gebhart/patrepeval huggingface dataset:
Metabolic interdependencies between phylogenetically novel fermenters and respiratory organisms in an unconfined aquifer (2014)

Fermentation-based metabolism is an important ecosystem function often associated with environments rich in organic carbon, such as wetlands, sewage sludge and the mammalian gut. The diversity of microorganisms and pathways involved in carbon and hydrogen cycling in sediments and aquifers and the impacts of these processes on other biogeochemical cycles remain poorly understood. Here we used metagenomics and proteomics to characterize microbial communities sampled from an aquifer adjacent to the Colorado River at Rifle, CO, USA, and document interlinked microbial roles in geochemical cycling. The organic carbon content in the aquifer was elevated via acetate amendment of the groundwater occurring over 2 successive years. Samples were collected at three time points, with the objective of extensive genome recovery to enable metabolic reconstruction of the community. Fermentative community members include organisms from a new phylum, Melainabacteria, most closely related to Cyanobacteria, phylogenetically novel members of the Chloroflexi and Bacteroidales, as well as candidate phyla genomes (OD1, BD1-5, SR1, WWE3, ACD58, TM6, PER and OP11). These organisms have the capacity to produce hydrogen, acetate, formate, ethanol, butyrate and lactate, activities supported by proteomic data. The diversity and expression of hydrogenases suggests the importance of hydrogen metabolism in the subsurface. Our proteogenomic data further indicate the consumption of fermentation intermediates by Proteobacteria can be coupled to nitrate, sulfate and iron reduction. Thus, fermentation carried out by previously unknown members of sediment microbial communities may be an important driver of nitrogen, hydrogen, sulfur, carbon and iron cycling.
An Efficient Reduced-Complexity Two-Stage Differential Sliding Correlation Approach for OFDM Synchronization in the AWGN Channel (2011)

In this paper, we propose a new scheme for data- aided time and frequency synchronization for OFDM systems, based on a single-symbol preamble. The preamble, of useful length $2^{m}-2$, is composed of two consecutive identical m-sequences (with length $2^{m-1}-1$ each). This preamble is extended by a cyclic prefix of convenient length. This stucture is adequate for a two-stage synchronization scheme, namely a reduced complexity coarse synchronization stage, followed by a finer synchronization one. The first stage, based on Cox and Schmidl-like sliding correlation, determines a reduced uncertainty interval over which the fine stage is carried. The second stage is indeed based on a differential correlation, which is more complex compared to the first stage. The combined use of m-sequences and differential correlation offers an almost perfect peak of the computed metric at the preamble start. To assess the performance degradation occasioned by the reduction of complexity characterizing the proposed two-stage approach, we also consider the brute force single-stage approach, where differential correlation is exclusively used. As a byproduct of our two-stage approach, the fractional frequency offset is estimated and its performance is assessed and compared for both two- stage and one-stage approaches. The brute force approach outperfoms all the considered benchmarks. Compared to the reduced complexity scheme, the brute force one provides similar performance, at the expense of a significant complexity overload. Only for SNR lower than $-5$ dB, the brute force scheme presents a slight enhancement with respect to the reduced complexity one. The simulation results show that the proposed method gives better performance than any other considered estimator. Although our technique is expected to be well suited to multipath channels, thanks to the underlying properties of m-sequences, in this paper we focus on the Additive White Gaussian Noise channel.
FX knockout CHO hosts can express desired ratios of fucosylated or afucosylated antibodies with high titers and comparable product quality (2016)

