieren und – in bestimmten Fällen – bis hinab zur Ebene einzelner Atome charakterisieren. Dieser Aufsatz behandelt neuere Entwicklungen hinsichtlich Synthese und Biokonjugation von Goldnanokonjugaten sowie deren Verwendung in Zellen. Es gibt heute viele Beispiele für hochempfindliche und selektive Assays auf der Basis von Goldkonjugaten. In den letzten Jahren war der Fokus auf den Einsatz solcher Materialien in der Therapie gerichtet. Strukturen, die als genregulierende Agentien, Wirkstofftransporter, Bildgebungsagentien und lichtempfindliche Therapeutika fungieren, wurden entwickelt und in Verbindung mit Zellen und vielen schwächenden Krankheiten erforscht. Diese Strukturen wurden nicht einfach als Alternativen zu molekularen Systemen gewählt, sondern weil ihre neuen physikalischen und chemischen Eigenschaften ihnen in zellulären und medizinischen Anwendungen erhebliche Vorteile verschaffen.
Plasma biomarker for detection of early-stage pancreatic cancer and risk factors for pancreatic malignancy using antibodies for apolipoprotein-A2 isoforms. (2016)

4106 Background: We have previously revealed that circulating levels of apolipoprotein A2 (apoA2) isoforms apoA2-ATQ/AT (C-terminal truncations of apoA2 homo-dimer) are significantly decreased in early-stage pancreatic cancer in comparison with healthy controls on mass spectrometry (MS)-based assays. We report here the development of novel enzyme-linked immunosorbent assays (ELISAs) for measuring apoA2-ATQ/AT and their clinical applicability for the early detection of pancreatic cancer. Methods: Plasma and serum concentrations of apoA2-isoforms were measured in three independent cohorts (two Japanese cohorts and one pancreatic reference set collected by the US National Cancer Institute’s Early Detection Research Network (NCI EDRN), each comprising healthy control subjects and patients with pancreatic cancer or gastroenterological disease (n = 1156). These cohorts included 151 cases of stage-I/II pancreatic cancer. Results: Significant reductions in apoA2-ATQ/AT levels were recognized in patients with pancreatic cancer in comparison with healthy controls in both independent Japanese cohorts (p = 1.34*10-18 and 5.09*10-39). Areas under the receiver operating characteristic curve (AUCs) were > 0.92 for distinguishing patients with stage-I/II pancreatic cancer from healthy controls in the Japanese cohorts. The AUCs of apoA2-ATQ/AT to distinguish patients with pancreatic cancer from healthy controls were higher than those of CA19-9 in both Japanese cohorts. Better discrimination of pancreatic cancer was also observed with apoA2-ATQ/AT than with CA19-9 in the blind test using NCI EDRN data; combining apoA2-ATQ/AT with CA19-9 led to significantly improved AUC compared to CA19-9 alone Conclusions: ELISA for apoA2-isoforms offers a good biomarker for early detection of pancreatic cancer. We have started experimental screening for pancreatic cancer in the Kobe Cancer Screening Network.
A disturb-alleviation scheme for 3D flash memory (2013)

Even though 3D flash memory presents a grand opportunity for huge-capacity non-volatile memory, it suffers from serious program disturb problems. Different from the past efforts in error correction codes or the work in trading the space utilization with reliability, we propose a disturb-alleviation scheme that can alleviate the negative effects caused by program disturb, especially inside a block, without introducing extra overheads on encoding or storing of extra redundant data. In particular, a methodology is proposed to reduce the data error rate by distributing unavoidable disturb errors over the flash-memory space of invalid data, with the considerations of the physical organization of 3D flash memory. A series of experiments was conducted based on real multi-layer 3D flash chips, and it showed that the proposed scheme could significantly enhance the reliability of 3D flash memory.
Antibacterial and Antioxidant Screening of Semi-Synthetic Naringin Based Hydrazone and Oxime Derivatives (2018)

Background: The semi-synthesis of drugs from natural products is still limited and complicated. Recently, there has been compelling global need to develop novel and potential antibacterial and antioxidant agents. Objectives: The current study aimed at semi-synthesizing new derivatives from naringin, to verify their chemical structures and assess their antibacterial and antioxidant potentials. Methods: The semi-synthesis of naringin was conducted in the presence of hydrazone and oxime derivatives in acidic solution, while elemental and spectral analytical methods were used to verify the chemical structures of the semi-synthesized molecules. Also, to assess their antibacterial activity, the micro-broth dilution method with different American type culture collection (ATCC) strains as Pseudomonas aeruginosa, Staphylococcus aureus, Escherichia coli, and clinical isolate methicillin-resistant Staphylococcus aureus (MRSA) were utilized. Moreover, 2, 2-Diphenyl-1-Picrylhydrazyl (DPPH) was used to assess the antioxidant activity of the derived compounds. Results: Three new hydrazone and oxime compounds were semi-synthesized from naringin and their chemical structures were identified by 13C NMR, IR, MS, and 1H NMR. Among the semi-synthesized compounds, the (2a) molecule showed the best antibacterial activity with a minimum inhibitory concentration (MIC) value of 62.5 Î¼g/mL. Also, this compound exhibited the best antioxidant activity with IC50 3.7 Î¼g/mL, in comparison with the other studied samples. Conclusions: Hydrazone (2a) compound could be used as a potent antioxidant and bacterial agent. Further studies are required to investigate other therapeutic effects of the (2a) molecule.