gebhart/patrepeval huggingface dataset:
Characterization and Description of <i>Anaeromyxobacter dehalogenans</i> gen. nov., sp. nov., an Aryl-Halorespiring Facultative Anaerobic Myxobacterium (2002)

Five strains were isolated which form a physiologically and phylogenetically coherent group of chlororespiring microorganisms and represent the first taxon in the Myxobacteria capable of anaerobic growth. The strains were enriched and isolated from various soils and sediments based on their ability to grow using acetate as an electron donor and 2-chlorophenol (2-CPh) as an electron acceptor. They are slender gram-negative rods with a bright red pigmentation that exhibit gliding motility and form spore-like structures. These unique chlororespiring myxobacteria also grow with 2,6-dichlorophenol, 2,5-dichlorophenol, 2-bromophenol, nitrate, fumarate, and oxygen as terminal electron acceptors, with optimal growth occurring at low concentrations (<1 mM) of electron acceptor. 2-CPh is reduced by all strains as an electron acceptor in preference to nitrate, which is reduced to ammonium. Acetate, H(2), succinate, pyruvate, formate, and lactate were used as electron donors. None of the strains grew by fermentation. The 16S ribosomal DNA (rDNA) sequences of the five strains form a coherent cluster deeply branching within the family Myxococcaceae within the class Myxobacteria and are mostly closely associated with the Myxococcus subgroup. With the exception of anaerobic growth and lack of a characteristic fruiting body, these strains closely resemble previously characterized myxobacteria and therefore should be considered part of the Myxococcus subgroup. The anaerobic growth and 9.0% difference in 16S rDNA sequence from those of other myxobacterial genera are sufficient to place these strains in a new genus and species designated Anaeromyxobacter dehalogenans. The type strain is 2CP-1 (ATCC BAA-258).
Measurement of Ultrasonic Attenuation Within Regions Selected from B-Scan Images (1983)

This paper describes the calculation of absolute ultrasonic attenuation as a function of frequency by processing backscattered signals obtained from a clinical imaging instrument. The signal processing steps are developed from a mathematical model of scattering in an attenuating medium with random inhomogeneities. Attenuation data are derived from the imaging system by recording amplitude-compressed ultrasonic echo waveforms along with transducer position information and time-varying gain values. The input-output characteristics of the receiver are employed to remove the effects of compression and gain. Attenuation values are calculated for selected regions within scans of two tissue phantoms and a normal breast. The values agree with other independent measurements and illustrate the requirements for incorporating quantitative attenuation measurements with clinical imaging.
Solderability Changes of Printed Wiring Board Surfaces during Electronic Assembly Operations (1993)

Today's electronic assembly manufacturing operations can be complex combinations of process steps such as IR reflow, wave soldering, special soldering of connectors or sensitive components, cleaning, rework, etc. Such multiple exposures to elevated temperatures and/or oxidising environments (e.g., aqueous cleaning) can have a negative effect on the solderability of printed wiring board (PWB) surfaces. This in turn may limit the effectiveness of subsequent soldering operations, such as wave soldering following an IR reflow step. The purpose of this study is to assess the impact of individual assembly process steps on the solderability of PWB surfaces. The PWB surfaces are initially treated with protective coatings of benzotriazole (BTA). The process steps investigated include: IR reflow in air and in nitrogen; vapour phase reflow; aqueous cleaning; adhesive cure; and wave soldering as a function of solder temperature and flux type. Meniscograph wettability testing is used to measure relative solderability changes, and Auger electron spectroscopy (AES) is used to monitor surface chemical changes, particularly oxide formation. The overall result is a body of fundamental information providing insight into optimisations of process flows, equipment operating specifications, process temperatures and selection of flux types.
Differential Expression of <i>var</i> Gene Groups Is Associated with Morbidity Caused by <i>Plasmodium falciparum</i> Infection in Tanzanian Children (2006)

