bluuebunny/crossref_metadata_2025_split huggingface dataset:
Alcohol, Volatile Fatty Acid, Phenol, and Methane Emissions from Dairy Cows and Fresh Manure
Authors: Sun Huawei , Trabue Steven L. , Scoggin Kenwood , Jackson Wendi A. , Pan Yuee , Zhao Yongjing , Malkina Irina L. , Koziel Jacek A. , Mitloehner Frank M. 
Published: February 2008

AbstractThere are approximately 2.5 million dairy cows in California. Emission inventories list dairy cows and their manure as the major source of regional air pollutants, but data on their actual emissions remain sparse, particularly for smog‐forming volatile organic compounds (VOCs) and greenhouse gases (GHGs). We report measurements of alcohols, volatile fatty acids, phenols, and methane (CH4) emitted from nonlactating (dry) and lactating dairy cows and their manure under controlled conditions. The experiment was conducted in an environmental chamber that simulates commercial concrete‐floored freestall cow housing conditions. The fluxes of methanol, ethanol, and CH4 were measured from cows and/or their fresh manure. The average estimated methanol and ethanol emissions were 0.33 and 0.51 g cow−1 h−1 from dry cows and manure and 0.7 and 1.27 g cow−1 h−1 from lactating cows and manure, respectively. Both alcohols increased over time, coinciding with increasing accumulation of manure on the chamber floor. Volatile fatty acids and phenols were emitted at concentrations close to their detection limit. Average estimated CH4 emissions were predominantly associated with enteric fermentation from cows rather than manure and were 12.35 and 18.23 g cow−1 h−1 for dry and lactating cows, respectively. Lactating cows produced considerably more gaseous VOCs and GHGs emissions than dry cows (P < 0.001). Dairy cows and fresh manure have the potential to emit considerable amounts of alcohols and CH4 and research is needed to determine effective mitigation.
On the Pathogenicity of Autoantigen-Specific T-Cell Receptors
Authors: Burton Amanda R. , Vincent Erica , Arnold Paula Y. , Lennon Greig P. , Smeltzer Matthew , Li Chin-Shang , Haskins Kathryn , Hutton John , Tisch Roland M. , Sercarz Eli E. , Santamaria Pere , Workman Creg J. , Vignali Dario A.A. 
Published: February 2008

OBJECTIVE—Type 1 diabetes is mediated by T-cell entry into pancreatic islets and destruction of insulin-producing β-cells. The relative contribution of T-cells specific for different autoantigens is largely unknown because relatively few have been assessed in vivo.RESEARCH DESIGN AND METHODS—We generated mice possessing a monoclonal population of T-cells expressing 1 of 17 T-cell receptors (TCR) specific for either known autoantigens (GAD65, insulinoma-associated protein 2 (IA2), IA2β/phogrin, and insulin), unknown islet antigens, or control antigens on a NOD.scid background using retroviral-mediated stem cell gene transfer and 2A-linked multicistronic retroviral vectors (referred to herein as retrogenic [Rg] mice). The TCR Rg approach provides a mechanism by which T-cells with broad phenotypic differences can be directly compared.RESULTS—Neither GAD- nor IA2-specific TCRs mediated T-cell islet infiltration or diabetes even though T-cells developed in these Rg mice and responded to their cognate epitope. IA2β/phogrin and insulin-specific Rg T-cells produced variable levels of insulitis, with one TCR producing delayed diabetes. Three TCRs specific for unknown islet antigens produced a hierarchy of insulitogenic and diabetogenic potential (BDC-2.5 &gt; NY4.1 &gt; BDC-6.9), while a fourth (BDC-10.1) mediated dramatically accelerated disease, with all mice diabetic by day 33, well before full T-cell reconstitution (days 42–56). Remarkably, as few as 1,000 BDC-10.1 Rg T-cells caused rapid diabetes following adoptive transfer into NOD.scid mice.CONCLUSIONS—Our data show that relatively few autoantigen-specific TCRs can mediate islet infiltration and β-cell destruction on their own and that autoreactivity does not necessarily imply pathogenicity.
Compact corigid objects in triangulated categories and co-t-structures
Authors: Pauksztello David 
Published: February 2008

