bluuebunny/crossref_metadata_2025_split huggingface dataset:
AN APPLICATION OF NEURAL NETWORKS TO SEQUENCE ANALYSIS AND GENRE IDENTIFICATION
Authors: BISANT DAVID 
Published: March 2005

This study borrowed a technique from molecular sequence analysis and applied it to genre identification, which is the process of determining the type or family of a given document. For example, is the document a letter, a news story, a horoscope, a joke, an advertisement, a pornographic story, etc. Genre identification allows a computer user to further filter email and web sites in a way that is totally different from topic-based methods. This study presents original research in an application of machine learning to the genre identification problem. The specific method selected for the application was neural modeling. The data for the study came from a database constructed by the author and his colleagues. The data consisted of descriptive features and the genre classification, as judged by a human, from over 5,000 different documents. Ten different genres were represented. The descriptive features consisted of 89 different measurements of each document such as average word length, the number of numeric terms, the proportion of present tense verbs, etc. The data was divided into two sets, with 75% set aside for training and 25% reserved separately for testing. The first neural network applied was a very basic single layer network that achieved 79% correct classifications on the testing data. This performance was equivalent to the previous best method on the problem, decision trees. When more complex neural networks were applied to the problem, performance increased significantly. The best performance of 86% correct classifications was achieved by a network with a single hidden layer of 300 units. Increasing the number of hidden layers, or changing the number of hidden units did not improve performance. The best score is also a significant improvement over scores obtained from topic-based filters. The neural networks were further used to determine which input features were most influential in the classifications by the networks. The average magnitude of the weights coming from each feature was computed after training. The analysis indicated that 10% of the features were not of any use to the networks. An additional 10% were very influential and were responsible for most of the performance of the networks. The remaining 80% varied between marginally useful to useful. The analysis of the features indicated that second-order information was being exploited by the networks for better performance. This means that on this problem, neural networks will outperform statistical models or other methods that only utilize first-order information.
Spatial Variations in Material Properties of Segmental Retaining Wall (SRW) Units, Part II: Sampling Considerations for Absorption Tests
Authors: Chan C , Hover KC , Folliard KJ 
Published: March 2005

Abstract
Part I (Observed Variations) of this article summarized observed spatial variations in material properties that could exist in Segmental Retaining Wall (SRW) units. As a continuation of Part I, Part II of this article examines in more detail the statistical significance of these observed variations and the implications of such variations on sampling and test result interpretation. It was demonstrated that the observed spatial variations were statistically significant along the casting direction (parabolic distribution) and in a direction away from the split face (linear distribution). As a result of these variations, an analysis involving test simulations showed that, depending on how specimens are sampled, a technician could interpret the SRW unit as being either very uniform or marginally uniform. The effect of increasing the quantity of specimens per test was only to modestly improve the expected value of the perceived test variation, though the range of possible values of perceived variation was substantially narrowed. This analysis also showed that variations in test results decreased with increasing soak time. Finally, an alternate method of specimen sampling (stratified random sampling) was explored and shown to yield slightly more consistent test results by reducing the overall variability in test results.
Zen and the Art (or Is It Science) of a Perfect Analysis
Authors: Nadkarni RAK 
Published: March 2005

Abstract
An analytical laboratory in any industry plays a crucial role in product quality management and ultimate customer satisfaction. Some factors need to be considered for an aspiring laboratory to become a perfect performer. These range from sampling, calibration, contamination control, and use of valid test methods to statistical quality assurance. Some approaches may be utilized to achieve a perfect analysis including: staff training, participation in proficiency testing, use of standard reference materials in the analytical sequence, internal and external audits, agency accreditation, continuous improvement program, benchmarking, etc. Laboratories managed in this way show demonstrated superiority in data precision and accuracy over the labs which do not practice such quality management. Well-managed industrial laboratories can have insignificant laboratory sigma compared with manufacturing variability in the plant production. For a flawless perfect analysis, determination to excel, mental discipline to stay the course, willingness to overcome inertia and resistance, and focus on producing a perfect analysis at all levels of laboratory staff are essential.
The Rate of Serious Bacterial Infections Among HIV-Infected Children With Immune Reconstitution Who Have Discontinued Opportunistic Infection Prophylaxis
Authors: Nachman Sharon , Gona Philimon , Dankner Wayne , Weinberg Adrianna , Yogev Ram , Gershon Anne , Rathore Mobeen , Read Jennifer S. , Huang Sharon , Elgie Carol , Hudgens Kim , Hughes Walter 
Published: March 2005

