gebhart/patrepeval huggingface dataset:
Barriers in the developing brain (1998)

Evidence is summarized that shows that proteins do not penetrate into immature brain. Some proteins reach cerebrospinal fluid (CSF) from plasma by a developmentally regulated transfer mechanism. There are also barriers at CSF-brain interfaces, not present in the adult. Thus there is specialization of barriers in the developing brain, some being unique to fetuses.
Realtime facial animation with on-the-fly correctives (2013)

We introduce a real-time and calibration-free facial performance capture framework based on a sensor with video and depth input. In this framework, we develop an adaptive PCA model using shape correctives that adjust on-the-fly to the actor's expressions through incremental PCA-based learning. Since the fitting of the adaptive model progressively improves during the performance, we do not require an extra capture or training session to build this model. As a result, the system is highly deployable and easy to use: it can faithfully track any individual, starting from just a single face scan of the subject in a neutral pose. Like many real-time methods, we use a linear subspace to cope with incomplete input data and fast motion. To boost the training of our tracking model with reliable samples, we use a well-trained 2D facial feature tracker on the input video and an efficient mesh deformation algorithm to snap the result of the previous step to high frequency details in visible depth map regions. We show that the combination of dense depth maps and texture features around eyes and lips is essential in capturing natural dialogues and nuanced actor-specific emotions. We demonstrate that using an adaptive PCA model not only improves the fitting accuracy for tracking but also increases the expressiveness of the retargeted character.
Epibionts from the Cerro Gordo Member of the Lime Creek Formation (Upper Devonian), Rockford, Iowa (1982)

Epibionts and borings are common on brachiopods from the Cerro Gordo Member of the Lime Creek Formation (Upper Devonian) at Rockford, Iowa. Occurrences and distributions of epibionts are best explained by attachment and subsequent growth on either living or dead brachiopods. Distribution of Spirorbis, a calcareous worm tube, is best explained by random attachment of worm larvae on living or dead brachiopods. Cornulites, a conical shell of uncertain affinity, commonly occurs with its aperture oriented toward the anterior commissure of brachiopods, suggesting attachment to living shells and subsequent growth in response to the feeding currents of the brachiopod. Some tabulate corals (auloporids) and some bryozoa (Hederella sp.) display growth patterns toward, or parallel to, the plane of commissure of brachiopods. Such patterns are understandable if these colonial epibionts grew on living brachiopods, taking advantage of the brachiopods' feeding currents. Circular borings and dendritic grooves are common on the brachiopod shells and may have caused the death of some brachiopods. Because the Cerro Gordo Member of the Lime Creek Formation was deposited on a muddy seafloor, attachment sites for small suspension feeders were limited. In this environment, brachiopod shells and horn corals provided relatively mud-free sites where epibionts could attach, grow, and survive.
Inside Microsoft .NET IL Assembler (2002)

From the Publisher:
.NET IL is the intermediate language that the .NET Common Language Runtime converts to machine language in .NET applications. Get the inside scoop on this critical low-level language with an architectural guide from the most reliable authoritythe language's designer, Serge Lidin. You'll discover common structures, functions, and rules for designing .NET applications, explanations for how .NET executables compile, details on the .NET IL Assembler, IL Disassembler and Metadata Validation tools, and more.

Design and develop more effective .NET applications by mastering the structure, rules of organization, and functionality of the .NET IL assembly language.

This in-depth architectural guide comes straight from the most reliable authority on .NET ILits designer, Serge Lidin.
Key Book Benefits: 
* Design better, faster .NET applications by mastering the structure, rules of organization, and functionality of the .NET IL assembly language

* Take your programming skills to the next level by learning how .NET executables compile, and how .NET IL Assembler, IL Disassembler, and Metadata Validation tools work

* Discover how to fully exploit the capabilities of the .NET Common Language Runtime by using IL Assembler to compile multi-language applications
Effects of maturation and storage on solubility, emulsion stability and gelation properties of isolated soy proteins (1990)

