bluuebunny/crossref_metadata_2025 huggingface dataset:
Asy1, a protein required for meiotic chromosome synapsis, localizes to axis-associated chromatin inArabidopsisandBrassica
Authors: Armstrong Susan J. , Caryl Anthony P. , Jones Gareth H. , Franklin F. Christopher H.
Published: November 2002

The Arabidopsis thaliana ASY1 gene is essential for homologous chromosome synapsis. Antibodies specific to Asy1 protein and its homologue BoAsy1 from the related crop species Brassica oleracea have been used to investigate the temporal expression and localization of the protein in both species. Asy1 is initially detected in pollen mother cells during meiotic interphase as numerous punctate foci distributed over the chromatin. As leptotene progresses the signal appears to be increasingly continuous and is closely associated with the axial elements but not to the extended chromatin loops associated with them. By the end of zygotene the signal extends almost the entire length of the synapsed homologues, although not to the telomeres. The protein begins to disappear as the homologues desynapse, until by late diplotene it is no longer associated with the chromosomes. Immunogold labelling in conjunction with electron microscopy established that Asy1 localizes to regions of chromatin that associate with the axial/lateral elements of meiotic chromosomes rather than being a component of the synaptonemal complex itself. These data together with the previously observed asynaptic phenotype of the asy1 mutant suggest that Asy1 is required for morphogenesis of the synaptonemal complex, possibly by defining regions of chromatin that associate with the developing synaptonemal complex structure.
The impact of various potential‐vorticity anomalies on multiple frontal cyclogenesis events
Authors: Zhang Da‐Lin , Cheng William Y. Y. , Gyakum John R.
Published: November 2002

The influences of various potential vorticity (PV) anomalies on multiple frontal cyclogenesis events are examined using 60 h simulations of a family of six frontal cyclones that developed over the western Atlantic between 0000 UTC 13 March and 1200 UTC 15 March 1992. The cyclogenesis events are characterized by pronounced low‐level baroclinicity along a large‐scale cold front moving over the warm ocean and by multiple propagating perturbations in the two PV rings on the cyclonic‐shear side of an upper‐level jet stream. It is found that the tracks of the frontal cyclones follow closely the distribution of the PV rings, whereas the cyclogenesis occurs in the cold‐frontal zone, and in close proximity to the propagating PV perturbations in the central portion of an upper‐level parent trough. A piecewise PV inversion reveals that the low‐level thermal advection (or the bottom thermal anomaly) contributes the most to the depths of two major frontal cyclones, followed by latent‐heat release and the upper‐level PV anomalies, whereas the opposite order is true for the remaining four weaker frontal cyclones.

A series of sensitivity experiments is performed to test the impact of removing the upper‐level PV anomalies individually, or collectively, on the development of a major frontal cyclone (MFC) as an initial‐value problem. It is found that the MFC genesis and its final intensity depend on how much its track departs from the upper‐level PV perturbations. Removing a PV anomaly associated with a major short‐wave trough delays the MFC genesis by 18 h and weakens its final depth by 13 hPa. The largest departure occurs when two upstream PV anomalies are removed collectively, delaying the MFC genesis by 36 h and weakening its final depth by 21 hPa. It appears that the MFC genesis in the first 36 h depends more on the PV anomalies in an inner PV ring, whereas its subsequent development depends more on the PV reservoir in an outer PV ring.

It is shown that most of the frontal cyclones can still develop in the absence of diabatic heating, indicating the important role of dry dynamics in controlling the multiple frontal cyclogenesis events. However, the ‘dry’ MFC fails to form a closed isobar when the trough‐related PV anomaly is removed. The associated PV inversion and sensitivity simulation results suggest that even though the low‐level thermal advection plays an important role in deepening the frontal cyclones, it is the upper‐level PV anomalies that provide the necessary forcing for its amplification and the frontal cyclogenesis.

It is concluded that the upper‐level propagating multiple PV anomalies play a major role in triggering, but a secondary role in determining the final depth of the multiple frontal cyclones. It is the subsequent growth of the bottom thermal anomaly that accounts for most of the final depth of the frontal cyclones. Copyright © 2002 Royal Meteorological Society
Two‐dimensional simulation of orographic effects on mesoscale boundary‐layer convection
Authors: Tian Wen‐Shou , Parker Douglas J.
Published: November 2002

In this paper, orographic effects on mesoscale boundary‐layer convection are studied through a series of idealized numerical experiments. It is found that hills tend to weaken convective activity at their summits under higher background winds, whilst strong updraughts can be observed at the summits, or slightly downwind of the peaks, under light‐wind conditions; these can be associated with so‐called convective cores. When the background winds are strong, the effects of the hill length on the results are only significant when the height of the hill reaches 500 m. The combined effect of a sensible‐heating maximum on the hill summit and baroclinic tendencies due to the elevated heating is a tendency to produce a convective core under reasonably light‐wind conditions. Under higher‐wind conditions, the strong ascents and descents on both sides of the hill, as well as the lee‐wave dynamics, seem to pose a more important impact on the convective features than the thermal forcing of the hill. A Richardson‐number balance has been proposed to explain these two kinds of response. Finally, under stronger‐wind conditions, the convective available potential energy (CAPE) is small at the summit and reaches its maximum value in the lee of the hill while, under light‐wind conditions, the air parcels at the summit have more buoyancy and the CAPE downwind of the top of the hill is slightly larger than that elsewhere. Copyright © 2002 Royal Meteorological Society
A climatology of mesoscale convective systems over Europe using satellite infrared imagery. I: Methodology
Authors: Morel C. , Senesi S.
Published: November 2002

An automated method aimed at producing a significant European mesoscale convective system (MCS) climatology is presented. It uses Meteosat infrared window channel images and is composed of two main tools: an automated cloud‐shield tracking method and a robust method of discriminating between convective and nonconvective cloud shields.

