gebhart/patrepeval huggingface dataset:
Rating the Relevance of QUORUM-Selected ASRS Incident Narratives to a "Controlled Flight into Terrain" Accident (1998)

An exploratory study was conducted to identify commercial aviation incidents that are relevant to a "controlled flight into terrain" (CFIT) accident using a NASA-developed text processing method. The QUORUM method was used to rate 67820 incident narratives, virtually all of the narratives in the Aviation Safety Reporting System (ASRS) database, according to their relevance to two official reports on the crash of American Airlines Flight 965 near Cali, Colombia in December 1995. For comparison with QUORUM's ratings, three experienced ASRS analysts read the reports of the crash and independently rated the relevance of the 100 narratives that were most highly rated by QUORUM, as well as 100 narratives randomly selected from the database. Eighty-four of 100 QUORUM-selected narratives were rated as relevant to the Cali accident by one or more of the analysts. The relevant incidents involved a variety of factors, including, over-reliance on automation, confusion and changes during descent/approach, terrain avoidance, and operations in foreign airspace. In addition, the QUORUM collection of incidents was found to be significantly more relevant than the random collection.
An N<sub>2</sub>S<sub>2</sub> Bifunctional Chelator for Technetium-99m and Rhenium:  Complexation, Conjugation, and Epimerization to a Single Isomer (1999)

A bifunctional chelator 6 was prepared bearing an N2S2 core for binding rhenium or technetium and a carboxylic acid group for conjugation to amino groups of biomolecules. Complexation of 6 with rhenium(V) resulted in two kinetic isomers, anti-7 and syn-7, being formed in approximately equal amounts. Epimerization with 0.5 M NaOH yields a single isomer anti-7, as determined by NMR spectroscopy and single-crystal X-ray analysis. The 99mTc complex was prepared at the tracer level by reaction of the ligand with 99mTcO4-, tin(II) chloride and sodium gluconate giving a mixture of two isomers, but showing a preference for the anti isomer. Chelation in the presence of 1 M NaOH results in anti-8 being formed as the sole product. The bifunctional ability of the ligand was explored by amide formation with (S)-alpha-phenethylamine, either by direct DCC coupling or through the N-hydroxy succinimidyl ester 9 intermediate. The deprotected bioconjugate 11 was complexed with rhenium, yielding similar amounts of two isomeric rhenium complexes, anti-12 and syn-12, which were isolated and characterized by NMR spectroscopy. Treatment of the kinetic mixture of anti-12 and syn-12 with 1 M NaOH resulted in quantitative conversion to a single rhenium complex anti-12. With technetium-99m in 0.1 M sodium acetate, bioconjugate 11 yielded both technetium-99m complexes anti-13 and syn-13, in a 2:1 ratio, respectively. In contrast, complexation in the presence of 1 M NaOH gave only one technetium-99m complex, assigned the structure anti-13.
Activatable Probes Based on Distance‐Dependent Luminescence Associated with Cerenkov Radiation (2013)

Let me get my nanoruler: Activatable probes based on radionuclide and quantum dots (QDs) were constructed using DNA as a linker. Cerenkov radiation from (64)Cu was used to excite the QDs in a distance-dependent manner. The luminescence was lowest nearest to the QD and increased with distance.
105. An interpretation of the Sandmeyer reaction. Part V. The comparative behaviour of cuprous, cupric, and ferric chlorides as catalysts (1944)

H. H. Hodgson and D. D. R. Sibbald, J. Chem. Soc., 1944, 393 DOI: 10.1039/JR9440000393
Preferential Use of Central Metabolism In Vivo Reveals a Nutritional Basis for Polymicrobial Infection (2015)

