gebhart/patrepeval huggingface dataset:
Integrated microbiome and metabolome analysis reveals a novel interplay between commensal bacteria and metabolites in colorectal cancer (2019)

<b>Rationale</b>: Colorectal cancer (CRC) is a malignant tumor with the third highest morbidity rate among all cancers. Driven by the host's genetic makeup and environmental exposures, the gut microbiome and its metabolites have been implicated as the causes and regulators of CRC pathogenesis. We assessed human fecal samples as noninvasive and unbiased surrogates to catalog the gut microbiota and metabolome in patients with CRC. <b>Methods</b>: Fecal samples collected from CRC patients (CRC group, n = 50) and healthy volunteers (H group, n = 50) were subjected to microbiome (16S rRNA gene sequencing) and metabolome (gas chromatography-mass spectrometry, GC-MS) analyses. The datasets were analyzed individually and integrated for combined analysis using various bioinformatics approaches. <b>Results</b>: Fecal metabolomic analysis led to the identification of 164 metabolites spread across 40 metabolic pathways in both groups. In addition, there were 42 and 17 metabolites specific to the H and CRC groups, respectively. Sequencing of microbial diversity revealed 1084 operational taxonomic units (OTUs) across the two groups, and there was less species diversity in the CRC group than in the H group. Seventy-six discriminatory OTUs were identified for the microbiota of H volunteers and CRC patients. Integrated analysis correlated CRC-associated microbes with metabolites, such as polyamines (cadaverine and putrescine). <b>Conclusions</b>: Our results provide substantial evidence of a novel interplay between the gut microbiome and metabolome (i.e., polyamines), which is drastically perturbed in CRC. Microbe-associated metabolites can be used as diagnostic biomarkers in therapeutic explorations.
Effect of osmopriming on rice seed germination and seedling growth (2012)

The experiment was conducted in the Agronomy Laboratory of Agrotechnology Discipline, Khulna University, Khulna from 29th August to 17th September, 2009. The experiment was laid out in a Completely Randomized Design (CRD) with two factors and three replications. The aim of the experiment was to study the efficacy of three osmopriming agents viz ., NaCl, KC1 and CaCb with control on seed germination and seedling growth of three T. aman rice varities viz., BRRI dhan40, BRRI dhan41 and BINA dhan7. Among the chemicals CaCb showed best as osmopriming agents and it enhanced all germination parameters. BRRI dhan41 showed the best performance. Better root length and shoot length were observed in control. Seeds of BRRI dhan41 when treated with NaCl showed the highest germination percentage (98.67%), germination energy (88%), germination speed (96.83%), but vigor index (10.63) was found highest in BRRI dhan40 when it was treated with KC1. BRRI dhan41 produced the largest root (8.56 cm) when seeds were treated with NaCl. BRRI dhan40 (10.51 cm) and BINA dhan7 (10.53 cm) produced the highest shoot length at controlled condition and CaCl2 treated seed, respectively. DOI: http://dx.doi.org/10.3329/jbau.v10i1.12013 J. Bangladesh Agril. Univ. 10(1): 1520, 2012
The Aging Process (1990)

The intricate cause of the aging process in humans and animals, at present a matter of intense speculation, has given rise to many theories. Despite its uncertain cause, aging constitutes the most significant and universal problem confronting physicians today. Age-related physiologic deterioration and age-associated diseases are of immense concern to physicians because of the "old-age boom" anticipated in the first part of the twenty-first century. Biomedical research achievements in the twentieth century have permitted more persons to approach the fixed upper limit of the human lifespan. We discuss the functional decline of the aging heart and the underlying mechanisms of that decline; quantitative and qualitative changes in the immune system; and normal aging of the human brain contrasted to the brain changes seen in Alzheimer disease. With our growing geriatric population, we greatly need to increase our understanding of both the causes of human aging and the goals of gerontology and geriatrics and to expand research into the significant problem of Alzheimer disease.
Nonlinearity in experimental modal analysis (2001)