The automated cloud‐tracking method defines cloud systems as connected sets of pixels, named ‘cells’, after temperature and area thresholding and it is based on the overlapping between cells in successive images. It handles splits and merges of cells and takes cell movement into account. It has three parameters: the temperature and area thresholds and a minimum overlapping threshold. It is concluded that it performs a correct tracking at any temperature threshold between −30°C and −55°C and for an area threshold greater than 1000 km2, so that it allows the tracking of MCSs during most of their life cycle.

The automated discrimination between convective and non‐convective cloud shields uses a discrimination parameter based on brightness‐temperature gradients on the edges of cells, because strong values of this gradient are observed at the beginning of the life cycle of MCSs when cold anvils develop. A seasonal study, and the sensitivity of the method to the temperature threshold, are presented. The method shows significant quality during the entire warm season (from April to September): it correctly discriminates 80% of MCSs and more than 90% of the most electrically active ones, while showing a low false‐alarm rate around 8%; therefore the method seems to be useful for climatological purposes. Copyright © 2002 Royal Meteorological Society
Error analysis of TMI rainfall estimates over ocean for variational data assimilation
Authors: Bauer Peter , Mahfouf Jean‐FrançOis , Olson William S. , Marzano Frank S. , Michele Sabatino Di , Tassa Alessandra , Mugnai Alberto
Published: November 2002

An intercomparison of retrieval errors from different Tropical Rainfall Measuring Mission (TRMM) passive microwave rainfall products was carried out to assess the definition of observation error for experiments of rainfall assimilation in a variational framework. Depending on algorithms and their spatial resolution and sampling, a large variety of error estimates occurred. The error propagation to the European Centre for Medium‐Range Weather Forecasts (ECMWF) model grid (here 45 and 60 km) was investigated from error simulations and observed data with and without accounting for spatial error correlation.

All algorithms used in this study (TRMM standard product 2A12 V.5 and two alternative algorithms, namely PATER and BAMPR) employ a Bayesian retrieval framework. The Bayesian errors obtained from each algorithm from different case‐studies showed values well above 100% at low rain rates (0.1 mm h−1) and around 50% at high rain rates (20–50 mm h−1) at the original product resolution and sampling. These Bayesian errors corresponded very well with those from an independent evaluation which was carried out by comparing TRMM microwave radiometer (TMI) estimates to precipitation radar retrievals at the same (here ≈27×40 km2) resolution.

The impact of spatial averaging on retrieval errors was simulated using fits to the Bayesian errors and realistic log‐normal rainfall probability distributions. By neglecting spatial correlation, the range of errors is reduced from 70–200% to 20–50% at low rain rates and from 25–70% to 5–20% at high rain rates. To account for spatial data correlation, TMI observations were first averaged to the ECMWF model grid. Then the decorrelation of rain rates as a function of separation distance from all products was calculated. The introduction of spatial error correlation affected both error reduction and dispersion of errors per rain‐rate interval. The final error estimates ranged from 50–150% at low rain rates to 20–50% at high rain rates. The analysis suggests that once the spatial correlation pattern of a product is known, the probability density distribution of real observations inside the model grid does not produce larger scatter and therefore a simple scaling may suffice to calculate rainfall retrieval errors at the model resolution. Copyright © 2002 Royal Meteorological Society
Determinants of environmental management systems standards implementation: evidence from Greek industry
Authors: Halkos George E. , Evangelinos Konstantinos I.
Published: November 2002

This paper employs logistic regression analysis to test a model that predicts the implementation or non‐implementation of Environmental Management Systems Standards (EMSSs) by considering various factors as explanatory variables. The dependent variable is dichotomous: industrial firms either implementing or not implementing EMSSs. From past experience we identify 15 major variables contributing to implementation of EMSSs. A sample of 259 respondents (84 implementing and 175 not) is used to estimate the parameters of the logistic regression model employing maximum likelihood. The results show an overall significant model with four of the 15 variables significant. The significance of management perception of environmental issues on their decision to implement EMSS was confirmed with regards to their perception on win–win possibilities. Pressure on companies to improve their environmental performance does not result in higher uptake of the standards. Company image and size are important factors in its decision to implement EMSS. Copyright © 2002 John Wiley & Sons, Ltd. and ERP Environment
Effect of delay interval on classical eyeblink conditioning in 5‐month‐old human infants
Authors: Klaflin Dragana I. , Stanton Mark E. , Herbert Jane , Greer Jennifer , Eckerman Carol. O.
Published: November 2002