Solubility, emulsion stability and gelation of isolated soy proteins and their 7S and 11S fractions from three stages of seed maturity were studied. The pH‐solubility profile was similar irrespective of maturation and six‐month storage. The 11S protein was more soluble in the acidic pH range than the 7S protein. Oil‐in‐water emulsion stability of isolated soy protein from mature soybeans was higher than that from the immature ones. This is due to the fact that there was more 7S fraction in the mature soybeans, and 7S protein was found to form a more stable emulsion than that formed from 11S protein. The result suggests that isolated soy protein from mature soybeans would serve as a better emulsifying agent. Heat‐induced soy protein gels became weaker as the soybeans became more mature. This can be attributed to the higher content in the immature soybeans of 11S fraction which gives a stronger gel than 7S fraction in the protein from immature soybeans.
p<i>K</i><sub>a</sub> Values and the pH Dependent Stability of the N-Terminal Domain of L9 as Probes of Electrostatic Interactions in the Denatured State. Differentiation between Local and Nonlocal Interactions (1999)

pKa values were measured for the 6 carboxylates in the N-terminal domain of L9 (NTL9) by following NMR chemical shifts as a function of pH. The contribution of each carboxylate to the pH dependent stability of NTL9 was estimated by comparing the pKa values for the native and denatured state of the protein. A set of peptides with sequences derived from NTL9 were used to model the denatured state. In the protein fragments, the pKa values measured for the aspartates varied between 3.8 and 4.1 and the pKa values measured for the glutamates varied between 4.1 and 4.6. These results indicate that the local sequence can significantly influence pKa values in the denatured state and highlight the difficulties in using standard pKa values derived from small compounds. Calculations based on the measured pKa values suggest that the free energy of unfolding of NTL9 should decrease by 4.4 kcal mol-1 when the pH is lowered from 6 to 2. In contrast, urea and thermal denaturation experiments indicate that the stability of the protein decreases by only 2.6 kcal mol-1 when the carboxylates are protonated. This discrepancy indicates that the protein fragments are not a complete representation of the denatured state and that nonlocal sequence effects perturb the pKa's in the denatured state. Increasing the salt concentration from 100 to 750 mM NaCl removes the discrepancy between the stabilities derived from denaturation experiments and the stability changes calculated from the pKa values. At high concentrations of salt there is also less variation of the pKa values measured in the protein fragments. Our results argue that in the denatured state of NTL9 there are electrostatic interactions between groups both local and nonlocal in primary sequence.
Gene expression patterns in the hippocampus and amygdala of endogenous depression and chronic stress models (2010)

The etiology of depression is still poorly understood, but two major causative hypotheses have been put forth: the monoamine deficiency and the stress hypotheses of depression. We evaluate these hypotheses using animal models of endogenous depression and chronic stress. The endogenously depressed rat and its control strain were developed by bidirectional selective breeding from the Wistar-Kyoto (WKY) rat, an accepted model of major depressive disorder (MDD). The WKY More Immobile (WMI) substrain shows high immobility/despair-like behavior in the forced swim test (FST), while the control substrain, WKY Less Immobile (WLI), shows no depressive behavior in the FST. Chronic stress responses were investigated by using Brown Norway, Fischer 344, Lewis and WKY, genetically and behaviorally distinct strains of rats. Animals were either not stressed (NS) or exposed to chronic restraint stress (CRS). Genome-wide microarray analyses identified differentially expressed genes in hippocampi and amygdalae of the endogenous depression and the chronic stress models. No significant difference was observed in the expression of monoaminergic transmission-related genes in either model. Furthermore, very few genes showed overlapping changes in the WMI vs WLI and CRS vs NS comparisons, strongly suggesting divergence between endogenous depressive behavior- and chronic stress-related molecular mechanisms. Taken together, these results posit that although chronic stress may induce depressive behavior, its molecular underpinnings differ from those of endogenous depression in animals and possibly in humans, suggesting the need for different treatments. The identification of novel endogenous depression-related and chronic stress response genes suggests that unexplored molecular mechanisms could be targeted for the development of novel therapeutic agents.
Cognitive Disorders Associated with Epilepsy: Diagnosis and Treatment (2008)

