bluuebunny/crossref_metadata_2025_split huggingface dataset:
A rapid method for detection of putative RNAi target genes in
genomic data
Authors: Horesh Yair , Amir Amihood , Michaeli Shulamit , Unger Ron 
Published: October 2003

Abstract
RNAi, inhibition of gene expression by double stranded RNA molecules, has rapidly become a powerful laboratory technique to study gene function. The effectiveness of the procedure raised the question of whether this laboratory technique may actually mimic a natural cellular control mechanism that works on similar principles. Indeed recent evidence is accumulating to suggest that RNAi is a natural control mechanism that might even serve as a primitive immune response against RNA viruses and retroposons. Three different interference scenarios seem to be utilized by various RNAi mechanisms. One of the mechanisms involves degradation of mRNA molecules. Here we suggest a method to systematically scan entire genomes simultaneously for RNAi elements and the presence of cellular genes that are degraded by these RNAi elements via exact short base-pair matching. The method is based on scanning the genomes using a suffix tree data structure that was specifically modified to identify sets of combinations of repeated and inverted repeated sequences of 20 bp or more. Initial scan suggest that a large number, about 7% of C.elegans and 3% of C.briggsae genes, have the potential to be subject to natural RNAi control. Two methods are proposed to further analyze these genes to select the cases that are more likely to be actual cases of RNAi control. One method involves looking for ESTs that can provide direct evidence that RNAi control element are indeed expressed. The other method looks for synteny between C.elegans and C.briggsae assuming that genes that might be under RNAi control in both organisms are more likely to be biological significant. Taken together, supportive evidence was found for about 70 genes to be under RNAi control. Among these genes are: transposase, hormone receptors, homeobox proteins, defensin, actins, and several types of collagens. While our method is not capable of detecting all cases of natural RNAi control, it points to a large number of potential cases that can be further verified by experimental work.
Key words: RNAi, Suffix tree, C.elegans, C.briggsae, control mechanism
Contact: ron@biocom1.ls.biu.ac.il
*To whom correspondence should be addressed.
Discovery of significant rules for classifying cancer diagnosis
data
Authors: Li Jinyan , Liu Huiqing , Ng See-Kiong , Wong Limsoon 
Published: October 2003

Abstract
Methods and Results: We introduce a new method to discover many diversified and significant rules from high dimensional profiling data. We also propose to aggregate the discriminating power of these rules for reliable predictions. The discovered rules are found to contain low-ranked features; these features are found to be sometimes necessary for classifiers to achieve perfect accuracy. The use of low-ranked but essential features in our method is in constrast to the prevailing use of an ad-hoc number of only top-ranked features. On a wide range of data sets, our method displayed highly competitive accuracy compared to the best performance of other kinds of classification models. In addition to accuracy, our method also provides comprehensible rules to help elucidate the translation between raw data and useful knowledge.
Supplementary information: http://sdmc.i2r.a-star.edu.sg/GEDatasets/supplementaldata/eccb2003/ECCB2003.html.
Contact: jinyan@i2r.a-star.edu.sg
*To whom correspondence should be addressed.
Finding optimal degenerate patterns in DNA sequences
Authors: Shinozaki Daisuke , Akutsu Tatsuya , Maruyama Osamu 
Published: October 2003

Abstract
Motivation: The problem of finding transcription factor binding sites in the upstream regions of given genes is algorithmically an interesting and challenging problem in computational biology. A degenerate pattern over a finite alphabet Σ is a sequence of subsets of Σ. A string over IUPAC nucleic acid codes is also a degenerate pattern over Σ = {A, C, G, T}, and is used as one of the major patterns modeling transcription factor binding sites in the upstream regions of genes. However, it is known that the problem of finding a degenerate pattern consistent with both positive and negative string sets is in general NP-complete. Our aim is to devise a heuristic algorithm to find a degenerate pattern which is optimal for positive and negative string sets w.r.t. a given score function.
Results: We have proposed an enumerative algorithm called SUPERPOSITION for finding optimal degenerate patterns with a pruning technique, which works with most all reasonable score functions. The performance score of the algorithm has been compared with those of other popular motif-finding algorithms YMF, MEME and AlignACE on various sets of co-regulated genes of yeast. In the computational experiment, SUPERPOSITION has outperformed the others on several gene sets.
Availability: The python script SUPERPOSITION is available at http://www.math.kyushu-u.ac.jp/~om/softwares.html
Contact: om@math.kyushu-u.ac.jp
*To whom correspondence should be addressed.
Sources of genetic and phenotypic variability
Authors: Taddei François 
Published: October 2003

