gebhart/patrepeval huggingface dataset:
Evaluation of ANSI/ASHRAE/USGBC/IES Standard 189.1-2009 (2010)

The National Renewable Energy Laboratory (NREL) evaluated ANSI/ASHRAE/USGBC/IES Standard 189.1-2009, 'The Standard for High-Performance Green Buildings Except Low-Rise Residential Buildings'. NREL performed this evaluation by examining the results of predictions for site energy use from a comprehensive set of EnergyPlus models. NREL has conducted an 'order-of-magnitude' analysis in this study toidentify the likely overall impact of adopting Standard 189.1-2009 over ANSI/ASHRAE/IESNA Standard 90.1-2007.
Genome-Wide Expression Analysis of Burkholderia pseudomallei Infection ina Hamster Model of Acute Melioidosis (2006)

Burkholderia pseudomallei is the causative agent of melioidosis and represents a potential bioterrorism threat. In the current studies we have examined gene expression in B. pseudomallei in an animal model of acute melioidosis using whole-genome microarrays. Gene expression profiles were generated by comparing transcriptional levels of B. pseudomallei-expressed genes in infected hamster organs including liver, lung, and spleen following intraperitoneal and intranasal routes of infection to those from bacteria grown in vitro. Differentially expressed genes were similar in infected livers irrespective of the route of infection. Reduced expression of a number of housekeeping genes suggested a lower bacterial growth rate during infection. Energy production during growth in vivo involved specific biochemical pathways such as isomerization of 3-phosphoglycerate, catabolism of d-glucosamine and inositol, and biosynthesis of particular amino acids. In addition, the induction of genes known to be involved in oxidative phosphorylation including ubiquinol oxidase, ferredoxin oxidoreductase, and formate dehydrogenase enzymes suggested the use of alternative pathways for energy production, while the expression of genes coding for ATP-synthase and NADH-dehydrogenase enzymes was reduced. Our studies have identified differentially expressed genes which include potential virulence genes such as those for a putative phospholipase C and a putative two-component regulatory system, and they have also provided a better understanding of bacterial metabolism in response to the host environment during acute melioidosis.
Investigation of the Scope of a Co‐Mediated O→C Ring Contraction. (2007)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
CagL polymorphisms between East Asian and Western Helicobacter pylori are associated with different abilities to induce IL-8 secretion (2021)

Helicobacter pylori colonizes human gastric mucosa. Its infection is associated with gastric diseases including gastric cancer. CagA is one of the most important toxins produced by H. pylori. It is related to gastric cancer which can be injected into host cells via a type IV secretion system (T4SS). CagL is a structural component of T4SS apparatus, which triggers host cell signaling pathway. It has been reported that CagL polymorphisms may influence the severity of disease development. To explore the contribution of CagL polymorphisms between East Asian and Western H. pylori in pathogenesis, cagL gene in G27 H. pylori was swapped by K74 cagL which is identical to East Asian CagL consensus sequence and by Western 26695 H. pylori, resulting in G27 ΔcagL/cagL<sup>K74</sup> and G27 ΔcagL/cagL<sup>26695</sup>, respectively. Intriguingly, G27 ΔcagL/cagL<sup>K74</sup> showed significantly less ability of IL-8 induction than G27 ΔcagL/cagL<sup>26695</sup> while displayed similar abilities of CagA phosphorylation, and cell elongation. Taken together, this study suggests that the CagL polymorphism may influence IL-8 induction, and K74 CagL has less ability to induce IL-8 secretion than G27 or 26695 CagL. Further research should address how the different capabilities of IL-8 induction between intraspecies-CagL are associated with the large differences of the incidence of gastric cancer between East Asian and Western countries.
Motion of the Cochlear Reticular Lamina Varies Radially Across Outer-Hair-Cell Rows (2022)