Abstract
In the work of Hoshino, Kato and Miyachi, [11], the authors look at t-structures induced by a compact object, $$
C
$$, of a triangulated category, $$
\mathcal{T}
$$, which is rigid in the sense of Iyama and Yoshino, [12]. Hoshino, Kato and Miyachi show that such an object yields a non-degenerate t-structure on $$
\mathcal{T}
$$ whose heart is equivalent to Mod(End($$
C
$$)op). Rigid objects in a triangulated category can the thought of as behaving like chain differential graded algebras (DGAs). Analogously, looking at objects which behave like cochain DGAs naturally gives the dual notion of a corigid object. Here, we see that a compact corigid object, $$
\mathcal{S}
$$, of a triangulated category, $$
\mathcal{T}
$$, induces a structure similar to a t-structure which we shall call a co-t-structure. We also show that the coheart of this non-degenerate co-t-structure is equivalent to Mod(End($$
\mathcal{S}
$$)op), and hence an abelian subcategory of $$
\mathcal{T}
$$.
Transformations preserving the Hausdorff-Besicovitch dimension
Authors: Albeverio Sergio , Pratsiovytyi Mykola , Torbin Grygoriy 
Published: February 2008

Abstract
Continuous transformations preserving the Hausdorff-Besicovitch dimension (“DP-transformations”) of every subset of R
1 resp. [0, 1] are studied. A class of distribution functions of random variables with independent s-adic digits is analyzed. Necessary and sufficient conditions for dimension preservation under functions which are distribution functions of random variables with independent s-adic digits are found. In particular, it is proven that any strictly increasing absolutely continuous distribution function from the above class is a DP-function. Relations between the entropy of probability distributions, their Hausdorff-Besicovitch dimension and their DP-properties are discussed. Examples are given of singular distribution functions preserving the fractal dimension and of strictly increasing absolutely continuous functions which do not belong to the DP-class.
Vector bundles on Hirzebruch surfaces whose twists by a non-ample line bundle have natural cohomology
Authors: Ballico Edoardo , Malaspina Francesco 
Published: February 2008

Abstract
Here we study vector bundles E on the Hirzebruch surface F
e such that their twists by a spanned, but not ample, line bundle M = $$
\mathcal{O}
$$
Fe(h + ef) have natural cohomology, i.e. h
0(F
e, E(tM)) > 0 implies h
1(F
e, E(tM)) = 0.
On the exact values of coefficients of coiflets
Authors: Černá Dana , Finěk Václav , Najzar Karel 
Published: February 2008

Abstract
In 1989, R. Coifman suggested the design of orthonormal wavelet systems with vanishing moments for both scaling and wavelet functions. They were first constructed by I. Daubechies [15, 16], and she named them coiflets. In this paper, we propose a system of necessary conditions which is redundant free and simpler than the known system due to the elimination of some quadratic conditions, thus the construction of coiflets is simplified and enables us to find the exact values of the scaling coefficients of coiflets up to length 8 and two further with length 12. Furthermore for scaling coefficients of coiflets up to length 14 we obtain two quadratic equations, which can be transformed into a polynomial of degree 4 for which there is an algebraic formula to solve them.
A numerically stable least squares solution to the quadratic programming problem
Authors: Übi E. 
Published: February 2008

Abstract
The strictly convex quadratic programming problem is transformed to the least distance problem — finding the solution of minimum norm to the system of linear inequalities. This problem is equivalent to the linear least squares problem on the positive orthant. It is solved using orthogonal transformations, which are memorized as products. Like in the revised simplex method, an auxiliary matrix is used for computations. Compared to the modified-simplex type methods, the presented dual algorithm QPLS requires less storage and solves ill-conditioned problems more precisely. The algorithm is illustrated by some difficult problems.
Induced Breeding of <i>Pila globosa</i> (Swainson 1822) (Gastropoda: Prosobranchia) for Commercial Farming
Authors: Jahan Md Sarwar , Islam Md Refiqul , Rahman Md Redwanur , Alam M Manjurul 
Published: February 2008

Studies were made on the number of egg clutch, copulating pairs, duration of mating, duration of egg laying, and weight of egg clutch of Pila globosa by inducing it with Pituitary Gland (PG) and Optic Tentacle cut (OT) under laboratory condition. The effect of inducing the animal with PG and OT cut showed that it resulted in an increase in the number of egg clutch in comparison with that of the control.
In control animals the number of egg clutch was found to be 0.30±0.02 which was 20.93% of total egg clutches laid. Whereas in animals with Pituitary Gland (PG) and Optic Tentacles (OT) cut the number of egg clutch were 0.43±0.61 and 0.70±0.86 which were 30.23% and 48.83% of total egg clutches laid respectively. The animals injected with pituitary gland extract and optic tentacle cut showed an increase in the number of egg clutch in comparison with that of the control animals.
In control animals, duration of mating, duration of egg laying, and weight of egg clutch were found as, 3.23±0.29hrs., 5.37±1.51hrs., and 8.38±g respectively. The pituitary gland (PG) injected and optic tentacle (OT) cut, duration of mating, duration of egg laying and weight of egg clutch were found as, 3.52±0.26hrs., 4.64±1.63hrs., and 8.54±2.10g.; 3.51±0.33hrs., 5.47±1.19hrs., and 8.45±2.53g respectively.