Abstract
The availability of hundreds of genomes allows us to learn rapidly about genomic differences between micro-organisms. Comparative genomics shows that horizontal gene transfer, mutations and rearrangements are frequent events in most species. The molecular mechanisms for these events have been described in laboratory experiments and sometimes even under ‘natural conditions’. Beside, when put in different environments, a given bacterial genome shows drastic change in its profile of expression (as evidenced by transcriptomic or proteomic experiments). Thus, clearly genetic differences and variation in environmental conditions lead to phenotypic variability (i.e. as text books say genotype X environment = phenotype). However, there might be other sources of phenotypic variability as experiments show that even with a given genome in a given environment one observes phenotypic variability. Even if this was recognized already in the 50’s, the causes and consequences of this other source of phenotypic variability remain to be described presumably by developping new interdisciplinary tools.
Contact: taddei@necker.fr
The fundamental thumb‐tip force vectors produced by the muscles of the thumb
Authors: Pearlman Jonathan L. , Roach Stephanie S. , Valero‐Cuevas Francisco J. 
Published: October 2003

AbstractA rigorous description of the magnitude and direction of the 3D force vector each thumb muscle produces at the thumb‐tip is necessary to understand the biomechanical consequences to pinch of a variety of paralyses and surgical procedures (such as tendon transfers). In this study, we characterized the 3D force vector each muscle produces at the thumb‐tip, and investigated if these thumb‐tip force vectors scaled linearly with tendon tension. In 13 cadaver specimens, we measured the output 3D thumb‐tip force vector produced by each tendon acting on the thumb, plus two common tendon transfers, as a function of input tendon tension. After fixing the hand to a rigid frame, we mounted the thumb by configuring it in standardized key or opposition pinch posture and coupling the thumb‐tip to a rigidly held 6 degree‐of‐freedom force/torque sensor. Linear actuators applied tension to the distal tendons of the four extrinsic thumb muscles, and to six Nylon cords reproducing the lines of action of (i) the four intrinsic thumb muscles and (ii) two alternative tendon transfers commonly used to restore thumb opposition following low median nerve palsy. Each computer‐controlled linear actuator ramped tendon tension from zero to 1/3 of predicted maximal muscle force expected at each tendon, and back to zero, while we measured the 3D force vector at the thumb‐tip. In test/re‐test trials, we saw thumb‐tip force vectors were quite sensitive to mounting procedure, but also sensitive to variations in the seating of joint surfaces. We found that: (i) some thumb‐tip force vectors act in unexpected directions (e.g., the opponens force vector is parallel to the distal phalanx), (ii) the two tendon transfers produced patently different force vectors, and (iii) for most muscles, thumb‐tip force vectors do not scale linearly with tendon tension—likely due to load‐dependent viscoelastic tendon paths, joint seating and/or bone motion. Our 3D force vector data provide the first quantitative reference descriptions of the thumb‐tip force vectors produced by all thumb muscles and two tendon transfers. We conclude that it may not be realistic to assume in biomechanical models that thumb‐tip force vectors scale linearly with tendon tensions, and that our data suggest the thumb may act as a “floating digit” affected by load‐dependent trapezium motion. © 2003 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Endothelin 1 and leptin in the pathophysiology of intrauterine growth restriction
Authors: Arslan M. , Yazici G. , Erdem A. , Erdem M. , Ozturk Arslan E. , Himmetoglu O. 
Published: October 2003