Modal analysis is established as one of the fundamental strategies in approaching structural dynamic problems. Despite its universal appeal, it is fundamentally a linear theory and cannot be applied to significantly nonlinear systems without incurring substantial difficulties in implementation and interpretation of results. This paper documents a number of attempts to reconcile nonlinearity with modal analysis. Three main approaches are discussed, each of which is characterized by a different philosophy.
Non-conventional expression systems for the production of vaccine proteins and immunotherapeutic molecules (2016)

The increasing demand for recombinant vaccine antigens or immunotherapeutic molecules calls into question the universality of current protein expression systems. Vaccine production can require relatively low amounts of expressed materials, but represents an extremely diverse category consisting of different target antigens with marked structural differences. In contrast, monoclonal antibodies, by definition share key molecular characteristics and require a production system capable of very large outputs, which drives the quest for highly efficient and cost-effective systems. In discussing expression systems, the primary assumption is that a universal production platform for vaccines and immunotherapeutics will unlikely exist. This review provides an overview of the evolution of traditional expression systems, including mammalian cells, yeast and E.coli, but also alternative systems such as other bacteria than E. coli, transgenic animals, insect cells, plants and microalgae, Tetrahymena thermophila, Leishmania tarentolae, filamentous fungi, cell free systems, and the incorporation of non-natural amino acids.
Design and implementation of DSP-based three-phase PFC (2011)

In this study, DSP based three phase PFC system for switching devices such as switching mode power supplies has been designed and implemented. The experimental set uses MATLAB/SIMULINK compatible eZdsp F2812 target equipped with a TI TMS320F2812 DSP. The DSP produces the driving signals by realizing control algorithm, current control and PWM modulation methods. MATLAB/SIMULINK software has been used to modeling of control algorithm, current control and PWM modulation techniques. Therefore more flexible control system has been carried out while reducing software writing time. Experimental results show that, input current of PFC system is in phase with utility voltage and its total harmonic distortion (THD) is in the range described at international standards.
Quantitative Evaluation of Mechanical Oil Spill Cleanup Devices (1973)

ABSTRACT A systematic quantitative method has been developed which can be used for preliminary screening and with the availability of more accurate performance data, used for final evaluation and selection of candidate oil removal devices. This method has been applied to various types of devices available commercially. Although the lack of precision in available performance data precludes selection between devices with close rating, an outstanding score of a device under the present method is an indication of its potential for further study or development. The result shows that for confined area operation inverted belts and a saucer weir with hydro-adjusting feature have high potential. A system based on the mechanized recovery of polyurethane foam rated high for the open area operation. The effectiveness indices for all of the open area devices considered fall in a narrow range, however, and final selection must be based on more accurate data from field and wave tank tests.
Regioselective Oxybromination of Activated Aromatic Compounds Catalysed by Ammonium Molybdate<sup>+</sup> (1994)

A highly regioselective, environmentally safe and economical method for oxybromination of both protected and unprotected anilines and phenols is possible through electrophilic substitution of bromine generated in situ from KBr using ammonium molybdate as a catalyst and H2O2 as a reoxidant for the first time.
Fine structure of hepatitis B virus surface antigen produced by recombinant yeast: comparison with HBsAg of human origin (1998)

The ultrastructure of hepatitis B virus surface antigen (HBsAg) particles produced by recombinant yeast cells was examined using high-resolution negative staining, and ice embedding, electron microscopy. With negative staining, the HBsAg particles were spherical to slightly ovoid with a mean diameter of 27.5 nm and consisted of many subunits each 4 nm in diameter. Subunits were marked with a minute central pore. With ice embedding, particles were mostly spherical to ovoid, with a mean diameter of 23.7 nm and a 7–8 nm thick cortex surrounding an electron translucent core. Human HBsAg particles, examined using the same methods, were smaller, apparently because of molecular differences in polypeptide structure.
Self-consistent field theory of directed self-assembly in laterally confined lamellae-forming diblock copolymers (2012)

