gebhart/patrepeval huggingface dataset:
Processing Pathway Dependence of Amorphous Silica Nanoparticle Toxicity: Colloidal vs Pyrolytic (2012)

We have developed structure/toxicity relationships for amorphous silica nanoparticles (NPs) synthesized through low-temperature colloidal (e.g., Stöber silica) or high-temperature pyrolysis (e.g., fumed silica) routes. Through combined spectroscopic and physical analyses, we have determined the state of aggregation, hydroxyl concentration, relative proportion of strained and unstrained siloxane rings, and potential to generate hydroxyl radicals for Stöber and fumed silica NPs with comparable primary particle sizes (16 nm in diameter). On the basis of erythrocyte hemolytic assays and assessment of the viability and ATP levels in epithelial and macrophage cells, we discovered for fumed silica an important toxicity relationship to postsynthesis thermal annealing or environmental exposure, whereas colloidal silicas were essentially nontoxic under identical treatment conditions. Specifically, we find for fumed silica a positive correlation of toxicity with hydroxyl concentration and its potential to generate reactive oxygen species (ROS) and cause red blood cell hemolysis. We propose fumed silica toxicity stems from its intrinsic population of strained three-membered rings (3MRs) along with its chainlike aggregation and hydroxyl content. Hydrogen-bonding and electrostatic interactions of the silanol surfaces of fumed silica aggregates with the extracellular plasma membrane cause membrane perturbations sensed by the Nalp3 inflammasome, whose subsequent activation leads to secretion of the cytokine IL-1β. Hydroxyl radicals generated by the strained 3MRs in fumed silica, but largely absent in colloidal silicas, may contribute to the inflammasome activation. Formation of colloidal silica into aggregates mimicking those of fumed silica had no effect on cell viability or hemolysis. This study emphasizes that not all amorphous silicas are created equal and that the unusual toxicity of fumed silica compared to that of colloidal silica derives from its framework and surface chemistry along with its fused chainlike morphology established by high-temperature synthesis (>1300 °C) and rapid thermal quenching.
Thermal Transport Characteristics of Human Skin Measured In Vivo Using Ultrathin Conformal Arrays of Thermal Sensors and Actuators (2015)

Measurements of the thermal transport properties of the skin can reveal changes in physical and chemical states of relevance to dermatological health, skin structure and activity, thermoregulation and other aspects of human physiology. Existing methods for in vivo evaluations demand complex systems for laser heating and infrared thermography, or they require rigid, invasive probes; neither can apply to arbitrary regions of the body, offers modes for rapid spatial mapping, or enables continuous monitoring outside of laboratory settings. Here we describe human clinical studies using mechanically soft arrays of thermal actuators and sensors that laminate onto the skin to provide rapid, quantitative in vivo determination of both the thermal conductivity and thermal diffusivity, in a completely non-invasive manner. Comprehensive analysis of measurements on six different body locations of each of twenty-five human subjects reveal systematic variations and directional anisotropies in the characteristics, with correlations to the thicknesses of the epidermis (EP) and stratum corneum (SC) determined by optical coherence tomography, and to the water content assessed by electrical impedance based measurements. Multivariate statistical analysis establishes four distinct locations across the body that exhibit different physical properties: heel, cheek, palm, and wrist/volar forearm/dorsal forearm. The data also demonstrate that thermal transport correlates negatively with SC and EP thickness and positively with water content, with a strength of correlation that varies from region to region, e.g., stronger in the palmar than in the follicular regions.
Cellulose-binding polypeptides from Cellulomonas fimi: endoglucanase D (CenD), a family A beta-1,4-glucanase (1993)