During antibody dependent cell cytotoxicity (ADCC) the target cells are killed by monocytes and natural killer cells. ADCC is enhanced when the antibody heavy chain's core N-linked glycan lacks the fucose molecule(s). Several strategies have been utilized to generate fully afucosylated antibodies. A commonly used and efficient approach has been knocking out the FUT8 gene of the Chinese hamster ovary (CHO) host cells, which results in expression of antibody molecules with fully afucosylated glycans. However, a major drawback of the FUT8-KO host is the requirement for undertaking two separate cell line development (CLD) efforts in order to obtain both primarily fucosylated and fully afucosylated antibody species for comparative studies in vitro and in vivo. Even more challenging is obtaining primarily fucosylated and FUT8-KO clones with similar enough product quality attributes to ensure that any observed ADCC advantage(s) can be strictly attributed to afucosylation. Here, we report generation and use of a FX knockout (FXKO) CHO host cell line that is capable of expressing antibody molecules with either primarily fucosylated or fully afucosylated glycan profiles with otherwise similar product quality attributes, depending on addition of fucose to the cell culture media. Hence, the FXKO host not only obviates the requirement for undertaking two separate CLD efforts, but it also averts the need for screening many colonies to identify clones with comparable product qualities. Finally, FXKO clones can express antibodies with the desired ratio of primarily fucosylated to afucosylated glycans when fucose is titrated into the production media, to allow achieving intended levels of FcγRIII-binding and ADCC for an antibody. Biotechnol. Bioeng. 2017;114: 632-644. © 2016 Wiley Periodicals, Inc.
Heterojunctions and superlattices based on silicon carbide (2006)

In addition to possessing unique electrical properties, silicon carbide (SiC) can crystallize in different modifications (polytypes). Having the same chemical nature, SiC polytypes may significantly differ in their electrical parameters. In recent years, the world's interest in the fabrication and study of heteropolytype structures based on silicon carbide has considerably increased. This review considers studies concerned with polytypism in SiC, fabrication technologies of various types of heterostructures constituted by different SiC polytypes and their electrical parameters. It is shown that heterostructures between SiC polytypes may have a better structural perfection than those constituted by semiconductors that differ in chemical nature. A conclusion is made that SiC-based heterostructures are promising for application in modern electronic devices.
PES News (2001)

This section of the magazine offers a vehicle that speeds publication of new results, discoveries, and developments. It affords authors the opportunity to publish contributions within a few months of submission to ensure rapid dissemination of ideas and timely archiving of developments in our rapidly changing field. Original and significant contributions in applications, case studies, and research in all fields of power engineering are invited. Of specific interest are contributions defining emerging problems and special needs in specific areas. For more information, contact M.E. El-Hawary, DalTech, Nova Scotia, Canada, +1 902 494 6198, fax +1 902 429 3011, e-mail elhawary@dal.ca. Editorial Board
Making Polycarbonates without Employing Phosgene:  An Overview on Catalytic Chemistry of Intermediate and Precursor Syntheses for Polycarbonate (2004)

Conventional production of aromatic polycarbonates (PCs) involves interfacial polycondensation between phosgene (COCl2) and bisphenol A (BPA). This COCl2 process has several drawbacks such as environmental and safety problems involved in using the highly toxic COCl2 as the reagent, which resulted in the formation of chlorine salts of a stoichiometric amount, and in using copious amounts of methylene chloride as the solvent. For these reasons, environmentally friendly processes for PC production without COCl2 have been developed such as melt transesterification of BPA and diphenyl carbonate (DPC). However, COCl2-free production of DPC is not easy yet because of its severe equilibrium constraint, and therefore obtaining DPC efficiently is the most important step to develop a successful COCl2-free PC process. DPC can be obtained via two methods without using COCl2: two-step synthesis of DPC from dimethyl carbonate (DMC) and phenol and direct oxidative carbonylation of phenol. The DPC reacts with BPA to form PC precursors, which are amenable to the subsequent polycondensation step to obtain high molecular weight PC. Alternatively, BPA can be directly carbonylated with DMC or CO. In this work, we review and discuss different reaction routes and the involved catalytic chemistry of possible COCl2-free PC syntheses based on literature as well as our own experimental results. We compare reaction characteristics and the nature of PC precursors produced from different synthetic routes and provide a perspective on an improved COCl2-free PC process
The influence of an attachable subcutaneous cuff for preventing triple lumen catheter infections in critically ill surgical and trauma patients. (1992)

One hundred and ninety-one triple lumen central venous catheters were placed into 107 sites in 81 surgical and trauma patients who were prospectively studied to determine the rate of catheter related infection using a subcutaneous cuff of biodegradable collagen containing bactericidal silver and a guide wire exchange protocol. Thirty-seven sites in 36 nonseptic patients (group 1) were compared with 70 sites in 45 septic patients (group 2). The data were also compared with data consecutively collected one year earlier, using the same exchange protocol without the cuff. Fourteen of 70 sites in group 2 had catheter related infections, with seven causing bloodstream infection. Five of 14 were the result of fungus, with three causing fungemia. Two of 37 sites in group 1 had catheter related infections (p = 0.044), with no associated bacteremia. The number of triple lumen catheter related infections and associated bacteremia or fungemia are higher in septic patients compared with nonseptic critically ill surgical and trauma patients. The cuff significantly prolongs time of catheter site use in patients who are nonseptic, but may be of no benefit in reducing infection rates or prolonging site use time in patients who are septic and may predispose to fungal colonization.
Multi-layer thin-film substrates for multi-chip packaging (1989)

