cssi/SciSciGPT-SciSciNet huggingface dataset:
On the expanding roles of tRNA fragments in modulating cell behavior

The fragments that derive from transfer RNAs (tRNAs) are an emerging category of regulatory RNAs. Known as tRFs, these fragments were reported for the first time only a decade ago, making them a relatively recent addition to the ever-expanding pantheon of non-coding RNAs. tRFs are short, 16-35 nucleotides (nts) in length, and produced through cleavage of mature and precursor tRNAs at various positions. Both cleavage positions and relative tRF abundance depend strongly on context, including the tissue type, tissue state, and disease, as well as the sex, population of origin, and race/ethnicity of an individual. These dependencies increase the urgency to understand the regulatory roles of tRFs. Such efforts are gaining momentum, and comprise experimental and computational approaches. System-level studies across many tissues and thousands of samples have produced strong evidence that tRFs have important and multi-faceted roles. Here, we review the relevant literature on tRF biology in higher organisms, single cell eukaryotes, and prokaryotes.
Laboratory testing and calibration of the upgraded MMT adaptive secondary mirror

The MMT Adaptive optics exoPlanet characterization System (MAPS) is a broad overhaul and upgrade of AO instrumentation at the 6.5-m MMT observatory, from deformable secondary mirror, through pyramid wavefront sensors in both the visible and near-infrared, to improved science cameras. MAPS is an NSF MSIP-funded program whose ultimate goal is a facility optimized for exoplanet characterization. Here we describe the laboratory testing and calibration of one MAPS component: the refurbished MMT adaptive secondary mirror (ASM). The new ASM includes a complete redesign of electronics and actuators, including simplified hub-level electronics and digital electronics incorporated into the actuators themselves. The redesign reduces total power to l300W, from the original system’s 1800W, which in turn allows us to eliminate liquid cooling at the hub with no loss of performance. We present testing strategies, results, and lessons learned from laboratory experience with the MAPS ASM. We discuss calibrations first on the level of individual actuators, including capacitive position sensing, force response function, and individual closed-loop position control with an improved control law. We then describe investigations into the full ASM system – hub, actuators, thin shell, and human – to understand how to optimize interactions between components for dynamical shape control using a feedforward matrix. Finally, we present our results in the form of feedforward matrix and control law parameters that successfully produce a desired mirror surface within 1ms settling time.
Artificial intelligence in pancreaticobiliary endoscopy

Artificial intelligence (AI) applications in health care have exponentially increased in recent years, and a few of these are related to pancreatobiliary disorders. AI-based methods were applied to extract information, in prognostication, to guide clinical treatment decisions and in pancreatobiliary endoscopy to characterize lesions. AI applications in endoscopy are expected to reduce inter-operator variability, improve the accuracy of diagnosis, and assist in therapeutic decision-making in real time. AI-based literature must however be interpreted with caution given the limited external validation. A multidisciplinary approach combining clinical and imaging or endoscopy data will better utilize AI-based technologies to further improve patient care.
Nanoscale Dynamics of Cellulose Digestion by the Cellobiohydrolase TrCel7A

Understanding the mechanism by which cellulases from bacteria, fungi, and protozoans catalyze the digestion of lignocellulose is important for developing cost-effective strategies for bioethanol production. Cel7A from the fungus Trichoderma reesei is a model exoglucanase that degrades cellulose strands from their reducing ends by processively cleaving individual cellobiose units. Despite being one of the most studied cellulases, the binding and hydrolysis mechanisms of Cel7A are still debated. Here, we used single-molecule tracking to analyze the dynamics of 11,116 quantum dot-labeled TrCel7A molecules binding to and moving processively along immobilized cellulose. Individual enzyme molecules were localized with a spatial precision of a few nanometers and followed for hundreds of seconds. Most enzyme molecules bound to cellulose in a static state and dissociated without detectable movement, whereas a minority of molecules moved processively for an average distance of 39 nm at an average speed of 3.2 nm/s. These data were integrated into a three-state model in which TrCel7A molecules can bind from solution into either static or processive states and can reversibly switch between states before dissociating. From these results, we conclude that the rate-limiting step for cellulose degradation by Cel7A is the transition out of the static state, either by dissociation from the cellulose surface or by initiation of a processive run. Thus, accelerating the transition of Cel7A out of its static state is a potential avenue for improving cellulase efficiency.
A parametric modeling study of thermal barrier coatings in low-temperature combustion engines

