gebhart/patrepeval huggingface dataset:
Clinically Feasible Biofilm Susceptibility Assay for Isolates of <i>Pseudomonas aeruginosa</i> from Patients with Cystic Fibrosis (2004)

Pseudomonas aeruginosa is the predominant cause of chronic airway infection in cystic fibrosis (CF). CF airway isolates are often tested for antibiotic susceptibility but are rarely eradicated by the antibiotics identified as potentially effective. The growth state of P. aeruginosa in CF airways is probably different from that exhibited under conventional susceptibility testing conditions and may represent a bacterial biofilm. Biofilm susceptibility testing methods were adapted to create an assay for implementation in a clinical microbiology laboratory. This assay gave reproducible results when examined in 300 paired determinations with 12 antimicrobial agents, with a serious error rate of 5.7%. The biofilm assay was used retrospectively to test these 12 agents against 94 isolates from 41 CF patients. The biofilm inhibitory concentrations (BICs) were much higher than the corresponding conventionally determined MICs for the beta-lactam antibiotics (median values: aztreonam, >128 microg/ml versus 4 microg/ml; ceftazidime, 128 microg/ml versus 2 microg/ml; piperacillin-tazobactam, 256 microg/ml versus 4 microg/ml; and ticarcillin-clavulanate, 512 microg/ml versus 16 microg/ml, respectively) and doxycycline (>64 microg/ml versus 16 microg/ml); and similar for meropenem (4 micro g/ml versus < or = 1 microg/ml), ciprofloxacin (0.5 microg/ml versus 1 microg/ml), and the aminoglycosides amikacin (32 microg/ml versus 16 microg/ml), gentamicin (16 microg/ml versus 8 microg/ml), and tobramycin (4 microg/ml versus 2 microg/ml). The median BIC for azithromycin was 2 microg/ml, whereas isolates were uniformly resistant when tested by standard methods. This demonstrates the feasibility of adapting biofilm susceptibility methods to the clinical microbiology laboratory and opens the way to examining whether biofilm testing might be used to select more effective antibiotic combinations for CF airway infections than methods in current use.
Addition of a magnetite layer onto a polysulfone water treatment membrane to enhance virus removal (2011)

The applicability of low-pressure membranes systems in distributed (point of use) water treatment is hindered by, among other things, their inability to remove potentially harmful viruses and ions via size exclusion. According to the USEPA and the Safe Drinking Water Act, drinking water treatment processes must be designed for 4-log virus removal. Batch experiments using magnetite nanoparticle (nano-Fe3O4) suspensions and water filtration experiments with polysulfone membranes coated with nano-Fe3O4 were conducted to assess the removal of a model virus (bacteriophage MS2). The membranes were coated via a simple filtration protocol. Unmodified membranes were a poor adsorbent for MS2 bacteriophage with less than 0.5-log removal, whereas membranes coated with magnetite nanoparticles exhibited a removal efficiency exceeding 99.99% (4-log). Thus, a cartridge of PSf membranes coated with nano-Fe3O4 particles could be used to remove viruses from water. Such membranes showed negligible iron leaching into the filtrate, thus obviating concern about coloured water. Further research is needed to reduce the loss of water flux caused by coating.
Corundum: statically-enforced persistent memory safety (2021)

Fast, byte-addressable, persistent main memories (PM) make it possible to build complex data structures that can survive system failures. Programming for PM is challenging, not least because it combines well-known programming challenges like locking, memory management, and pointer safety with novel PM-specific bug types. It also requires logging updates to PM to facilitate recovery after a crash. A misstep in any of these areas can corrupt data, leak resources, or prevent successful recovery after a crash. Existing PM libraries in a variety of languages -- C, C++, Java, Go -- simplify some of these problems, but they still require the programmer to learn (and flawlessly apply) complex rules to ensure correctness. Opportunities for data-destroying bugs abound.
Novel self-convergent programming method using source-induced band-to-band hot electron injection (2002)

The authors describe a novel self-converging programming method using the source-induced band-to-band hot electron (SIBE) injection. This method features low current, high speed, and good reliability, and automatically converges at the desired threshold voltage state without any conventional verification operations. The programming leakage current of this method is only about 3 μA/μm, and the programming time is as low as 30 μs. A threshold voltage model is also proposed and shows good consistency with measured results.
Plasma chemical degradation of phenol in solution by gas–liquid gliding arc discharge (2005)

