gebhart/patrepeval huggingface dataset:
Measuring information storage and transfer in swarms (2011)

Spatial aggregation of animal groups give individuals many benefits that they would not be able to obtain otherwise.One of the key questions in the study of these animal groups, or "swarms", concerns the way in which information is propagated through the group.In this paper, we examine this propagation using an information-theoretic framework of distributed computation.Swarm dynamics is interpreted as a type of distributed computation.Two localized informationtheoretic measures (active information storage and transfer entropy) are adapted to the task of tracing the information dynamics in a kinematic context.The observed types of swarm dynamics, as well as transitions among these types, are shown to coincide with well-marked local and global optima of the proposed measures.Specifically, active information storage tends to maximize as the swarm is becoming less fragmented and the kinematic history begins to strongly inform an observer about the next state.The peak of transfer entropy is observed to appear at the final stages of merging of swarm fragments, near the "edge of chaos" where the system actively computes its next stable configuration.Both measures tend to minimize for either unstable or static swarm configurations.The results here show these measures can be applied to non-trivial models, most importantly, they can tell us about the dynamics within these model where we can not rely on visual intuitions.
Supplementary Figure 2 from Distinct Roles of HES1 in Normal Stem Cells and Tumor Stem-like Cells of the Intestine (2023)

&lt;p&gt;Hes3 and Hes5 do not compensate for Hes1 deficiency in adult NSCs.&lt;/p&gt;
Solution Syntheses of Protected Type II Lewis Blood Group Oligosaccharides: Study for Automated Synthesis. (2005)

Glycosyl phosphate and trichloroacetimidate monosaccharide building blocks were used in a stepwise\nsolution-phase synthesis of three Lewis blood group oligosaccharides. The syntheses were conducted\nto establish general routes for the automated assembly of the oligosaccharide portion of biologically\nimportant glycolipids. The H-type II pentasaccharide, Le&lt;i&gt;&lt;sup&gt;x&lt;/sup&gt;&lt;/i&gt;&lt;sup&gt;&lt;/sup&gt; pentasaccharide, and Le&lt;i&gt;&lt;sup&gt;y&lt;/sup&gt;&lt;/i&gt;&lt;sup&gt;&lt;/sup&gt; hexasaccharide\nwere prepared in high yield. These syntheses served to evaluate the utility and limitations of the\n2-(azidomethyl)benzoate ester (AZMB) for the construction of complex carbohydrates. Development\nof a glucosamine building block containing a &lt;i&gt;N&lt;/i&gt;-trichloroacetamide group to mask the C2 amine\nimproved coupling yields and was key for completion of the Le&lt;i&gt;&lt;sup&gt;x&lt;/sup&gt;&lt;/i&gt;&lt;sup&gt;&lt;/sup&gt; and Le&lt;i&gt;&lt;sup&gt;y&lt;/sup&gt;&lt;/i&gt;&lt;sup&gt;&lt;/sup&gt; structures.
A reduced complexity partial sampling MMSE receiver for asynchronous MC-CDMA systems (2002)

In multi-carrier CDMA (MC-CDMA) system, timing of the starting point of the desired signal must be estimated to demodulate the desired signal. Especially for asynchronous MC-CDMA systems, rather a complicated timing estimation is needed, due to the random delays of all users. Zong, Wang and Bar-Ness (see VTC2001)proposed a partial sampling MMSE (PS-MMSE) receiver which does not require timing estimation. However, it requires several times more filter's taps than the conventional MC-CDMA receiver. The number of taps is a multiple of, and depends on, the number of subcarriers (i.e., the processing gain). A reduced complexity partial sampling MMSE (RPS-MMSE) receiver is proposed, which can be adaptively implemented by using the least-mean-square (LMS) algorithm. The proposed structure allows one to choose the number of taps independent of the number of subcarriers, hence having more flexibility in choosing the number of taps than with PS-MMSE receiver. With this structure, we can use fewer taps than with the PS-MMSE receiver and still can obtain comparable performance.
An evaporated aluminum metallization for high efficiency GaAs solar cells (2002)