Objective. Receipt of highly active antiretroviral therapy is associated with a decrease in the incidence of opportunistic infections (OIs) among HIV-infected adults. The goal of Pediatric AIDS Clinical Trials Group protocol 1008 was to evaluate prospectively the incidence of serious bacterial infections (SBIs) and other OIs after discontinuation of OI and/or Pneumocystis jiroveci pneumonia (PCP) prophylaxis among HIV-infected pediatric subjects who experienced immune reconstitution while receiving stable antiretroviral therapy.
Methods. HIV-infected children and adolescents, 2 to 21 years of age, who had received OI and/or PCP prophylaxis for ≥6 months were enrolled if they had sustained responses (&gt;16 weeks before study entry) to antiretroviral therapy, with CD4+ cell percentages of ≥20% for patients &gt;6 years of age or ≥25% for patients 2 to 6 years of age. Prophylaxis was discontinued at entry. To identify whether any correlation existed between functional immune reconstitution and protection from OIs, subjects were immunized with the hepatitis A virus vaccine. The association between the humoral immune response and the likelihood of developing an OI was evaluated.
Results. A total of 235 HIV-infected subjects from 43 participating sites had a median follow-up period of 132 weeks, yielding 547 person-years of observation. Twenty SBIs were observed among 19 subjects, resulting in an incidence rate of 3.66 SBIs per 100 person-years (95% confidence interval: 2.24–5.66 SBIs per 100 person-years). Sixteen of the events were presumed bacterial pneumonia, with 4 proven SBIs. One participant experienced 2 separate pneumonia episodes, of presumed bacterial cause. Ten subjects who developed SBIs had baseline CD4+ cell counts of ≥750 cells per mm3, and 15 had CD4+ cell percentages of ≥25% at the time of their SBIs. Two subjects died as a result of non–SBI-related causes. There were no statistically significant differences in changes over time in CD4+ cell counts or CD4+ cell percentages between subjects who experienced primary end points and those who did not. There was no evidence that baseline protease inhibitor use, gender, race/ethnicity, age, or CD4+ cell count or percentage affected the time to development of a SBI.
Conclusions. OI or PCP prophylaxis can be withdrawn safely for HIV-infected pediatric patients who experience CD4+ cell recovery while receiving stable antiretroviral therapy. More studies are needed to assess the association between antibody responses to neoantigens and the development of SBIs.
An Evaluation of Mark–Recapture Estimates of Black Crappie Population Size Determined by Trap-Netting during Fall and Spring in Minnesota Lakes
Authors: McInerny Michael C. , Cross Timothy K. 
Published: March 2005