A gas–liquid gliding arc (glidarc) discharge reactor is used to degrade high concentration phenol solution. Phenol solution with 1878 mg L−1 initial chemical oxygen demand (COD) is treated by spraying directly into the plasma zone formed between two electrodes through a gas–liquid two phase atomizing nozzle. A number of parameters such as voltage waveform, solution concentration, electrode material, nature of the carrier gases and the gas–liquid ratio are examined. It is found that the voltage waveform of gas–liquid gliding arc discharge is more irregular than that of gas gliding arc discharge, and the breakdown voltage of gas–liquid gliding arc discharge is lower than that of gas gliding arc discharge. The COD abatement of phenol solution with stainless steel as the electrode material is higher than that with brass and aluminium. The increasing electrode thickness and the increasing gas–liquid ratio and carrier gas such as oxygen can increase the degradation of phenol. The final COD of the solution is 173 mg L−1; either air or oxygen is used as the carrier gas, and the solution treated is acidic. The variation of pH and conductivity and the formation of hydrogen peroxide and ozone are measured. The occurrence of CO2 is detected during the plasma treatment: the maximum concentration is 18 000 ppm. While H2 and NOx are also detected during the plasma phase, p-nitrosophenol (C6H5NO2) and p-nitrophenol (C6H5NO3) are detected in the solution treated.
A Methodology for Automated Trajectory Prediction Analysis (2004)

A number of air traffic management decision support tools (DST) are being developed to help air traffic managers and controllers improve capacity, efficiency, and safety in the National Airspace System. Although DST functionality may vary widely, trajectory prediction algorithms can be found at the core of most DST. A methodology is presented for the automated statistical analysis of trajectory prediction accuracy as a function of phase of flight (level-flight, climb, descent) and look-ahead time. The methodology is focused on improving trajectory prediction algorithm performance for DST applications such as conflict detection and arrival metering. The methodology has been implemented in software and tested with air traffic data. Aggregate trajectory prediction accuracy statistics are computed and displayed in histogram format based on 2,774 large commercial jet flights from five different days of Fort Worth Center air traffic data. The results show that trajectory prediction anomalies can be detected by examining error distributions for large numbers of trajectory predictions. The ability of the trajectory analysis methodology to detect the effects of subsequent changes to the trajectory prediction algorithm and to aircraft performance model parameters was also demonstrated.
Anorganische Bi(cyclopentasilanyle): Synthese und spektroskopische Charakterisierung (1995)

Abstract Ausgehend von Nonachlor‐ bzw. Nonabromcyclopentasilan, die durch Abspaltung der Phenylgruppen in Nonaphenylcyclopentasilan mit HX/AlX 3 (X = Cl, Br) zugänglich sind, gelingt durch Kopplung mit ( t ‐bu) 2 Hg die Synthese der bicyclischen Oligosilane Bi(nonachlorcyclopentasilanyl) ( 7 ) und Bi(nonabromcyclopentasilanyl) ( 8 ). Bi(nonaphenylcyclopentasilanyl) ( 6 ), das mit HX/AlX 3 ebenfalls in 7 oder 8 überführt werden kann, läßt sich aus Bromnonaphenylcyclopentasilan mit Naphthyllithium darstellen. Die Hydrierung von 7 und 8 mit LiAlH 4 liefert neben dem erwarteten Bi(cyclopentasilanyl) etwa 15% Cyclopentasilan, was auf eine bemerkenswerte Labilität der zentralen SiSi‐Bindung gegenüber nucleophilen Reagenzien schließen läßt. Massenspektroskopische Untersuchungen ergeben keine Hinweise auf eine geringere Bindungsstärke der mittelständigen SiSi‐Bindung in 7 und 9 .
The Prevalence of Proteolytic Antibodies against Factor VIII in Hemophilia A (2002)

Proteolysis is a mechanism by which IgG antibodies against factor VIII can inactivate factor VIII.
Role of Monosaccharide Transport Proteins in Carbohydrate Assimilation, Distribution, Metabolism, and Homeostasis (2012)