Abstract In-cylinder thermal barrier coatings (TBCs) reduce heat transfer losses and increase thermal efficiency. It has been shown that thick TBCs negatively impact the performance of conventional combustion modes by degrading volumetric efficiency and increasing the propensity for end-gas knock. Low-temperature combustion (LTC) is an advanced combustion strategy that offers high efficiencies and low emissions. Due to the nature of kinetics-driven autoignition, LTC is fundamentally different from the conventional combustion modes, where the benefits and tradeoffs of thick TBCs need to be re-evaluated. Previous experimental studies showed the feasibility and the efficiency gains associated with a 2 mm thick TBC applied to the piston surface, as well as the reduction in the required intake temperature with no observable deterioration on the high load limit. However, the effects of TBCs and their independent thermophysical properties on LTC have not been systematically explored. It is necessary to perform a comprehensive study on the effects of TBC on LTCs from a fundamental thermodynamic perspective, which serves as the motivation for the current study. This study couples a 0D engine thermodynamic model to a 1D transient heat transfer model of the coating and piston. The model was first validated against the metal piston baseline, followed by validation against experimental data of the TBC cases at different engine loads. With confidence established in the model’s fidelity, three parameters are investigated independently: thermal conductivity (k), coating thickness, and volumetric heat capacity (s). The results revealed that the volumetric efficiency actually increases by 7.4 percentage points with a thicker coating due to a reduction in heat transfer during the compression stroke, which allows for a lower intake temperature requirement to reach autoignition. However, there is a thickness limit before the intake temperature becomes impractically low. The results show that elevating surface temperature is directly proportional to higher efficiency. Therefore, the optimal coating configuration for kinetically-controlled LTC is a combination of the lowest k, thickest coating before reaching the limit, and the lowest s, where the low k and high thickness contribute the most thermal efficiency gains (4.1 percentage points) and increased exhaust enthalpy (5.7%).
A multidimensional approach to evaluating the vulnerability of drinking water systems

Safe, affordable, reliable drinking water is central to public health, strong communities, economic development, and a healthy environment. Drinking water policy and management tends to rely on reg...
The Effect of Ag/Ag2O Doping on the Low Temperature Sintering of Superconducting Composites

Practical applications of the high-Tc ceramic superconductors will require electrical, mechanical and thermal stabilization of the superconducting phase. Non-noble metal superconducting particulate composites have been formed with various metals, in order to achieve some of the desirable properties. One of the critical parameters in forming superconducting composites with non-noble metals is the processing temperature of the composites, which is dictated primarily by the need to sinter the ceramic particles into a continuous superconducting skeleton. The possilbility to lower the processing temperature of the composites, by the use of Ag/Ag2O is explored. The relative effect of Ag and Ag2O on the low temperature sintering of Y1Ba2Cu3O7−x is discussed. The major difficulty in forming superconducting composites at low temperatures seems to be associated with poor contacts between the individual ceramic particles within the composite.
flrB, a regulatory locus controlling branched-chain amino acid biosynthesis in Salmonella typhimurium.

Salmonella typhimurium strain CV123 (ara-9 gal-205 flrB1), isolated as a mutant resistant to trifluoroleucine, has derepressed and constitutive levels of enzymes forming branched-chain amino acids. This strain grows more slowly than the parent at several temperatures, both in minimal medium and nutrient broth. It overproduces and excretes sizeable amounts of leucine, valine, and isoleucine in comparison with the parental strain. Both leuS (coding for leucyl-transfer ribonucleic acid [tRNA]synthetase) and flrB are linked to lip (min 20 to 25) by P1 transduction, whereas only leuS is linked to lip by P22 transduction. Strain CV123 containing an F′ lip+ episome from Escherichia coli has repressed levels of leucine-forming enzymes, indicating that flrB+ is dominant to flrB. Leucyl-tRNA synthetase from strain CV123 appears to be identical to the leucyl-tRNA synthetase in the parent. No differences were detected between strain CV123 and the parent with respect to tRNA acceptor activity for a number of amino acids. Furthermore, there was no large difference between the two strains in the patterns of leucine tRNA isoaccepting species after fractionation on several different columns. Several other flrB strains exhibited temperature-sensitive excretion of leucine, i.e., they excreted leucine at 37 C but not 25 C. In one such strain, excretion at 37 C was correlated with derepression of some enzymes specified by ilv and leu. These latter results suggest that flrB codes for a protein.
Expansion of opiate agonist treatment: an historical perspective.

Untreated opiate addiction remains a major health care crisis in New York and in most other urban centers in America. Optimism for closing the gap between need and demand for treatment and its availability has greeted the recent approval of a new opiate medication for addiction, buprenorphine – which unlike methadone may be prescribed by independent, office-based practitioners. The likelihood of buprenorphine fulfilling its potential is assessed in the light of the massive expansion of methadone treatment more than 30 years earlier. It is concluded that the key, indispensable ingredient of success will be true commitment on the part of Government to provide care to all those who need it.
Softcast: exposing a waveform interface to the wireless channel for scalable video broadcast