The human genitourinary tract is a common anatomical niche for polymicrobial infection and a leading site for the development of bacteremia and sepsis. Most uncomplicated, community-acquired urinary tract infections (UTI) are caused by Escherichia coli, while another bacterium, Proteus mirabilis, is more often associated with complicated UTI. Here, we report that uropathogenic E. coli and P. mirabilis have divergent requirements for specific central pathways in vivo despite colonizing and occupying the same host environment. Using mutants of specific central metabolism enzymes, we determined glycolysis mutants lacking pgi, tpiA, pfkA, or pykA all have fitness defects in vivo for P. mirabilis but do not affect colonization of E. coli during UTI. Similarly, the oxidative pentose phosphate pathway is required only for P. mirabilis in vivo. In contrast, gluconeogenesis is required only for E. coli fitness in vivo. The remarkable difference in central pathway utilization between E. coli and P. mirabilis during experimental UTI was also observed for TCA cycle mutants in sdhB, fumC, and frdA. The distinct in vivo requirements between these pathogens suggest E. coli and P. mirabilis are not direct competitors within host urinary tract nutritional niche. In support of this, we found that co-infection with E. coli and P. mirabilis wild-type strains enhanced bacterial colonization and persistence of both pathogens during UTI. Our results reveal that complementary utilization of central carbon metabolism facilitates polymicrobial disease and suggests microbial activity in vivo alters the host urinary tract nutritional niche.
Hypersensitive teeth. Experimental studies of dentinal desensitizing agents. (1990)

The effect of dentinal desensitizing agents on nerve activity was tested. Effective agents such as KNO3 reduce dentinal sensory nerve activity. This effect is due to the depolarizing action of the K+ ion.
Disease Gene Candidates Revealed by Expression Profiling of Retinal Ganglion Cell Development (2007)

To what extent do postmitotic neurons regulate gene expression during development or after injury? We took advantage of our ability to highly purify retinal ganglion cells (RGCs) to profile their pattern of gene expression at 13 ages from embryonic day 17 through postnatal day 21. We found that a large proportion of RGC genes are regulated dramatically throughout their postmitotic development, although the genes regulated through development in vivo generally are not regulated similarly by RGCs allowed to age in vitro. Interestingly, we found that genes regulated by developing RGCs are not generally correlated with genes regulated in RGCs stimulated to regenerate their axons. We unexpectedly found three genes associated with glaucoma, optineurin, cochlin, and CYP1B1 (cytochrome P450, family 1, subfamily B, polypeptide 1), previously thought to be primarily expressed in the trabecular meshwork, which are highly expressed by RGCs and regulated through their development. We also identified several other RGC genes that are encoded by loci linked to glaucoma. The expression of glaucoma-linked genes by RGCs suggests that, at least in some cases, RGCs may be directly involved in glaucoma pathogenesis rather than indirectly involved in response to increased intraocular pressure. Consistent with this hypothesis, we found that CYP1B1 overexpression potentiates RGC survival.
Secchi disk science: Visual optics of natural waters1 (1986)

The Secchi disk is a circular white disk that is lowered into a natural body of water by a human observer until it disappears from view. The depth of disappearance is a visual measure of the clarity of the water. This review examines the physical and physiological basis of the Secchi disk procedure. The theory of the white disk is detailed to show the underlying assumptions and the consequent strengths and limitations of the procedure. The theory shows how to use a calibrated Secchi disk to predict illuminance levels as a function of depth. In particular it is shown how to predict the euphotic depth of a medium. Ten laws of the Secchi disk are stated verbally and in mathematical form. The laws show how variations in properties of the disk and the surrounding light field affect the depth of disappearance of the disk. Theory and examples lead to the following three main conclusions of this paper: (i) the Secchi disk reading z sd (in meters) yields a quantitative estimate of a single apparent optical property (a + K ) (in meter −1 ) of a natural hydrosol, where a is the (photopic) beam attenuation coefficient and K the (photopic) diffuse attenuation coefficient of the medium; (ii) the primary function of a Secchi disk is to provide a simple visual index of water clarity via z sd or α + K ; (iii) to extend the use of the Secchi disk by auxiliary objective electronic measurements of a or of K, or both, is to risk obviating or abusing this primary function.
Robust closed-loop control of isometric muscle force using pulsewidth modulation (1988)