Abstract The facilitated diffusion of glucose, galactose, fructose, urate, myoinositol, and dehydroascorbic acid in mammals is catalyzed by a family of 14 monosaccharide transport proteins called GLUTs. These transporters may be divided into three classes according to sequence similarity and function/substrate specificity. GLUT1 appears to be highly expressed in glycolytically active cells and has been coopted in vitamin C auxotrophs to maintain the redox state of the blood through transport of dehydroascorbate. Several GLUTs are definitive glucose/galactose transporters, GLUT2 and GLUT5 are physiologically important fructose transporters, GLUT9 appears to be a urate transporter while GLUT13 is a proton/myoinositol cotransporter. The physiologic substrates of some GLUTs remain to be established. The GLUTs are expressed in a tissue specific manner where affinity, specificity, and capacity for substrate transport are paramount for tissue function. Although great strides have been made in characterizing GLUT‐catalyzed monosaccharide transport and mapping GLUT membrane topography and determinants of substrate specificity, a unifying model for GLUT structure and function remains elusive. The GLUTs play a major role in carbohydrate homeostasis and the redistribution of sugar‐derived carbons among the various organ systems. This is accomplished through a multiplicity of GLUT‐dependent glucose sensing and effector mechanisms that regulate monosaccharide ingestion, absorption, distribution, cellular transport and metabolism, and recovery/retention. Glucose transport and metabolism have coevolved in mammals to support cerebral glucose utilization. © 2012 American Physiological Society. Compr Physiol 2:863‐914, 2012.
Barth syndrome: <i>TAZ</i> gene mutations, mRNAs, and evolution (2005)

Barth syndrome (MIM 302060) is an X-linked condition that includes dilated cardiomyopathy, neutropenia, failure to thrive, abnormal mitochondria, and 3-methylglutaconic aciduria. The mutated gene, TAZ, first described in 1996, appeared to produce a large set of alternatively spliced mRNAs with initiations of transcription upstream of exons 1 and 3. Since then, disease-causing mutations have been found in all exons including, most recently, a missense mutation in the controversial exon 5. Because of the initially described second initiation of transcription in intron 2, with in-frame initiation of translation in exon 3, we hypothesized that subjects with mutations in exons 1 and 2 would produce more normal "short product" that might attenuate their phenotype. Moreover, it was of interest to determine which splice variants were potentially functional as exon 5 is not present in yeast and rodents, and the variant lacking this exon is the most abundant. Using RT-PCR, we characterized TAZ mRNAs in cultured lymphocytes from nine subjects with Barth syndrome and two healthy controls. The TAZ genes and mRNAs of primates were also included. We found the following: (1) there is only one site for initiation of transcription, and the normal alternatively spliced assortment is limited to full-length, delta5, delta7, delta5delta7; (2) there are two alternative splice sites within introns 1 and 2 that could potentially produce an in-frame product; (3) exon 5 evolved into "exonhood" in the primate lineage after the split between Old World monkeys and hominoid primates; and (4) our results suggest that only two functional protein variants exist in lymphocytes: delta5 and full-length. Although exon 5 does not appear to be required for TAZ function in yeast and monkeys, its evolution to a highly conserved spliced exon in hominoid primates and the recent finding of an exon 5 mutation in a patient with Barth syndrome suggest that the full-length variant is important to TAZ function.
SUBAQUEOUS GEOMORPHOLOGY AND SEDIMENTS OF HANAS LAKE IN XINJIANG (1993)

测量表明,哈纳斯湖最大水深达188.5m,平均水深达120.1m,优质淡水容量达53.78×10<sup>8</sup>m<sup>3</sup>,均在我国湖泊中居突出地位。横断面为罕见的典型箱形,断陷作用仍在强烈进行之中。湖底表层沉积物粒度参数之分布主要受纵向搬运作用控制,局部受横向搬运作用影响。沉积物的矿物学特征与元素分布特征明显受沉积环境控制。沉积物中营养元素含量总体偏低。<sup>210</sup>Pb法测得平均沉积速率为0.52mm/a,难以补偿断陷作用,湖盆将继续加深。;Lake survey shows that Hanas Lake, with maximun water depth of 188. 5m, mean water depth of 120.1m and excellent fresh water capacity of 5.378km<sup>3</sup>, is one of very prominent lakes in China. The cross section of the lake bottom shows an unusual chest-like form and the lake faults are still in intensive action now. The grain size distribution is controlled chiefly by longitudinal transportation, and influnced by traverse transportation in the local area with quite low concentration of the most nutrient elements in the sediments. Minerals and chemical elements of the sediments are obviously under the control of sedimentary environments, with quite low concentration of the most elements in the sediments. Its sedimentary rate is measured 0.52mm/a by <sup>210</sup>Pb,but insufficient to compensate the lake faulting,as a result,the lake depth will get increased even more.
Modified z-source DC circuit breaker topologies (2014)