Abstract The basilar membrane (BM) is connected to the reticular lamina (RL) through three rows of Y-shaped structures consisting of an outer hair cell (OHC) and a Deiters’ cell (DC) with a phalangeal process (PhP) that forms part of the RL mosaic surface. Morphological differences in the anatomy of the Y-shaped structures across the three OHC rows suggest differences in motion across the rows. Here we report OoC transverse motions measured across several radial locations for the gerbil basal region corresponding to ~45 kHz. Cross-sectional imaging and vibrometry measurements were made using a high-resolution (2.23 um axially in water) spectral-domain optical-coherence-tomography (SD-OCT) system. The stimuli were pure tones (2–63 kHz) at ear-canal sound pressure levels (SPLs) of 30–95 dB SPL in anesthetized gerbils (N=9) with healthy cochleae. We report displacements at the RL regions of OHC rows 1–3 (RL 1–3 ), at the OHC-DC junctions of OHC rows 1–3 (OHC-DC-junction 1–3 ), and at the arcuate zone, arcuate-pectinate junction, and pectinate zone of the BM (BM AZ , BM APJ , and BM PZ , respectively). The in vivo BM displacements showed classic compressive nonlinearity and traveling-wave delays. The RL gain was similar to the BM gain at low frequencies (&lt;20 kHz), but increased with frequency. Near the best frequency (BF), the RL gain was greater than the high-level BM gain by 40 ±5 dB (mean±std), and had greater compressive nonlinearity. RL motion varied radially, and the RL 3 gain was significantly greater than that of RL 1 by 10 ±1 dB (p&lt;0.001). In contrast, the OHC-DC-junction gain varied little radially across OHCs. At low frequencies the OHC-DC-junction gain was constant across SPLs, and 14 ± 3 dB greater than the BM gain. As the frequency increased, the OHC-DC-junction gain decreased to a level similar to the BM gain at BF. The RL 2, 3 phase was advanced by 0.25–0.375 cycles relative to the BM phase at low frequencies, but the RL 2, 3 phase lead decreased as the frequency increased, became similar to the BM phase at BF, and lagged behind the BM phase by 0.25–0.5 cycles above BF. The OHC-DC-junction phases were mostly similar to the BM phase at low frequencies, but became delayed relative to the BM as the frequency increased, typically by 0.25–0.5 cycles near BF and by up to 1 cycle above BF. Our results show the most detailed picture of motion around the three OHC rows yet published, indicating that RL motion varied radially. Surprisingly, there was little motion difference across the three OHC rows in the OHC-DC-junction region, indicating that the tops of the DCs move in unison. Our data show a rich array of OoC amplitude and phase variations that are not explained by current theories.
Network-Coded Multiple Access on Unmanned Aerial Vehicle (2018)

This paper presents the first network-coded multiple access (NCMA) downlink system on unmanned aerial vehicle (UAV). The use of UAV as a mobile aerial base station has received much attention in the 5G community in the context of highly mobile and flexible-configurable communication systems. As UAVs are limited by their flight time in the air, achieving high spectral and power efficiency while they are inflight is of great importance. Non-orthogonal multiple access (NOMA) is a promising technique to increase the spectral and power efficiency. Conventional NOMA downlink that makes use of superposition coding in combination with successive interference cancellation (SIC) decoding does not work well in scenarios where the channel conditions of different downlink users are not readily available at the transmitter side. This is the case, for example, in the UAV scenario in which the UAV transmitter moves quickly, causing the channel conditions to vary in a very dynamic manner. This paper investigates a new NOMA downlink architecture, referred to as network-coded multiple access. In the absence of channel information, an NCMA transmitter allocates equal power to the superposed signals of different downlink users. A key challenge is how to achieve high NOMA throughput under such equal power allocation. Toward this end, NCMA makes joint use of physical-layer network coding (PNC) and multiuser decoding (MUD) together with a new superposition coding scheme, referred to as NCMA-based superposition coding. In NCMA-based superposition coding, equal powers are allocated to the signals of different users, but a relative phase offset between the signals is introduced to optimize PNC and MUD decodings. To demonstrate the feasibility and advantage of the NCMA downlink, we implemented our designs on a software-defined radio and UAV. Our experimental results show that NCMA is robust against varying channel conditions. Moreover, the throughput of NCMA can outperform the state-of-the-art SIC-based superposition coding system and the time-division multiple access system by 50% and 80%, respectively, demonstrating that NCMA is a practical solution to boost throughput in UAV NOMA.
Figure S4 from The Highly Recurrent PP2A Aα-Subunit Mutation P179R Alters Protein Structure and Impairs PP2A Enzyme Function to Promote Endometrial Tumorigenesis (2023)

&lt;p&gt;Supplemental data for the classical and enhanced sampling molecular dynamics simulations&lt;/p&gt;
Assessment by flow cytometry of intracellular cytokine production in the peripheral blood cells of renal transplant recipients (2004)

