bluuebunny/crossref_metadata_2025_split huggingface dataset:
Raney nickel catalyst of improved stability and reactivity in the hydrogenation of triglycerides
Authors: Tɒmer H. V. , Feuge R. O. , Cousins E. R. 
Published: January 2009

AbstractThe degree of activity of Raney nickel catalysts in the hydrogenation of triglycerides has been found to vary considerably with and to depend upon unknown factors in the original alloy. Highly active preparations of Raney nickel rapidly lost their activity when stored in absolute ethanol due to the formation of acetaldehyde. Loss of activity was associated with the amount of residual aluminum in the catalyst. The nickel was found to dissolve to some extent in the acetal‐dehyde‐ethanol solution. Catalysts deactivated by acetaldehyde could be reactivated to a greater degree of activity than that possessed originally by treating with acetic acid. The activity of the original Raney nickel catalyst was preserved to a greater extent by storage in dioxane instead of ethanol.
Factors affecting the rate of deterioration in the frying qualities of fats. 1 i. exposure to air
Authors: Rock S. P. , Roth H. 
Published: January 2009

AbstractThe effect of heating fats in air and the effect of heating fats in an inert atmosphere were compared, and the relationship of air to changes in the frying characteristics of fat studied. The frying characteristics of a fat did not change to an extent that is commercially significant even after 48 hr heating at 375F in the absence of air; fats heated under identical conditions but in the presence of air, changed radically. It was found, also, that fat which had changed appreciably in frying characteristics when heated in air did not continue to change significantly when heated further under nitrogen. Hence, presence of oxygen was shown to be a necessary condition for the deterioration of the frying qualities of fat at frying temp. Rate of change of the frying characteristics was found to be directly proportional to the degree of exposure of fat surface to the oxygen.
Molecular weight distribution of nonionic surfactants. III. Foam, wetting, detergency, emulsification and solubility properties of normal distribution and homogeneous p,t‐octylphenoxyethoxyethanols
Authors: Crook E. H. , Fordyce D. B. , Trebbi G. F. 
Published: January 2009

AbstractThe effect of mol wt distribution on the foaming, wetting, detergency, emulsification and solubility properties of p,t‐octylphenoxyethoxy‐ethanols (OPE's) has been studied by comparing normal distribution and homogeneous compounds: Ross‐Miles foam studies indicate that, although homogeneous OPE7‐10 are higher in initial foam height than normal distribution OPE7‐10, their foam stability is poorer. Hard surface and textile wetting were studied by contact angle determinations and the Draves' skein test, respectively. An exact correlation exists between hard surface wetting by solutions of OPE's of a Teflon surface and surface tension lowering. Normal distribution OPE's are, in general, better hard surface wetting agents than the corresponding homogeneous compounds. In textile wetting, normal distribution OPE5‐10 are approximately equivalent in performance and by implication are probably equivalent in wetting performance to the corresponding homogeneous compounds. Hard surface detergency studies show that normal distribution OPE's are generally slightly superior in detersive power to homogeneous OPE's at corresponding ethylene oxide chain lengths. OPE10 is the best hard surface detergent of the OPE series, there being no distinguishable difference in performance between homogeneous and normal distribution OPE10. Emulsification studies on the system, water‐isooctane, show that only normal distribution OPE5 is capable of forming stable o/w emulsions. Both homogeneous and normal distribution OPE3 and OPE4 form stable w/o (invert) emulsions. Solubility studies in isooctane and Ultrasene show that homogeneous OPE4 is soluble at lower temp than the corresponding normal distribution compound. Studies of aqueous OPE solutions at temp above their cloud points show that solubility of both homogeneous and normal distribution materials is of the same order of magnitude as their critical micelle concn and that homogeneous OPE4 is more soluble than normal distribution OPE4.
The preparation and plasticizing characteristics of pipendides of long chain fatty acids and n‐fatty acyl derivatives of other cyclic imines
Authors: Mod R. R. , Magne F. C. , Skau E. L. 
Published: January 2009

