bluuebunny/crossref_metadata_2025_split huggingface dataset:
Performance of methods for SARS-CoV-2 variant detection and abundance estimation within mixed population samples
Authors: Kayikcioglu Tunc , Amirzadegan Jasmine , Rand Hugh , Tesfaldet Bereket , Timme Ruth E. , Pettengill James B. 
Published: January 2023

Background
The accurate identification of SARS-CoV-2 (SC2) variants and estimation of their abundance in mixed population samples (e.g., air or wastewater) is imperative for successful surveillance of community level trends. Assessing the performance of SC2 variant composition estimators (VCEs) should improve our confidence in public health decision making. Here, we introduce a linear regression based VCE and compare its performance to four other VCEs: two re-purposed DNA sequence read classifiers (Kallisto and Kraken2), a maximum-likelihood based method (Lineage deComposition for Sars-Cov-2 pooled samples (LCS)), and a regression based method (Freyja).

Methods
We simulated DNA sequence datasets of known variant composition from both Illumina and Oxford Nanopore Technologies (ONT) platforms and assessed the performance of each VCE. We also evaluated VCEs performance using publicly available empirical wastewater samples collected for SC2 surveillance efforts. Bioinformatic analyses were performed with a custom NextFlow workflow (C-WAP, CFSAN Wastewater Analysis Pipeline). Relative root mean squared error (RRMSE) was used as a measure of performance with respect to the known abundance and concordance correlation coefficient (CCC) was used to measure agreement between pairs of estimators.

Results
Based on our results from simulated data, Kallisto was the most accurate estimator as it had the lowest RRMSE, followed by Freyja. Kallisto and Freyja had the most similar predictions, reflected by the highest CCC metrics. We also found that accuracy was platform and amplicon panel dependent. For example, the accuracy of Freyja was significantly higher with Illumina data compared to ONT data; performance of Kallisto was best with ARTICv4. However, when analyzing empirical data there was poor agreement among methods and variations in the number of variants detected (e.g., Freyja ARTICv4 had a mean of 2.2 variants while Kallisto ARTICv4 had a mean of 10.1 variants).

Conclusion
This work provides an understanding of the differences in performance of a number of VCEs and how accurate they are in capturing the relative abundance of SC2 variants within a mixed sample (e.g., wastewater). Such information should help officials gauge the confidence they can have in such data for informing public health decisions.
Service recovery: a framework and empirical investigation
Authors: Miller Janis L , Craighead Christopher W , Karwan Kirk R 
Published: July 2002

AbstractAlthough recovery activities are primarily managed by the operations function, service recovery has received little attention in the operations management literature. This paper outlines a framework for examining the service recovery process and then reports on an empirical study to test this framework. The results not only validate much of what is anecdotally claimed by researchers and casual observers of service industries, but also highlight the role of operational activities in service recovery. The paper then points to the need for an array of operations‐based research efforts that will lead to better understanding of the recovery process and to more empirically based descriptive and prescriptive models.
REMOVING SERVICE BARRIERS FOR WOMEN WITH PHYSICAL DISABILITIES: PROMOTING ACCESSIBILITY IN THE GYNECOLOGIC CARE SETTING
Authors: Schopp Laura H. , Sanford Tiffany C. , Hagglund Kristofer J. , Gay John W. , Coatney Mary Ann 
Published: July 2002

ABSTRACTAlthough women with disabilities constitute a substantial segment of the population, their gynecologic health care needs often go unrecognized or untreated. Women with disabilities encounter a variety of obstacles to receiving health services including attitudinal, environmental, economic, and informational barriers. Standard screening and preventive services, such as pelvic examinations and mammograms, can be especially difficult to obtain, potentially placing women with disabilities at greater risk for diseases such as breast cancer and cervical cancer. This article reviews the current status of gynecologic care for women with disabilities and provides strategies for women's health care providers seeking to increase the accessibility of their practice settings.
Subcutaneous pseudomembranous fat necrosis: new observations/linkr>
Authors: Diaz‐Cascajo Carlos , Borghi Susanna 
Published: July 2002