We use Self-Consistent Field Theory (SCFT) to study the directed self-assembly of laterally confined diblock copolymers. In this study, we focus on systems where the self-assembled lamellae are oriented parallel to the selective sidewalls of the channel. While well-ordered, perfect lamellae are observed both experimentally and numerically, undesirable defective structures also emerge. We therefore investigate the energetics of two isolated defects, dislocations and disclinations, for various chain lengths and channel dimensions and establish conditions that favor the formation of defects. We also determine the energy barrier and the transition path between the defective and perfect state using the string method.
[Mortality in the French paper and pulp industry]. (1998)

In absence of any prior hypothesis, it is difficult to assign an occupational origin to these observed excesses. The future results of the international study will enable us to interpret these results more precisely.
PointRCNN: 3D Object Proposal Generation and Detection From Point Cloud (2019)

In this paper, we propose PointRCNN for 3D object detection from raw point cloud. The whole framework is composed of two stages: stage-1 for the bottom-up 3D proposal generation and stage-2 for refining proposals in the canonical coordinates to obtain the final detection results. Instead of generating proposals from RGB image or projecting point cloud to bird's view or voxels as previous methods do, our stage-1 sub-network directly generates a small number of high-quality 3D proposals from point cloud in a bottom-up manner via segmenting the point cloud of the whole scene into foreground points and background. The stage-2 sub-network transforms the pooled points of each proposal to canonical coordinates to learn better local spatial features, which is combined with global semantic features of each point learned in stage-1 for accurate box refinement and confidence prediction. Extensive experiments on the 3D detection benchmark of KITTI dataset show that our proposed architecture outperforms state-of-the-art methods with remarkable margins by using only point cloud as input. The code is available at https://github.com/sshaoshuai/PointRCNN.
Development of a broad-host-range sacB-based vector for unmarked allelic exchange (2008)

The broad-host-range vector for marker-free allelic exchange described here, pCM433, has the advantages of a high copy, general Escherichia coli replicon for easy cloning, an IncP oriT enabling conjugal transfer, an extensive set of restriction sites in its polylinker, three antibiotic markers, and sacB (encoding levansucrase) for negative selection upon sucrose plates. These traits should permit pCM433 to be broadly applied across many bacterial taxa for marker-free allelic exchange, which is particularly important if multiple manipulations or more subtle genetic manipulations such as point mutations are desired.
Hydrolysis of Samples for Amino Acid Analysis (2003)

There is no single hydrolysis method that will effectively cleave all proteins to single amino acids completely and quantitatively. This is owing to the varying stability of the peptide bonds between the different amino acids and the amino acid side chains, which are themselves susceptible to the reagents and conditions used to cleave the peptide bonds (see Table 1). The classical hydrolysis conditions, to which all other methods are compared, is liquid-phase hydrolysis in which the protein or peptide sample is heated in 6 M hydrochloric acid under vacuum at 110°C for 18-24 h (1). The various methods of hydrolysis described here are summarized in Table 2.
[Escherichia coli O157:H7 strains carrying Shiga toxin 2 variant slt2vha were isolated from Xuzhou City of Jiangsu Province]. (2003)

The predominant Shiga toxin types of E. coli O157:H7 in Xuzhou changed 1999 - 2000, which may be related to the changes of epidemiological features of E. coli O157:H7 infection in Xuzhou. A genotyping method based on restriction fragment length polymorphism (RFLP) analysis of a B-subunit-encoding DNA fragment obtained by PCR described in this study is a useful tool to identify slt2 gene and slt2 variant gene in epidemiological studies with O157:H7 strains.
Cleavage Fracture of Brittle Semiconductors from the Nanometre to the Centimetre Scale (2005)