Flow cytometry is a potentially useful method for quantifying cytokine production by PBMCs of renal transplant recipients. The technique is sensitive enough to detect differences between distinct test groups but could not find differences between recipients with and without CAN. This probably reflects the lack of a true difference because pathological changes within the long-term allograft may simply not be reflected or detected in the total population of PBMCs. Further studies should explore the usefulness of this technique in assaying more defined populations of PBMCs (such as those activated by donor allopeptides) and in serial monitoring of individual patients.
Cross-talk Modeling of Wnt, BMP and ERK Pathways during Osteochondrogenic Differentiation (2009)

peer reviewed
Plasma-Induced Crystallization of TiO2 Nanotubes (2019)

Facile crystallization of titanium oxide (TiO₂) nanotubes (NTs), synthesized by electrochemical anodization, with low pressure non-thermal oxygen plasma is reported. The influence of plasma processing conditions on TiO₂ NTs crystal structure and morphology was examined by X-ray diffraction (XRD) and scanning electron microscopy (SEM). For the first time we report the transition of amorphous TiO₂ NTs to anatase and rutile crystal structures upon treatment with highly reactive oxygen plasma. This crystallization process has a strong advantage over the conventional heat treatments as it enables rapid crystallization of the surface. Thus the crystalline structure of NTs is obtained in a few seconds of treatment and it does not disrupt the NTs' morphology. Such a crystallization approach is especially suitable for medical applications in which stable crystallized nanotubular morphology is desired. The last part of the study thus deals with in vitro biological response of whole blood to the TiO₂ NTs. The results indicate that application of such surfaces for blood connecting devices is prospective, as practically no platelet adhesion or activation on crystallized TiO₂ NTs surfaces was observed.
Hydrogen absorption in non-acidic H{sub 2}S environment (1996)

Hydrogen absorption of steel in non-acidic H{sub 2}S-NH{sub 3} environments has not been experimentally confirmed yet in spite of a lot of experiences of hydrogen damage in refineries. This study clarified that (1) HS{sup {minus}}, which is dissociated from H{sub 2}S and the predominant cathodic reactant over pH 7, prevents hydrogen absorption by passivating steel at room temperature, (2) if the passivation current increases with elevating temperature or by adding EDTA to form complex ions with iron, steel remains in an active state and absorbs hydrogen, and (3) if the cathodic current of reduction of HS{sup {minus}} decreases with lowering partial pressure of H{sub 2}S, steel is not passivated and absorbs hydrogen.
On the key equation for n-dimensional cyclic codes. Applications to decoding (1992)

We introduce the key equation of a multidimensional code. This equation exhibits the error-locator polynomial as product of univariate polynomials and the error-evaluator polynomial as a multivariate polynomial. Then we reinterpret these polynomials in a multidimensional linear recurring sequence context. In particular, using the concept of section, we reduce the solution of the decoding problem to a succession of application of the Berlekamp-Massey algorithm. However, it must be noted that multidimensional codes which are usefull for applications and which are decodable by our algorithm are left to be found.
The anomalous Dispersion of the disorder-induced and the second order Raman bands in carbon nanotubes (2001)

In this work we have studied the dispersion of the disorder-induced (D) and the second-order (G') Raman bands in single wall carbon nanotubes using several laser excitation energies (E laser) in the range 1.5-3.0 eV. An anomalous step-like behavior was observed in the E laser dependence of the G'-band frequency. This result is interpreted as a manifestation of the one-dimensional (1D) behavior of the phonon spectrum in carbon nanotubes.
Clock domain verification challenges and scalable solutions (2010)

With chip-design risk at worrying levels, a verification methodology based on just linting and simulation does not cut it. Real Intent has demonstrated that identifying specific sources of verification complexity and deploying automatic customized technologies to tackle them surgically has benefit. Automatic and customized don't go together at first glance. Whereas automatic deals with maximizing productivity in setup, analysis and debug, customized ensures comprehensiveness. That's the challenge for clock-domain verification as well as for the plethora of other failure modes in modern chips. Clockdomain verification is certainly a case in point. Its complexity has grown tremendously:
Oxidatively Stable Fluorinated Sulfones Electrolytes for High Voltage High Energy Li-Ion Batteries (2018)