Abstract
We evaluated mark–recapture population estimates of black crappies Pomoxis nigromaculatus 200 mm and longer made with trap-net catches during fall or spring in eight Minnesota lakes (18–168 ha). We estimated population size N during fall by use of marking and recapture in fall (FF estimates) and marking in fall and recapture during the following spring (FS estimates). We estimated spring N by use of marking and recapture after ice-out in early spring (ES estimates) and marking after ice-out and recapture during late spring (LS estimates). The FF and ES estimates were multiple-census estimates, whereas the FS and LS estimates were two-census estimates even though sampling occurred over many days. The most precise estimates were the LS estimates (median 95% confidence limits (CLs) were within 36% of 1/N), and FF estimates were least precise (median 95% CLs were within 51% of 1/N) among sampling scenarios. The median trap-net effort needed to achieve 95% CLs within 25% of 1/N estimates ranged from 160 (ES estimates) to 490 trap-net sets (FS estimates), and the effort needed for this level of precision decreased with increasing density of marked fish at large. The ES and LS estimates for the same lakes and years differed significantly (P &lt; 0.05), and FF estimates did not exceed LS estimates from the following spring, which indicates that either the estimates from one or more scenarios were biased or that the catchable portions of populations differed temporally. Probable sources of bias included unequal capture probabilities, unequal mortality, and unequal emigration between marked and unmarked individuals during or after marking, as well as immigration of unmarked individuals after marking. Although marking occurred over short time periods, mortality, emigration, and immigration were possible, and therefore populations may not have been closed. Comparisons of N estimated from the same sampling scenario are the most meaningful because the similarity in biases or catchable portions of populations should be highest.
Near‐Room‐Temperature Production of Diameter‐Tunable ZnO Nanorod Arrays through Natural Oxidation of Zinc Metal
Authors: Zhang Zhongping , Yu Haidong , Shao Xiaoqiong , Han Mingyong 
Published: March 2005

AbstractA simple, low‐temperature strategy has been developed for the low‐cost and large‐area fabrication of ZnO nanoarrays on a zinc substrate by the natural oxidation of zinc metal in formamide/water mixtures. The one‐step, wet‐chemical approach has exhibited well‐controlled growth of highly oriented and densely packed ZnO nanoarrays with large‐area homogeneity and consisting of nanorods or nanowires with predictable morphologies, such as tunable diameters and identical lengths. The chemical‐liquid‐deposition process, an analogue to the widely used chemical‐vapor‐deposition technique, has been used for the near‐room‐temperature production of ZnO nanoarrays through continuous supply, transport, and thermal decomposition of zinc complexes in a liquid phase.
A Novel Human Hair Protein Fiber Prepared by Watery Hybridization Spinning
Authors: Hirao Yoshitoshi , Ohkawa Kousaku , Yamamoto Hiroyuki , Fujii Toshihiro 
Published: March 2005

AbstractSummary: A novel human hair protein hybrid fiber was developed by combining (i) the high‐efficiency extraction technique for preparing human hair proteins and (ii) the watery hybridization spinning method using gellan and chitosan. The resulting human hair protein‐gellan‐chitosan hybrid fibers are conveniently produced by simply mixing the 7–35 wt.‐% human hair protein‐1.0 wt.‐% gellan aqueous solution and the 1.0 wt.‐% chitosan‐0.15 M acetic acid solution at 50 °C, followed by pulling out to spin the human hair protein‐gellan‐chitosan ternary complex thus formed at the aqueous solution interface. By use of this simple procedure and ambient spinning condition, the human hair proteins were successfully incorporated into the fiber matrix of gellan‐chitosan, without any denaturation and degradation. The hybrid fiber can also be recognized as a new type of the regenerated human hair keratin fiber, because of its high purity and content of human hair keratin types I and II. Mechanical strength of the human hair protein‐gellan‐chitosan fiber varies from 108 to 153 MPa, depending on the contents of the human hair proteins. SEM observation revealed that the incorporated human hair proteins were found as the particles (1–10 μm) on the fiber surface. The type I and II keratins in the fiber matrices were rapidly biodegraded by chymotrypsin within 30 min, and the digested fragments slowly released from the fiber matrices. Thus, the human hair hybrid fiber is a very promising material to have a broad spectrum of applications as the engineering fibers, particularly for the medical uses, because the human hair proteins are easily available, biocompatible, and bioresorbable materials.Gellan‐chitosan hybrid fiber (a), human hair protein‐gellan‐chitosan hybrid fiber (b).magnified imageGellan‐chitosan hybrid fiber (a), human hair protein‐gellan‐chitosan hybrid fiber (b).
Enhanced large intestinal potassium permeability in end‐stage renal disease
Authors: Mathialahan T , Maclennan KA , Sandle LN , Verbeke C , Sandle GI 
Published: March 2005