Five cellulose-binding polypeptides were detected in Cellulomonas fimi culture supernatants. Two of them are CenA and CenB, endo-beta-1,4-glucanases which have been characterized previously; the other three were previously uncharacterized polypeptides with apparent molecular masses of 120, 95, and 75 kDa. The 75-kDa cellulose-binding protein was designated endoglucanase D (CenD). The cenD gene was cloned and sequenced. It encodes a polypeptide of 747 amino acids. Mature CenD is 708 amino acids long and has a predicted molecular mass of 74,982 Da. Analysis of the predicted amino acid sequence of CenD shows that the enzyme comprises four domains which are separated by short linker polypeptides: an N-terminal catalytic domain of 405 amino acids, two repeated sequences of 95 amino acids each, and a C-terminal domain of 105 amino acids which is > 50% identical to the sequences of cellulose-binding domains in Cex, CenA, and CenB from C. fimi. Amino acid sequence comparison placed the catalytic domain of CenD in family A, subtype 1, of beta-1,4-glycanases. The repeated sequences are more than 40% identical to the sequences of three repeats in CenB and are related to the repeats of fibronectin type III. CenD hydrolyzed the beta-1,4-glucosidic bond with retention of anomeric configuration. The activities of CenD towards various cellulosic substrates were quite different from those of CenA and CenB.
Dextran microsphere embolization: experimental and clinical experience with radiologic-pathologic correlation. Work in progress. (1986)

The radiologic and pathologic effects of canine renal embolization with dextran microspheres of two size ranges (40-150 micron and 100-300 micron) were studied 30 minutes and 1, 2, 4, and 6 weeks after embolization. Dramatic occlusions occurred with very small quantities of these particles, which reached more distally and were suspended and embolized more easily than other solid embolic agents. Because of these qualities, however, they should be used with more caution. They can be injected through 2-F catheters, calibrated-leak balloons, and open-ended guide wires. Embolization with dextran microspheres was also used for epistaxis, meningioma, dural arteriovenous malformation, renal tumors, bone metastasis, multiple myeloma, or peripheral angioma in ten patients. The technique was safe and effective, but special attention should be directed to proper dilution and gentle embolization with careful monitoring to avoid excessive embolization or reflux.
Isolation and characterization of type IV procollagen, laminin, and heparan sulfate proteoglycan from the EHS sarcoma (1982)

We have studied the extractability of type IV collagen, laminin, and heparan sulfate proteoglycan from EHS tumor tissue growth in normal and lathyritic animals. Laminin and heparan sulfate proteoglycan were readily extracted with chaotropic solvents from both normal and lathyritic tissue. The collagenous component was only solubilized from lathyritic tissue in the presence of a reducing agent. These results indicate that lysine-derived cross-links and disulfide bonds stabilize the collagenous component in the matrix but not the laminin or the heparan sulfate proteoglycan. The majority of the collagen present in the extracts had a native triple helix based upon the pattern of peptides resistant to pepsin digestion and visualization in the electron microscope by the rotary shadow technique. This protein was composed of chains (Mr 185000 and 170000) identical in migration to the chains of newly synthesized type IV procollagen. This finding confirms earlier work that indicates that the biosynthetic form, type IV procollagen, is incorporated as such in the basement membrane matrix. Material with smaller chains (Mr 160000 and 140000) appeared on storage in acetic acid solutions. These results indicate that the lower molecular weight collagen in acid extracts of basement membrane arises artifactually due to an endogenous acid-active protease.
Turkish word segmentation using morphological analyzer (2001)

This paper describes an algorithm to segment an input Turkish string without any spaces, which may be an output of a speech-to-text application, into words by using morphological analyzer. It is quite possible to use the algorithm on other languages, which has a morphological analysis component, as well. Turkish morphological analyzer is designed and implemented as the linguistic engine of the algorithm. The construction of the analyzer proposes a technique that attempts to achieve group vise morpheme recognition instead of searching suffixes one by one in a word.
Database Management for Interactive Display of Large Architectural Models (1996)

This paper describes algorithms for predictive database management used in The UC Berkeley Building Walkthrough System. The algorithms forecast a range of possible observer viewpoints during upcoming frames and use precomputed cell visibility information to determine a set of objects likely to be visible to the observer in the near future. For each of these objects, detail elision techniques determine which levels of detail must be stored in a memory resident cache. Cache management algorithms determine which objects to load into memory from disk, and which to replace when the cache is full. Using these algorithms, the system is able to maintain real-time frame rates during interactive visualization of large building models with furniture and radiosity illumination.
Cloning of a Sphingomonas paucimobilis SYK-6 Gene Encoding a Novel Oxygenase That Cleaves Lignin-Related Biphenyl and Characterization of the Enzyme (1998)