A thick aluminum grid metallization for p-n GaAs solar cells which can be deposited completely by evaporation has been developed. The contacts are weldable, have low specific contact resistance (5*10/sup -6/ Omega -cm/sup 2/) to p-GaAs, and are compatible with the subsequent processing steps used on a GaAs solar cell pilot line. The total metallization is approximately 4 mu m thick with nearly vertical sidewalls, and height-to-width aspect ratios greater than one can be achieved. This cross-sectional geometry provides sufficient current-carrying capacity with minimum obscuration. Large-area (4 cm/sup 2/) devices have been fabricated with this aluminum metal scheme, resulting in a median efficiency of 20.52% (one sun, AM0). Fabrication details, test results for large-area cells, and applications for high-temperature stability, and concentrator cells are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Genetic Modification of Human Hematopoietic Cells: Preclinical Optimization of Oncoretroviral-mediated Gene Transfer for Clinical Trials (2009)

This chapter provides information about the oncoretroviral transduction of human hematopoietic stem/ progenitor cells under clinically applicable conditions. We describe in detail a short -60 h transduction protocol which consistently yields transduction efficiencies in the range of 30-50% with five different oncoretroviral vectors. We discuss a number of parameters that affect transduction efficiency, including the oncoretroviral vector characteristics, the vector stock collection, the source of CD34+ cells and transduction conditions.
Monitoring Antigen-Specific Biologics (2013)

An increasing number of antigen-specific biologics have been introduced into clinical practice, and the ones that arrived first have already reached the end of their patented life span. Despite the use of these agents for over a decade, individualized dosing is not standard practice. Most patients are treated according to treatment protocols, with a fixed dose administered at fixed time intervals. Although the between-subject variability in the volume of distribution is small, there is a moderate to high between-subject variability in the clearance of these biologics. The formation of neutralizing antidrug antibodies (ADAs) further contributes to the variability in the pharmacokinetics and pharmacodynamics. After the development of assays to detect biologic drug serum concentrations and ADA titers, the first clinical studies in immune-mediated diseases such as rheumatology, gastroenterology, and dermatology have now shown clear concentration-effect relationships. By monitoring the serum trough concentrations of biologics, patients with high drug exposure could be identified and dose reductions in those patients may lead to improved safety and substantial cost savings. Low biologic drug serum concentrations may be due to the development of ADAs, and if these are detected, a switch to an alternative treatment is indicated. We envision a vast expansion of therapeutic drug monitoring to support the use of biologics, and we urge the International Association of Therapeutic Drug Monitoring and Clinical Toxicology to embark on initiatives to investigate the contribution of therapeutic drug monitoring to this field.
Gene‐Environment Interaction between Twist and Thyroid Hormone Results in Extreme Craniosynostotic Phenotypes in Mice (2013)

Craniosynostosis (CS) is the premature fusion of one or more cranial sutures; it can both hinder the growth of the brain and result in severe craniofacial dysmorphology. Although several genes have been implicated with CS, it is unclear how these genotypes lead to widely variable phenotypes. One possibility is gene‐environment interaction. A CDC study found several environmental risk factors associated CS, including maternal hyperthyroidism. We hypothesize that predisposed genotypes will result in more extreme CS phenotypes when exposed to thyroid hormone. To test this we introduced thyroxine to the maternal environment of a genetic CS mouse model, Twist+/−. TWIST has been linked with CS and this model exhibits variable phenotypic expression of CS. Twist+/− and WT control pregnant dams were given thyroxine‐laced water at E13, before suture formation. We sacrificed neonates at P15 and scanned the skulls using μCT. We collected landmarks from the 3D reconstructions and analyzed them using geometric morphometrics. Our preliminary results show that thyroxine has a clear affect on the shape of both Twist+/− and WT skulls and it affects the two groups differently. Exposed Twist+/− mice have higher cranial vaults, wider calvaria, shorter maxilla lengths and wider midfaces compared to both WT and Twist+/− unexposed mice; these shape changes are similar to those associated with CS. Grant Funding Source : Cleft Palate Foundation
The High- T c Superconductor Bi 2 Sr 2 CaCu 2 O x As a Superconducting Superlattice (1992)