Developing a high-voltage enabling electrolyte is extremely critical for the success of the next generation high-energy density lithium-ion battery especially for electric vehicles. Material scientists have developed new cathode materials with improved specific capacity[1,2] and operating voltage (5 V vs. Li + /Li).[3,4] However, designed for a 4V-class lithium-ion chemistry, the conventional electrolyte suffers from oxidation instability on the charge cathode/electrolyte interface at high charging voltages which leads to severe transition metal (TM) dissolution and rapid capacity fading. The voltage instability of electrolyte becomes the bottleneck for the extensive application of the high voltage cathode materials. Thus, new electrolytes with elevated voltage stability has been widely explored.[5-8] Here we report a new class of fluorinated electrolytes comprising novel fluorinated sulfones including ((trifluoromethyl)sulfonyl)ethane (FMES), 1-((trifluoromethyl)sulfonyl)propane (FMPS) and 2-((trifluoromethyl)sulfonyl)propane (FMIS).[9] These compounds have been synthesized via new synthetic routes and evaluated as electrolyte materials under high voltage operation. The results indicate that sulfones with an α-trifluoromethyl group possess enhanced oxidative potential and reduced viscosity as compared to their non-fluorinated counterparts. The α-fluorinated sulfones also show enhanced wetting ability with polyolefin separator. A facile synthesis method for a reported sulfone 1,1,1-trifluoro-3-(methylsulfonyl)propane (FPMS) was also developed. With the new reaction method, large quantity of material was obtained and comprehensive electrochemical properties of FPMS as high voltage electrolyte was evaluated. Unlike the α-fluorinated sulfones, the γ-fluorinated sulfones resemble the property of the non-fluorinated ones. References: [1] Nyten, A.; Abouimrance, A.; Armand, M.; Gustafsson, T.; Thomas, J. O. Electrochem. Commun. , 2005 , 7 , 156-160. [2] Ellis, B. L.; Makahnoul, R. M.; Makimura, Y.; Toghill, K.; Nazar, L. F., Nat. Mater. , 2007 , 6 , 749-753. [3] Hu, M.; Pang, X.; Zhou, Z. J., Power Sources , 2013 , 237 , 229-242. [4] Santhanam, R.; Rambabu, B. J., Power Sources , 2010 , 195 , 5442-5451. [5] He, M.; Su, C. C.; Feng, Z.; Zeng, L.; Wu, T.; Bedzyk, M. J.; Fenter, P.; Wang, Y.; Zhang, Z., Adv. Energy Mater., 2017 , 7 , 1700109. [6] He, M.; Su, C. C.; Peebles, C.; Feng, F.; Connell, J. G.; Liao, C.; Wang, Y.; Shkrob, I. A.; Zhang, Z., ACS Appl. Mater. Interface , 2016, 8 (18), 11450-11458. [7] Kunduraciz, M.; Amatucci, G.G., J. Electrochem. Soc., 2006 , 153 , A1345-A1352. [8] Wolfenstine, J.; Aleen, J., J. Power Sources , 2005 , 142 , 389-390. [9] Su, C. C.; He, M.; Redfern, P. C.; Curtiss, L. A.; Shkrob, I. A.; Zhang, Z., Energy Environ. Sci., 2017 , 10 , 900-904. Figure 1
Systematic comparison of two whole-genome amplification methods for targeted next-generation sequencing using frozen and FFPE normal and cancer tissues (2017)

Sequencing key cancer-driver genes using formalin-fixed, paraffin-embedded (FFPE) cancer tissues is becoming the standard for identifying the best treatment regimen. However, about 25% of all samples are rejected for genetic analyses for reasons that include too little tissue to extract enough high quality DNA. One way to overcome this is to do whole-genome amplification (WGA) in clinical samples, but only limited studies have tested different WGA methods in FFPE cancer specimens using targeted next-generation sequencing (NGS). We therefore tested the two most commonly used WGA methods, multiple displacement amplification (MDA-Qiagen REPLI-g kit) and the hybrid or modified PCR-based method (Sigma/Rubicon Genomics Inc. GenomePlex kit) in FFPE normal and tumor tissue specimens. For the normalized copy number analysis, the FFPE process caused none or very minimal bias. Variations in copy number were minimal in samples amplified using the GenomePlex kit, but they were statistically significantly higher in samples amplified using the REPLI-g kit. The pattern was similar for variant allele frequencies across the samples, which was minimal for the GenomePlex kit but highly variable for the REPLI-g kit. These findings suggest that each WGA method should be tested thoroughly before using it for clinical cancer samples.
Performance and User Experience of Touchscreen and Gesture Keyboards in a Lab Setting and in the Wild (2015)