Sphingomonas paucimobilis SYK-6 transforms 2,2'-dihydroxy-3,3'-dimethoxy-5,5'-dicarboxybiphenyl (DDVA), a lignin-related biphenyl compound, to 5-carboxyvanillic acid via 2,2',3-trihydroxy-3'-methoxy-5,5'-dicarboxybiphenyl (OH-DDVA) as an intermediate (15). The ring fission of OH-DDVA is an essential step in the DDVA degradative pathway. A 15-kb EcoRI fragment isolated from the cosmid library complemented the growth deficiency of a mutant on OH-DDVA. Subcloning and deletion analysis showed that a 1.4-kb DNA fragment included the gene responsible for the ring fission of OH-DDVA. An open reading frame encoding 334 amino acids was identified and designated ligZ. The deduced amino acid sequence of LigZ had 18 to 21% identity with the class III extradiol dioxygenase family, including the beta subunit (LigB) of protocatechuate 4,5-dioxygenase of SYK-6 (Y. Noda, S. Nishikawa, K.-I. Shiozuka, H. Kadokura, H. Nakajima, K. Yano, Y. Katayama, N. Morohoshi, T. Haraguchi, and M. Yamasaki, J. Bacteriol. 172:2704-2709, 1990), catechol 2,3-dioxygenase I (MpcI) of Alcaligenes eutrophus JMP222 (M. Kabisch and P. Fortnagel, Nucleic Acids Res. 18:3405-3406, 1990), the catalytic subunit of the meta-cleavage enzyme (CarBb) for 2'-aminobiphenyl-2,3-diol from Pseudomonas sp. strain CA10 (S. I. Sato, N. Ouchiyama, T. Kimura, H. Nojiri, H. Yamane, and T. Omori, J. Bacteriol. 179:4841-4849, 1997), and 2,3-dihydroxyphenylpropionate 1,2-dioxygenase (MhpB) of Escherichia coli (E. L. Spence, M. Kawamukai, J. Sanvoisin, H. Braven, and T. D. H. Bugg, J. Bacteriol. 178:5249-5256, 1996). The ring fission product formed from OH-DDVA by LigZ developed a yellow color with an absorption maximum at 455 nm, suggesting meta cleavage. Thus, LigZ was concluded to be a ring cleavage extradiol dioxygenase. LigZ activity was detected only for OH-DDVA and 2,2',3,3'-tetrahydroxy-5,5'-dicarboxybiphenyl and was dependent on the ferrous ion.
Town and country planning association (Victoria) turns 100 (2018)

The Town and Country Planning Association Inc. is a politically independent, not-for-profit association. Its members and supporters represent a wide cross-section of land use, environmental and transport planning expertise and interests. Town and Country Planning Association (TCPA) began life as the Victorian Town Planning and Parks Association (VTPPA), which was formed in Melbourne in 1914. In 1918, the name was changed to the Town Planning Association Victoria (TPAV) and, in 1941, to the TCPA. The TCPA was incorporated in Victoria in 1994.
The Evolution of the Protein Corona around Nanoparticles: A Test Study (2011)

The importance of the protein corona formed around nanoparticles upon entering a biological fluid has recently been highlighted. This corona is, when sufficiently long-lived, thought to govern the particles' biological fate. However, even this long-lived "hard" corona evolves and re-equilibrates as particles pass from one biological fluid to another, and may be an important feature for long-term fate. Here we show the evolution of the protein corona as a result of transfer of nanoparticles from one biological fluid (plasma) into another (cytosolic fluid), a simple illustrative model for the uptake of nanoparticles into cells. While no direct comparison can be made to what would happen in, for example, the uptake pathway, the results confirm that significant evolution of the corona occurs in the second biological solution, but that the final corona contains a "fingerprint" of its history. This could be evolved to map the transport pathways utilized by nanoparticles, and eventually to predict nanoparticle fate and behavior.
Application of complex-trace analysis to seismic data for random-noise suppression and temporal resolution improvement (2006)