Structures in the conductance which are periodic in bias voltage have been observed in very weakly coupled Bi2Sr2CaCu2Ox/W point-contact tunneling junctions. These reproducible features appear to result from geometrical resonances of the order parameter, as would be found in superconductor-normal multilayers, rather than from Coulomb-staircase or multiple-gap effects. The data and its analysis strongly suggest the validity of treating even microscopic properties of Bi2Sr2CaCu2Ox using multilayer models with geometrical parameters inferred from the placement and thicknesses of the CuO2 conductive sheets within the unit cell.
Thermolysis of trimethylsilyl esters: an ultraviolet photoelectron spectroscopy study (1988)

The thermolytic behaviour of trimethylsilyl trifluoromethanesulfonate, 1, trimethylsilyl trifluoroacetate, 2, and trimethylsilyl acetate, 3, has been investigated by ultraviolet photoelectron spectroscopy. Acetate 3 undergoes decomposition only to a small extent at 800 °C via the mechanism shown in Scheme 1 (X = Si); only acetic acid and starting material are detected. In contrast[Formula: see text]with this result, 1 and 2 decompose completely at 725–800 °C and yield products which cannot be derived via the mechanism shown in Scheme 1. Evidence is presented to support our proposal that the thermolysis of 1 yields trimethylsilyl fluoride, 6, and difluorooxathirane dioxide, 7, as primary products. The photoelectron spectra of 1, 2, 3, 6 and trimethylsilanol, 9, are presented. Molecular orbital eigenvalues of dimethylsilene, 4, dimethylsilanone, 5 (calculated using AMPAC and Gaussian 82), 6 and 9 (AMPAC) are reported. Molecular orbital contour diagrams are given for selected MOs of 6 and 9.
Mutational Analysis of Residues Implicated in the Interaction between Protein Kinase CK2 and Peptide Substrates (1997)

Sixteen derivatives of the optimal peptide substrate RRRA-DDSDDDDD in which aspartic acids were singly or multiply substituted by alanine have been assayed for their phosphorylation efficiency by either wild type protein kinase CK2 or CK2 alpha mutants defective in substrate recognition. With wild type CK2, the only detrimental single substitutions were those at positions +3 and +1. Each of these caused a 5-fold increase of Km and a 2-fold decrease of the Vmax values. If both aspartic acids at n + 1 and n + 3 were substituted however, the Km rose 24-fold and the Vmax decreased 16-fold. Multiple substitutions tend to have a more than additive effect even if they affect individually dispensable aspartic acids; thus, double, triple, and quintuple substitutions at positions n - 2 and -1, and n + 2, +4, and +5 had detrimental consequences comparable to those observed with substitutions at n + 1 and n + 3. These data indicate that additional acidic residues besides those at n + 1 and n + 3 are collectively required for efficient phosphorylation of CK2 substrates. They are also consistent with a flexible mode of binding of the substrate, where acidic residues may play interchangeable roles. Among twelve CK2 mutants in which basic residues suspected to be implicated in substrate recognition have been replaced by alanine, only K74-77A, K79R80K83A, R191,195K198A, and K198A showed substantially increased Km values with the optimal substrate RRRA-DDSDDDDD, symptomatic of a reduced ability to bind it. However, if the suboptimal substrate RRRA-AASDDDDD was used, the single mutants K49A, K71A, K77A, R80A, and H160A also exhibited Km values significantly higher than those of wild type CK2. Kinetic analysis with singly substituted derivatives of peptide RRRA-DDSDDDDD revealed that K49 is implicated in the recognition of the determinant at position n + 2, K77 cooperates with other residues nearby in the interaction with the determinants at n + 3 and n + 4, while K198 plays a prominent role in the recognition of the determinant at n + 1.
NEXAFS Spectroscopy Reveals the Molecular Orientation in Blade-Coated Pyridal[2,1,3]thiadiazole-Containing Conjugated Polymer Thin Films (2015)