Associative learning was evaluated in human infants with simple delay classical eyeblink conditioning. A tone conditioned stimulus (CS) was paired with an airpuff unconditioned stimulus (US) at three different delay intervals (250, 650, and 1,250 ms). Independent groups of healthy, full‐term 5‐month‐old human infants were assigned to these three paired conditions and received two identical training sessions 1 week apart. The two longer delays resulted in associative conditioning, as confirmed by comparison with unpaired control groups. However, only at the 650‐ms delay were associative eyeblinks adaptively timed to avoid the airpuff. The delay function at 5 months of age appears much sharper than is observed in adults. Together with the findings of A. H. Little, L. P. Lipsitt, and C. Rovee‐Collier (1984), the present study suggests a downward shift in the optimal delay interval for associative eyeblink conditioning between 1 and 6 months of age. However, this delay remains longer than what is typically reported in adults. © 2002 Wiley Periodicals, Inc. Dev Psychobiol 41: 329–340, 2002. Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/dev.10050
Holmium laser for management of ureterocele calculi
Authors: Jones J. Stephen
Published: November 2002

Background and Objectives

Although most ureteral calculi will pass spontaneously, those in a ureterocele will usually not pass beyond the stenotic orifice. We address both the stone and the underlying anatomic abnormality of a ureterocele using the holmium:YAG laser.

Study Design/Materials and Methods

We report the first use of the holmium laser to treat ureteral calculi and the ureteroceles responsible for their retention.

Results

Two patients have been successfully treated using the described procedure.

Conclusions

The flexibility to treat both the underlying anatomic abnormality and the resultant stone with a single minimally invasive device makes the holmium laser ideal in this situation. Lasers Surg. Med. 31:297–298, 2002. © 2002 Wiley‐Liss, Inc.
Evaluation of pulse‐duration on purpuric threshold using extended pulse pulsed dye laser (cynosure V‐star)
Authors: Tanghetti Emil , Sierra Rafael A. , Sherr Evan A. , Mirkov Mirko
Published: November 2002

Background and Objectives

Pulsed dye lasers (PDL) with extended pulse‐durations create new opportunities in the treatment of vascular lesions. Development of extended pulse methods requires understanding of tissue effects of extended pulse‐durations. We evaluated tissue effects of extended pulse‐duration PDL (EPDL) with cooling. Effects of increasing pulse‐duration, fluence, and multiple passes were evaluated to determine purpuric threshold and delayed purpuric response.

Study Design/Patients and Methods

Ten patients were treated with EPDL and air‐cooling on normal buttocks skin. Exposure pulse‐durations of 0.5, 2, 20, and 40 milliseconds and increasing fluences 3–20 J/cm2, pulse‐duration dependent. Exposures were evaluated 0.5, 1, and 24 or 48 hours determining purpuric threshold and side effects.

Results

Immediate purpuric threshold increased from 6.2 to 8, 10.4, and 13.8 J/cm2 at pulse‐durations of 0.5, 2, 20, and 40 milliseconds, respectively. Purpuric threshold dropped after 24 hours to 5.2, 7.1, 9.3, and 11.9 J/cm2, respectively. Multi‐pass treatment lowered purpuric threshold by 1 J/cm2. EPDL purpura resolved in less time than traditional PDL. No side effects were noted.

Conclusions

EPDL exhibits increasing purpuric threshold with increasing pulse‐durations, and risk of delayed onset of purpura. Lasers Surg. Med. 31:363–366, 2002. © 2002 Wiley‐Liss, Inc.
Cerebral Reorganization and Plasticity: From Meuroscience
to Rehabilitation: Cerebral Reorganization of Function
after Brain Damage, Harvey S. Levin and Jordan Grafman
(Eds.). 2000. New York: Oxford University Press. 392 pp.,
$55.00.
Authors: Anderson Vicki
Published: November 2002

Cerebral reorganization and functional plasticity are topics
central to the practice of neuropsychology. Clinicians are
frequently required to make choices regarding the most efficacious
rehabilitation methods, comment on recovery and outcome patterns,
or predict nature and severity of residual deficits. Unfortunately,
insufficient available information makes such judgments problematic
at best.
More Practice Effect Tables for More Effective
Practice: Practitioner's Guide to Evaluating Change
with Intellectual Assessment Instruments, R.J. McCaffrey,
K. Duff, and H.J. Westervelt (Eds.). 2001. New York: Kluwer
Academic/Plenum. 280 pp., $69.95 (PB).
Authors: Lezak Muriel D.
Published: November 2002

Clinicians owe a debt of gratitude to McCaffrey and his team
for developing not just one (McCaffrey et al., 2000) but now
a second set of tables providing an extensive compilation of
test–retest data for tests commonly used in
neuropsychological assessment. The newest Practitioner's
Guide presents the retest findings for all four versions
of the adult Wechsler Intelligence Scale [Wechsler-Bellevue,
the original Wechsler Adult Intelligence Scale (WAIS), and its
variants: WAIS–R, WAIS–III, WAIS–RNI],
plus the Wechsler Intelligence Scale for Children (WISC) with
its variants (WISC–R, WISC–III) and the Wechsler
Preschool and Primary Scale of Intelligence. For each of
Wechsler's batteries this guide provides retest data for
the scores in common use (e.g., IQ, VIQ, PIQ, each individual
test, and WAIS–III index scores). In addition retest findings
are given for the North American Reading Test, Raven's
Progressive Matrices, Shipley-Hartford Institute of Living Scale,
and for 13 Stanford-Binet studies (form L-M, judging from study
dates; all but five are IQ scores).
Memory in multiple sclerosis: Contextual encoding deficits
Authors: THORNTON ALLEN E. , RAZ NAFTALI , TUCKER KAREN A.
Published: November 2002