AbstractObjectives: To evaluate the relationship of endothelin 1 (ET‐1) and leptin concentrations in women and newborns following a pregnancy complicated with intrauterine growth restriction (IUGR). Methods: Twenty‐five women with a pregnancy complicated with IUGR at 19 different gestational ages were matched with women with uncomplicated pregnancies. Blood samples from the umbilical artery and maternal peripheral venous circulation were collected at delivery, and ET‐1 and leptin levels were determined from the blood samples. Data relating to obstetric complications (e.g., pregnancy‐induced hypertension), delivery (e.g. mode, birth weight, signs of intrapartum fetal distress, and Apgar scores) were also recorded. Results: Mean maternal ET‐1 (13.4±6.2–9.9±2.9 pmol/l) and mean fetal ET‐1 (14.5±4.2–11.7±3.1 pmol/l) concentrations were significantly higher when women had experienced pregnancies complicated with IUGR than when they had had normal pregnancies. Mean fetal leptin concentration was significantly lower in the study group (6.8±2.2 ng/ml) than in the control group (10.6±3.6 ng/ml (P<0.05). However, fetal leptin per kilogram of fetal weight was not significantly different in the study group (3.16±1.18 ng/ml) than in the control group (3.23±0.96 ng/ml) (P>0.05, paired t‐test). However, a statistically significant correlation was observed between fetal leptin concentrations per kilogram of fetal weight and fetal endothelin concentrations in pregnancies complicated with IUGR (r=0.546; P<0.05). Conclusions: These results suggest the intertwined roles of ET‐1 and leptin in the pathophysiology of IUGR. Further studies concerning interaction between these peptides in different pregnancy conditions may provide important information about the actions of ET‐1 and leptin on fetal growth.
Umbilical cord prolapse and perinatal outcomes
Authors: Kahana B. , Sheiner E. , Levy A. , Lazer S. , Mazor M. 
Published: October 2003

AbstractObjectives: To determine obstetric risk factors and perinatal outcomes of pregnancies complicated by umbilical cord prolapse. Methods: A population‐based study was performed comparing all deliveries complicated by cord prolapse to deliveries without this complication. Statistical analysis was performed using multiple logistic regression models. Results: Prolapse of the umbilical cord complicated 0.4% (n=456) of all deliveries included in the study (n=121 227). Independent risk factors for cord prolapse identified by a backward, stepwise multivariate logistic regression model were: malpresentation (OR=5.1; 95% CI 4.1–6.3), hydramnios (OR=3.0; 95% CI 2.3–3.9), true knot of the umbilical cord (OR=3.0; 95% CI 1.8–5.1), preterm delivery (OR=2.1; 95% CI 1.6–2.8), induction of labor (OR=2.2; 95% CI 1.7–2.8), grandmultiparity (>five deliveries, OR=1.9; 95% CI 1.5–2.3), lack of prenatal care (OR=1.4; 95% CI 1.02–1.8), and male gender (OR=1.3; 95% CI 1.1–1.6). Newborns delivered after umbilical cord prolapse graded lower Apgar scores, less than 7, at 5 min (OR=11.9, 95% CI 7.9–17.9), and had longer hospitalizations (mean 5.4±3.5 days vs. 2.9±2.1 days; P<0.001). Moreover, higher rates of perinatal mortality were noted in the cord prolapse group vs. the control group (OR=6.4, 95% CI 4.5–9.0). Using a multiple logistic regression model controlling for possible confounders, such as preterm delivery, hydramnios, etc., umbilical cord prolapse was found to be an independent contributing factor to perinatal mortality. Conclusions: Prolapse of the umbilical cord is an independent risk factor for perinatal mortality.
How significant is 98.5% ‘junk’ in mammalian
genomes?
Authors: Brosius Jürgen 
Published: October 2003