Abstract Time-dependent amplitude and phase information of stacked seismic data are processed independently using complex trace analysis in order to facilitate interpretation by improving resolution and decreasing random noise. We represent seismic traces using their envelopes and instantaneous phases obtained by the Hilbert transform. The proposed method reduces the amplitudes of the low-frequency components of the envelope, while preserving the phase information. Several tests are performed in order to investigate the behavior of the present method for resolution improvement and noise suppression. Applications on both 1D and 2D synthetic data show that the method is capable of reducing the amplitudes and temporal widths of the side lobes of the input wavelets, and hence, the spectral bandwidth of the input seismic data is enhanced, resulting in an improvement in the signal-to-noise ratio. The bright-spot anomalies observed on the stacked sections become clearer because the output seismic traces have a simplified appearance allowing an easier data interpretation. We recommend applying this simple signal processing for signal enhancement prior to interpretation, especially for single channel and low-fold seismic data.
A phase 1b study of placenta‐derived mesenchymal stromal cells in patients with idiopathic pulmonary fibrosis (2014)

Intravenous MSC administration is feasible and has a good short-term safety profile in patients with moderately severe IPF.
The Biology of Haemophilus influenzae Type b Vaccination Failure (1992)

Vaccination with unconjugated polysaccharide vaccine against Haemophilus influenzae type b (Hib) disease at a median age of 25 months was not effective in a group of children who developed Hib disease at a median age of 35 months. This group had normal serum immunoglobulin concentrations but impaired anticapsular antibody responses to Hib infection and to reimmunization with unconjugated polysaccharide. Another group vaccinated with conjugated polysaccharide vaccine at a median age of 18 months developed Hib disease at a median age of 24 months. Of this group, 40% had subnormal immunoglobulin concentrations, particularly IgG2, and showed impaired antibody responses to Hib infection, whereas those with normal immunoglobulin concentrations showed high antibody responses to Hib infection. In both vaccination failure groups, low antibody responders to infection responded to revaccination with Hib conjugate, and most children expressed the idiotype HibId-1 in convalescent or postrevaccination sera. The presence of this idiotype implies that vaccination failure did not result from an inability to use the V kappa II A2 variable region gene, which is used in the anticapsular antibody response of most healthy children.
Procuring Universal Telephone Service (1997)

One of the hallmarks of modern society is its pervasive reliance on telecommunications. Progress in telecommunications has deeply changed the nature of social relations, politics and commerce. Individuals and communities with limited access to modern communications are disadvantaged in their efforts to keep abreast of current news, to participate in public debates, and to make their opinions known to the rest of the world. Business firms need electronic communications to integrate their far-flung operations. Much more than in the past, firms can now depend on distant suppliers to be well enough informed to react quickly to their changing needs. Combining rapid communications with flexible manufacturing technologies enables firms to make customized products that respond to individual customers’ changing demands (Milgrom and Roberts, 1987).
Effects of Platelet Glycoprotein IIb/IIIa Blockade With Tirofiban on Adverse Cardiac Events in Patients With Unstable Angina or Acute Myocardial Infarction Undergoing Coronary Angioplasty (1997)

In patients undergoing coronary angioplasty for acute coronary syndromes, tirofiban protects against early adverse cardiac events related to thrombotic closure. At 30 days, however, the reduction in adverse cardiac events was no longer statistically significant. The bleeding observed with tirofiban was not statistically different from that observed with placebo.
Mathematical Modeling and Simulation of Ventricular Activation Sequences: Implications for Cardiac Resynchronization Therapy (2012)