Abstract The objective of this paper is to present the fundamental phenomena occurring during the scribing and subsequent fracturing process usually performed when preparing surfaces of brittle semiconductors. In the first part, an overview of nano‐scratching experiments of different semiconductor surfaces (InP, Si and GaAs) is given. It is shown how phase transformation can occur in Si under a diamond tip, how single dislocations can be induced in InP wafers and how higher scratching load of GaAs wafer leads to the apparition of a crack network below the surface. A nano‐scratching device, inside a scanning electron microscope (SEM), has been used to observe how spalling (crack and detachment of chips) and/or ductile formation of chips may happen at the semiconductor surface. In the second part cleavage experiments are described. The breaking load of thin GaAs (100) wafers is directly related to the presence of initial sharp cracks induced by scratching. By performing finite element modelling (FEM) of samples under specific loading conditions, it is found that the depth of the median crack below the scratch determines quantitatively the onset of crack propagation. By carefully controlling the position and measuring the force during the cleavage, it is demonstrated that crack propagation through a wafer can be controlled. Besides, the influence of the loading configuration on crack propagation and on the cleaved surface quality is explained.
Contributions to variance in force-plate analysis of gait in dogs. (1993)

Coefficients of variation were calculated for peak vertical force and for vertical, cranial, and caudal impulses recorded from the left forelimb and left hind limb of 5 dogs that were trotted across a force plate 5 times by 5 handlers. To determine the percentages of variance attributable to dogs, handlers, and trial repetitions, data recorded for each force measurement were analyzed according to a two-factor ANOVA. Coefficients of variation for peak vertical forces and for vertical impulses varied between 5.8 and 8.5%. Coefficients of variation for the forelimb cranial and caudal impulses and for the hind limb cranial and caudal impulses were 26.4 and 30.5%, and 63.0 and 25.9%, respectively. The percentage of the total variance attributable to dogs and to trial repetitions ranged from 14 to 69% and from 29 to 85%, respectively, depending on the force or impulse evaluated. The percentage of variance attributable to handlers varied between 0 and 7%. The trivial amount of variation attributable to handlers indicated that multiple handlers may be used in experiments without an appreciable influence on the results.
Self-Diffusion and Constraint Release in Isotropic Entangled Rod–Coil Block Copolymers (2015)

Understanding dynamic relaxation mechanisms in self-diffusion and constraint release processes of rod–coil block copolymers is important for many technological applications that employ neat melts or concentrated solutions. Using a model system composed of poly(alkoxyphenylenevinylene) rods and polyisoprene coils, reptation theories of entangled rod–coil block copolymers are investigated in the isotropic melt state. Self-diffusion was measured by forced Rayleigh scattering using a red laser line and a new blue photoswitchable dye that allow operation above the bandgap of most semiconducting polymers. In contrast to previous tracer studies where the diffusion of rod–coils through a coil homopolymer matrix is slowed relative to coil homopolymers because of a mismatch in the curvature of the rod and coil entanglement tubes, slowed diffusion is only present in self-diffusion measurements above a critical molecular weight. An activated reptation mechanism with constraint release is proposed as a modification to the description of entangled rod–coil block copolymer dynamics, where the slowing occurs when the time scale of rod block reptation is faster than the reorganization of the surrounding entanglement tube. This mechanism is supported by additional tracer diffusion experiments on polyalanine-b-poly(ethylene oxide) diblocks in aqueous entangled poly(ethylene oxide) matrix solutions and Kremer–Grest simulations where the matrix molecular weight is varied. The slowing of tracer diffusion in rod–coil block copolymers relative to coil homopolymers is significantly weaker for smaller matrix polymers, confirming the proposed constraint release effects.
Densification, phase transformation and hardness of mullite-cubic BN composites prepared by spark plasma sintering (2010)

Mullite-cubic boron nitride (cBN) composites were prepared using mullite and cBN powders by spark plasma sintering at temperatures of 1500-1700°C for a holding time of 600 s under a pressure of 100 MPa. Densification, microstructure and hardness of the mullite-BN composites and the phase transformation of cBN to hexagonal BN (hBN) in the mullite-BN composites were studied. Fully dense mullite-cBN composites originally containing 10-30 vol% cBN with relative density of over 95% were obtained at 1500°C without the phase transformation of cBN. At the cBN content of 10 vol%, the densification of the mullite-BN composite was not inhibited. When more than 20 vol% cBN was added to mullite, the densification of the mullite-BN composites was suppressed. The phase transformation of cBN in the mullite-BN composites started at 1600-1700°C. The hardness of mullite-BN composites originally containing 20 vol% cBN sintered at 1500°C without the phase transformation of cBN reached a maximum value of 16 GPa.
High-energy ultraviolet I/sub 2/ laser (1983)