AbstractForty‐six N‐acyl derivatives of cyclic imines have been prepared, characterized, and screened as primary plasticizers for poly (vinyl chloridevinyl acetate) copolymer. Among these were the piperidides of decanoic, palmitic, stearic, oleic, erucic, ricinoleic, epoxystearic, epoxyoleic, diepoxystearic, sebacic, pinic, cottonseed, hydrogenated cottonseed, rapeseed,Limnanthes douglasii, animal, 2‐ethylhexanoic, naphthenic, and dimer acids, as well as the N‐oleoyl derivatives of a number of substituted piperidines and other cyclic imines including pyrrolidine, piperazine, hexamethylenimme, tetrahydroquinolme, 3‐azabicyclo [3.2.2] nonane, dipyridylamine, and carbazole.In general these amides of the 5‐,6‐, and 7‐membered cyclic imines exhibited exceptionally high plasticizing efficiencies. The compatibilities observed were the best to date for fatty acid derivatives on the basis of both individual and ternary fatty acid composition‐compatibility data. Several of these amides exhibited low‐temp characteristics in the adipate plasticizer range without the adverse volatility characteristics of the adipates. There are indications that some of them have appreciable antifungal activity. It has been concluded that cyclic imines will, in general, produce fatty acid derivatives of better than average compatibility as vinyl plasticizers.
Rehabilitation Needs of Combat‐Injured Service Members Admitted to the VA Polytrauma Rehabilitation Centers: The Role of PM&R in the Care of Wounded Warriors
Authors: Sayer Nina A. , Cifu David X. , McNamee Shane , Chiros Christine E. , Sigford Barbara J. , Scott Steve , Lew Henry L. 
Published: January 2009

ObjectiveTo describe the rehabilitation course of combat‐injured service members who sustained polytraumatic injuries during the current wars in and around Iraq and Afghanistan.DesignRetrospective descriptive analysis.SettingDepartment of Veterans Administration Polytrauma Rehabilitation Centers (PRCs).ParticipantsOne hundred eighty‐eight consecutive, acutely combat‐injured service members suffering polytraumatic injuries requiring inpatient rehabilitation and being treated at PRCs between October 2001 and January 2006.InterventionsNot applicable.Main Outcome MeasuresMedications prescribed, devices used, injuries and impairment information, and consultative services.ResultsNinety‐three percent of the patients had sustained a traumatic brain injury (TBI) and more than half of these were incurred secondary to blast explosions. Over half of the patients had infections or surgeries prior to PRC admission that required continued medical attention during their stay. Pain and mental health issues were present in 100% and 39%, respectively, of all patients admitted and added complexity to the brain injury rehabilitation process. Common treatment needs included cognitive‐behavioral interventions, pain care, assistive devices, mental health interventions for both patients and their families, and specialty consultations, in particular to ophthalmology, otolaryngology, and neurology.ConclusionsCombat‐injured polytrauma patients have complex rehabilitation needs that require a high level of specialized training and skill. Physical medicine and rehabilitation specialists treating war injured service members need a high level of expertise in assessment and treatment of co‐occurring pain, TBI, and stress disorders. Physiatrists are playing an important role in providing and coordinating the rehabilitation care for individuals with significant polytraumatic war injuries from the Operation Enduring Freedom/Operation Iraqi Freedom (OEF/OIF) conflicts.
Practice Parameter: The Evaluation of Distal Symmetric Polyneuropathy: The Role of Laboratory and Genetic Testing (An Evidence‐Based Review)
Authors: England J.D. , Gronseth G.S. , Franklin G. , Carter G.T. , Kinsella L.J. , Cohen J.A. , Asbury A.K. , Szigeti K. , Lupski J.R. , Latov N. , Lewis R.A. , Low P.A. , Fisher M.A. , Herrmann D.N. , Howard J.F. , Lauria G. , Miller R.G. , Polydefkis M. , Sumner A.J. 
Published: January 2009

BackgroundDistal symmetric polyneuropathy (DSP) is the most common variety of neuropathy. Since the evaluation of this disorder is not standardized, the available literature was reviewed to provide evidence‐based guidelines regarding the role of laboratory and genetic tests for the assessment of DSP.MethodsA literature review using MEDLINE, EMBASE, Science Citation Index and Current Contents was performed to identify the best evidence regarding the evaluation of polyneuropathy published between 1980 and March 2007. Articles were classified according to a four‐tiered level of evidence scheme and recommendations were based upon the level of evidence.Results and Conclusions1. Screening laboratory tests may be considered for all patients with polyneuropathy (Level C). Those tests that provide the highest yield of abnormality are blood glucose, serum B12 with metabolites (methylmalonic acid with or without homocysteine) and serum protein immunofixation electrophoresis (Level C). If there is no definite evidence of diabetes mellitus by routine testing of blood glucose, testing for impaired glucose tolerance may be considered in distal symmetric sensory polyneuropathy (Level C). 2. Genetic testing is established as useful for the accurate diagnosis and classification of hereditary neuropathies (Level A). Genetic testing may be considered in patients with cryptogenic polyneuropathy who exhibit a hereditary neuropathy phenotype (Level C). Initial genetic testing should be guided by the clinical phenotype, inheritance pattern, and electrodiagnostic (EDX) features and should focus on the most common abnormalities which are CMT1A duplication/HNPP deletion, Cx32 (GJB1), and MFN2 mutation screening. There is insufficient evidence to determine the usefulness of routine genetic testing in patients with cryptogenic polyneuropathy who do not exhibit a hereditary neuropathy phenotype (Level U).
Module networks revisited: computational assessment and prioritization of model predictions
Authors: Joshi Anagha , De Smet Riet , Marchal Kathleen , Van de Peer Yves , Michoel Tom 
Published: January 2009