The var gene family of Plasmodium falciparum encodes the variant surface antigen Plasmodium falciparum erythrocyte membrane protein 1 (PfEMP1). PfEMP1 is considered an important pathogenicity factor in P. falciparum infection because it mediates cytoadherence to host cell endothelial receptors. var genes can be grouped into three major groups, A, B, and C, and the conserved var genes, var1-4, according to sequence similarities in coding and noncoding upstream regions. Using real-time quantitative PCR in a study conducted in Tanzania, the var transcript abundances of the different var gene groups were compared among patients with severe, uncomplicated, and asymptomatic malaria. Transcripts of var group A and B genes were more abundant in patients with severe malaria than in patients with uncomplicated malaria. In general, the transcript abundances of var group A and B genes were higher for children with clinical malaria than for children with asymptomatic infections. The var group C and var1-like transcript abundances were similar between the three sample groups. A transcript abundance pattern similar to that for var group A was observed for var2csa and var3-like genes. These results suggest that substantial and systematic differences in var gene expression exist between different clinical presentations.
Two-Dimensional Porphyrin Array Assembled by Self-Coordination (2004)

A novel cross-shaped porphyrin pentamer having four imidazolyl-porphyrinatozinc(II) moieties, one at each meso-position, was prepared. AFM measurements confirmed the formation of a large twodimensional porphyrin array structure: a thin layer of 6∼7 porphyrins was assembled over a 350 × 350nm2 area, representing linkage of approximately 120 pentamer units along the line of the cross. Keywords: porphyrin, nanostructure, scanning probe microscopy, self-assembly, supramolecular chemistry, confocal fluorescence microscopy
Expression of the 3-hydroxy-3-methylglutaryl coenzyme A-reductase and LDL-receptor genes in human embryonic tumours and in normal foetal tissues. (1987)

The expression of the HMG-CoA-reductase and LDL-receptor genes was examined in primary human embryonic tumours and in normal human first trimester foetal tissues. All embryonic and extra-embryonic tissues examined contained RNA that hybridized with the HMG-CoA-reductase and LDL-receptor cDNA-probes. However, the transcript levels varied considerably between organs. By using Northern blotting, we confirmed that normal foetal tissues contained HMG-CoA-reductase and LDL-receptor transcripts of normal size (4.2 kB and 5.3 kB, respectively). All human developmental tumours examined were characterized by high levels of HMG-Co-A-reductase RNA. However, when the quality of this RNA was examined in greater detail it was found that the 4.2 kB band only accounted for a minor portion of the RNA. Instead we found a range of other transcripts (3.1, 1.1., 0.95, 0.78 and 0.55 kB) that hybridized with the probe. There was a qualitative difference in that only the non-seminomas contained high levels of the three smaller transcripts (0.95, 0.78 and 0.55 kB). In contrast, only one tumor--an embryonal carcinoma--contained increased levels of LDL-receptor transcript. This was found to be of the expected size (5.3 kB).
Human recombinant DNA‐derived antihaemophilic factor (factor VIII) in the treatment of haemophilia A: conclusions of a 5‐year study of home therapy (1999)

Fifty-eight previously treated haemophilic subjects were treated exclusively with the recombinant FVIII (rFVIII-KOGENATE) produced by Bayer Corporation (Berkeley, CA) in an international multicentre prospective study of more than 5 years duration. Fifty-four of the 58 had severe haemophilia (< 2% FVIII) and four had moderate haemophilia (2-5% FVIII); 23/58 (40%) were seropositive for HIV, while 35/58 (60%) were HIV seronegative. Patients were monitored for safety and efficacy over a median period of 4.7 years (range 0.9-5.9 years) and received 17 922 infusions totalling 25.7 million units of rFVIII. Of 7107 bleeding episodes reported in home diaries, 5831 (82%) required only one treatment with rVIII. Twenty-five invasive surgical procedures in 17 patients, including eight joint replacements, were successfully accomplished and 13 serious bleeding episodes in eight patients were successfully treated. FVIII recovery performed on 885 occasions using 39 different lots of rFVIII showed mean incremental recovery of 2.48% IU-1 kg-1 (+/- 0.64). Adverse events were associated with 42 infusions (0.2%); none caused discontinuation of therapy. Immunological parameters remained stable in HIV-seronegative subjects treated with rFVIII; a small decrease in CD4 counts was noted in HIV-seropositive individuals (mean - 37.2 cells mm-3 yr-1). No de novo formation of inhibitors to FVIII was noted; and no clinical allergic reactions occurred to murine or hamster proteins. These conclusions from the longest monitored safety study ever performed for a haemophilia treatment product (with more than 5 years of observation) confirm previous interim study reports that rFVIII is well tolerated over the long-term, has biological activity comparable to that of plasma-derived FVIII, and is safe and efficacious for the treatment of haemophilia A.
Shear wave elastography for breast masses is highly reproducible (2011)