It is commonly recognized that multiple chip module (MCM) packaging offers great advantages in system performance by virtue of the elimination of an entire level of interconnection. Multilayer thin-film module technologies for high-performance multiple chip packaging were developed and integrated. The technologies, which feature four copper layers, polyimide dielectric, controlled-impedance transmission lines, and solder bump assembly, were demonstrated on a variety of vehicles including, recently, a 4-kbyte RAM module operating at above 100-MHz clock frequency. The generic MCM substrate technology is described. The process can be designed to be compatible with a number of substrate materials as required for specific applications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Human Fibroblasts Prefer Mannose over Glucose as a Source of Mannose for N-Glycosylation (1997)

Mannose in N-linked oligosaccharides is assumed to be derived primarily from glucose through phosphomannose isomerase (PMI). The discovery of mammalian mannose-specific transporters that function at physiological concentrations suggested that mannose might directly contribute to oligosaccharide synthesis. To determine the relative contribution of glucose and mannose, human fibroblasts were labeled with either [2-3H]mannose or [1,5,6-3H]glucose at the same specific activity, and the N-linked chains were released by PNGase F digestion. Most of the trichloroacetic acid-precipitable [3H]mannose label was released by this digestion, but only about 10% of the trichloroacetic acid-precipitable material was released from cells labeled with [1,5,6-3H]glucose. Both sugars labeled a similar array of oligosaccharides, and acid hydrolysis of these chains showed that [2-3H]mannose contributed 65-75% of the [3H]mannose in cells labeled for 1 h, despite the 100-fold higher concentration of exogenous glucose. Mannose consumption and [2-3H]mannose utilization were within the range of rates expected for mannose transport via the mannose-specific transporter. About 7-14% of the [2-3H]mannose is used for glycosylation, while the rest (86-93%) is catabolized to 3H2O via PMI. Increasing the exogenous mannose concentration beyond mannose transporter saturation results in the conversion of >99% of [2-3H]mannose into 3H2O. Long term labeling of cells with [2-3H]mannose showed that the specific activity of mannose in glycoproteins reached 77% of the specific activity of [2-3H]mannose added to the medium. These results show that when fibroblasts are provided with physiological concentrations of mannose, they use the mannose-specific transporter to supply the majority of mannose needed for glycoprotein synthesis. PMI may normally be used to catabolize excess mannose rather than to primarily supply Man-6-P for glycoprotein synthesis.
Wiskott‐Aldrich syndrome: a comprehensive review (2013)

Wiskott-Aldrich syndrome (WAS) is a rare X-linked primary immunodeficiency characterized by microthrombocytopenia, eczema, recurrent infections, and an increased incidence of autoimmunity and malignancies. The disease is caused by mutations in the WAS gene expressed exclusively in hematopoietic cells. WAS protein (WASp) is a multidomain protein that exists in complex with several partners that play important roles in its function. WASp belongs to a family of proteins that relay signals from the surface of the cell to the actin cytoskeleton. Mutations in the WAS gene have various effects on the level of WASp, which, in turn, correlates with the severity of the disease. In addition to WAS, mutations in the WAS gene can result in the mild variant X-linked thrombocytopenia, or in X-linked neutropenia, characterized by neutropenia with myelodysplasia. The absence of functional WASp leads to a severe clinical phenotype that can result in death if not diagnosed and treated early in life. The treatment of choice with the best outcome is hematopoietic stem cell transplantation, preferably from a matched related donor.
A Scalable 0.128–1 Tb/s, 0.8–2.6 pJ/bit, 64-Lane Parallel I/O in 32-nm CMOS (2013)