Abstract
Motivation: The solution of high-dimensional inference and prediction problems in computational biology is almost always a compromise between mathematical theory and practical constraints, such as limited computational resources. As time progresses, computational power increases but well-established inference methods often remain locked in their initial suboptimal solution.
Results: We revisit the approach of Segal et al. to infer regulatory modules and their condition-specific regulators from gene expression data. In contrast to their direct optimization-based solution, we use a more representative centroid-like solution extracted from an ensemble of possible statistical models to explain the data. The ensemble method automatically selects a subset of most informative genes and builds a quantitatively better model for them. Genes which cluster together in the majority of models produce functionally more coherent modules. Regulators which are consistently assigned to a module are more often supported by literature, but a single model always contains many regulator assignments not supported by the ensemble. Reliably detecting condition-specific or combinatorial regulation is particularly hard in a single optimum but can be achieved using ensemble averaging.
Availability: All software developed for this study is available from http://bioinformatics.psb.ugent.be/software.
Contact: tom.michoel@psb.ugent.be
Supplementary information: Supplementary data and figures are available from http://bioinformatics.psb.ugent.be/supplementary_data/anjos/module_nets_yeast/.
Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery
Authors: Davey Norman E. , Shields Denis C. , Edwards Richard J. 
Published: January 2009

Abstract
Motivation: Short linear motifs (SLiMs) are important mediators of protein–protein interactions. Their short and degenerate nature presents a challenge for computational discovery. We sought to improve SLiM discovery by incorporating evolutionary information, since SLiMs are more conserved than surrounding residues.
Results: We have developed a new method that assesses the evolutionary signal of a residue in its sequence and structural context. Under-conserved residues are masked out prior to SLiM discovery, allowing incorporation into the existing statistical model employed by SLiMFinder. The method shows considerable robustness in terms of both the conservation score used for individual residues and the size of the sequence neighbourhood. Optimal parameters significantly improve return of known functional motifs from benchmarking data, raising the return of significant validated SLiMs from typical human interaction datasets from 20% to 60%, while retaining the high level of stringency needed for application to real biological data. The success of this regime indicates that it could be of general benefit to computational annotation and prediction of protein function at the sequence level.
Availability: All data and tools in this article are available at http://bioware.ucd.ie/~slimdisc/slimfinder/conmasking/.
Contact: r.edwards@southampton.ac.uk
Supplementary information: Supplementary data are available at Bioinformatics online.
Multiperm: shuffling multiple sequence alignments while approximately preserving dinucleotide frequencies
Authors: Anandam Parvez , Torarinsson Elfar , Ruzzo Walter L. 
Published: January 2009

Abstract
Summary: Assessing the statistical significance of structured RNA predicted from multiple sequence alignments relies on the existence of a good null model. We present here a random shuffling algorithm, Multiperm, that preserves not only the gap and local conservation structure in alignments of arbitrarily many sequences, but also the approximate dinucleotide frequencies. No shuffling algorithm that simultaneously preserves these three characteristics of a multiple (beyond pairwise) alignment has been available to date. As one benchmark, we show that it produces shuffled exonic sequences having folding free energy closer to native sequences than shuffled alignments that do not preserve dinucleotide frequencies.
Availability: The Multiperm GNU Cb++ source code is available at http://www.anandam.name/multiperm
Contact: anandam@u.washington.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
Profiling model T-cell metagenomes with short reads
Authors: Warren René L. , Nelson Brad H. , Holt Robert A. 
Published: January 2009