Video broadcast and mobile video challenge the conventional wireless design. In broadcast and mobile scenarios the bit-rate supported by the channel differs across receivers and varies quickly over time. The conventional design however forces the source to pick a single bit-rate and degrades sharply when the channel cannot support it. This thesis presents SoftCast, a clean-slate design for wireless video where the source transmits one video stream that each receiver decodes to a video quality commensurate with its specific instantaneous channel quality. To do so, SoftCast ensures the samples of the digital video signal transmitted on the channel are linearly related to the pixels' luminance. Thus, when channel noise perturbs the transmitted signal samples, the perturbation naturally translates into approximation in the original video pixels. Hence, a receiver with a good channel (low noise) obtains a high fidelity video, and a receiver with a bad channel (high noise) obtains a low fidelity video. SoftCast's linear design in essence resembles the traditional analog approach to communication, which was abandoned in most major communication systems, as it does not enjoy the theoretical opimality of the digital separate design in point-to-point channels nor its effectiveness at compressing the source data. In this thesis, I show that in combination with decorrelating transforms common to modern digital video compression, the analog approach can achieve performance competitive with the prevalent digital design for a wide variety of practical point-to-point scenarios, and outperforms it in the broadcast and mobile scenarios. Since the conventional bit-pipe interface of the wireless physical layer (PHY) forces the separation of source and channel coding, to realize SoftCast, architectural changes to the wireless PHY are necessary. This thesis discusses the design of RawPHY, a reorganization of the PHY which exposes a waveform interface to the channel while shielding the designers of the higher layers from much of the perplexity of the wireless channel. I implement SoftCast and RawPHY using the GNURadio software and the USRP platform. Results from a 20-node testbed show that SoftCast improves the average video quality (i.e., PSNR) across diverse broadcast receivers in our testbed by up to 5.5 dB in comparison to conventional single- or multi-layer video. Even for a single receiver, it eliminates video glitches caused by mobility and increases robustness to packet loss by an order of magnitude. (Copies available exclusively from MIT Libraries, Rm. 14-0551, Cambridge, MA 02139-4307. Ph. 617-253-5668; Fax 617-253-1690.)
The role of adjuvant therapy in Stage I ovarian cancer

Women with Stage I epithelial carcinoma of the ovary were initially treated by an extirpative operation and were subsequently randomized to either no further treatment, radiotherapy, or chemotherapy. Only two patients (6%) treated with chemotherapy developed recurrence, compared to five (17%) and seven (30%) patients in the no-treatment and radiotherapy regimens, respectively (P < 0.05). All patients, with the possible exception of those with Stage IA(1)g1, appeared to benefit from adjuvant chemotherapy compared to no treatment or radiotherapy.
Species-level classification of the vaginal microbiome

The application of next-generation sequencing to the study of the vaginal microbiome is revealing the spectrum of microbial communities that inhabit the human vagina. High-resolution identification of bacterial taxa, minimally to the species level, is necessary to fully understand the association of the vaginal microbiome with bacterial vaginosis, sexually transmitted infections, pregnancy complications, menopause, and other physiological and infectious conditions. However, most current taxonomic assignment strategies based on metagenomic 16S rDNA sequence analysis provide at best a genus-level resolution. While surveys of 16S rRNA gene sequences are common in microbiome studies, few well-curated, body-site-specific reference databases of 16S rRNA gene sequences are available, and no such resource is available for vaginal microbiome studies. We constructed the Vaginal 16S rDNA Reference Database, a comprehensive and non-redundant database of 16S rDNA reference sequences for bacterial taxa likely to be associated with vaginal health, and we developed STIRRUPS, a new method that employs the USEARCH algorithm with a curated reference database for rapid species-level classification of 16S rDNA partial sequences. The method was applied to two datasets of V1-V3 16S rDNA reads: one generated from a mock community containing DNA from six bacterial strains associated with vaginal health, and a second generated from over 1,000 mid-vaginal samples collected as part of the Vaginal Human Microbiome Project at Virginia Commonwealth University. In both datasets, STIRRUPS, used in conjunction with the Vaginal 16S rDNA Reference Database, classified more than 95% of processed reads to a species-level taxon using a 97% global identity threshold for assignment. This database and method provide accurate species-level classifications of metagenomic 16S rDNA sequence reads that will be useful for analysis and comparison of microbiome profiles from vaginal samples. STIRRUPS can be used to classify 16S rDNA sequence reads from other ecological niches if an appropriate reference database of 16S rDNA sequences is available.
What Is the Universe Made of

Having considered the nature of space and time, we now turn our attention to the stuff of the universe: what do we know about the things—both material and immaterial—which inhabit space and time? The state of our current understanding of matter and energy is both highly detailed and very incomplete. We still have a lot to learn. As already hinted in Chap. 2, Einstein’s theory of general relativity is very successful at describing physics on the large scale (planetary, stellar, galactic, and so forth), but is completely incompatible with quantum mechanics—an equally successful model of physics, but at the subatomic scale. The ongoing quest to resolve this incompatibility is one of the most interesting and open fields of physics research. In this chapter we will explore various properties of materials, including some of the latest developments in materials science. But we will begin with a look at the fundamental building blocks of matter and one of the most intriguing questions of modern physics: What is the universe made of?
The Democratic Effects of the Internet, 1994—2003 A Cross-National Inquiry of 152 Countries

/ Since its inception and subsequent diffusion, the Internet has been lauded as a potent democratizing agent. Using macro-level panel data from 1994 to 2003, this study examined 152 countries and found that increased Internet diffusion was a meaningful predictor of more democratic regimes. This was shown to be most true in developed countries, where non-linear fixed effects regression models showed the highest coefficient estimates and largest observed associations. Consistent with media system dependency theory, greater effects were also demonstrated for countries that already were at least partially democratic where the Internet was more prevalent and thus more likely to fulfill a greater number of information functions. In addition, Internet diffusion and democracy demonstrated a positive, statistically significant relationship (but with a marginal observed association size) in developing countries where the average level of sociopolitical instability was much higher. The Internet therefore should not ...
Nitric oxide inhibition increases aortic wall matrix metalloproteinase-9 expression.