The heterogeneity of different types of epilepsy makes case-control studies difficult; however, thanks to the growing interest in the neuropsychological deficits associated with epilepsy, we now know some factors that could lead to the appearance of these disorders and their prognosis. Special care must be taken to detect cognitive side effects associated with AEDs, which seem to be more common with classic than with new AEDs, and in those patients receiving polytherapy. Neuropsychological assessment should be routinely performed before epilepsy surgery to predict possible postsurgical cognitive deficits.
IMing, Text Messaging, and Adolescent Social Networks (2006)

Building on previous research in computer-mediated communication, social and communication networks, and adolescent development, this article raises three issues regarding adolescent use of socially interactive technologies (SITs) and their relationship to offline social networks: 1) whether adolescents are creating more, but weaker ties using SITs, 2) to what extent adolescent SIT-facilitated networks overlap with friendship networks, and 3) whether SIT relationships are important for adolescents who have fewer offline peer ties. In order to investigate these questions, network data collection and analysis were integrated with more traditional questionnaire methodology and statistical analysis. The results show that the adolescents in the study were not creating more ties using SITs, nor were they necessarily creating weaker SIT-based ties; that there was little overlap between SIT-facilitated and offline social networks; and that socially isolated adolescents were less likely than other adolescents to use SITs.
Volume 176, No. 1 (1988)

1. The abilities of botulinum neurotoxins, types A and B (single and two-chain forms) to inactivate an intraneuronal component required for transmitter release were quantified in a phrenic-nerve-diaphragm preparation, cerebrocortical synaptosomes or the buccal ganglion of Aplysia californica and compared with the mouse toxicity assay. 2. Homogeneous preparations of the individually renatured polypeptide chains of both toxin types showed low residual toxicity in the whole animal and had no effect on neurotransmission in all three systems, when tested singly. 3. Mixtures of individually renatured heavy chain, from type A or B, and either light chain proved very effective in blocking the evoked release of acetylcholine when bath-applied to the buccal ganglion of Aplysia whilst they were relatively inactive on mammalian nerve terminals, indicating a less efficient uptake of the polypeptides in the latter. 4. When renatured together, the homologous, but not the heterologous, chains of each toxin type yielded toxic, disulphide-linked two-chain species. 5. A role for the heavy chain alone in acceptor recognition and membrane translocation was implicated by the blockade of acetylcholine release produced when light chain was applied to a ganglion of Aplysia previously bathed in heavy chain and washed extensively. No blockade was observed when the order of application of the two chains was reversed. 6. These findings are discussed in the context of the intracellular requirement for both the constituent toxin chains for toxicity, and in the apparent need for these chains to be linked via a disulphide bond for uptake in rodents but not in Aplysia.
Alternative single-reference coupled cluster approaches for multireference problems: The simpler, the better (2011)

We report a general implementation of alternative formulations of single-reference coupled cluster theory (extended, unitary, and variational) with arbitrary-order truncation of the cluster operator. These methods are applied to compute the energy of Ne and the equilibrium properties of HF and C(2). Potential energy curves for the dissociation of HF and the BeH(2) model computed with the extended, variational, and unitary coupled cluster approaches are compared to those obtained from the multireference coupled cluster approach of Mukherjee et al. [J. Chem. Phys. 110, 6171 (1999)] and the internally contracted multireference coupled cluster approach [F. A. Evangelista and J. Gauss, J. Chem. Phys. 134, 114102 (2011)]. In the case of Ne, HF, and C(2), the alternative coupled cluster approaches yield almost identical bond length, harmonic vibrational frequency, and anharmonic constant, which are more accurate than those from traditional coupled cluster theory. For potential energy curves, the alternative coupled cluster methods are found to be more accurate than traditional coupled cluster theory, but are three to ten times less accurate than multireference coupled cluster approaches. The most challenging benchmark, the BeH(2) model, highlights the strong dependence of the alternative coupled cluster theories on the choice of the Fermi vacuum. When evaluated by the accuracy to cost ratio, the alternative coupled cluster methods are not competitive with respect to traditional CC theory, in other words, the simplest theory is found to be the most effective one.
Function and 3D Structure of the N-Glycans on Glycoproteins (2012)