Background: Pseudomembranous fat necrosis is a peculiar manifestation of necrosis of adipose tissue characterized by formation of pseudocystic cavities lined by crenulated membranes. The underlying mechanism for the formation of pseudomembranes is unknown and numerous hypotheses have been proposed. Despite divergent interpretations, most authors consider necrotic fat cells to be the anatomic substrate for the formation of pseudomembranes.Methods: A total of 341 panniculitides were reviewed for the presence of pseudomembranous fat necrosis. The specific diagnoses were established after correlation of all available clinical and laboratory data with the histopathology. Special attention was given to the time in the evolution of the disease when the biopsy was taken. Additional immunohistochemical studies were performed in 12 cases.Results: Thirty of 341 cases of different types of panniculitides were found to show pseudomembranous fat necrosis, namely: 10 of 15 cases of sclerosing panniculitis (lipodermatosclerosis), 6 of 95 cases of erythema nodosum, 7 of 34 cases of traumatic panniculitis, 1 of 7 cases of lupus panniculitis, 1 of 20 cases of erythema induratum Bazin (nodular vasculitis), 1 of 9 cases of necrobiosis lipoidica, 1 of 4 cases of sclerotic lipogranuloma, 1 of 9 cases of infectious panniculitis (erysipelas), 1 of 2 cases of pancreatic panniculitis, and 1 of 4 cases of subcutaneous sarcoidosis. Pseudomembranous fat necrosis labelled strongly for the histiocytic markers CD68 and lysozyme.Conclusions: Our series provides data suggesting that pseudomembranous fat necrosis represents a dynamic process that varies according to the evolution of the lesion at the time of the biopsy. In biopsies taken from early foci of panniculitides pseudomembranes show vescicular or picnotic nuclei. Later, pseudomembranes retain their crenulated appearance but lack nuclear elements. Furthermore, we present histopathologic, histochemical, and immunohistochemical evidence that pseudomembranous fat necrosis results from the interaction of residual products of disintegrated fat cells and macrophages. Histiocytic markers such as CD68 and lysozyme may be used as reliable tools in order to detect pseudomembranes in panniculitides.
Oral manifestations in 101 Cambodian patients with HIV infection and AIDS
Authors: Bendick C. , Scheifele C. , Reichart P. A. 
Published: July 2002

AbstractBackground: The HIV/AIDS epidemic in Cambodia has become a major problem in the last 7–8 years, mainly because in this formerly war‐stricken country the socioeconomic situation is only slowly improving. Since only very few studies have been published to date on the oral health status of Cambodian HIV/AIDS patients, it was the purpose of the present investigation to study oral manifestations in Cambodian patients with HIV disease.Methods: One hundred one Cambodian patients with HIV infection or AIDS were examined for the presence of oral manifestations in one medical center in Phomh Penh, Cambodia.Results: Sixty‐three men and 38 women with a median age of 32 years were examined (age range 7.5–63.5 years). Of these patients, 42.6% were smokers, 46.5% of men were heavy drinkers and 90.5% of men were promiscuous compared with 5.3% of women. The most frequent AIDS‐defining diseases were wasting syndrome (54.5%),Pneumocystis carinii pneumonia(PcP) (19.8%) and tuberculosis (18.8%). Puritic papular eruption, a common cutaneous manifestation in HIV‐infected patients, was seen in 17.8% of patients. Candida‐associated infections of the oral cavity were most common. Among the patients, 52.5% revealed pseudomembranous candidiasis and 35.6% had bilateral hairy leukoplakia. Only 10% of patients had no oral lesions. Also common were necrotising ulcerative gingivo‐periodontal diseases (27.7%).Conclusion: The general health status of 101 Cambodian patients with HIV infection and AIDS was poor, and they demonstrated a large number of oral manifestations. Antiretroviral therapy is presently not available and only a fraction of patients receives antimycotic treatment (25.7%). HIV infection and the AIDS epidemic in Cambodia have become a serious problem and patients urgently need adequate diagnosis and antiretroviral therapies.
The authority of complexity*
Authors: Stehr Nico , Grundmann Reiner 
Published: July 2002

ABSTRACTThe assertion about the unique ‘complexity’ or the peculiarly intricate character of social phenomena has, at least within sociology, a long, venerable and virtually uncontested tradition. At the turn of the last century, classical social theorists, for example, Georg Simmel and Emile Durkheim, made prominent and repeated reference to this attribute of the subject matter of sociology and the degree to which it complicates, even inhibits the development and application of social scientific knowledge. Our paper explores the origins, the basis and the consequences of this assertion and asks in particular whether the classic complexity assertion still deserves to be invoked in analyses that ask about the production and the utilization of social scientific knowledge in modern society. We present John Maynard Keynes' economic theory and its practical applications as an illustration. We conclude that the practical value of social scientific knowledge is not dependent on a faithful, in the sense of complete, representation of social reality. Instead, social scientific knowledge that wants to optimize its practicality has to attend and attach itself to elements of social situations that can be altered or are actionable.
A dependency syndrome related to areca nut use: some medical and psychological aspects among areca nut users in the Gujarat community in the UK
Authors: Winstock A. R. , Trivedy C. R. , Warnakulasuriya K. A. A. S. , Peters T. J. 
Published: July 2002