Abstract
Conversion of genetic information from RNA into DNA by reverse transcription is ancient and was instrumental for the transition from the RNP world to modern cells (Brosius, 1999a, Nat. Genet. , 22, 8–9; Brosius, 2003, J. Struct. Funct. Genom. , 3, 1–17). Surprisingly, in many eukaryotic lineages, the process of retroposition is still very active. All types of RNAs (Brosius, 1999b, Gene , 238, 115–134) can be reverse transcribed and their cDNA copies reintegrated into genomes as retronuons (a nuon is any discrete segment of nucleic acid (Brosius and Gould, 1992, Proc. Natl Acad. Sci. USA , 89, 10706–10710)). About 38% or 42% of the mouse and human genomes, respectively, consist of discernible retronuons (excluding mRNA-derived retroposons). Only 1.5% of the human genome consists of exons coding for proteins. Even considering DNA transposons (∼1–3% discernible), slippage during replication and a relatively large fraction derived from segmental duplications it is conceivable that the remainder of mammalian genomes is probably derived from ancient, today non-discernible retronuons. Hence, the vast majority of mammalian genomes have been contributed by retroposition. Retroposition predominantly leads to ‘junk DNA’. However, mRNA-derived retronuons are known to give rise to active genes, often with different expression patterns than their respective founder genes (Brosius and Gould, 1992, Proc. Natl Acad. Sci. USA , 89, 10706–10710; Brosius, 1991, Science , 251, 753). Retronuons derived from small non-messenger RNAs (snmRNAs) generate novel snmRNA genes (such as the neuron-specific BC1 and BC200 RNAs) (Brosius, 1999b, Gene , 238, 115–134; Brosius and Gould, 1992, Proc. Natl Acad. Sci. USA , 89, 10706–10710). Frequently, retronuons are exapted (co-opted) as regulatory elements that may alter expression or processing of targeted genes (Brosius and Gould, 1992, Proc. Natl Acad. Sci. USA , 89, 10706–10710) (for compilations see http://www-ifi.uni-muenster.de/exapted-retrogenes/tables.html). Consequently, retronuons are a major driving force of evolution and perhaps even speciation. Comparison of the human genome with that of other mammals such as mouse or, in particular, chimpanzee reveals that neither contains numerous additional genes. Instead, one observes exaptation of novel exons (often involving alternative splicing) from previously nonaptive intronic (as predicted by Gilbert, 1978, Nature , 271, 501) or flanking sequences originally generated by retroposition. Furthermore, the differential expression of shared genes with respect to developmental onset and/or cell-type specificity, that is triggered by de novo insertions of retronuons, will turn out to be a recurrent theme in species differences at the genomic level.
Contact: RNA.worldwuni-muenster.de
Mechanobiological predictions of growth front morphology in developmental hip dysplasia
Authors: Shefelbine Sandra J. , Carter Dennis R. 
Published: October 2003

AbstractDevelopmental dysplasia of the hip (DDH) is the most common orthopedic problem of newborn children. Most clinicians and researchers agree that the primary cause of DDH is abnormal mechanical forces on the head of the femur due to limb position, pressure from the womb, or ligament laxity. The abnormal mechanical forces result in altered growth and bony deformities, in particular large neck‐shaft and anteversion angles in the proximal femur and a shallow acetabulum. Previous studies have suggested that intermittent octahedral shear stress promotes growth and ossification, while intermittent hydrostatic compressive stress inhibits growth and ossification. We implemented these mechanobiological principles into a finite element model to predict the rate of progression of the growth front and the formation of coxa valga (large neck‐shaft angle) in DDH. Under the assumed normal fetal loading conditions the hydrostatic stress was even across the growth front, but the octahedral shear stress was higher in the center than at the edges. This stress profile promoted growth in the center and a produced a convex growth front shape. Under loading conditions of the dysplastic hip, the octahedral shear stress was much larger on the medial side than on the lateral side, which promoted growth on the medial side and resulted in coxa valga. These results indicate that abnormal forces on the prenatal hip might influence total bone morphology and the development of DDH. These findings might help in understanding the etiology and pathology of other developmental bone deformities. © 2003 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
Age and paleoclimatic significance of late Holocene lakes in the Carson Sink, NV, USA
Authors: Adams Kenneth D. 
Published: October 2003