Glycosylation is one of the most common post-translational modifications in eukaryotic cells and plays important roles in many biological processes, such as the immune response and protein quality control systems. It has been notoriously difficult to study glycoproteins by X-ray crystallography since the glycan moieties usually have a heterogeneous chemical structure and conformation, and are often mobile. Nonetheless, recent technical advances in glycoprotein crystallography have accelerated the accumulation of 3D structural information. Statistical analysis of "snapshots" of glycoproteins can provide clues to understanding their structural and dynamic aspects. In this review, we provide an overview of crystallographic analyses of glycoproteins, in which electron density of the glycan moiety is clearly observed. These well-defined N-glycan structures are in most cases attributed to carbohydrate-protein and/or carbohydrate-carbohydrate interactions and may function as "molecular glue" to help stabilize inter- and intra-molecular interactions. However, the more mobile N-glycans on cell surface receptors, the electron density of which is usually missing on X-ray crystallography, seem to guide the partner ligand to its binding site and prevent irregular protein aggregation by covering oligomerization sites away from the ligand-binding site.
Solving Multiclass Learning Problems via Error-Correcting Output Codes (1995)

Multiclass learning problems involve finding a definitionfor an unknown function f(x) whose range is a discrete setcontaining k &gt; 2 values (i.e., k ``classes''). Thedefinition is acquired by studying collections of training examples ofthe form [x_i, f (x_i)]. Existing approaches tomulticlass learning problems include direct application of multiclassalgorithms such as the decision-tree algorithms C4.5 and CART,application of binary concept learning algorithms to learn individualbinary functions for each of the k classes, and application ofbinary concept learning algorithms with distributed outputrepresentations. This paper compares these three approaches to a newtechnique in which error-correcting codes are employed as adistributed output representation. We show that these outputrepresentations improve the generalization performance of both C4.5and backpropagation on a wide range of multiclass learning tasks. Wealso demonstrate that this approach is robust with respect to changesin the size of the training sample, the assignment of distributedrepresentations to particular classes, and the application ofoverfitting avoidance techniques such as decision-tree pruning.Finally, we show that---like the other methods---the error-correctingcode technique can provide reliable class probability estimates.Taken together, these results demonstrate that error-correcting outputcodes provide a general-purpose method for improving the performanceof inductive learning programs on multiclass problems.
Time-domain optical and thermal properties of blood undergoing laser photocoagulation (2001)

We have examined the temporal characteristics of the optical properties of blood undergoing laser-induced photocoagulation during long pulse (10 ms) 532-nm irradiation. The time-domain optical properties were probed at 532 nm, 594 nm, 633 nm and 1064 nm using a newly developed pump-probe technique in a double integrating sphere apparatus. During the 10 ms illumination period, blood evolves from liquid to a liquid blood-coagulum mixture to a system at the liquid/vapor transition in an essentially adiabatic manner. As with previous studies, a sharp rise in the 532 nm signal remitted from the sample can be linked to the onset of coagulation and a concomitant increase in scattering caused by microscopic coagulum particles. We also observe a subsequent decay in this remittance and, at sufficiently high radiant exposures, acoustic and visual transients indicating the onset of microvaporization. Probing the sample at the other wavelengths, we show that the optical properties of the system display highly complex behavior in multiple time frames. We believe that this rich behavior results from the interplay of: i) a time/temperature-dependent red-shift in the absorption spectrum of the oxy-hemoglobin chromophore, ii) coagulation dynamics occurring on at least two distinct time and length scales, and, iii) the creation of at least one new chemical species possessing a different absorption spectrum to that of oxy-hemoglobin. The thermal properties of the system were measured in a time- and spatially-resolved manner using a newly developed technique, and modeled using finite-element analysis incorporating the effects of time-dependent changes in the absorption coefficients of the blood, and phase changes representing coagulation and the liquid/vapor transition. Cross-correlating the optical and thermal studies, we show that the temporal properties of the 532 nm and 633 nm remittance signals can potentially be used to develop a sensitive real-time probe of the onset of coagulation, which in turn will lead to accurate dosimetry during clinical procedures. We also show that the three features of the coagulation highlighted above have profound implications for the design of lasers for vascular therapeutic applications.
Naive Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy (2007)