The characterization of the microstructure and molecular orientation is critical to understanding the performance of conjugated polymer semiconductors. In this work, near-edge X-ray absorption fine structure (NEXAFS) spectroscopy was used to study the molecular orientation of blade-coating thin films of regioregular PCDTPT (poly[4-(4,4-dihexadecyl-4H-cyclopenta[1,2-b:5,4-b′]dithiophen-2-yl)-alt-[1,2,5]thiadiazolo[3,4-c]pyridine]) on substrates with and without uniaxial nanogrooves. The prediction of NEXAFS spectra through density functional theory calculations allowed for the interpretation of the experimental spectral features and provided information about molecular orientation. Using the polarization dependence of the Nitrogen 1s to π*-resonance signals, the molecular orientation was quantified through calculations of the order parameters S (out-of-plane) and η (in-plane) for both the top side and bottom side of the film. All films have out-of-plane orientation where the conjugated backbones have a preferential "edge-on" alignment relative to the substrate surface. On the other hand, with increasing blade-coating rates, the greatest degree of in-plane polymer-chain orientation occurs on the bottom side of a film deposited on a nanogrooved substrate. The results demonstrate the utility of the nanogroove method to induce alignment of solution-processed semiconducting polymers.
Effect of short‐scale turbulence on kilometer wavelength irregularities in the equatorial electrojet (1990)

The kilometer scale irregularities in the daytime equatorial electrojet are studied within the framework of a two‐fluid, nonlocal theory of the gradient drift instability. A separation of scales is introduced into the equations in order to model the effects of the subgrid, short‐wavelength (λ &lt; 100 m) modes. The presence of the short‐scale turbulence is included in the large‐scale equations through the average nonlinear flux due to the small‐scale nonlinear terms. With the use of the linear ion continuity equation the nonlinear flux is expressed in terms of the large‐scale quantities and of the small‐scale density fluctuation spectrum. It is shown that the small‐scale turbulence contributes to the large‐scale equations through turbulent mobility and diffusion coefficients. For a particular choice for the small‐scale density fluctuation spectrum (modeled after some of the available rocket data), the turbulent mobility is determined as a function of altitude, and its peak equals a few times the classical Pedersen mobility value. The equilibrium solutions of the large‐scale equations are also derived in the presence of the short‐wavelength turbulence. The localization of the current layer is seen to shift toward higher altitudes, and the current density profile conforms well with some of the available experimental data. Neglecting at this point the large‐scale nonlinearities, the local and nonlocal linear growth rates of the long‐wavelength modes are also obtained and discussed. The renormalized linear nonlocal equations for the large scales are integrated numerically, and the effects of the turbulent mobility and of velocity shear are observed and discussed. Nonlocal modes with horizontal wavelengths in the kilometer range dominate the linear stage of the instability, thus providing a possible explanation for the experimentally observed predominance of such wavelengths in the electrojet's wave spectrum. The dispersive nature of the large‐scale modes is also discussed and reconsidered in the presence of the turbulent mobility term.
[Treatment of hypertrophic and keloid cicatrices with thiomucase]. (1975)

As hypertrophic and keloid scars are formed essentially by fibrous connective tissue, the therapeutic response of an enzyme with specific action on mucopolysaccharides of the fundamental connective tissue substance (Thiomucase) was studied. This compound has been used with desamethazone phosphate in the ratio of 1:1 with promising results.
Femtosecond Applications for Anterior Segment Surgery (2010)

Femtosecond laser technology has greatly improved on the ability to perform numerous anterior segment procedures that cannot be performed with mechanical microkeratomes. The increased predictability and safety of femtosecond laser in situ keratomileusis flap creation over mechanical microkeratomes are now well accepted.
Whipworm-Associated Intestinal Microbiome Members Consistent Across Both Human and Mouse Hosts (2021)