Long-term memory (LTM) is one of the diverse cognitive functions
adversely affected by multiple sclerosis (MS). The LTM deficits
have often been attributed to failure of retrieval, whereas
encoding processes are presumed intact. However, support for
this view comes primarily from studies in which encoding and
retrieval operations were not investigated systematically. In
the current study, we used an encoding specificity paradigm
to examine the robustness of encoding in MS and to specifically
evaluate the impact of the disease on contextual memory. We
hypothesized that persons with MS would exhibit a selective
impairment in retrieving items from LTM when required to generate
new cue-target associations at encoding, but not when cues held
a strong preexisting relationship to the targets. The findings
supported the hypotheses. We conclude that the mnemonic deficits
associated with MS affect both encoding and retrieval.
Specifically, problems with binding of contextual information
at encoding impair effective retrieval of memories. Nonetheless,
access to these memories can be gained through preexisting
associations organized in the semantic network. (JINS,
2002, 8, 395–409.)
Olfactory event-related potentials in Alzheimer's disease
Authors: MORGAN CHARLIE D. , MURPHY CLAIRE
Published: November 2002

Areas of the brain affected in the early stages of
Alzheimer's disease are also areas heavily involved in
the processing of olfactory information. Olfactory event-related
potentials (OERPs) and auditory ERPs were recorded from the
Fz, Cz, and Pz electrode sites in 12 Alzheimer's disease
(AD) patients and 12 age and gender matched normal controls
(NC) in a single-stimulus paradigm with a 45 s inter-trial
interval, using amyl acetate as the olfactory stimulus, and
in a separate session a 500 Hz tone as the auditory stimulus.
Odor identification (ID) was also used to assess ability to
identify odors. The results indicate that (1) OERP P2 and P3
latencies were significantly longer in AD patients than normal
controls; (2) olfactory ERP latency measures correlated
significantly with dementia status as measured by the Dementia
Rating Scale (DRS), indicating that as participants performed
more poorly on the DRS, reflecting increased dementia, OERP
latencies increased; (3) olfactory ERP latency measures better
differentiated AD patients from normal controls than auditory
ERP latency measures; (4) olfactory ERP measures alone correctly
classified up to 92% of participants; (5) odor ID measures,
namely the UPSIT and San Diego-Odor-ID tests also classified
participants at a high rate. Combining scores for odor
identification with olfactory P3 latency measures resulted in
a correct classification rate of 100%. The results strongly
support the use of olfactory measures in the assessment of AD.
(JINS, 2002, 8, 753–763.)
The application of “dysexecutive syndrome” measures
across cultures: Performance and checklist assessment in
neurologically healthy and traumatically brain-injured Hong
Kong Chinese volunteers
Authors: CHAN RAYMOND C.K. , MANLY TOM
Published: November 2002

Deficits in planning, self-regulation and attention are a
relatively common consequence of traumatic brain injury (TBI).
Such “dysexecutive” deficits tend to be most exposed
in complex, real world situations. Consequently, clinicians
often have to rely on interviews, questionnaires and observation
in their assessments. While there is little doubt that dysexecutive
symptoms occur across different cultures, the expression of
those symptoms, the way in which they are experienced by others,
and the propensity of friends/relatives to report negative features
may vary considerably. The cross-cultural use of standardized
checklists and measures that have predominantly been studied
with English speaking, Western groups therefore requires empirical
support. Here a group of 68 healthy Chinese speaking volunteers
were asked to complete translations of 2 UK developed
questionnaires (the Dysexecutive Questionnaire and Cognitive
Failures Questionnaire) measures and to perform 2
“executive” tasks (The Six Elements Test and the
Tower of Hanoi). Their self ratings and the ratings of close
relatives were very close to those seen in the original UK
standardization samples—as was their performance on the
2 tasks. Accordingly, the conditions for assessing their clinical
sensitivity were met. Comparison between 30 Chinese patients
with TBI and matched controls showed that both questionnaires
and tests were sensitive to the deficits in this group.
(JINS, 2002, 8, 771–780.)
Effect of mild head injury on event-related potential correlates
of Stroop task performance
Authors: POTTER DOUGLAS D. , JORY SUSAN H. , BASSETT MARTIN R.A. , BARRETT KENNETH , MYCHALKIW WASYL
Published: November 2002