Key words: Pila globosa, induced breeding, Commercial Farming.

Univ. j. zool. Rajshahi Univ. Vol. 26, 2007. pp. 35-39
Measurement of Aminoacylases
Authors: Pushkin Alexander , Kurtz Ira 
Published: February 2008

AbstractThe unit describes the assays for aminoacylase activity, with specific emphasis on aminoacylase III. The methods are based on the determination of deacetylated products of the aminoacylase‐catalyzed reactions in fluorescence and absorbance assays. The unit also provides methods for isolation of the aminoacylase III from tissues and bacterial or mammalian cells and subsequent purification and analysis.Curr. Protoc. Toxicol. 35:6.14.1‐6.14.20. © 2008 by John Wiley & Sons, Inc.
Experimental Models of Hypoxic‐Ischemic Encephalopathy: Hypoxia‐Ischemia in the Immature Rat
Authors: Carloni Silvia , Balduini Walter 
Published: February 2008

AbstractThe development of experimental models to study the mechanisms of perinatal hypoxic‐ischemic encephalopathy and stroke and effective therapies represents an important goal in perinatal medicine. However, due to the complexity of this pathological condition in humans, to date there is no ideal animal model that completely reproduces this condition. This unit describes the most widely used rodent animal model for the study of hypoxic‐ischemic encephalopathy during development. The model consists of 7‐day‐old pup rats subjected to unilateral carotid artery ligation followed by timed hypoxia exposure, and incorporates both focal cerebral ischemia and reperfusion. Its strength lies in the relative ease of the surgical procedure, the low mortality rate, and the possibility of performing long‐term experiments, a necessity for preclinical therapeutic trials. Over the years, this model has been extensively characterized, and most information on the mechanisms responsible for neurodegeneration and possible therapeutic approaches following hypoxia‐ischemia during brain development derives from studies performed using this model. Curr. Protoc. Toxicol. 35:11.15.1‐11.15.11. © 2008 by John Wiley & Sons, Inc.
The Syrian Hamster Embryo (SHE) Low pH Cell Transformation Assay
Authors: Pant Kamala , Aardema Marilyn J. 
Published: February 2008

AbstractThe Syrian hamster embryonic (SHE) cell transformation assay (CTA) at pH 6.7 can determine the ability of a test article to induce morphological transformation (MT) in cultured SHE cells. The assay uses SHE cells prepared at gestation day ∼13 and frozen. Target cells are seeded onto a layer of feeder cells (X‐ray irradiated SHE cells) and treated with test article for 24 hr or 7 days. After a growth period of 7 days, the cells are fixed, stained, and evaluated for MT. Normal colonies typically contain a monolayer of cells with an organized, often flowing, pattern of growth and minimal cell criss‐crossing at a confluent density. Transformed colonies contain randomly oriented, stacked cells, with cell criss‐crossing throughout the colony. The transformed cells are frequently more basophilic than their normal counterparts, with increased nuclear/cytoplasmic ratios. This assay provides a valuable tool for evaluating the carcinogenic potential of a test article. Curr. Protoc. Toxicol. 35:20.3.1‐20.3.16. © 2008 by John Wiley & Sons, Inc.
MultiBac: Multigene Baculovirus‐Based Eukaryotic Protein Complex Production
Authors: Bieniossek Christoph , Richmond Timothy J. , Berger Imre 
Published: February 2008