• Shear wave ultrasound elastography can measure the stiffness of breast tissue • It provides a qualitatively and quantitatively interpretable colour-coded map of tissue stiffness • Intraobserver reproducibility of SWE is almost perfect while intraobserver reproducibility of SWE proved to be moderate to substantial • The most reproducible SWE features between observers were SWE image homogeneity and maximum elasticity.
New Perspectives in Cell Delivery Systems for Tissue Regeneration: Natural-derived Injectable Hydrogels (2012)

Natural polymers, because of their biocompatibility, availability, and physico-chemical properties have been the materials of choice for the fabrication of injectable hydrogels for regenerative medicine. In particular, they are appealing materials for delivery systems and provide sustained and controlled release of drugs, proteins, gene, cells, and other active biomolecules immobilized.In this work, the use of hydrogels obtained from natural source polymers as cell delivery systems is discussed. These materials were investigated for the repair of cartilage, bone, adipose tissue, intervertebral disc, neural, and cardiac tissue. Papers from the last ten years were considered, with a particular focus on the advances of the last five years. A critical discussion is centered on new perspectives and challenges in the regeneration of specific tissues, with the aim of highlighting the limits of current systems and possible future advancements.
Stem Cells Genetically Modified With the Developmental Gene MT1-MMP Improve Regeneration of the Supraspinatus Tendon-to-Bone Insertion Site (2010)

Biologic augmentation of repaired rotator cuffs with MT1-MMP-transduced MSCs may reduce the incidence of retears. However, further studies are needed to determine if this remains safe and effective in larger models.
A rapid immunoassay method for the direct detection of PCR products: application to detection of TEM  -lactamase genes (1996)

A rapid immunoassay for the detection of specific PCR products is described in which a positive PCR amplification result is detected, usually in less than 5 min, by applying a few drops of the diluted PCR end-product to a small immunoassay sample device. The method was evaluated in comparison with conventional susceptibility tests and isoelectric focusing (IEF) for the detection of TEM-family beta-lactamase genes in 477 Escherichia coli isolates from urine samples. Of 187 isolates identified as presumptive TEM beta-lactamase producers by conventional methods, 185 generated a positive signal in the PCR immunoassay system. Two further signal-positive isolates were recognised when the PCR was repeated. In addition, one of the 276 ampicillin-susceptible isolates gave a positive signal in repeated PCR-immunoassay experiments despite being ampicillin susceptible and failing to give a TEM-type enzyme band in iso-electric focusing experiments.
Development of techniques to genetically manipulate members of the genera Cytophaga, Flavobacterium, Flexibacter, and Sporocytophaga (1996)

The Bacteroides-Cytophaga-Flavobacterium branch of the eubacterial phylogenetic tree contains a diverse group of bacterial species. Techniques for the genetic manipulation of Bacteroides spp. are well developed (A. A. Salyers, N. B. Shoemaker, and E. P. Guthrie, Crit. Rev. Microbiol. 14:49-71, 1987). Recently we developed techniques to genetically manipulate the gliding bacterium Cytophaga johnsonae (M. J. McBride and M. J. Kempf, J. Bacteriol. 178:583-590, 1996). We now demonstrate that some of these techniques allow genetic manipulation of a number of environmentally or medically significant bacteria in this group. The Bacteroides transposon Tn4351 was introduced into Cytophaga hutchinsonii, Cytophaga succinicans, Flavobacterium meningosepticum, Flexibacter canadensis, Flexibacter sp. strain FS1, and Sporocytophaga myxococcoides by conjugation. Tn4351 integrated itself into the host chromosomes and conferred erythromycin resistance. We isolated several auxotrophic mutants of Flavobacterium meningosepticum following Tn4351 mutagenesis. The C. johnsonae-Escherichia coli shuttle vector pCP11 functioned in C. succinicans but not in the other bacteria. pLYL03 did not replicate in any of these bacteria and should function as a convenient suicide vector. The identification of a system of gene transfer, a selectable marker, a suicide vector, and a transposon that functions in these diverse bacteria allows genetic manipulations to be performed.
A miniaturized dual-band dipole antenna with a modified meander line for laptop computer application in the 2.5 and 5.25 GHz WLAN band (2006)