The effect of mild head injury on event-related potential (ERP)
correlates of Stroop task performance was explored with the
aim of further elucidating the basis of processing impairments
after mild head injury. Computer- and card-based Stroop tasks
were employed to assess attention function. A sequence of
incongruent color words were presented followed by a sequence
of congruent color words (printed in congruent colors). Control
performance was equivalent on computer- and card-based versions
of the incongruent task and faster on the congruent card task
than the preceding congruent computer task. The mild head injury
group were as fast as controls on the computer-based task but
made more errors. However, they were relatively slower on both
the congruent and incongruent parts of the card-based task and
made more errors in the incongruent task. ERP correlates of
computer-based Stroop task performance suggested a greater
allocation of attention resources in the incongruent condition
in both groups in the form of relatively greater negativity
in the latency range 350 to 450 ms with a distribution consistent
with the activation of the anterior cingulate gyrus. In addition
the mild head injured group showed relatively greater enhancement
than the control group in this latency range in both congruent
and incongruent conditions. There was, however no evidence of
reduced amplitude P1, N1, N2, or P3b deflections. Trails, digit
symbol, digit span and auditory verbal learning tests (AVLT)
were also administered. Mild head injured participants were
impaired only on the AVLT. The finding of greater ERP negativity
in the mild head injured group is consistent with greater
allocation of attention resources to achieve equivalent performance
in the computer-based Stroop task. (JINS, 2002,
8, 828–837.)
Cross-modal semantic priming in schizophrenia
Authors: SURGULADZE SIMON , ROSSELL SUSAN , RABE-HESKETH SOPHIA , DAVID ANTHONY S.
Published: November 2002

Work on implicit memory in normal subjects has demonstrated
the influence of stimulus modality on the retrieval of semantic
information. The present study examined the effects of auditory
and visual semantic priming on the recognition of visual words
using a lexical decision task. Performance was studied in a
group of 20 patients with DSM–IV schizophrenia and 26
normal volunteers of similar age and sex. There were two versions
of the task: ipsimodal, in which the word or nonword visual
target followed 400 ms after the onset of a visual word prime
which may or may not be semantically related to the target;
and cross-modal, in which the visual target followed 400 ms
after the onset of an auditory word prime. Both groups showed
significant priming in both modality conditions, although the
schizophrenia patients exhibited significantly greater priming
in the cross-modal condition. Priming effects in the ipsimodal
condition did not differ substantially between patients and
controls. The priming effects in the two conditions correlated
with each other in the schizophrenia patients only. The results
suggest that priming may occur through amodal semantic
representations. In schizophrenia, there appears to be increased
cross-modal connectivity (reduced modality modularity and
informational encapsulation) between lexical representations
that could result in impaired language, particularly speech,
processing. (JINS, 2002, 8, 884–892.)
Child Neuropsychology and Neurophysiology
Authors: Butler Robert W.
Published: November 2002

The Handbook of Clinical Child Neuropsychology
(2nd ed.), as is obvious from the title, is an updated
edition of the editors' first book, originally published
in 1989. At that time the subspecialty of child neuropsychology
was just beginning to unfold its wings, and little was
available in terms of a broad and encompassing handbook
resource.

The book Biological and Neuropsychological Mechanisms:
Life-Span Developmental Psychology is an example of how the
above problems can be manifested even with a good attempt at
execution. The chapters in this book cover a wide range of topics
within developmental neuropsychology, including a developmental
theory of behavior, mathematical modeling, electrophysiology,
lateralization, and adolescent substance abuse.
Double Vision
Authors: Corballis Michael C.
Published: November 2002

“The asymmetry of the mammalian brain,”
goes the first sentence in this book, “took hundreds
of years to discover.” This is not a promising beginning.
Hundreds of years from when? And do the authors really
mean the mammalian brain? We are indeed beginning
to discover all kinds of asymmetries in the brains of mammals,
from mice to chimpanzees, but the only mammal that features
in the book is Homo sapiens. Cerebral asymmetry
in humans is scarcely news, having been discovered by Dax
as early as 1836, and a great many volumes have been produced
on the subject.
Numerical skills and aphasia
Authors: DELAZER MARGARETE , GIRELLI LUISA , SEMENZA CARLO , DENES GIANFRANCO
Published: November 2002

The aim of this study was to investigate numerical
difficulties in 50 patients with left hemispheric lesions.
Aphasic patients were grouped according to their type of
aphasia diagnosed by the Aachener Aphasia Test. The overall
error rate in various transcoding and calculation tasks
was clearly correlated with the severity of the language
deficit, global aphasics being the most impaired patients.
Broca's and Wernicke's aphasics scored similarly
at the quantitative level, and amnesic aphasics were less
impaired. Interestingly, qualitative analysis of the errors
indicated that each group presented with specific difficulties,
partially reflecting the nature of the language problems.
In simple calculation, multiplication was found to be the
most impaired operation, in particular in Broca's
aphasics. This result supports the hypothesis that the
retrieval of multiplication facts is preferentially mediated
by verbal processing. Calculation procedures were mainly
impaired in Wernicke's and global aphasics. (JINS,
1999, 5, 213–221.)
Uptake and Trafficking of Mildly Oxidized LDL and Acetylated
LDL in THP-1 Cells Does Not Explain the Differences in Lysosomal
Metabolism of These Two Lipoproteins
Authors: Yancey Patricia G. , Miles Stacia , Schwegel Jennifer , Jerome W. Gray
Published: November 2002