A scalable 64-lane chip-to-chip I/O, with per-lane data rate of 2-16 Gb/s is demonstrated in 32-nm low-power CMOS technology. At maximum aggregate bandwidth of 1.024 Tb/s across 50-cm channel length, the link consumes 2.7 W from a 1.08-V supply, corresponding to 2.6 pJ/bit. As bandwidth demand decreases, scaling the per-lane data rate to 4 Gb/s and power supply to 0.65 V provides 1/4 of the maximum bandwidth while consuming 0.2 W. Across a 1-m channel, the link operates at a maximum per-lane data rate of 16 Gb/s; thus, providing up to 1.024 Tb/s of aggregate bandwidth with 3.2 pJ/bit power efficiency from a 1.15-V supply. A length-matched dense interconnect topology allows clocking to be shared across multiple lanes to reduce area and power. Reconfigurable current/voltage mode transmitter driver and CMOS clocking enable a highly scalable power-efficient link. Optional low-dropout regulators provide >22-dB supply noise rejection at the package resonance frequency of 200 MHz. System-level optimization of duty-cycle and quadrature error correctors across the clock hierarchy provides optimized clock phase placement and, thus, enhances link performance and power. A lane failover mechanism provides design robustness to mitigate channel or circuit defects. The active circuitry occupies 1.3 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> .
Electrophilic fluorination using a hypervalent iodine reagent derived from fluoride (2013)

The air and moisture stable fluoroiodane 8, readily prepared on a 6 g scale by nucleophilic fluorination of the hydroxyiodane 7 with TREAT-HF, has been used as an electrophilic fluorinating reagent for the first time to monofluorinate 1,3-ketoesters and difluorinate 1,3-diketones in good isolated yields.
Deciphering the landscape of host barriers to<i>Listeria monocytogenes</i>infection (2017)

<i>Listeria monocytogenes</i> is a common food-borne pathogen that can disseminate from the intestine and infect multiple organs. Here, we used sequence tag-based analysis of microbial populations (STAMP) to investigate <i>L</i><i>monocytogenes</i> population dynamics during infection. We created a genetically barcoded library of murinized <i>L</i><i>monocytogenes</i> and then used deep sequencing to track the pathogen's dissemination routes and quantify its founding population (<i>N</i><sub>b</sub>) sizes in different organs. We found that the pathogen disseminates from the gastrointestinal tract to distal sites through multiple independent routes and that <i>N</i><sub>b</sub> sizes vary greatly among tissues, indicative of diverse host barriers to infection. Unexpectedly, comparative analyses of sequence tags revealed that fecally excreted organisms are largely derived from the very small number of <i>L. monocytogenes</i> cells that colonize the gallbladder. Immune depletion studies suggest that distinct innate immune cells restrict the pathogen's capacity to establish replicative niches in the spleen and liver. Finally, studies in germ-free mice suggest that the microbiota plays a critical role in the development of the splenic, but not the hepatic, barriers that prevent <i>L. monocytogenes</i> from seeding these organs. Collectively, these observations illustrate the potency of the STAMP approach to decipher the impact of host factors on population dynamics of pathogens during infection.
Negative Thermal Expansion in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:msub><mml:mi>ZrW</mml:mi><mml:mn>2</mml:mn></mml:msub><mml:msub><mml:mi mathvariant="normal">O</mml:mi><mml:mn>8</mml:mn></mml:msub></mml:math>: Mechanisms, Rigid Unit Modes, and Neutron Total Scattering (2005)

The local structure of the low-temperature ordered phase of the negative thermal expansion (NTE) material ${\mathrm{ZrW}}_{2}{\mathrm{O}}_{8}$ has been investigated by reverse Monte Carlo (RMC) modeling of neutron total scattering data. We obtain, for the first time, quantitative measurements of the extent to which the ${\mathrm{WO}}_{4}$ and ${\mathrm{ZrO}}_{6}$ polyhedra move as rigid units, and we show that these values are consistent with the predictions of rigid unit mode theory. We suggest that rigid unit modes are associated with the NTE. Our results do not support a recent interpretation of x-ray-absorption fine structure spectroscopy data in terms of a larger rigid structural component involving the Zr-O-W linkage.
Determination of Exchangeable Calcium of Calcareous and Gypsiferous Bentonites (2010)