The design of feedback controllers to accurately and robustly regulate the properties of electrically stimulated muscle is considered. Reliable, precise control is necessary for the development of neuroprosthetic devices to improve gradation and repeatability of force. A digital closed-loop controller has been developed which regulates muscle force by modulating the pulsewidth of a constant-amplitude electrical simulation pulse train. This controller has been evaluated in slow- and fast-twitch muscles (cat soleus and plantaris) in acute experiments. In isometric tests, it was found to regulate muscle force with low sensitivity to modeling errors and disturbances while satisfying stability, repeatability, linearity, and step/ramp response criteria over a wide range of commands.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Synthesis and Lithium Insertion into Nanophase MgTi<sub>2</sub>O<sub>5</sub> with Pseudo-Brookite Structure (2008)

Micrometer-sized and nanometer-sized samples of MgTi2O5 were prepared by solid state reaction and polymerizable complex methods. Electrochemical lithium insertion was studied for the first time. We observe a remarkable change in the material response when particle size is reduced from micrometer to nanometer regime. In micrometer sized samples, 0.8 Li per formula unit could be inserted, and no reversible extraction of lithium is observed. In case of nanometer-sized samples, 2.1Li are inserted and 1Li can be reversibly extracted even after 50 cycles. In the case of nanometer sized samples, formation of a new phase with approximate composition Li2MgTi2O5 is evident form ex situ XRD studies. HRTEM studies reveal that the new phase can be considered as a distorted analogue of the parent phase.
Large eddy simulation of the turbulence and fiber motion in a headbox (2009)

This thesis describes numerical simulations of the mean flow and the large-scale turbulence structures in a typical paper machine headbox. Parallel computational methods and a large eddy simulation (LES) model are used. Turbulent flow through the converging section is modelled and is then used, with a suitable fiber model, to make predictions of the statistical fiber orientation in the headbox. The present large eddy simulations have been made with a new parallel computational code developed by the author for this purpose. Techniques for parallel computation of LES are discussed. In this code, the incompressible Navier-Stokes equations are solved using a staggered finite volume method for a generalized curvilinear coordinate system. The fractional step method is used to solve the momentum equations. A Poisson equation for pressure is obtained to satisfy the continuity equation. The Smagorinsky constant, the dynamic subgrid scale models and the approximate deconvolution model (ADM) are used in the large eddy simulations to account for the effects of the unresolved turbulent motions. Satisfactory validation of the new code is obtained through comparisons with experiments and computations of fully developed channel flow. The parallel efficiency is higher than 80% for the present parallel computation of LES. For the converging section flow representing the headbox, the computed values of the mean velocity agree well with the measured values. For the rms fluctuations, there are some differences between the numerical and the measured results over the first third of the converging section. These differences appear to be related to the impossiblity to set accurately the flow in the experiment and to the inflow data used in the simulations. A modified method for the simulation of inflow conditions is proposed, and used, and better agreement with experimental data is obtained with the new inflow conditions. The LES computer code is coupled with a suitable fiber model to predict the statistical orientation of nylon "fibers" in the converging section. The numerical methods give statistical results which are similar to existing experimental data for the fiber orientation. Finally, high Reynolds number large eddy simulations are carried out for a commercial sized headbox of generic geometry. Two inflow conditions for the converging section are investigated and some conclusions are drawn.
Hiding communication latency and coherence overhead in software DSMs (1996)