The z-source breaker has been introduced as a new circuit for quickly and automatically switching off in response to faults. A modified z-source breaker design is introduced for operation at medium-voltage dc with future applications in naval ship power systems. Compared to existing designs the respective design will allow for step changes in load. This new design also limits capacitor current in the circuit and can be easily modified for fault detection. Analysis of the breaker operation is presented during both fault and step changes in load. Low voltage laboratory validation of the breaker was carried out on two different versions of the proposed circuit.
Motor primitive discovery (2012)

We present a method for autonomous on-line discovery of motor primitives for Markov decision processes with high-dimensional continuous action spaces. These biologically-inspired motor primitives require overhead to compute but form a compressed representation of the action set that allows for improved performance on subsequent learning tasks that have similar dynamics.
Profile for Datagram Congestion Control Protocol (DCCP) Congestion Control ID 3: TCP-Friendly Rate Control (TFRC) (2006)

This document contains the profile for Congestion Control Identifier
3, TCP-Friendly Rate Control (TFRC), in the Datagram Congestion
Control Protocol (DCCP). CCID 3 should be used by senders that want a
TCP-friendly sending rate, possibly with Explicit Congestion
Notification (ECN), while minimizing abrupt rate changes. [STANDARDS-
TRACK]
Text Line Extraction in Handwritten Document with Kalman Filter Applied on Low Resolution Image (2006)

In this paper we present a method to extract text lines in handwritten documents. Indeed, line extraction is a first interesting step in document structure recognition. Our method is based on a notion of perceptive vision: at a certain distance, text lines of documents can be seen as line segments. Therefore, we propose to detect text line using a line segment extractor on low resolution images. We present our extractor based on the theory of Kalman filtering. Our method makes it possible to deal with difficulties met in ancient damaged documents: skew, curved lines, overlapping text lines. We present results on archive documents from the 18th and 19th century
Polarimetry using liquid-crystal variable retarders: theory and calibration (2000)

A Mueller-matrix polarimeter in transmission mode using two electronically controlled liquid-crystal variable retarders has been developed. Its design, theory and calibration are described. Although liquid crystals have been proposed earlier, this paper is focused on the process of the calculation of the Mueller matrix by a matrix-inversion method, oriented to static systems and in vitro samples. By driving the retarders with appropriate voltages, nine independent pairs of polarization states can be produced (incomplete polarimetry), while the other additional seven pairs are obtained by placing two quarter-wave plates (in the input and output optical paths respectively). This configuration allows extraction of 16 independent measurements of intensity. The Mueller matrix of the sample is calculated from them. The results of Mueller matrices for air, a linear polarizer and a quarter-wave plate are presented. Additional polarization parameters such as retardation, ellipticity or degree of polarization were also computed and some applications of the system are proposed.
A millimeter-wave fabry-perot antenna with high-gain and circular polarization operation (2014)

A Fabry-Perot (F-P) antenna operating at Ka-band with high gain and circular polarization operation is presented. The circular polarization wave is excited by an aperture-coupled rectangular patch with truncated corners. The F-P cavity consists of a ground plane and a frequency selective surface (FSS) cover. In order to further improve the antenna gain, the FSS cells are printed on a circular substrate plate. The simulated results show that the antenna has an impedance bandwidth (S11 <; -10 dB) of greater than 12.5% and an axial-ratio bandwidth (AR <; 3 dB) of 7.1%. A peak gain of 18.1 dBi is obtained at 35 GHz. The antenna has the characteristics of high-gain, circular polarization and easy integration, which can be used as the receiving antenna of millimeter wave communication or wireless power transmission systems.
Characterization of Native and Recombinant Falcipain-2, a Principal Trophozoite Cysteine Protease and Essential Hemoglobinase ofPlasmodium falciparum (2000)