Objective. Nitric oxide (NO) may mediate vessel wall remodeling by regulating expression of matrix metalloproteinases (MMPs) and tissue inhibitors of metalloproteinases (TIMPs). This study tested the hypothesis that nitric oxide synthase (NOS) inhibition in whole aortic wall causes increases in cytokine-stimulated MMP and TIMP expression. Methods. Cultured infrarenal aortic segments from Sprague-Dawley rats were exposed to increasing concentrations (0, 0.1, 0.5, 1, and 5 mM; n = 6 per concentration) of NG-monomethyl-l-arginine (L-NMMA), a known inhibitor of NOS. This was in the presence of 2 ng/ml of interleukin-1β, a known inducer of NOS, MMP, and TIMP expression. Media nitrate and nitrite (NOx) were measured at 72 h using the Saville method. Media MMP activity was measured using gelatin zymography. MMP-2 and -9 protein and mRNA levels were determined by Western blot and reverse transcriptase-polymerase chain reaction (RT-PCR). TIMP activity and mRNA levels were evaluated by reverse zymography and RT-PCR. Data were analyzed using ANOVA. Results. Increasing concentrations of L-NMMA produced a dose-dependent decrease in NOx (2214 ± 405 to 347 ± 37 ng/mg, P < 0.001). Zymography demonstrated a dose-dependent increase in 92-kDa MMP (pro-MMP-9) activity (P < 0.001) with corresponding increases in pro-MMP-9 protein (P = 0.03) and mRNA levels (P = 0.004). While there was a dose-dependent increase in 72-kDa MMP (pro-MMP-2) activity (P = 0.001), pro-MMP-2 protein and mRNA levels were unchanged. Reverse zymography demonstrated a dose-dependent increase in 29-kDa TIMP-1 activity (P = 0.01), but there was no change in TIMP-1 mRNA levels. Conclusions. NOS inhibition in ex vivo aortic tissue causes a dose-dependent increase in MMP-9 expression and activity. It is speculated that deficiencies of NO in vivo alter MMP and TIMP homeostasis, favoring matrix degradation.
Theoretical analysis of particle trajectories and sieving in a two-dimensional cross-flow filtration system

Particle deposition and fouling are critical factors governing the performance of microfiltration systems. Particle trajectories in cross-flow filtration were evaluated by numerical integration of the Langevin equation accounting for the combined effects of electrostatic repulsion, enhanced hydrodynamic drag, Brownian diffusion, inertial lift and van der Waals attraction. The membrane remains completely free of particles below a critical filtration velocity due to the electrostatic repulsion between the charged particles and the charged membrane. This critical flux increases with increasing surface potential and decreasing ionic strength due to the increase in electrostatic repulsion. The critical flux also increases with increasing wall shear rate due to the reduction in residence time over the pore. Brownian motion provides a random character to the particle trajectories, allowing particles to enter the pores even at operation below the critical flux. Particle transmission increases with increasing filtrate flux and ionic strength, and decreases with increasing particle size, wall shear rate and electrostatic potential.
A relation between diagonal and unconditional basis constants

This note establishes an inequality relating the weakly nuclear norm of the identity on a finite dimensional space with the diagonal symmetry constant of the space. An application shows the non-existance of"good" diagonally symmetric bases in L(l~), the space of linear operators on n-dimensional Hilbert space. More precisely, for any basis (bi)i _n t/2 It u 11/18. In addition it is shown that there are spaces with diagonal symmetry constant one, but with unconditional basis constant greater than one.
Variability of precision pinch movements caused by carpal tunnel syndrome.

Purpose Carpal tunnel syndrome (CTS) impairs the performance of fine motor tasks of the hand, leading to clumsiness. Precision pinch by the thumb and index finger is a frequent task that requires the fine control of each digit as well as the coordination of the 2 digits. The purpose of this study was to examine the performance of precision pinch movements impaired by CTS. Methods Sixteen CTS subjects and 16 gender- and age-matched control subjects were instructed to repetitively perform the precision pinch movement with the thumb and index finger. A marker-based motion analysis method was used to obtain the kinematic data of the thumb and index finger during the precision pinch movements. Pinch performance was quantified by the variability of tip positions, joint angles, and tip distance at the pinch closures in the repeated movements. Results The CTS subjects performed the precision pinch movements less consistently compared with performance of the control subjects. The inconsistency was demonstrated by the increased variability of the tip positions of the 2 digits and the joint angles of the index finger. However, the variability of thumb joint angles was not significantly different between the 2 groups. The tip-to-tip distance, an indicator of thumb and index finger coordination, was relatively reproducible for both groups. Still, the CTS subjects showed a 50% greater variability of the tip distance compared with that of the control subjects. Conclusions Carpal tunnel syndrome impairs the performance of precision pinch movement as indicated by the increased variability. The results correlate with the observed clumsiness or lack of dexterity for patients with CTS.
Pairing and radio-frequency spectroscopy in two-dimensional Fermi gases