Foam cells in the atherosclerotic lesion have substantial
cholesterol stores within large, swollen lysosomes. This feature
is mimicked by incubating THP-1 macrophages with mildly oxidized
low density lipoprotein (LDL). Incubation of THP-1 cells with
acetylated LDL produces cytoplasmic cholesteryl ester accumulation
rather than lysosomal storage. The differences could be due
to differences in uptake and delivery of lipoprotein to lysosomes
or to lysosomal and post-lysosomal processing events. We compared
uptake and lysosomal trafficking of acetylated and oxidized
LDL using colloidal gold-labeled lipoproteins. Labeling did
not alter cellular cholesterol accumulation. We found that uptake
and delivery to lysosomes are not different for acetylated and
oxidized LDL. In fact, both oxidized and acetylated LDL can
be delivered to the same lysosomes. Sequential incubation with
oxidized LDL followed by acetylated LDL showed that the
lipid-engorged lysosomes are long-lived structures, continuously
accepting newly ingested lipoprotein. Comparison of acetylated
and oxidized LDL in mouse peritoneal macrophages, a cell which
does not accumulate substantial lysosomal lipid, also revealed
no differences in uptake. This indicates that in THP-1 cells,
the differences in metabolism of oxidized and acetylated LDL
are due to cell-specific lysosomal or post-lysosomal events
not present in B6C3F1 mouse
macrophages.
The Nanostructures of Amorphous Silicas
Authors: Hobbs Linn W. , Yuan Xianglong , Qin L.C. , Pulim Vinay , Coventry Alexander
Published: November 2002

Topologically modeled amorphized silica structures have been
refined using a molecular dynamics simulation technique. Several
metastable structures with substantially different medium-range
connectivities, as characterized by primitive ring statistics,
were obtained. Whereas the total correlation function is
insensitive to these differences, the first sharp diffraction
peak derived from energy-filtered electron diffraction shows
a promising correlation to medium-range structure.
Inferring Alternative Splicing Patterns in Mouse from a Full-Length cDNA Library and Microarray Data
Authors: Kochiwa Hiromi , Suzuki Ryosuke , Washio Takanori , Saito Rintaro , Phase The RIKEN Genome Exploration Resear , Bono Hidemasa , Carninci Piero , Okazaki Yasushi , Miki Rika , Hayashizaki Yoshihide , Tomita Masaru
Published: November 2002

Although many studies on alternative splicing of specific genes have been reported in the literature, the general mechanism that regulates alternative splicing has not been clearly understood. In this study, we systematically aligned each pair of the 21,076 cDNA sequences ofMus musculus, searched for putative alternative splicing patterns, and constructed a list of potential alternative splicing sites. Two cDNAs are suspected to be alternatively spliced and originating from a common gene if they share most of their region with a high degree of sequence homology, but parts of the sequences are very distinctive or deleted in either cDNA. The list contains the following information: (1) tissue, (2) developmental stage, (3) sequences around splice sites, (4) the length of each gapped region, and (5) other comments. The list is available athttp://www.bioinfo.sfc.keio.ac.jp/intron. Our results have predicted a number of unreported alternatively spliced genes, some of which are expressed only in a specific tissue or at a specific developmental stage.
Mosaic Organization of Orthologous Sequences in Grass Genomes
Authors: Song Rentao , Llaca Victor , Messing Joachim
Published: November 2002

Although comparative genetic mapping studies show extensive genome conservation among grasses, recent data provide many exceptions to gene collinearity at the DNA sequence level. Rice, sorghum, and maize are closely related grass species, once sharing a common ancestor. Because they diverged at different times during evolution, they provide an excellent model to investigate sequence divergence. We isolated, sequenced, and compared orthologous regions from two rice subspecies, sorghum, and maize to investigate the nature of their sequence differences. This study represents the most extensive sequence comparison among grasses, including the largest contiguous genomic sequences from sorghum (425 kb) and maize (435 kb) to date. Our results reveal a mosaic organization of the orthologous regions, with conserved sequences interspersed with nonconserved sequences. Gene amplification, gene movement, and retrotransposition account for the majority of the nonconserved sequences. Our analysis also shows that gene amplification is frequently linked with gene movement. Analyzing an additional 2.9 Mb of genomic sequence from rice not only corroborates our observations, but also suggests that a significant portion of grass genomes may consist of paralogous sequences derived from gene amplification. We propose that sequence divergence started from hotspots along chromosomes and expanded by accumulating small-scale genomic changes during evolution.

[GenBank Accession Numbers: Rice (Oryza sativa L. ssp. japonica)php200725 region: AF119222; rice (Oryza sativa L. ssp. indica) php200725 region: AF128457; sorghum (Sorghum bicolor) php200725 region: AF114171,AF527807, AF727808, AF527809; maize (Zea mays)php200725 region: AF090447, AF528565; rice chromosome 10 region (2.9 Mb): AC073391, AC087549, AC027657, AC087547, AC027658,AC087546, AC027659, AC087550, AC025905, AC087545, AF229187, AC027660,AC087544, AC027661, AC027662, AC087543, AC073392, AC087542, AC025906,AC073393, AC025907.]
Factors Influencing the Identification of Transcription Factor Binding Sites by Cross-Species Comparison
Authors: McCue Lee Ann , Thompson William , Carmack C. Steven , Lawrence Charles E.
Published: November 2002

As the number of sequenced genomes has grown, the questions of which species are most useful and how many genomes are sufficient for comparison have become increasingly important for comparative genomics studies. We have systematically addressed these questions with respect to phylogenetic footprinting of transcription factor (TF) binding sites in the γ-proteobacteria, and have evaluated the statistical significance of our motif predictions. We used a study set of 166Escherichia coligenes that have experimentally identified TF binding sites upstream of the gene, with orthologous data from nine additional γ-proteobacteria for phylogenetic footprinting. Just three species were sufficient for ∼74.0% of the motif predictions to correspond to the experimentally reportedE. colisites, and important characteristics to consider when choosing species were phylogenetic distance, genome size, and natural habitat. We also performed simulations using randomized data to determine the critical maximum a posteriori probability (MAP) values for statistical significance of our motif predictions (P = 0.05). Approximately 60% of motif predictions containing sites from just three species had average MAP values above these critical MAP values. The inclusion of a species very closely related toE. coliincreased the number of statistically significant motif predictions, despite substantially increasing the critical MAP value.