Trophozoites of the malaria parasite Plasmodium falciparum hydrolyze erythrocyte hemoglobin in an acidic food vacuole to provide amino acids for parasite protein synthesis. Cysteine protease inhibitors block hemoglobin degradation, indicating that a cysteine protease plays a key role in this process. A principal trophozoite cysteine protease was purified by affinity chromatography. Sequence analysis indicated that the protease is encoded by a previously unidentified gene, falcipain-2. Falcipain-2 was predominantly expressed in trophozoites, was concentrated in food vacuoles, and was responsible for at least 93% of trophozoite soluble cysteine protease activity. A construct encoding mature falcipain-2 and a small portion of the prodomain was expressed in Escherichia coli and refolded to active enzyme. Specificity for the hydrolysis of peptide substrates by native and recombinant falcipain-2 was very similar, and optimal at acid pH in a reducing environment. Under physiological conditions (pH 5.5, 1 mm glutathione), falcipain-2 hydrolyzed both native hemoglobin and denatured globin. Our results suggest that falcipain-2 can initiate cleavage of native hemoglobin in the P. falciparum food vacuole, that, following initial cleavages, the protease plays a key role in rapidly hydrolyzing globin fragments, and that a drug discovery effort targeted at this protease is appropriate.
Estimation of Origin-Destination Matrices Using Traffic Counts - A Literature Survey (1998)

The Origin-Destination (OD) matrix is important in describing transportation in a region. This matrix has information on the travel and transportation made between different zones of a region. The OD matrix can be estimated using traffic counts on links in the transport network and other available information. This information on the travel is often contained in a &quot;target OD matrix. The target OD matrix may be an old (probably outdated) matrix or a result from a sample survey. From these two data sources various approaches to estimating an OD matrix has been developed and tested. This survey provides a survey of generic approaches and an annotated bibliography of some individual contributions. Some models and methods are in another paper tested in medium sized applications in a congested region. Keywords: Estimation of OD matrix, OD matrix estimation using traffic counts. -- iii -- Acknowledgments I gratefully acknowledge my supervisors, Professor Lars Lundqvist, KTH, and Professor J...
OctoPath: An OcTree-Based Self-Supervised Learning Approach to Local Trajectory Planning for Mobile Robots (2021)

Autonomous mobile robots are usually faced with challenging situations when driving in complex environments. Namely, they have to recognize the static and dynamic obstacles, plan the driving path and execute their motion. For addressing the issue of perception and path planning, in this paper, we introduce OctoPath, which is an encoder-decoder deep neural network, trained in a self-supervised manner to predict the local optimal trajectory for the ego-vehicle. Using the discretization provided by a 3D octree environment model, our approach reformulates trajectory prediction as a classification problem with a configurable resolution. During training, OctoPath minimizes the error between the predicted and the manually driven trajectories in a given training dataset. This allows us to avoid the pitfall of regression-based trajectory estimation, in which there is an infinite state space for the output trajectory points. Environment sensing is performed using a 40-channel mechanical LiDAR sensor, fused with an inertial measurement unit and wheels odometry for state estimation. The experiments are performed both in simulation and real-life, using our own developed GridSim simulator and RovisLab's Autonomous Mobile Test Unit platform. We evaluate the predictions of OctoPath in different driving scenarios, both indoor and outdoor, while benchmarking our system against a baseline hybrid A-Star algorithm and a regression-based supervised learning method, as well as against a CNN learning-based optimal path planning method.
Near-Field Heat Transfer in a Scanning Thermal Microscope (2005)

We present measurements of the near-field heat transfer between the tip of a thermal profiler and planar material surfaces under ultrahigh vacuum conditions. For tip-sample distances below 10(-8) m, our results differ markedly from the prediction of fluctuating electrodynamics. We argue that these differences are due to the existence of a material-dependent small length scale below which the macroscopic description of the dielectric properties fails, and discuss a heuristic model which yields fair agreement with the available data. These results are of importance for the quantitative interpretation of signals obtained by scanning thermal microscopes capable of detecting local temperature variations on surfaces.