AbstractMultiprotein complexes are an emerging focus in current biology, resulting in a demand for advanced heterologous expression systems. This unit provides protocols for the expression of eukaryotic multiprotein complexes using multigene expression vectors. Homologous and site‐specific recombinases facilitate their assembly. Thus, modification of individual subunits for revised expression studies is achieved with comparative ease. The strategy outlined here employs the MultiBac baculoviral expression system for multiprotein complexes as an example. Baculoviral expression does not require particular safety precautions due to the replication incompetence of baculovirus in mammalian hosts. The MultiBac system provides for improved protein production due to deletion of specific viral genes (V‐cath, chiA). Most of the steps described in this unit are tailored for high‐throughput approaches. The general strategy of rapidly combining encoding DNAs by recombination into multigene expression vectors for protein complex expression can also be applied to other prokaryotic or mammalian expression systems. Curr. Protoc. Protein Sci. 51:5.20.1‐5.20.26. © 2008 by John Wiley & Sons, Inc.
Phage Display for Generating Peptide Reagents
Authors: Brigati Jennifer R. , Samoylova Tatiana I. , Jayanna Prashanth K. , Petrenko Valery A. 
Published: February 2008

AbstractThis unit presents detailed protocols for selection and propagation of landscape phages, which are fusions of filamentous phage fd (or its close relatives M13 and f1) and foreign DNA that result in chimeric phage virions with foreign peptides (8 to 9 amino acids long) covering the entire surface of the phage particles. These landscape phages bind specifically to mammalian and bacterial cells, spores, or discrete molecular targets. Curr. Protoc. Protein Sci. 51:18.9.1‐18.9.27. © 2008 by John Wiley & Sons, Inc.
Utilizing Peptide SPOT Arrays to Identify Protein Interactions
Authors: Cushman Ian 
Published: February 2008

AbstractSPOT arrays consist of synthesized peptides 12‐ to 18‐amino acids long, with overlapping sequences that cover the entire sequence of a protein, covalently linked to a solid support. This unit describes how to construct peptide SPOT arrays, biotinylate recombinant proteins, and conduct overlay assays to identify binding interactions. In addition, directions describing how to analyze results to determine single amino acid binding contributions are included. The two techniques in this unit describe how to scan protein sequences to find binding motifs and how to conduct site‐directed mutagenesis studies. Curr. Protoc. Protein Sci. 51:18.10.1‐18.10.9. © 2008 by John Wiley & Sons, Inc.
Carcinoembryonic Antigen Transgenic Mouse Models for Immunotherapy and Development of Cancer Vaccines
Authors: Bhattacharya‐Chatterjee Malaya , Saha Asim , Foon Kenneth A. , Chatterjee Sunil K. 
Published: February 2008

AbstractThe goal of cancer therapy remains as the long‐term eradication of tumor cells without adverse effects on normal tissue. Conventional approaches utilizing chemotherapy and radiotherapy are limited by both their toxicity and lack of specificity. In recent years, investigators have carried out several studies designed to evaluate whether human tumor‐associated antigens (TAAs) can be exploited as targets for immunotherapy, specifically for human cancer vaccine development. A major limitation in immunotherapy studies of human cancer is the general lack of appropriate preclinical models. Clinical studies can be difficult to implement, particularly when a clear understanding of the potential efficacy, limitation, and safety of an immunotherapeutic strategy is not available from relevant animal investigations. However, mice carrying a transgene for a human tumor self‐antigen may provide a more acceptable experimental model in which knowledge about immunotherapeutic strategies aiming at the TAA of interest can be enhanced prior to initiating clinical trials. Since the different strategies in experimental immunotherapy of cancer have been directed to activate different immune system components, a variety of transgenic mouse models have been generated expressing either TAA, human leukocyte antigen (HLA), oncogene, or immune effector cell molecules. These models may serve as an excellent platform for the identification of novel targets for immunotherapy as well as to evaluate the efficacy of targeted therapies and will lead to the development of clinical trials for cancer patients. In this unit, a brief overview of the generation and study of different vaccine approaches in carcinoembryonic antigen (CEA) transgenic mouse models and the experimental findings in mouse models that spontaneously develop gastrointestinal tumors and express the CEA transgene is provided. Curr. Protoc. Immunol. 80:20.8.1‐20.8.12. © 2008 by John Wiley & Sons, Inc.
Aminoacyl tRNASynthetases, Chemistry of
Authors: Nawaz Mir Hussain , Martinis Susan A. 
Published: February 2008

AbstractAminoacyl‐tRNA synthetases (aaRSs) compose a family of essential enzymes that attach amino acids covalently to tRNA molecules during protein synthesis. Some aaRSs possess a hydrolytic amino acid editing function to ensure the fidelity of protein synthesis. In addition, aminoacylation can occur by indirect pathways that rely on mischarged tRNA intermediates and enzymes other than aaRSs. Throughout evolution, structural and functional divergence of aaRSs has yielded diverse secondary roles. Likewise, aaRS‐like proteins with either sequence or structural similarities to synthetases exhibit functions that may or may not be related to aminoacylation. Many of these diverse aaRSs and aaRS‐like proteins have been capitalized on by the microbial world and by medical research as targets for therapeutic agents such as antibiotics.
BacterialDNAPolymerases, Chemistry of
Authors: Pomerantz Richard T. , O'Donnell Mike 
Published: February 2008