We theoretically study the normal phase properties of strongly interacting two-component Fermi gases in two spatial dimensions. In the limit of weak attraction, we find that the gas can be described in terms of effective polarons. As the attraction between fermions increases, we find a crossover from a gas of noninteracting polarons to a pseudogap regime. We investigate how this crossover is manifested in the radio-frequency (rf) spectroscopy. Our findings qualitatively explain the differences in the recent rf spectroscopy measurements of two-dimensional Fermi gases [Sommer et al., Phys. Rev. Lett. 108, 045302 (2012) and Zhang et al., Phys. Rev. Lett. 108, 235302 (2012)].
Electrical Properties of the Venus Surface from Bistatic Radar Observations

A bistatic radar experiment in 1994, involving reception on Earth of a specularly reflected, linearly polarized 13-centimeter-wavelength signal transmitted from the Magellan spacecraft in orbit around Venus, has established that the surface materials viewed at low and intermediate altitudes on Venus have a relative dielectric permittivity of 4.0 ± 0.5. However, bistatic results for the Maxwell Montes highlands imply an electrically lossy surface with an imaginary dielectric permittivity of − i 100 ± 50, probably associated with a specific conductivity of about 13 mhos per meter. Candidates for highlands surface composition include ferroelectrics, a thin frost of elemental tellurium, or a plating of magnetite or pyrites.
Microtubules and tubulin sheet polymers elongate from isolated axonemes in vitro as observed by negative-stain electron microscopy

Abstract Microtubules are an important cytoskeletal component involved in cell motility and morphogenesis. They are unique polymers because they are highly dynamic in vivo and in vitro , displaying spontaneous transitions between phases of elongation and rapid shortening. This property has been termed microtubule dynamic instability. Here we describe the application of negative-stain electron microscopy to examine the morphology of microtubules. The purpose was to provide insight into the structural basis of dynamic instability. Highly purified porcine brain tubulin was seeded from isolated axoneme seeds and the morphologies of the tubulin polymers were examined. As previously reported, tubulin polymer sheets in addition to intact MTs were observed during elongation. Cross-sections of identical preparations displayed intact circles (MTs) and c-shaped polymers. The fraction of sheets (28%) observed by negative staining was identical to the fraction of c-shaped polymers in cross-sections. These results suggest that tubulin polymer elongation is not strictly helical due to the lack of helical symmetry of tubulin sheets. Finally, we document the novel effect of glutaraldehyde fixation on MTs. Fixation of MTs in 1% glutaraldehyde for longer than 2 min severely disrupted MT protofilament structure and induced MT curvature at a gross level. Even at 1 min, thin, thread-like structures were observed that were only present in glutaraldehyde-fixed samples. It is therefore an advantage to minimize the extent of glutaraldehyde fixation.
Measurement of hemolysin transfer using untreated red blood cells.

SummaryA modified method is. described for measurement of the avidity of rabbit anti-sheep hemolysin in terms of the proportional transfer of the antibody from one population of erythrocytes to another. It is simple, involves colorimetric measurements only, eliminates the need for pretreatment (e.g., Cr51- labeling) of one of the 2 cell populations, yet yields results comparable to those obtained using an isotopic label.
Functional Domains of ExsA, the Transcriptional Activator of the Pseudomonas aeruginosa Type III Secretion System

The opportunistic pathogen Pseudomonas aeruginosa utilizes a type III secretion system (T3SS) to evade phagocytosis and damage eukaryotic cells. Transcription of the T3SS regulon is controlled by ExsA, a member of the AraC/XylS family of transcriptional regulators. These family members generally consist of an approximately 100-amino acid carboxy-terminal domain (CTD) with two helix-turn-helix DNA binding motifs and an approximately 200-amino acid amino-terminal domain (NTD) with known functions including oligomerization and ligand binding. In the present study, we show that the CTD of ExsA binds to ExsA-dependent promoters in vitro and activates transcription from ExsA-dependent promoters both in vitro and in vivo. Despite possessing these activities, the CTD lacks the cooperative binding properties observed for full-length ExsA at the P(exsC) promoter. In addition, the CTD is unaffected by the negative regulatory activity of ExsD, an inhibitor of ExsA activity. Binding studies confirm that ExsD interacts directly with the NTD of ExsA. Our data are consistent with a model in which a single ExsA molecule first binds to a high-affinity site on the P(exsC) promoter. Protein-protein interactions mediated by the NTD then recruit an additional ExsA molecule to a second site on the promoter to form a complex capable of stimulating wild-type levels of transcription. These findings provide important insight into the mechanisms of transcriptional activation by ExsA and inhibition of ExsA activity by ExsD.
On the resolvability of the tris(catecholato) aluminate ion