Abstract
Motivation: T-cell receptor (TCR) diversity in peripheral blood has not yet been fully profiled with sequence level resolution. Each T-cell clonotype expresses a unique receptor, generated by somatic recombination of TCR genes and the enormous potential for T-cell diversity makes repertoire analysis challenging. We developed a sequencing approach and assembly software (immuno-SSAKE or iSSAKE) for profiling T-cell metagenomes using short reads from the massively parallel sequencing platforms.
Results: Models of sequence diversity for the TCR β-chain CDR3 region were built using empirical data and used to simulate, at random, distinct TCR clonotypes at 1–20 p.p.m. Using simulated TCRβ (sTCRβ) sequences, we randomly created 20 million 36 nt reads having 1–2% random error, 20 million 42 or 50 nt reads having 1% random error and 20 million 36 nt reads with 1% error modeled on real short read data. Reads aligning to the end of known TCR variable (V) genes and having consecutive unmatched bases in the adjacent CDR3 were used to seed iSSAKE de novo assemblies of CDR3. With assembled 36 nt reads, we detect over 51% and 63% of rare (1 p.p.m.) clonotypes using a random or modeled error distribution, respectively. We detect over 99% of more abundant clonotypes (6 p.p.m. or higher) using either error distribution. Longer reads improve sensitivity, with assembled 42 and 50 nt reads identifying 82.0% and 94.7% of rare 1 p.p.m. clonotypes, respectively. Our approach illustrates the feasibility of complete profiling of the TCR repertoire using new massively parallel short read sequencing technology.
Availability: ftp://ftp.bcgsc.ca/supplementary/iSSAKE
Contact: rwarren@bcgsc.ca
Supplementary information: Supplementary methods and data are available at Bioinformatics online.
Tyrosine and Phenylalanine Are Synthesized within the Plastids in Arabidopsis
Authors: Rippert Pascal , Puyaubert Juliette , Grisollet Delphine , Derrier Laure , Matringe Michel 
Published: January 2009

Abstract
While the presence of a complete shikimate pathway within plant plastids is definitively established, the existence of a cytosolic postchorismate portion of the pathway is still debated. This question is alimented by the presence of a chorismate mutase (CM) within the cytosol. Until now, the only known destiny of prephenate, the product of CM, is incorporation into tyrosine (Tyr) and/or phenylalanine (Phe). Therefore, the presence of a cytosolic CM suggests that enzymes involved downstream of CM in Tyr or Phe biosynthesis could be present within the cytosol of plant cells. It was thus of particular interest to clarify the subcellular localization of arogenate dehydrogenases (TYRAs) and arogenate dehydratases (ADTs), which catalyze the ultimate steps in Tyr and Phe biosynthesis, respectively. The aim of this study was to address this question in Arabidopsis (Arabidopsis thaliana) by analysis of the subcellular localization of the two TYRAAts and the six AtADTs. This article excludes the occurrence of a spliced TYRAAt1 transcript encoding a cytosolic TYRA protein. Transient expression analyses of TYRA- and ADT-green fluorescent protein fusions reveal that the two Arabidopsis TYRA proteins and the six ADT proteins are all targeted within the plastid. Accordingly, TYRA and ADT proteins were both immunodetected in the chloroplast soluble protein fraction (stroma) of Arabidopsis. No TYRA or ADT proteins were immunodetected in the cytosol of Arabidopsis cells. Taken together, all our data exclude the possibility of Tyr and/or Phe synthesis within the cytosol, at least in green leaves and Arabidopsis cultured cells.
Rearrangement of Actin Cytoskeleton Mediates Invasion ofLotus japonicusRoots byMesorhizobium loti
Authors: Yokota Keisuke , Fukai Eigo , Madsen Lene H. , Jurkiewicz Anna , Rueda Paloma , Radutoiu Simona , Held Mark , Hossain Md Shakhawat , Szczyglowski Krzysztof , Morieri Giulia , Oldroyd Giles E.D. , Downie J. Allan , Nielsen Mette W. , Rusek Anna Maria , Sato Shusei , Tabata Satoshi , James Euan K. , Oyaizu Hiroshi , Sandal Niels , Stougaard Jens 
Published: January 2009