AbstractAll DNA polymerases share a common two‐metal ion catalyzed chemistry of nucleotide incorporation. Structure analysis, however, suggests that DNA polymerases share one of two different ancestors, which converged to employ the same mechanism.Escherichia coli, the prototypical bacterium, encodes five different DNA polymerases. The chromosomal replicase functions closely with clamps, clamp‐loaders, and other proteins. Oxidative damage to DNA during normal cell growth requires interplay among the several distinct DNA polymerases, which enable the replicase to circumvent these obstacles and complete chromosomal replication. Additional processes involving DNA polymerases are brought into action during heightened levels of DNA damage. We review here DNA polymerase structure, catalytic mechanism, and several pathways in which various bacterial DNA polymerases act.
Calcium Signaling
Authors: Brini Marisa , Fedrizzi Laura , Carafoli Ernesto 
Published: February 2008

AbstractCalcium is a universal second messenger that controls many cellular reactions. Considering its pleiotropic role, it seems evident that the cells, to get a specific message in the proper time and manner, need precise and efficient mechanisms to encode and decode Ca2+signals. Generally, extracellular stimuli are converted in a transient increase in cytosolic Ca2+concentration, [Ca2+]c, which, in turn, modulates cell function. In the last two decades, improvements in the development of probes and instrumentation for Ca2+imaging have led to the discovery that the coordinated action of different players is responsible for a complex spatio‐temporal organization of the Ca2+signal. It is intriguing to observe that cells can encode and discriminate Ca2+signals not only according to their magnitude but also according to their localization (microdomains) and shape; i.e., cells can discriminate between sustained and oscillatory signals. Even more, in the case of oscillations, messages can be read differently according to the frequency of the oscillatory signals. The mechanisms by which cells decode Ca2+signals are now explored in numerous laboratories. This article focuses on the autoregulation properties of the Ca2+signals. It will show that Ca2+itself is central in the regulation of the Ca2+signal. It will also show that it can act as a first and second messenger and that it can modulate the activity and the availability of the other players in the signaling operation.
Catalytic Antibodies (Abzymes), Synthetic
Authors: Brogan Andrew P. , Dickerson Tobin J. , Janda Kim D. 
Published: February 2008

AbstractCatalytic antibodies have emerged as powerful tools for the chemical biologist, enabling the design and realization of specific catalysis for a wide range of chemical reactions. Catalytic antibodies are grounded upon transition state theory and envisioned as programmable mimics of enzyme catalysis. Affinity maturation of the immune response for a small‐molecule hapten elicits binding site complementarity within an antibody that facilitates chemical catalysis. The evolution of hapten design strategies for chemical catalysis is presented, including the transition state analog approach, strain‐induced hapten design, “bait‐and‐switch,” and “reactive immunization.” The range and scope of antibody catalysis is examined by reaction class, highlighting structural and mechanistic investigations to explore the roots of chemical catalysis by these designer biocatalysts. Recently, antibodies, regardless of disposition or origin, have been shown to catalyze the oxidation of water, equipping the antibody with a mechanism for antigen decomposition. These recent developments are presented along with the utilization of this pathway in the oxidative degradation of a commonly abused drug. The achievements in antibody catalysis have enriched our scientific understanding of chemical catalysis, particularly by biological molecules in aqueous systems. However, realizing more operative rate enhancements on the same order as natural enzymes remains as the “holy grail” of this field.
Cell Membrane Dynamics
Authors: Kenworthy Anne K. 
Published: February 2008

AbstractCell membranes are two‐dimensional fluids that exhibit a wide range of dynamic behaviors. Recent technical advances have enabled unprecedented views of membrane dynamics in living cells. In this technical review, we provide a brief overview of three well‐studied examples of membrane dynamics: lateral diffusion of proteins and lipids in the plane of the membrane, vesicular trafficking between intracellular compartments, and exchange of proteins on and off membranes. We then discuss experimental approaches to monitor membrane protein and lipid dynamics, and we place a special emphasis on the use of genetically encoded fluorescent probes and live cell‐imaging techniques.