[Supplemental material is available online athttp://www.genome.org. In addition, our motif predictions for the study set and the entireE. coligenome are available online athttp://www.wadsworth.org/resnres/bioinfo/.]
Polycapillary focusing optic for small-sample neutron crystallography
Authors: Gibson W. M. , Schultz A. J. , Chen-Mayer H. H. , Mildner D. F. R. , Gnäupel-Herold T. , Miller M. E. , Prask H. J. , Vitt R. , Youngman R. , Carpenter J. M.
Published: November 2002

The relatively low flux from neutron sources means that structural analysis using neutron diffraction requires large crystals that are often not available. The feasibility of a polycapillary focusing optic to produce a small intense spot of size < ∼0.5 mm for small crystals has been explored and such an optic has been tested both on a monochromatic and on a polychromatic beam. In a diffraction measurement from an α-quartz crystal using a 2.1° convergent beam from a pulsed neutron source, six diffraction peaks in the 1.5–4 Å wavelength bandwidth transmitted by the optic were observed. These diffraction spots show an intensity gain of 5.8 ± 0.9 compared with a direct beam diffracting from the same sample volume as that illuminated by the convergent beam.
Separating the recrystallization and deformation texture components by high-energy X-rays
Authors: Wang Y. D. , Wang X.-L. , Stoica A. D. , Almer J. D. , Lienert U. , Haeffner D. R.
Published: November 2002

High-energy synchrotron diffraction offers great potential for experimental study of recrystallization kinetics. Measurements on partially recrystallized samples using a monochromatic high-energy synchrotron beam show that recrystallized grains generate sharp diffraction spots, whereas the intensity from the deformed matrix varies smoothly along the Debye–Scherrer rings. Based on these observations, a method has been developed to separate the recrystallization texture components from those originating from the deformation matrix. The validity of this method is demonstrated with partially recrystallized interstitial-free steel.
Diffraction thermometry and differential thermal analysis
Authors: Kisi E. H. , Riley D. P.
Published: November 2002

A unit-cell parameter anomaly observed during the precipitation and growth of Ti3SiC2from a Si-substituted TiC phase is interpreted as the release of latent heat. The observations are used to propose a powder diffraction method for conducting differential thermal analysis as part ofin situphase transition studies.
Geoff Bible’s class
Authors: Chapman S
Published: November 2002

Geoffrey Bible, former CEO of Philip Morris, faces a life of luxury during his retirement—and has quit smoking to ensure he lives long enough to enjoy it
A novelchk1-dependent G1/M checkpoint in fission yeast
Authors: Synnes Marianne , Nilssen Esben A. , Boye Erik , Grallert Beáta
Published: November 2002

Fission yeast cells with a temperature-sensitive Orp1 protein, a component of the origin recognition complex, cannot perform DNA replication at the restrictive temperature. Seventy percent of orp1-4 cells arrest with a 1C DNA content, whereas 30% proceed to mitosis (`cut'). The arrest depends upon the checkpoint Rad proteins and, surprisingly, the Chk1 protein, which is thought to act only from late S phase. The arrested cells maintain a 1C DNA content, as judged by flow cytometry, and the early origin ars3001has not been initiated, as judged by 2D gel analysis. We show that in G1-arrested orp1-4 cells, Wee1 phosphorylates and inactivates Cdc2. Activation of Chk1 occurs earlier than Cdc2 phosphorylation, indicating a novel role for Chk1, namely to induce and/or maintain Cdc2 phosphorylation upon checkpoint activation in G1. We also show that commitment to cutting occurs already in early G1 phase.
Cytokinetic actomyosin ring formation and septation in fission yeast are dependent on the full recruitment of the polo-like kinase Plo1 to the spindle pole body and a functional spindle assembly checkpoint
Authors: Mulvihill Daniel P. , Hyams Jeremy S.
Published: November 2002