The Ribosomal Database Project (RDP) Classifier, a naïve Bayesian classifier, can rapidly and accurately classify bacterial 16S rRNA sequences into the new higher-order taxonomy proposed in Bergey's Taxonomic Outline of the Prokaryotes (2nd ed., release 5.0, Springer-Verlag, New York, NY, 2004). It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. The majority of classifications (98%) were of high estimated confidence (> or = 95%) and high accuracy (98%). In addition to being tested with the corpus of 5,014 type strain sequences from Bergey's outline, the RDP Classifier was tested with a corpus of 23,095 rRNA sequences as assigned by the NCBI into their alternative higher-order taxonomy. The results from leave-one-out testing on both corpora show that the overall accuracies at all levels of confidence for near-full-length and 400-base segments were 89% or above down to the genus level, and the majority of the classification errors appear to be due to anomalies in the current taxonomies. For shorter rRNA segments, such as those that might be generated by pyrosequencing, the error rate varied greatly over the length of the 16S rRNA gene, with segments around the V2 and V4 variable regions giving the lowest error rates. The RDP Classifier is suitable both for the analysis of single rRNA sequences and for the analysis of libraries of thousands of sequences. Another related tool, RDP Library Compare, was developed to facilitate microbial-community comparison based on 16S rRNA gene sequence libraries. It combines the RDP Classifier with a statistical test to flag taxa differentially represented between samples. The RDP Classifier and RDP Library Compare are available online at http://rdp.cme.msu.edu/.
A Novel Monte Carlo Noise Reduction Operator (2005)

Monte Carlo noise appears as outliers and as interpixel incoherence in a typical image rendered at low sampling density. Unfortunately, none of the previous approaches can reduce both types of noise in a unified way. In this article, we propose such a unified Monte Carlo noise reduction approach using bilateral filtering. We extended the standard bilateral filtering method and built a new local adaptive noise reduction kernel. The new operator suppresses the outliers and interpixel incoherence in a noniterative way.
Economic impact of reduced milk production associated with Johne's disease on dairy operations in the USA (2005)

Accurately assessing the economic impacts of diseases and other factors that affect milk production requires that the demand for milk be taken into account. Because demand for milk in the USA is relatively inelastic (i.e., consumers generally purchase a somewhat fixed amount over a given time frame, regardless of fluctuations in price), consumers tend to reap much of the benefit of enhanced production. An examination of the economic impacts of Johne's disease indicated that reduced milk production, associated with the determination of dairy operations as Johne's-positive, reduced consumer surplus by 770 million dollars+/- 690 million dollars, and resulted in a total loss of 200 million dollars+/- 160 million dollars to the US economy in 1996. Most of the economic surplus lost by consumers was transferred to producers, whose economic surplus increased by 570 million dollars+/- 550 million dollars as a result of the reduced milk production associated with Johne's disease. Uncertainty analysis showed that the estimated reduction in milk production on Johne's-positive dairy operations accounted for most of the uncertainty in the economic-impact estimates. If Johne's disease had not been present on US dairy operations, then an additional 580 million+/-460 million kg of milk would have been produced, but the price would have fallen by 1.1+/-1.0 cents/kg, and the total value of the milk would have decreased by 580 million dollars+/- 560 million dollars.