Abstract Repeated attempts to resolve the tris (cathecholato) aluminate ion using reported procedures were uniformly unsuccessful. All instances where rotations were observed could be attributed to residual resolving agent. An examination of the ligand exchange with 4-chlorocatechol shows that such exchange is rapid at a pH of 8·6 at 25°C. In contrast to this, the residual optical activity observed with solutions in which the presumably resolved complex was present showed no noticeable change over a period of days.
Claim-Evidence Structures in Environmental Science Writing: Modifying Toulmin's Model to Account for Multimodal Arguments

This article develops a multimodal model for how claims and evidence work across linguistic, numeric, and visual modes in the professional writing of environmental scientists. I coded and analyzed two reports (Bacey & Barry, 2008; Levine et al., 2005) written by research scientists working for California's Department of Pesticide Regulation (DPR) by applying concepts from studies of argument, genre, and visual representations in science. The claim-evidence patterns show initial and summative claims as well as warrants being presented in linguistic forms; however, supporting evidence (i.e., data and backing) is found in numeric, visual, and linguistic forms. These findings highlight the need to extend Toulmin's understanding of claim-evidence relationships into a more robust multimodal model.
Four-point probe resistivity measurements of dicing damage in (100) and (111) single crystal silicon wafers

Dicing damage in single crystal Czochralski (Cz) silicon wafers ((100) and (111) n-type) with initial resistivities of 0.057 and 13.89 Ω cm was investigated by forming grooves at room temperature with dicing blades lubricated with de-ionized water. The grooves were purposely misoriented by 10 °, 20 °, and 30 ° relative to the [110]. The groove surfaces were examined by optical microscopy and scanning electron microscopy while the subsurface deformation was examined after bevel polishing. The subsurface damage was quantified by four-point probe measurements along the groove length including the bevelled region with the probe tips straddling the groove. The results show that the resistivity varies with position along the groove. A maximum increase on the resistivity of 9.7% for the (100) and 8.0% for the (111) was formed for a dicing blade misorientation of 20 °. Microscopy of the bevelled region shows that the damage is composed of microcracks: the depth is 0.122mm for the (100) and 0.186 mm for the (111) at the 20 ° blade misorientation.
A silicon phthalocyanine and a silicon naphthalocyanine: synthesis, electrochemistry, and electrogenerated chemiluminescence

Abstract : The synthesis, spectral characterization, and electrochemical behavior of bis(tri-n-hexylsiloxy)-2,3-phthalocyaninatosilicon (SiPc(OR)2), its dimer (RO(SiPcO)2R), and its naphthalocyanine analog (SiNc(OR)2) are described. All compounds show near UV absorption corresponding to Soret and N bands and intense absorption in the visible-near IR region corresponding to Q-bands. In CH2Cl2, within the solvent stability limit, there are two reductions and one oxidation for SiPc(OR)2 and two reductions and two oxidations for RO(SiPcO)2R and SiNc(OR)2; all appear as reversible one electron waves, although n=2 for the dimer. The difference in the peak potentials of the first oxidation and first reduction waves agrees well with the excitation energy and fluorescence (corresponding to Q-bands) of SiPc(OR)2 and SiNc(OR)2.
Alternative Research Perspectives

Waldron begins the final section of her letter with the claim that the data for all but 16 of the 48 children with suspected DAS should be discounted, noting that even the 16 subjects "have widely ...
Ligand-based photooxidations of dithiomaltolato complexes of Ru(II) and Zn(II): photolytic CH activation and evidence of singlet oxygen generation and quenching.

The complex [Ru(bpy)2(ttma)]+ (bpy = 2,2′-bipyridine; ttma = 3-hydroxy-2-methyl-thiopyran-4-thionate, 1, has previously been shown to undergo an unusual C–H activation of the dithiomaltolato ligand upon outer-sphere oxidation. The reaction generated alcohol and aldehyde products 2 and 3 from C–H oxidation of the pendant methyl group. In this report, we demonstrate that the same products are formed upon photolysis of 1 in presence of mild oxidants such as methyl viologen, [Ru(NH3)6]3+ and [Co(NH3)5Cl]2+, which do not oxidize 1 in the dark. This reactivity is engendered only upon excitation into an absorption band attributed to the ttma ligand. Analogous experiments with the homoleptic Zn(ttma)2, 4, also result in reduction of electron acceptors upon excitation of the ttma absorption band. Complexes 1 and 4 exhibit short-lived visible fluorescence and long-lived near-infrared phosphorescence bands. Singlet oxygen is both generated and quenched during aerobic excitation of 1 or 4, but is not involved in the C–H activation process.
Non-meanfield deterministic limits in chemical reaction kinetics

A general mechanism is proposed by which small intrinsic fluctuations in a system far from equilibrium can result in nearly deterministic dynamical behaviors which are markedly distinct from those realized in the meanfield limit. The mechanism is demonstrated for the kinetic Monte Carlo version of the Schnakenberg reaction where we identified a scaling limit in which the global deterministic bifurcation picture is fundamentally altered by fluctuations. Numerical simulations of the model are found to be in quantitative agreement with theoretical predictions.
The Effects of Androgen Administration on Phallic Androgen Receptor Expression