In this paper we propose the use of a PCI-based programmable protocol controller for hiding communication and coherence overheads in software DSMs. Our protocol controller provides three different types of overhead tolerance: a) moving basic communication and coherence tasks away from computation processors; b) prefetching of diffs; and c) generating and applying diffs with hardware assistance. We evaluate the isolated and combined impact of these features on the performance of TreadMarks. We also compare performance against two versions of the Shrimp-based AURC protocol. Using detailed execution-driven simulations of a 16-node network of workstations, we show that the greatest performance benefits provided by our protocol controller come from our hardware-supported diffs. Reducing the burden of communication and coherence transactions on the computation processor is also beneficial but to a smaller extent. Prefetching is not always profitable. Our results show that our protocol controller can improve running time performance by up to 50% for TreadMarks, which means that it can double the TreadMarks speedups. The overlapping implementation of TreadMarks performs as well or better than AURC for 5 of our 6 applications. We conclude that the simple hardware support we propose allows for the implementation of high-performance software DSMs at low cost. Based on this conclusion, we are building the NCP 2 parallel system at COPPE/UFRJ.
Dendrimers as Antibacterial Agents (2012)

No more than 100 years ago, if a person acquired a bacterial infection, the body had to clear the infection by itself or else the infection would eventually result in death. After penicillin and many other effective antibiotics were discovered, however, that changed. In the decades after penicillin was discovered in 1928, a number of powerful antibiotics were developed. They were used plentifully and often carelessly prescribed needlessly for certain bacterial infections and even for viral infections where they have no effect. Farmers found that animals fed low levels of antibiotics grow faster and are less subject to disease, so thousands of tons of antibiotics were (and still are) added to animal feed. The problem: unlike disinfectants, antibiotics generally act against a single component of a bacterium. Thus, in environments where antibiotics are present, there is great selective pressure toward bacteria that can make the relatively minor mutations needed to render them resistant. Once a single bacterium has developed resistance to an antibiotic, it can be amplified across bacterial species by quick propagation and the tendency to share antibiotic resistance genes with other bacteria. In the last decade, resistance to antibiotics even antibiotics once thought to be “last ditch” treatments has increased remarkably and is continually on the rise. Doctors are finding many once-treatable infections are now deadly (e.g. highly publicized Methicillinresistant Staphylococcus aureus (MRSA) infections). Large pharmaceutical companies, once major sources of new antibiotics, have exhausted most “easy” targets for new antibiotics and have shifted their research and development focus to long-term, chronic diseases rather than antibiotic discovery to increase profits (Tanner, 2009).
ATM Activation by Oxidative Stress (2010)

The ataxia-telangiectasia mutated (ATM) protein kinase is activated by DNA double-strand breaks (DSBs) through the Mre11-Rad50-Nbs1 (MRN) DNA repair complex and orchestrates signaling cascades that initiate the DNA damage response. Cells lacking ATM are also hypersensitive to insults other than DSBs, particularly oxidative stress. We show that oxidation of ATM directly induces ATM activation in the absence of DNA DSBs and the MRN complex. The oxidized form of ATM is a disulfide-cross-linked dimer, and mutation of a critical cysteine residue involved in disulfide bond formation specifically blocked activation through the oxidation pathway. Identification of this pathway explains observations of ATM activation under conditions of oxidative stress and shows that ATM is an important sensor of reactive oxygen species in human cells.
AApeptides as a New Class of Peptidomimetics to Regulate Protein-Protein Interactions (2012)

In human physiology, proteins at all times are synthesized, processed, degraded and posttranslationally modified to varying degrees and at different rates, for their participations in a wide variety of activities to maintain normal functions of the body (Murray et al. 2007). In the successful proceedings of all the biological events, signals are consistently received and sent via physical contacts between proteins (Murray et al. 2007). The communication between proteins or the alternatively called non-covalent protein-protein interactions are thereby considered as important as proteins’ own functions (Murray et al. 2007). Disruptions of these signaling pathways by either mutational changes or deregulation of one of the protein partners would result in a series of diseases (Murray et al. 2007). On the other hand, therapeutic approaches based on chemical agents could potentially inhibit protein-protein interactions, thereby restoring the balance of signaling pathways, and leading to the cure of diseases (Murray et al. 2007). However, it is quite challenging to develop chemical agents which can target protein-protein interactions (Arkin et al. 2004; Whitty et al. 2006). Unlike the traditional medicinal chemistry approach, in which small molecule inhibitors are developed to target the hydrophobic pocket of enzymes / kinases, chemical agents are now required to bind to large surfaces of proteins that are usually amphiphilic and flexible (Murray et al. 2007). Yet a number of successful stories have been reported (Murray et al. 2007). Taking the p53/MDM2 system as an example, the p53/MDM2 has been a model system for the inhibition of protein-protein interactions, and has been reported to be the targets of a wide variety of inhibitors (Oren 1999; Balint et al. 2001; McLure et al. 2004; Brooks et al. 2006).
The Nature of BH<sub>4</sub><sup>–</sup> Reorientations in Hexagonal LiBH<sub>4</sub> (2011)