In this paper, a reduced size dual-band balanced antenna is presented and tested in a lid of a laptop computer. The antenna size is only 0.28 lambda <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> , which is 44% smaller than the conventional dipole antenna and is comparable to the size of unbalanced antenna. A modified meander line technology is used in the particular antenna configuration to achieve dual-band operation in the 2.5 and 5.25 GHz WLAN bands
Performance analysis of a spectrally compliant ultra-wideband pulse design (2005)

We present a performance analysis of an ultra-wideband (UWB) system. The UWB system utilizes a new pulse design that made the performance analysis possible, since the new pulse not only has a short duration to reduce collision, but is also spectrally compliant to the recent U.S. Federal Communications Commission regulation on UWB systems. We present the performance analysis of UWB systems based on different pulse shapes and number of users. New simulation results on multiuser performance of the impulse radio are also presented.
Wavelength switched hybrid TDMA/WDM (TWDM) PON: A flexible next-generation optical access solution (2012)

In this paper, we propose the system concepts of a next-generation wavelength switched hybrid time division multiple access and wavelength division multiplexing (TWDM) passive optical network (PON) architecture. In this architecture, wavelength selective switches (WSSs) are used at the remote node to improve flexibility, data security and power budget compared to other TWDM-PON variants. We map the proposed architecture to the requirements of next-generation optical access networks in a 2020 perspective. Finally, we benchmark the proposed architecture with other proposed TWDM-PON solutions.
The effect of communicational signals on drivers' subjective appraisal and visual attention during interactive driving scenarios (2015)

Communicational signals (e.g. lights and horns) are imperative for on-road interaction between drivers. The aim of the present study was to explore how these signals affect drivers' subjective appraisal and visual attention, and how drivers decode the signals from other vehicles within a variety of interactive contexts. Twenty-five male participants (20 valid samples, ranging from 21 to 29 years of age) were recruited to watch film clips of pre-designed interactive scenarios involving common vehicle signals in a full-view simulator (i.e. including road view and mirror views). Participants' attitudes towards the interacting vehicle's behaviours, emotional responses, fixation metrics, and decoded meanings were recorded and analysed. The majority of tested signals, with the exception of the horn used in the behind vehicles, significantly improved drivers' attitudes and pleasure. All signals significantly increased emotional arousal, as well as the total fixation time and mean fixation duration on the interacting vehicle. When the interacting vehicle was visible in mirrors, the signal usage significantly increased the fixation frequency towards it. Meanwhile, a significant decrease in total fixation time and mean fixation duration on the road was reported. The results also demonstrated that the decoded signal contained several meanings simultaneously depending on both the signal type and its interactive context. This study quantified the communication process via vehicular signals under typical situations involving other vehicles, and also suggested new ideas on how to establish more advanced communication between drivers.
Monitoring Wind Farms With Performance Curves (2012)

Three different operational curves-the power curve, rotor curve, and blade pitch curve-are presented for monitoring a wind farm's performance. A five-year historical data set has been assembled for constructing the reference curves of wind power, rotor speed, and blade pitch angle, with wind speed as an input variable. A multivariate outlier detection approach based on <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">k</i> -means clustering and Mahalanobis distance is applied to this data to produce a data set for modeling turbines. Kurtosis and skewness of bivariate data are used as metrics to assess the performance of the wind turbines. Performance monitoring of wind turbines is accomplished with the Hotelling <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">T</i> <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> control chart.
Molecular and functional characterization of the plastid‐localized Phosphoenolpyruvate enolase (ENO1) from <i>Arabidopsis thaliana</i> (2009)