AbstractNew dating in the Carson Sink at the termini of the Humboldt and Carson rivers in the Great Basin of the western United States indicates that lakes reached elevations of 1204 and 1198 m between 915 and 652 and between 1519 and 1308 cal yr B.P., respectively. These dates confirm Morrison's original interpretation (Lake Lahontan: Geology of the Southern Carson Desert, Professional Paper 40, U.S. Geol. Survey, 1964) that these shorelines are late Holocene features, rather than late Pleistocene as interpreted by later researchers. Paleohydrologic modeling suggests that discharge into the Carson Sink must have been increased by a factor of about four, and maintained for decades, to account for the 1204-m lake stand. The hydrologic effects of diversions of the Walker River to the Carson Sink were probably not sufficient, by themselves, to account for the late Holocene lake-level rises. The decadal-long period of increased runoff represented by the 1204-m lake is also reflected in other lake records and in tree ring records from the western United States.
An audit of the management of induced abortion in England and Wales
Authors: Thomas J. , Paranjothy S. , Templeton A. 
Published: October 2003

AbstractObjectives: To assess the quality of care provided to women undergoing induced abortion. Methods: The design was a single round audit questionnaire aimed at the providers of abortion services throughout England and Wales (NHS hospitals, clinics under NHS, agency agreements and private units. The levels of care were assessed against agreed audit criteria. Results: Responses were received from 240 (74%) of the 324 units providing abortion care in England and Wales. These units undertook 80% of the 176 000 termination procedures. Generally standards of care were appropriate, but there were clear areas for improvement including choice of method, infection screening, and delays in referral. A number of unnecessary investigations were still evident, including cross‐matching, while lower doses and alternative drug regimens might reduce costs. Only half of the units audited procedures and complications. Conclusions: This audit was carried out prior to the publication of the RCOG evidence‐based guideline and a further round of audit to assess the impact of the guideline should now be considered.
Induction of labor with vaginal misoprostol for second trimester termination of pregnancy in the scarred uterus
Authors: Herabutya Y. , Chanarachakul B. , Punyavachira P. 
Published: October 2003

AbstractObjectives: To assess the safety of vaginal misoprostol for second trimester pregnancy termination in patients with a history of cesarean section. Methods: A consecutive series of 593 women with pregnancies of 14–26 weeks were studied. A cohort of 56 cases had undergone previous cesarean section delivery. The 528 cases who had no history of prior uterine surgery served as the controls. The termination was carried out according to the regimen used at the time of enrolment, either 600 μg applied at every 6 or every 12 h, or 800 μg applied at every 12 h using the vaginal route. Results: The median induction to abortion time in the previous cesarean section group (15.1 h) was not significantly different from that of the controls (15.8 h). The median total dosage of misoprostol used was the same for both groups (1200 μg). The rates of incomplete abortion and analgesia usage were significantly higher in the previous cesarean section group as compared with the controls. Conclusions: Vaginal misoprostol was effective for the second trimester pregnancy termination but the safety of misoprostol in the scarred uterus cannot be assumed from this study. A large series is needed to reach the power to see the difference.
Creating ‘Virtuous and Talented’ Officials for the Twentieth Century: Discourse and Practice in Xinzheng China
Authors: Strauss Julia C. 
Published: October 2003

‘It must be considered that there is nothing more difficult to carry out, nor more doubtful of success, nor more dangerous to handle, than to initiate a new order of things.’ Machiavelli, The PrinceCentral Xinzheng Reform and the Twentieth-Century Chinese StateThe effort of the Qing dynasty to transform itself and forge a new set of relationships with society in its last decade has been one of the less explored areas in the scholarship on modern China. Although this set of radical initiatives, collectively known as the xinzheng (‘New Policy’) reforms attracted a good deal of commentary from its contemporaries, until recently it has been relatively understudied. There are two reasons for this neglect. First, conventional periodization has divided historical turf between Qing historians (for the Qing dynasty 1644–1911), Republican historians (for the period between 1911 and 1949 ) and political scientists (who cover 1949 to the present). Second, since the dramatic narrative for the first three-quarters of the twentieth century has been largely understood as a process of ever more radical forms of revolutionary change, scholars have understandably been more taken with exploring the antecedents of revolution and/or locally based studies of elite transformation than they have been with exploring a case of seemingly bona fide failure.The central government-initiated xinzheng reform period (1902–1911) has thus borne the full brunt of a Whiggish interpretation of history; too late to command the attention of most Qing historians, too early for the majority of Republican historians, at best a prologue for the real revolution to come, and at worst an abortive failure.