AbstractPurpose: Whether androgens down regulate the androgen receptor during penile development is controversial. We investigated the effects of androgens on penile androgen receptor expression.Materials and Methods: We injected prepubertal hypogonadotropic hypogonadal microphallic rats with testosterone or dihydrotestosterone. Specimens were obtained at 3 (prepuberty), 9 (puberty to early postpuberty) and 12 weeks (late postpuberty). At necropsy we compared penile size and androgen receptor expression of these animals to those of age matched nontreated hypogonadotropic hypogonadal and normal controls.Results: At age 3 weeks prepubertal androgens up regulated androgen receptor expression and significantly increased penile size compared to normal and untreated hypogonadotropic hypogonadal controls. By 9 weeks the normal down regulation of androgen receptor that occurs with maturation was present. Prepubertal androgens failed to accelerate or exaggerate the normal maturational loss of the androgen receptor...
Thickness Design of PCC/FBC Composites for Secondary/County Roads

Tests were conducted in the laboratory and field to determine the extent to which fluidized bed combustion (FBC) spent bed and pulverized coal combustion (PCC) fly ash, by products of the coal industry, can be used in low-volume county and secondary roads. Various proportions of prehydrated FBC spent bed (as a secondary aggregate and an agent to activate pozzolan oxides), PCC fly ash (as a primary cementitious binder), natural fine aggregate (as a primary filler), and a low dosage of Portland cement (as a secondary cementitious compound) were blended and compacted at their optimum moisture content to ascertain their suitability as base course materials. These tests and experiments were used to assess the performance of the selected PCC/FBC base course composites. On the basis of the results, thickness-design tables of PCC/FBC base courses were developed. Results indicate that the engineering properties of the PCC/FBC composites exceed those of the conventional mixes used in low-volume roads. The field results verified that the engineering characteristics of the laboratory mixtures can be easily duplicated in field.
Lead Poisoning: Rapid Formation of Intranuclear Inclusions

A single dose of lead (0.05 milligram per gram of body weight) induced characteristic intranuclear inclusions in the epithelium of proximal tubules in rat kidney within 1 to 6 days. The development of the intranuclear inclusions is thus an acute manifestation of lead poisoning, not a delayed one, as has been thought hitherto. Cytoplasmic structures resembling the intranuclear inclusions and situated in the vicinity of endoplasmic reticulum were regularly found in cells bearing the pathognomonic intranuclear inclusions. The latter and the cytoplasmic structures may be derived from a common precursor, perhaps a soluble protein-lead complex.
Habitat Segregation Among Larval Mosquitoes (Diptera: Culicidae) in Tire Yards in Indiana, USA

Mosquito larvae in tires were sampled at 6 tire disposal areas in St. Joseph Co., Indiana, USA. Larvae were present in 85% (123/145) of the sun-exposed tires and in 93% (125/135) of the shaded tires. In shaded tires, Aedes triseriatus and Culex restuans accounted for 93% of the total larvae. In the exposed tires Cx. restuans and Aedes atropalpus constituted 74% of the total larvae. Aedes triseriatus larvae were found predominantly in shaded tires and Ae. atropalpus occurred most frequently in exposed tires. Culex pipiens , Cx. restuans and Culex tetiitans showed no preference for either sun or shade. Larval densities of Ae. triseriatus were 3 times higher in shaded tires than in exposed tires. Densities of the other 4 most common species were not significantly different between the 2 tire types. Unique multispecies associations were found in exposed and shaded tires.
Cultivation of bovine fetal and adult endometrial epithelial cells

Primary epithelial cell cultures were developed from fetal caruncular, adult intercaruncular pregnant, and adult intercaruncular nonpregnant endometrium. Endometrial cells were obtained from both collagenase dispersion or from explant outgrowth, although the explant method was more consistent. Cultures derived from fetal endometrium grew more rapidly and were more viable after subculturing and cryopreservation than were adult-derived cultures. These cultures provide an in vitro system for the study of bovine endometrial physiology and pathology.
Research on Character of Sandlayer in Heidimiao Oil Layer in Yingtai Area

Based on the division and correlation of sand groups in Heidimiao, synthesizing the information of 3D seism data, drilling data, logging data and core data, well ties profile, sandstone contrast diagram and oil reservoir profile are drawn in this article in a way of combining the data of logging and seism. Furthermore, spatial distribution rules of sandlayer in Heidimiao oillayer are expected to be analyzed in this article through the data of stratum thickness, sandstone thickness, the thickness ratio of sandstone to stratum, and porosity isogram. The rules are described as: the Heidimiao oil layer is thick in east and north but thin in the west and south as a whole. Little sandstone is found in H3 (Nen 2) but that is highly developed in H2 (Nen 3) and H1 (Nen 4) in which lenticular sandlayer can also be found. Sandstones in each oil group are developed with varying thickness, great depth difference and complex lateral connectivity. What’s more, sandstones in the research area manifest a decline in layers and thickness from east to west. The thinner and smaller-scale sandstones in the west have weak lateral connectivity but strong control of oil and water distribution, which results in the formation of concealed lithological reservoir uncontrolled by geological structure.
The effect of glucagon on fructose metabolism in diabetic and non-diabetic human beings