We study the performance and user experience of two popular mainstream mobile text entry methods: the Smart Touch Keyboard (STK) and the Smart Gesture Keyboard (SGK). Our first study is a lab-based ten-session text entry experiment. In our second study we use a new text entry evaluation methodology based on the experience sampling method (ESM). In the ESM study, participants installed an Android app on their own mobile phones that periodically sampled their text entry performance and user experience amid their everyday activities for four weeks. The studies show that text can be entered at an average speed of 28 to 39 WPM, depending on the method and the user's experience, with 1.0% to 3.6% character error rates remaining. Error rates of touchscreen input, particularly with SGK, are a major challenge; and reducing out-of-vocabulary errors is particularly important. Both SGK and STK have strengths, weaknesses, and different individual awareness and preferences. Two-thumb touch typing in a focused setting is particularly effective on STK, whereas one-handed SGK typing with the thumb is particularly effective in more mobile situations. When exposed to both, users tend to migrate from STK to SGK. We also conclude that studies in the lab and in the wild can both be informative to reveal different aspects of keyboard experience, but used in conjunction is more reliable in comprehensively assessing input technologies of current and future generations.
Uplink non-orthogonal access with MMSE-SIC in the presence of inter-cell interference (2012)

This paper investigates the system-level throughput performance of non-orthogonal access with minimum mean squared error-based linear filtering followed by a successive interference canceller (MMSE-SIC) in the cellular uplink. Although non-orthogonal access employing the MMSE-SIC achieves the entire region of the multiuser capacity in a multiple access channel (MAC), which should be beneficial in enhancing the total user throughput and cell-edge user throughput simultaneously compared to orthogonal access, the multiplexing of multiple users within the same frequency block increases the inter-cell interference in the context of the cellular uplink. The aim of the transmission power control method investigated in this paper is to mitigate the inter-cell interference increase due to non-orthogonal user multiplexing. We employ a weighted proportional fair (PF)-based multiuser scheduling scheme to achieve a good tradeoff between the total user throughput and cell-edge user throughput. Simulation results show that non-orthogonal access employing the MMSE-SIC using the proposed transmission power control significantly enhances the system-level throughput performance compared to orthogonal access, which is widely used in 3.9 and 4G mobile communication systems.
Observation of boundary induced chiral anomaly bulk states and their transport properties (2022)

The most useful property of topological materials is perhaps the robust transport of topological edge modes, whose existence depends on bulk topological invariants. This means that we need to make volumetric changes to many atoms in the bulk to control the transport properties of the edges in a sample. We suggest here that we can do the reverse in some cases: the properties of the edge can be used to induce chiral transport phenomena in some bulk modes. Specifically, we show that a topologically trivial 2D hexagonal phononic crystal slab (waveguide) bounded by hard-wall boundaries guarantees the existence of bulk modes with chiral anomaly inside a pseudogap due to finite size effect. We experimentally observed robust valley-selected transport, complete valley state conversion, and valley focusing of the chiral anomaly bulk states (CABSs) in such phononic crystal waveguides. The same concept also applies to electromagnetics.
DNA-damage-induced Checkpoint Pathways in the Nematode Caenorhabditis elegans (2000)

Genomic instability is believed to be an enabling characteristic of cancer (Hanahan and Weinberg 2000).Therefore, it is not surprising that sophisticated mechanisms exist to maintain the integrity of the genome. Damage to DNA triggers checkpoint controls that result in cellcycle arrest and repair of the lesion (Nurse 1997, 2000;Weinert 1998). In multicellular organisms, when DNAdamage is extensive, these potentially harmful cells areeliminated by apoptosis (Enoch and Norbury 1995; Evanand Littlewood 1998). Defects in communications between DNA damage and the apoptotic program leads tothe survival of cells with unstable genomes vulnerable tooncogene activation, ultimately leading to tumor development (Morgan and Kastan 1997; Orr-Weaver andWeinberg 1998; Hanahan and Weinberg 2000). Geneticwork in yeast has greatly improved our understanding ofthe molecular mechanisms of DNA-damage-inducedcheckpoint arrest and repair. On the other hand, DNAdamage-induced apoptosis cannot be studied in yeasts, asthe apoptotic program is missing in both Saccharomycescerevisiae and Schizosaccharomyces pombe (Fraser andJames 1998)...