AbstractThe capacity of the colon for potassium (K+) secretion increases in end‐stage renal disease (ESRD), to the extent that it makes a substantial contribution to K+ homeostasis. This colonic K+ adaptive response may reflect enhanced active K+ secretion, and be associated with an increase in apical membrane K+ permeability. In this study, this hypothesis was tested in patients with normal renal function or ESRD, by evaluating the effect of barium ions (a K+ channel inhibitor) on rectal K+ secretion using a rectal dialysis technique, and the expression of high conductance (BK) K+ channel protein in colonic mucosa by immunohistochemistry. Under basal conditions, rectal K+ secretion was almost threefold greater (p < 0.02) in ESRD patients (n = 8) than in patients with normal renal function (n = 10). Intraluminal barium (5 mmol/l) decreased K+ secretion in the ESRD patients by 45% (p < 0.05), but had no effect on K+ transport in patients with normal renal function. Immunostaining using a specific antibody to the BK channel α‐subunit revealed greater (p < 0.001) levels of BK channel protein expression in surface colonocytes and crypt cells in ESRD patients (n = 9) than in patients with normal renal function (n = 9), in whom low levels of expression were mainly restricted to surface colonocytes. In conclusion, these results suggest that enhanced colonic K+ secretion in ESRD involves an increase in the apical K+ permeability of the large intestinal epithelium, which most likely reflects increased expression of apical BK channels. Copyright © 2005 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Randomized Clinical Trial Comparing Blunt Tapered and Standard Needles in Closing Abdominal Fascia
Authors: Nordkam Rob A.G. , Bluyssen Simone J. M. , van Goor Harry 
Published: March 2005

AbstractGlove perforation frequently occurs during the course of surgical procedures, introducing risks for both surgeons and patients. The aim of this study was to compare the use of blunt tapered and “sharp” needles during abdominal wall closure with respect to the incidence of glove perforation and the convenience of needle handling. A series of 200 patients undergoing laparotomy in a 6‐month period for general surgical disorders were randomized to two groups; in one, the abdominal fascia was closed with a blunt tapered needle; in the other, a sharp needle was used. The main outcome measures were glove perforation and convenience of handling the needle. Univariate and multivariate analyses were performed. In all, 56 glove perforations occurred during 40 (20%) surgical procedures.Perforation rates differed significantly: 12% for the blunt (n = 100) tapered needle and 28% (n = 100) for the sharp needle (p = 0.003). Only in 12 cases (21%) was the glove perforation detected at surgery. The type of needle (odds ratio 0.35, p = 0.006) and time taken to close the fascia (odds ratio 1.001, p = 0.05) significantly affected the risk of glove perforation. At multivariate logistic regression analysis the type of needle (odds ratio 0.23, p = 0.004) and the visual analog linear scale (VAS) for ease of needle handling (odds ratio 1.18, p = 0.019) were important predictive factors for glove perforation. With the blunt tapered needle, the VAS was significantly (p = 0.0003) higher at primary laparotomy than at relaparotomy. Use of the blunt tapered needle reduces the incidence of glove perforation. Laborious closure predicts glove perforation. Blunt tapered needles are less convenient in closing a scarred abdominal fascia.
A Putative Nucleoporin 96 Is Required for Both Basal Defense and Constitutive Resistance Responses Mediated bysuppressor of npr1-1,constitutive 1
Authors: Zhang Yuelin , Li Xin 
Published: March 2005