The human whipworm <i>Trichuris trichiura</i> infects 289 million people worldwide, resulting in substantial morbidity. Whipworm infections are difficult to treat due to low cure rates and high reinfection rates. Interactions between whipworm and its host's intestinal microbiome present a potential novel target for infection control or prevention but are very complicated and are identified using inconsistent methodology and sample types across the literature, limiting their potential usefulness. Here, we used a combined 16S rRNA gene OTU analysis approach (QIIME2) for samples from humans and mice infected with whipworm (<i>T. trichiura</i> and <i>T. muris</i>, respectively) to identify for the first time, bacterial taxa that were consistently associated with whipworm infection spanning host species and infection status using four independent comparisons (baseline infected vs uninfected and before vs after deworming for both humans and mice). Using these four comparisons, we identified significant positive associations for seven taxa including <i>Escherichia</i>, which has been identified to induce whipworm egg hatching, and <i>Bacteroides</i>, which has previously been identified as a major component of the whipworm internal microbiome. We additionally identified significant negative associations for five taxa including four members of the order <i>Clostridiales</i>, two from the family <i>Lachnospiraceae</i>, including <i>Blautia</i> which was previously identified as positively associated with whipworm in independent human and mouse studies. Using this approach, bacterial taxa of interest for future association and mechanistic studies were identified, and several were validated by RT-qPCR. We demonstrate the applicability of a mouse animal model for comparison to human whipworm infections with respect to whipworm-induced intestinal microbiome disruption and subsequent restoration following deworming. Overall, the novel cross-species analysis approach utilized here provides a valuable research tool for studies of the interaction between whipworm infection and the host intestinal microbiome.
NAV-LINES--KEEPING IN SAFE WATERS WITH DIGIPLOT (1977)

The technique speeds up the conventional time tested piloting procedure and does not introduce new methodology that the watch officer may find difficult to grasp, or easy to ignore in times of stress. NAV-LINES provides a simple, easy-to-use integrated automatic radar plotting aid that can continously and directly define safe waters and potential collision threats on the same DIGIPLOT P.P.I. display. Rather than frequent, time consuming, error prone, tedious radio or radar position fixing, the lines, without manual involvement, continuously show the viewer where the ship ought not to be and the course to steer to avoid hazards. The Captain, navigator and pilot are thus provided a digital electronics aid to assist them in maintaining safe ship's passage in pilotage waters. The paper will explain the concept, its relative merits and also describe in detail the use of the NAV-LINE option for a typical situation of a ship entering a harbor from open sea and operating in confined coastal waters.
Isolation and Properties of 7β-(4-Carboxybutanamido)cephalosporanic Acid Acylase-producing Bacteria (1981)

A search was undertaken for microorganisms that produce an enzyme capable of deacylating 7β-(4-carboxybutanamido)cephalosporanic acid (glutaryl 7-ACA, GL-7-ACA) to 7-aminocephalo-sporanic acid. Pseudomonas putida ATCC 950 was selected from our stock cultures, and Pseudomonas SY-77-1 was isolated from soil. Adding glutaric acid to the growth media enhanced the production of GL-7-ACA acylase by Pseudomonas SY-77-1. A β-lactamase-deficient mutant, Pseudomonas NS-2, was derived from Pseudomonas SY-77-1 treated with a mutagen. The cell suspension of Pseudomonas NS-2 specifically hydrolyzed cephalosporin compounds having aliphatic dicarboxylic acid in the acyl side chain.
Plant biotechnology approaches: from breeding to genome editing. (2018)

This chapter focuses on the role of biotechnology in improving the resistance of various economically important crops to plant parasitic nematodes. Information on the various biotechnological approaches currently used in improving crop resistance of plant parasitic nematodes, such as PCR, next generation sequencing, RNAi, genome editing and genetic engineering, among others, are also presented.
GLay: community structure analysis of biological networks (2010)

http://brainarray.mbni.med.umich.edu/glay/.
Dense Branching Morphology in Electrodeposition Experiments: Characterization and Mean-Field Modeling (2000)

Dense branching morphologies (DBM) obtained in thin gap electrodeposition cells are characterized by a dense array of branches behind a flat advancing envelope. In this Letter, we show the existence in DBM of a new (porous) phase, qualitatively different from a (compact) metal deposit. The local porosity inside the branches is found to be much more robust than geometric characteristics such as the width or the distance between branches. This fact seems to be unreported in previous modeling of DBM. A mean-field model is proposed that displays overall features observed in the experiments, such as concentration profiles, front velocity, and branched internal structure.