The Arabidopsis thaliana gene At1g74030 codes for a putative plastid phosphoenolpyruvate (PEP) enolase (ENO1). The recombinant ENO1 protein exhibited enolase activity and its kinetic properties were determined. ENO1 is localized to plastids and expressed in most heterotrophic tissues including trichomes and non-root-hair cells, but not in the mesophyll of leaves. Two T-DNA insertion eno1 mutants exhibited distorted trichomes and reduced numbers of root hairs as the only visible phenotype. The essential role of ENO1 in PEP provision for anabolic processes within plastids, such as the shikimate pathway, is discussed with respect to plastid transporters, such as the PEP/phosphate translocator.
A new learning algorithm for a forecasting neuro-fuzzy network (2003)

The article addresses the problem of adaptive learning in a neuro-fuzzy network based on Sugeno-type fuzzy inference. A new learning algorithm for tuning of both the antecedent and consequent parts of the fuzzy rules is proposed. The algorithm is der
Cas9/gRNA targeted excision of cystic fibrosis-causing deep-intronic splicing mutations restores normal splicing of CFTR mRNA (2017)

Cystic Fibrosis is an autosomal recessive disorder caused by mutations in the CFTR gene. CRISPR mediated, template-dependent homology-directed gene editing has been used to correct the most common mutation, c.1521_1523delCTT / p.Phe508del (F508del) which affects ~70% of individuals, but the efficiency was relatively low. Here, we describe a high efficiency strategy for editing of three different rare CFTR mutations which together account for about 3% of individuals with Cystic Fibrosis. The mutations cause aberrant splicing of CFTR mRNA due to the creation of cryptic splice signals that result in the formation of pseudoexons containing premature stop codons c.1679+1634A>G (1811+1.6kbA>G) and c.3718-2477C>T (3849+10kbC>T), or an out-of-frame 5' extension to an existing exon c.3140-26A>G (3272-26A>G). We designed pairs of Cas9 guide RNAs to create targeted double-stranded breaks in CFTR either side of each mutation which resulted in high efficiency excision of the target genomic regions via non-homologous end-joining repair. When evaluated in a mini-gene splicing assay, we showed that targeted excision restored normal splicing for all three mutations. This approach could be used to correct aberrant splicing signals or remove disruptive transcription regulatory motifs caused by deep-intronic mutations in a range of other genetic disorders.
Heavy ion beam probe energy analyzer for measurements of plasma potential fluctuations (1987)

The operation of a Proca and Green type 30° parallel plate electrostatic energy analyzer is modeled in a new manner that permits high-resolution heavy ion beam probe measurements of fluctuating plasma potential. Systematic calibration procedures permit detection of potential changes smaller than 0.01% of the probing beam energy at frequencies up to a megahertz. Most recent applications of beam probes have made use of this new capability.
Measuring the modified early warning score and the Rothman Index: Advantages of utilizing the electronic medical record in an early warning system (2013)

Early detection of an impending cardiac or pulmonary arrest is an important focus for hospitals trying to improve quality of care. Unfortunately, all current early warning systems suffer from high false-alarm rates. Most systems are based on the Modified Early Warning Score (MEWS); 4 of its 5 inputs are vital signs. The purpose of this study was to compare the accuracy of MEWS against the Rothman Index (RI), a patient acuity score based upon summation of excess risk functions that utilize additional data from the electronic medical record (EMR). MEWS and RI scores were computed retrospectively for 32,472 patient visits. Nursing assessments, a category of EMR inputs only used by the RI, showed sharp differences 24 hours before death. Receiver operating characteristic curves for 24-hour mortality demonstrated superior RI performance with c-statistics, 0.82 and 0.93, respectively. At the point where MEWS triggers an alarm, we identified the RI point corresponding to equal sensitivity and found the positive likelihood ratio (LR+) for MEWS was 7.8, and for the RI was 16.9 with false alarms reduced by 53%. At the RI point corresponding to equal LR+, the sensitivity for MEWS was 49% and 77% for RI, capturing 54% more of those patients who will die within 24 hours.