AbstractThe Arabidopsis thaliana suppressor of npr1-1, constitutive 1 (snc1) mutant contains a gain-of-function mutation in a Toll Interleukin1 receptor-nucleotide binding-Leu-rich repeat–type resistance gene (R-gene), which leads to constitutive activation of disease resistance response against pathogens. In a screen for suppressors of snc1, a recessive mutation, designated mos3 (for modifier of snc1,3), was found to suppress the constitutive pathogenesis-related gene expression and resistance to virulent Pseudomonas syringae maculicola ES4326 and Peronospora parasitica Noco2 in snc1. In addition, mos3 is also compromised in resistance mediated by Resistance to Peronospora parasitica 4 (RPP4), Resistance to Pseudomonas syringae pv maculicola (RPM1), and Resistance to Pseudomonas syringae 4 (RPS4). Single mutant mos3 plants exhibited enhanced disease susceptibility to P. s. pv maculicola ES4326, suggesting that MOS3 is required for basal resistance to pathogens as well. mos3-1 was identified by map-based cloning, and it encodes a protein with high sequence similarity to human nucleoporin 96. Localization of the MOS3-green fluorescent protein fusion to the nuclear envelope further indicates that MOS3 may encode a nucleoporin, suggesting that nuclear and cytoplasmic trafficking plays an important role in both R-gene–mediated and basal disease resistance.
Single nucleotide polymorphisms in the corticotrophin‐releasing hormone and pro‐opiomelancortin genes are associated with growth and carcass yield in beef cattle
Authors: Buchanan F. C. , Thue T. D. , Yu P. , Winkelman‐Sim D. C. 
Published: March 2005

SummaryA single nucleotide polymorphism (SNP) in the corticotrophin‐releasing hormone gene (CRH C22G) alters the fourth amino acid in the signal sequence from proline to arginine. Two other SNPs (CRH A145G and C240G) occur in the propeptide region at residue positions 45 and 77, respectively, that result in serine/asparagine and histidine/aspartic acid substitutions respectively. These SNPs, as well as SNPs in pro‐opiomelancortin (POMC), leptin (LEP) and melanocortin‐4 receptor (MC4R), were evaluated for associations with average daily gain, end‐of‐test rib‐eye area, shipping weight and hot carcass weight in a group of 256 steers using a general linear model. The CRH C22G SNP was associated with end‐of‐test rib‐eye area (P < 0.034) and hot carcass weight (P < 0.0015). The SNP in POMC was associated with shipping weight (P < 0.0078) and hot carcass weight (P = 0.006) while it approached significance for average daily gain (P < 0.07). The SNP in MC4R approached significance for hot carcass weight (P < 0.085) while no significance was observed between the leptin SNP and the above listed traits. Because both CRH and POMC regulate appetite, potential interaction effects between these two genes were assessed. The absence of an interaction effect between CRH and POMC with hot carcass weight suggests that these genes act independently to increase carcass yield. These gene effects used singularly or together could result in an economic benefit to the beef industry.
Trait‐associated sequence variation in the bovine growth hormone receptor 1A promoter does not affect promoter activity in vitro
Authors: Zhou Y. , Jiang H. 
Published: March 2005

SummaryGrowth hormone (GH) plays a central role in growth and metabolism in cattle by binding to growth hormone receptor (GHR) and stimulating production of insulin‐like growth factor 1 (IGF1). Two sequence variations in the promoter transcribing a major GHR mRNA variant, GHR 1A mRNA, have been reported to be associated with quantitative differences in growth rate or blood concentration of IGF1 in cattle. One such variation is in the length of a TG‐repeat, being 11 or 16–20; the other variation is in the nucleotide 155 bp upstream from the transcription start site, being G or A. In this study, we determined whether these sequence variations would affect the activity of GHR 1A promoter. We cloned GHR 1A promoters bearing different sequence variations and linked each of them to a reporter gene. Transient transfection analyses revealed that these promoter–reporter constructs did not differ in reporter gene expression. Cotransfection analyses demonstrated that they also did not differ in activation by hepatocyte nuclear factor 4α, hepatocyte nuclear factor 4γ and nuclear receptor subfamily 2 group F member 2, known transcription factors for bovine GHR 1A promoter. These in vitro results, together with a previous observation that neither the nucleotide 155 bp upstream from the transcription start site nor the TG‐repeat was part of the GHR 1A promoter region interacting with nuclear proteins from bovine liver, do not support a cause–effect relationship between the reported sequence variations and the associated changes in growth rate or blood IGF1 concentration in cattle.