Abstract The aim of the present study was to find methodological tools to obtain reasonable results for exchangable Ca 2+ of gypsiferous bentonites. Cation exchange capacity (CEC) is an important property of clays. Numerous methods for calculating CEC and exchangeable cations exist; determination of exchangeable Ca 2+ fails, however, when gypsiferous clays are examined because gypsum is dissolved throughout the exchange experiment, which in turn increases measureable Ca 2+ concentrations. Several new methods (AgTU calcite , CoHex calcite , and Cu-trien 5×calcite ) have been developed to overcome a similar problem occurring with calcite by using exchange solutions saturated with respect to calcite prior to the experiment. In the present study these three solutions were also pre-treated with gypsum and labeled AgTU CcGp , CoHex CcGp , and Cu-trien 5×CcGp . The special solutions were applied first to a gypsum- and calcite-free bentonite with known reference values for exchangeable Ca 2+ . The resulting exchangeable Ca 2+ values obtained did not match with reference values. The solutions were then applied to natural calcareous and gypsiferous bentonites but only the proposed AgTU CcGp test method was successful. The performance of AgTU CcGp was relatively poor when applied to calcareous non-gypsiferous bentonites, the third group of test materials. Reasonable values for exchangeable Ca 2+ of gypsiferous clays were obtained using a combination of two separate results: (1) calcite saturation of exchange solution ( e.g. Cu-trien 5×calcite ) and (2) quantification of gypsum with suitable mineralogical methods. Result 1 eliminates errors caused by calcite dissolution though it is still incorrect because it contains significant amounts of Ca 2+ from gypsum dissolution. After proving that gypsum was completely dissolved during the exchange experiment, result 2 was used to subtract the theoretical Ca 2+ portion of gypsum from result 1. The initial concentration of gypsum of the samples studied was <1 wt.%, typical of many commercial bentonites. Using this combined procedure the sum of exchangeable cations is very close to the CEC, though it still exceeds the CEC by, on average, 3%, which is a satisfactory improvement. The resulting exchangeable Ca 2+ values can be considered as operationally correct using this approach. Ca 2+ saturation (Ca/CEC in %) of seven gypsiferous bentonites ranges from 1 to 69%.
Interaction of enrofloxacin with breast cancer resistance protein (BCRP/ABCG2): influence of flavonoids and role in milk secretion in sheep (2006)

The ATP-binding cassette (ABC) transporter breast cancer resistance protein (BCRP)/ABCG2 is a high-capacity efflux transporter with wide substrate specificity located in apical membranes of epithelia, which is involved in drug availability. BCRP is responsible for the active secretion of clinically and toxicologically important substrates to milk. The present study shows BCRP expression in sheep and cow by immunoblotting with MAb (BXP-53). Vanadate-sensitive ATPase activity with specific BCRP substrates and inhibitors was measured in bovine mammary gland homogenates. To assess the role of BCRP in ruminant mammary gland we tested the fluoroquinolone enrofloxacin (ENRO). In polarized cell lines, ENRO was transported by Bcrp1/BCRP with secretory/absorptive ratios of 6.5 and 2 respectively. The efflux was blocked by the BCRP inhibitor Ko143. ENRO pharmacokinetics in plasma and milk was studied in sheep after co-administration of drug (2.5 mg/kg, i.v.) and genistein (0.8 mg/kg, i.m.) or albendazole sulfoxide (2 mg/kg, i.v) as BCRP inhibitors. Concomitant administration of BCRP inhibitors with ENRO had no significant effect on the plasma disposition kinetics of ENRO but decreased ENRO concentrations in milk.
A Comparison of Peak Linear and Angular Headform Accelerations Using Ice Hockey Helmets (2008)

Abstract The objective of this study was to quantify the ability of hockey helmets to manage peak angular and linear acceleration of the center of gravity of a Hybrid III headform at six impact locations and three velocities (5, 7, and 9 m/s). The method was intended to represent a reconstruction of helmet, shoulder, and elbow strikes to the head. Six different ice hockey helmets were impacted using a pneumatic linear impactor at velocities similar to those encountered in ice hockey. The results were then compared to impacts to an unhelmeted headform. The data demonstrated that under certain conditions, peak angular accelerations were above estimated injury thresholds, while peak linear accelerations remained below. This confirmed the importance of measuring peak angular acceleration and peak linear acceleration in order to better predict minor traumatic brain injuries.