In dividing cells, the assembly and contraction of the cytokinetic actomyosin ring (CAR) is precisely coordinated with spindle formation and chromosome segregation. Despite having a cell wall, the fission yeast Schizosaccharomyces pombe forms a CAR reminiscent of the structure responsible for the cleavage of cells with flexible boundaries. We used the myo2-gc fission yeast strain in which the chromosomal copy of the type II myosin gene, myo2+, is fused to the gene encoding green fluorescent protein (GFP) to investigate the dynamics of Myo2 recruitment to the cytokinetic actomyosin ring in living cells. Analysis of CAR formation in relation to spindle pole body (SPB) and centromere separation enabled us to pinpoint the timing of Myo2 recruitment into a stable CAR structure to the onset of anaphase A. Depolymerisation of actin with latrunculin B did not affect the timing of Myo2 accumulation at the cell equator (although Myo2 no longer formed a ring), whereas depolymerisation of microtubules with either thiabendazole (TBZ) or methyl 2-benzimidazolecarbamate (MBC) resulted in a delay of up to 90 minutes in CAR formation. Microtubule depolymerisation also delayed the localisation of other CAR components such as actin and Mid1/Dmf1. The delay of cytokinesis in response to loss of microtubule integrity was abolished in cells lacking the spindle assembly checkpoint protein Mad2 or containing non-functional Cdc16, a component of the fission yeast septation initiation network (SIN). The delay was also abolished in cells lacking Zfs1, a component of the previously described S. pombe cytokinesis checkpoint. Recruitment of the polo-related kinase, Plo1, a key regulator of CAR formation, to the SPBs was substantially reduced in TBZ in a Mad2-dependent manner. Loading of Cdc7, a component of the SIN and downstream of Plo1 in the cytokinesis pathway, onto the the SPBs was also delayed in TBZ to the same extent as CAR formation. We conclude that CAR formation is subject to regulation by the spindle assembly checkpoint via the loading of Plo1 onto the SPBs and the consequent activation of the SIN.
Reduced IRS-2 and GLUT4 expression in PPARγ2-induced adipocytes derived from C/EBPβ and C/EBPδ-deficient mouse embryonic fibroblasts
Authors: Yamamoto Hiroyasu , Kurebayashi Shogo , Hirose Takahisa , Kouhara Haruhiko , Kasayama Soji
Published: November 2002

In adipose tissue, the ability of cells to respond to insulin and to express genes such as those encoding fatty-acid-binding protein (422/aP2),lipoprotein lipase (LPL), adipsin and glucose transporter 4 (GLUT4) is acquired during their differentiation into mature adipocytes. It has been recognized that peroxisome proliferator-activated receptor γ(PPARγ) and CCAAT/enhancer-binding proteins (C/EBPs) play critical roles in adipocyte differentiation. However, it remained uncertain whether PPARγ or which C/EBP is involved in the acquisition of these characteristics. We introduced PPARγ2 into C/EBPβ/δ-double deficient mouse embryonic fibroblasts (MEFs), followed by stimulation with its ligands, in order to define the roles of C/EBPβ and C/EBPδ in phenotypic acquisition during adipocyte differentiation. This procedure resulted in differentiation of these MEFs into mature adipocytes morphologically similar to wild-type MEFs. However, the adipocytes derived from the C/EBPβ/δ-deficient MEFs showed lower expression of GLUT4 and adipsin mRNA than those derived from wild-type MEFs, although aP2 and LPL mRNA levels were similar in both types. The C/EBPβ/δ-deficient adipocytes also expressed lower amounts of insulin receptor substrate 2(IRS-2) than the adipocytes derived from wild-type MEFs, whereas the amounts of insulin receptor and IRS-1 were similar. Finally, insulin-responsive 2-deoxyglucose uptake was lower in the C/EBPβ/δ-deficient cells. It could thus be demonstrated that C/EBPβ and C/EBPδ are involved in the acquisition of IRS-2 and GLUT4 expression as well as in insulin-sensitive glucose uptake during adipocyte differentiation.
Normal modes of deep atmospheres. II: f–F‐plane geometry
Authors: Thuburn John , Wood Nigel , Staniforth Andrew
Published: November 2002

Numerical results have shown that, for a rotating spherical atmosphere with terrestrial parameters, making the shallow‐atmosphere approximation has only a very small impact on the frequency of linear, unforced normal modes, compared with those obtained from the full, unapproximated equations. In nearly all cases the normal‐mode frequencies are smaller in magnitude when the shallow‐atmosphere approximation is relaxed. Relaxing the approximation was also found to have only a small impact on the structures of normal modes, with the exception of long‐zonal‐wavelength internal acoustic modes. These results are particularly surprising in the tropics where the inclusion of the F = 2Ω cosϕ Coriolis terms (which are dropped in the shallow‐atmosphere approximation) might be expected to dominate the usual f=2Ωsinϕ Coriolis terms. The complexity of the full equations, however, prevents analysis of why this insensitivity to the extra terms arises.

In this paper normal modes are examined under the f–F‐plane approximation and compared with those on the more usual f‐plane. The resulting equations are more amenable to analysis than the full equation set, and analytic expressions for the dispersion relation and for the normal‐mode structures are obtained for the particular case of an isothermal reference profile. This simplified geometry allows the effects of the F Coriolis terms to be examined while eliminating the geometrical effects of relaxing the shallow‐atmosphere approximation, giving some insight into the relative importance of the two types of effect as well as the physical mechanisms at work. The F Coriolis terms are found to be responsible for the structural changes to long‐zonal‐wavelength internal acoustic modes, and can also affect extremely shallow and extremely deep gravity modes. However, these terms are found to have only a small effect on normal‐mode frequencies, and geometrical effects, rather than these Coriolis terms, are responsible for the systematic reduction in the magnitude of normal‐mode frequencies in a deep spherical atmosphere.

In planar geometry the inclusion of the F terms gives rise to a new kind of normal mode in addition to the usual Rossby, gravity, and acoustic modes. The new modes are inertial in character, have frequency very close to f, and have extremely strong vertical tilt. © Royal Meteorological Society, 2002. N. Wood's and A. Staniforth's contributions are Crown copyright.