Abstract Glucagon substantially modified the plasma pyruvate and lactate responses to a fructose load in diabetic and non-diabetic human subjects. Addition of glucagon (60 μg. per minute for 30 minutes) at the 60th minute of a fructose infusion was followed by a prompt and complete reversal of the elevation of plasma pyruvate produced by the fructose alone. Lactate concentrations also decreased after glucagon, but the change was much less pronounced, so that the lactate-pyruvate ratio increased. These results appear to indicate that glucagon thwarted hepatic utilization of the carbohydrate load and concomitantly altered intra-hepatic redox potential.
Analysis of Fatigue Data for Lifetime Predictions for Ceramic Materials

Accuracy in data analysis is of utmost importance because lifetime predictions are extremely sensitive to experimental uncertainty in the crack growth parameters. The limitations of the conventional data reduction techniques used for analysing static and dynamic fatigue data are reviewed and new, statistical methods of data reduction that offer advantages over the conventional techniques are discussed.
Interchangeable Stage and Probe Mechanisms for Microscale Universal Mechanical Tester

A microfabricated mechanical test platform has been designed, fabricated, and operated. This system consists of a reusable chip capable of large-displacement actuation, which interfaces to a test coupon chip compatible with synthesis conditions for many nanomaterials. Because only normal forces are used for mechanical interfacing, the two chips are not permanently connected, allowing exchange of the test coupon chips. The actuated test platform chip contains a thermal actuator driving a compliant displacement amplification transmission, and a bulk-micromachined well in which the test coupon chips may be placed and removed. The displacement amplification structure provides 40 of output displacement, extending a probe over the well and into contact with the test coupon. The test coupon contains compliant structures that are actuated by the probe from the test platform.
Modulatory effects of activation of metabotropic glutamate receptors on GABAergic circuits in the mouse cortex.

Metabotropic glutamate receptors (mGluRs) are widely distributed in the central nervous system and modulate the release of neurotransmitters in different ways. We have previously shown that activation of presynaptic group II mGluRs reduces the gain of GABAergic inputs in both primary visual and auditory cortices (V1 and A1). In the present study, we sought to determine whether activation of mGluRs can also affect the inhibitory inputs in thalamus. Using whole cell recordings in a mouse slice preparation, we studied two GABAergic inputs to thalamic relay cells: that of the thalamic reticular nucleus (TRN) to cells of the ventral posteromedial nucleus (VPM) and that of interneurons to cells of the lateral geniculate nucleus (LGN). We found that activation of mGluRs significantly reduced the amplitudes of inhibitory postsynaptic currents (IPSCs) evoked from TRN inputs to VPM cells, and further experiments indicated that this was due to activation of presynaptic group I and group II mGluRs. Similar results were found in the interneuronal inputs to LGN cells. Activation of presynaptic group I (type 1 but not type 5) and group II mGluRs significantly reduced the amplitudes of evoked IPSCs of the axonal inputs to relay cells, and additional experiments were consistent with previous observations that activation of type 5 mGluRs on the dendritic terminals of interneurons enhanced postsynaptic IPSCs. We concluded that group I and II mGluRs may generally reduce the amplitude of evoked GABAergic IPSCs of axonal inputs to thalamic relay cells, operating through presynaptic mechanisms, and this extends our previous findings in cortex.
The effects of behavioral control over stress on GABAergic spontaneous inhibitory postsynaptic currents in prefrontal cortical pyramidal neurons

Traumatic events may lead to anxiety, depression and post-traumatic stress disorder (PTSD). However, the majority of individuals exposed to trauma do not develop these disorders. The stressor controllability paradigm has been widely used as a model for understanding the neurobiology underlying factors that confer vulnerability and resilience to the outcome of traumatic events. In this paradigm rats receive a series of tail shocks: one group of rats have control over the termination of the shock by means of turning a wheel (escapable shock, ES), while the other “yoked” group of rats receive physically identical shocks but have no control over shock termination (inescapable shock, IS). In subsequent behavioral tests that model components of anxiety and depression, IS rats without control show increased signs of behavioral depression, while ES rats that have control over the shock behave as naive home caged (HC) rats. We have previously reported that individual deep layer pyramidal neurons from the ventral medial prefrontal cortex (vmPFC) exhibit changes in their intrinsic excitability following ES. To examine if there is a corresponding reduction in synaptic inhibition, we tested IS, ES and HC deep layer pyramidal neurons under identical conditions. Collecting such electrophysiological data from pyramidal neurons after exposure to stress is a technical challenge, yet very useful for conductance-based neural simulations and computational modeling. Here we present a data set of spontaneous inhibitory postsynaptic currents (sIPSCs) gathered from whole-cell patch-clamp recordings of individual prefrontal cortical deep layer neurons from adult rats (60-70 days old) after exposure to ES, IS or HC. In order to analyze the data, we provide our script used for the detection of synaptic events written for the scientific/engineering program Igor Pro that allows users to define their own event detection parameters.