Excitation of the I/sub 2/ laser occurs when pump photons with a 20-nm band centered at lambda = 190 nm are absorbed by the I/sub 2/ D formed from X band, whose peak absorption cross section is 3(+/-1) x 10-/sup 17/ cm/sup 2/. A moderately high pressure of buffer gas (approx.0.5-3 atm) collisionally relaxes the population into the D' state, from which lasing occurs to the A' state. This weakly bound state quickly dissociates, leading to rapid reformation of ground-state I/sub 2/ species. Exploding metal films and wires were used to optically pump the 342-nm I/sub 2/ laser. Specific output energies as high as 18 joules/liter and electrical efficiencies up to 0.27% were measured. Several parametric studies were conducted.
[A contribution to the stabilisation of the MVA-vaccine (author's transl)]. (1979)

The titre of the MVA-vaccine remains constant at -20 degrees C with human serum albumin, sorbitol, Haemaccel, Rheomacrodex and cysteine within 8 month. At -20 degrees C the stability of the MVA-virus is equivalent to the Vaccinia-virus, stabilized by peptone and sorbitol. Storing the MVA-Virus at +4 degrees C, +20 degrees C for 8 month or at 27 degrees C for 4 weeks, 1% human serum albumin and 5% sorbitol preserves the virustitre best, but the stability of Vaccinia-virus with 5% peptone and 5% sorbitol can, however, not be obtained by the MVA-virus under these conditions.
Teleoperation of a mobile robot through haptic feedback (2003)

Teleoperation systems have been developed in order to allow a human operator to perform complex tasks in remote environments. Mobile robots can be considered as a particular example of telemanipulation systems, since they can be operated remotely to perform particular tasks. As an example, the inspection of underwater structures and the removal of mines are performed by mobile platforms controlled by a remote operator, which generally takes advantage only of the visual feedback provided by vision systems. In this sense, the nature and completeness of the data provided to the operator about the state of the remote system are of crucial importance for proper task execution, and it is generally accepted that a more efficient achievement of the task can be obtained by increasing the amount of data feedback and using proper MMI. In this paper, the use of a haptic interface is proposed in order to increase a user's perception of the workspace of a mobile robot. In particular, a virtual interaction force is computed on the basis of obstacles surrounding the mobile vehicle in order to prevent dangerous contacts, so that navigation tasks can be carried out with generally better performances. In addition, passivity of the overall system is taken into account, so that stability of the virtual interaction is guaranteed.
Laboratory experiments to test relativistic gravity (1977)

Advancing technology will soon make possible a new class of gravitation experiments: pure laboratory experiments with laboratory sources of non-Newtonian gravity and laboratory detectors. This paper proposes seven such experiments; and for each one it describes, briefly, the dominant sources of noise and the technology required. Three experiments would utilize a high-$Q$ torque balance as the detector. They include (i) an "Amp\`ere-type" experiment to measure the gravitational spin-spin coupling of two rotating bodies, (ii) a search for time changes of the gravitation constant, and (iii) a measurement of the gravity produced by magnetic stresses and energy. Three experiments would utilize a high-$Q$ dielectric crystal as the detector. They include (i) a "Faraday-type" experiment to measure the "electric-type" gravity produced by a time-changing flux of "magnetic-type" gravity, (ii) a search for "preferred-frame" and "preferred-orientation" effects in gravitational coupling, and (iii) a measurement of the gravitational field produced by protons moving in a storage ring at nearly the speed of light. One experiment would use a high-$Q$ toroidal microwave cavity as detector to search for the dragging of inertial frames by a rotating body.