AbstractInfection thread–dependent invasion of legume roots by rhizobia leads to internalization of bacteria into the plant cells, which is one of the salient features of root nodule symbiosis. We found that two genes, Nap1 (for Nck-associated protein 1) and Pir1 (for 121F-specific p53 inducible RNA), involved in actin rearrangements were essential for infection thread formation and colonization of Lotus japonicus roots by its natural microsymbiont, Mesorhizobium loti. nap1 and pir1 mutants developed an excess of uncolonized nodule primordia, indicating that these two genes were not essential for the initiation of nodule organogenesis per se. However, both the formation and subsequent progression of infection threads into the root cortex were significantly impaired in these mutants. We demonstrate that these infection defects were due to disturbed actin cytoskeleton organization. Short root hairs of the mutants had mostly transverse or web-like actin filaments, while bundles of actin filaments in wild-type root hairs were predominantly longitudinal. Corroborating these observations, temporal and spatial differences in actin filament organization between wild-type and mutant root hairs were also observed after Nod factor treatment, while calcium influx and spiking appeared unperturbed. Together with various effects on plant growth and seed formation, the nap1 and pir1 alleles also conferred a characteristic distorted trichome phenotype, suggesting a more general role for Nap1 and Pir1 in processes establishing cell polarity or polar growth in L. japonicus.
Disruption of the Ao
pex11-1
Gene Involved in Peroxisome Proliferation Leads to Impaired Woronin Body Formation in
Aspergillus oryzae
Authors: Escaño Cristopher Salazar , Juvvadi Praveen Rao , Jin Feng Jie , Takahashi Tadashi , Koyama Yasuji , Yamashita Shuichi , Maruyama Jun-ichi , Kitamoto Katsuhiko 
Published: January 2009

ABSTRACT

The Woronin body, a unique organelle found in the
Pezizomycotina
, plugs the septal pore upon hyphal damage to prevent excessive cytoplasmic bleeding. Although it was previously shown that the Woronin body buds out from the peroxisome, the relationship between peroxisomal proliferation/division and Woronin body differentiation has not been extensively investigated. In this report, we examined whether Pex11 required for peroxisomal proliferation participates in Woronin body formation in
Aspergillus oryzae. A. oryzae
contained two orthologous
PEX11
genes that were designated Ao
pex11-1
and Ao
pex11-2
. Deletion of Ao
pex11
genes revealed that only the ΔAo
pex11-1
strain showed reduced growth and enlarged peroxisomes in the presence of oleic acid as a sole carbon source, indicating a defect in peroxisomal function and proliferation. Disruption of Ao
pex11-1
gene impaired the Woronin body function, leading to excessive loss of the cytosol upon hyphal injury. Dual localization analysis of the peroxisome and Woronin body protein AoHex1 demonstrated that Woronin bodies fail to fully differentiate from peroxisomes in the ΔAo
pex11-1
strain. Furthermore, distribution of AoHex1 was found to be peripheral in the enlarged peroxisome or junctional in dumbbell-shaped peroxisomes. Electron microscopy of the ΔAo
pex11-1
strain revealed the presence of Woronin bodies that remained associated with organelles resembling peroxisomes, which was supported from the sucrose gradient centrifugation confirming that the Woronin body protein AoHex1 overlapped with the density-shifted peroxisome in the ΔAo
pex11-1
strain. In conclusion, the present study describes the role of Pex11 in Woronin body differentiation for the first time.
Flagellar Biogenesis of
Xanthomonas campestris
Requires the Alternative Sigma Factors RpoN2 and FliA and Is Temporally Regulated by FlhA, FlhB, and FlgM
Authors: Yang Tsuey-Ching , Leu Yu-Wei , Chang-Chien Hui-Chen , Hu Rouh-Mei 
Published: January 2009

ABSTRACT

In prokaryotes, flagellar biogenesis is a complicated process involving over 40 genes. The phytopathogen
Xanthomonas campestris
pv. campestris possesses a single polar flagellum, which is essential for the swimming motility. A σ
54
activator, FleQ, has been shown to be required for the transcriptional activation of the flagellar type III secretion system (F-T3SS), rod, and hook proteins. One of the two
rpoN
genes,
rpoN2
, encoding σ
54
, is essential for flagellation. RpoN2 and FleQ direct the expression of a second alternative sigma FliA (σ
28
) that is essential for the expression of the flagellin FliC. FlgM interacts with FliA and represses the FliA regulons. An
flgM
mutant overexpressing FliC generates a deformed flagellum and displays an abnormal motility. Mutation in the two structural genes of F-T3SS,
flhA
and
flhB
, suppresses the production of FliC. Furthermore, FliA protein levels are decreased in an
flhB
mutant. A mutant defective in
flhA
, but not
flhB
, exhibits a decreased infection rate. In conclusion, the flagellar biogenesis of
Xanthomonas campestris
requires alternative sigma factors RpoN2 and FliA and is temporally regulated by FlhA, FlhB, and FlgM.