Next to clinical and experimental research, mathematical modeling plays a crucial role in medicine. Biomedical research takes place on many different levels, from molecules to the whole organism. Due to the complexity of biological systems, the interactions between components are often difficult or impossible to understand without the help of mathematical models. Mathematical models of cardiac electrophysiology have made a tremendous progress since the first numerical ECG simulations in the 1960s. This paper briefly reviews the development of this field and discusses some example cases where models have helped us forward, emphasizing applications that are relevant for the study of heart failure and cardiac resynchronization therapy.
Langerhans Cells Are Not Required for the CD8 T Cell Response to Epidermal Self-Antigens (2009)

Langerhans cells (LC) are APC that reside at the barrier surfaces. Mice expressing an OVA peptide in the epidermis (K14-OVAp) were used to study CD8(+) T cell responses to an epidermal self-Ag. Earlier results suggested that LC were the predominant APC, inducing a robust T cell response and autoimmunity. In this study, we used a whole protein model system, the K14-mOVA mouse, in which a transmembrane form of OVA was expressed in keratinocytes. In contrast to K14-OVAp mice, T cells in K14-mOVA mice were activated, but did not expand and instead died by apoptosis. Furthermore, in double-transgenic mice expressing both mOVA and OVAp, robust OT-I expansion occurred, indicating that tolerance to this Ag is not dominant and was due to lack of activating signals. We sought to identify the relevant APC in K14 mice using bone marrow chimeras and found that radioresistant cells (presumably LC) were able to cross-present the OVA Ag from keratinocytes to naive T cells in the lymph node. However, use of LC-deficient mice indicated that LC were not required for the expansion of OT-I in K14-OVAp or the deletion of OT-I in K14-mOVA mice. These data suggest that radioresistant non-LC present self-Ag in K14-OVAp mice and drive a robust CD8 T cell response.
Performance Characteristics of High RAP Bio-modified Asphalt Mixtures (2012)

The purpose of this study was to evaluate the effect of a bio-modified binder on the performance and workability of asphalt mixtures designed with and without a high Reclaimed Asphalt Pavement (RAP) content. The bio-modified binder was prepared by modifying a virgin asphalt binder with bio-binder produced from swine manure. The four mixtures that were designed and evaluated were: a control mixture incorporating virgin materials, the control mixture incorporating 40% RAP, the control mixture incorporating the bio-modified binder and the control mixture incorporating the bio-modified binder and 40% RAP. The effect of the bio-modified binder on the stiffness and workability of the control mixture with and without RAP was evaluated by measuring the dynamic modulus and the torque resistance of the mixtures respectively. The performance of each mixture was evaluated for fatigue cracking (Overlay Tester) and moisture susceptibility/rutting potential (Hamburg Wheel Tracking Device). Finally, the degree of blending between the virgin and RAP binders was evaluated for each mixture. The data indicated that the addition of bio-modified binder helped reduce the stiffness of the control mixture with 40% RAP to a level closer to the stiffness of the same mixture without RAP. Correspondingly, the mixture workability for the control mixture with 40% RAP was improved. The data indicated that the bio-modified binder improved the cracking characteristics and had no negative effect on the moisture susceptibility/rutting characteristics of the control mixture with 40% RAP. Overall, data indicated that there was a good degree of blending between the virgin/bio-modified and RAP binders.
Analysis of the trinucleotide repeat expansion in Italian families affected with Huntington disease (1994)

150 subjects affected with HD and 45 at high risk for the disease were typed for the CAG trinucleotide repeat at the 5' end of IT15. In all of them we find expanded segments showing marked instability upon transmission. Their length distribution matches those previously reported and inversely correlates (-0.686) with age at onset. Two at risk sibs from a large HD pedigree show expanded segments that overlap the normal distribution and can represent reductions from the HD to the normal range. A case of instability on a normal chromosome is also reported. Finally, an analysis of the CAG repeat as a function of three polymorphic DNA markers at D4S127 and D4S95 loci shows no significant difference in the average repeat length on HD chromosomes grouped according to the cosegregating allele of each marker or to the corresponding haplotype. Despite the marked heterogeneity in repeat length among HD families, haplotypes are not associated with different values around which the repeat length fluctuates.