Lithium borohydride (LiBH4) has lately been the subject of intense inquiry within the hydrogen storage community. Quasi-elastic neutron scattering spectra were measured for LiBH4 in the high-temperature hexagonal crystal phase. The elastic incoherent structure factor associated with the rapid BH4– anion reorientations was determined at 400, 410, and 420 K for momentum transfers as high as 4.2 Å–1. The results strongly suggest a BH4– reorientational mechanism approaching quasi-free, trigonal-axis rotation of three borohydride H atoms, combined with reorientational jump exchanges between these delocalized “orbiting” H atoms and the remaining axial borohydride H atom. This mechanism is consistent with previously reported diffraction and spectroscopy studies.
Trends and Connections in the Flour-milling and Wheat-growing Industries of Early South Australia, 1836-1860 (1985)

For a time after the colony of South Australia was founded (this was at the end of 1836) very little progress was made towards establishing a useful local grain-growing industry. As a result much damage was done to the infant colonial economy; flour had to be imported (and paid for) in considerable quantities to feed a substantial population, while the colony's earnings from its own exports remained at a low level. A number of factors were responsible - among them the absence of mills of any kind to process whatever grain might be produced by the farmers of the region. Eventually, however, local inertia was overcome. Wheat at last began to be grown in increasing quantities, and a milling industry was established with a certain amount of difficulty. An export trade was initiated, first in grain alone, and later in both whole grain and flour. Both wheat production and the milling industry in South Australia expanded rapidly over the years of the mid to late 19th century, and both changed quite significantly in character. This paper examines the unusual circumstances of the two industries in their early years, their dependence upon each other over time, and their evidently similar rates of progress. Attention is also directed to the manner in which the circumstances and practices of both industries changed as they developed.
Principles of the <i>Kenzan</i> Method for Robotic Cell Spheroid-Based Three-Dimensional Bioprinting <sup/> (2016)

Bioprinting is a technology with the prospect to change the way many diseases are treated, by replacing the damaged tissues with live de novo created biosimilar constructs. However, after more than a decade of incubation and many proofs of concept, the field is still in its infancy. The current stagnation is the consequence of its early success: the first bioprinters, and most of those that followed, were modified versions of the three-dimensional printers used in additive manufacturing, redesigned for layer-by-layer dispersion of biomaterials. In all variants (inkjet, microextrusion, or laser assisted), this approach is material ("scaffold") dependent and energy intensive, making it hardly compatible with some of the intended biological applications. Instead, the future of bioprinting may benefit from the use of gentler scaffold-free bioassembling methods. A substantial body of evidence has accumulated, indicating this is possible by use of preformed cell spheroids, which have been assembled in cartilage, bone, and cardiac muscle-like constructs. However, a commercial instrument capable to directly and precisely "print" spheroids has not been available until the invention of the microneedles-based ("Kenzan") spheroid assembling and the launching in Japan of a bioprinter based on this method. This robotic platform laces spheroids into predesigned contiguous structures with micron-level precision, using stainless steel microneedles ("kenzans") as temporary support. These constructs are further cultivated until the spheroids fuse into cellular aggregates and synthesize their own extracellular matrix, thus attaining the needed structural organization and robustness. This novel technology opens wide opportunities for bioengineering of tissues and organs.