AbstractUse of betel nut (areca nut) and its products is widespread, particularly in the Indo‐Chinese continents, being the fourth most widely used substance after tobacco, alcohol and caffeine, affecting approximately 20% of the world's population. Betel nut, with or without admixed tobacco, is widely used among UK Indo‐Asian immigrants, particularly Gujurate speakers. To date most research has concentrated on oral submucous fibrosis and malignancy. This paper reports detailed socio‐demographic, clinical, laboratory and psychological studies in 11 current and former heavy betel nut users, referred by an Oral Medicine Unit in NW London. The patients, nine males, two females, had a high incidence of cardiovascular disease and truncal obesity. Laboratory investigations showed a high incidence of reduced serum B12 levels (4/9) and raised urinary cotinine levels (6/11), although none were current cigarette smokers. These findings are consistent with heavy usage of tobacco‐areca combinations by this group. Routine biochemical and haematological investigations and clinical examination revealed no consistent abnormalities. Subjects had used areca for an average of 35 years with the mean age of first use being 13 years. Most subjects reported beneficial psychosocial effects. Ten subjects reported cessation withdrawal effects with the mean Severity of Dependence Score of 7.3. These findings are consistent with the existence of a dependency syndrome among those who use areca nut products. Further research is required to delineate the relative contributions of areca nut and tobacco to this clinical picture. Use of the areca nut, especially with tobacco, represents an area of health prevention among the UK minority populations that has, to date, been overlooked.
GOS.SP.ASS.'98: an assessment for speech disorders associated with cleft palate and/or velopharyngeal dysfunction (revised)
Authors: Sell Debbie , Harding Anne , Grunwell Pamela 
Published: July 2002

AbstractIn 1994 the present authors proposed a speech assessment protocol for speech disorders associated with cleft palate and/or velopharyngeal dysfunction known as GOS.SP.ASS. (Great Ormond Street Speech Assessment). In a recent survey undertaken to review the different speech assessment protocols used in six cleft palate centres in the UK, GOS.SP.ASS. was selected from six protocols as the optimal procedure for clinical and research purposes. The process of identifying an optimal procedure involved analysis of completed forms for each assessment. Analysis of the completed GOS.SP.ASS. forms revealed significant ambiguities in the protocol which led to differences in form completion. This paper describes important revisions to the original GOS.SP.ASS. protocol in order to ensure comparable data from different clinicians. This detailed speech assessment is now complemented by the Cleft Audit Protocol for Speech (CAPS), a tool recommended for clinical audit. As a result of close collaboration in their preparation, the results are directly comparable. In addition, the speech elicitation sentences and the phonetic diagram have been modified.
The Autophagic and Endocytic Pathways Converge at the Nascent Autophagic Vacuoles
Authors: Liou Willisa , Geuze Hans J. , Geelen Math. J.H. , Slot Jan W. 
Published: July 2002

We used an improved cryosectioning technique in combination with immunogold cytochemistry and morphometric analysis to study the convergence of the autophagic and endocytic pathways in isolated rat hepatocytes. The endocytic pathway was traced by continuous uptake of gold tracer for various time periods, up to 45 min, while the cells were incubated in serum-free medium to induce autophagy. Endocytic structures involved in fusion with autophagic vacuoles (AV) were categorized into multivesicular endosomes (MVE) and vesicular endosomes (VE). Three types of AV—initial (AVi), intermediate (AVi/d), and degradative (AVd)—were defined by morphological criteria and immunogold labeling characteristics of marker enzymes.
The entry of tracer into AV, manifested as either tracer-containing AV profiles (AV+) or fusion profiles (FP+) between AV and tracer-positive endosomal vesicles/vacuoles, was detected as early as 10 min after endocytosis. The number of AV+ exhibited an exponential increase with time. FP+ between MVE or VE and all three types of AV were observed. Among the 112 FP+ scored, 36% involved VE. Of the AV types, AVi and AVi/d were found five to six times more likely to be involved in fusions than AVd. These fusion patterns did not significantly change during the period of endocytosis (15–45 min). We conclude that the autophagic and endocytic pathways converge in a multistage fashion starting within 10 min of endocytosis. The nascent AV is the most upstream and preferred fusion partner for endosomes.
Interphase Nuclei of Many Mammalian Cell Types Contain Deep, Dynamic, Tubular Membrane-bound Invaginations of the Nuclear Envelope
Authors: Fricker Mark , Hollinshead Michael , White Nick , Vaux David 
Published: July 2002

The nuclear envelope consists of a doublemembraned extension of the rough endoplasmic reticulum. In this report we describe long, dynamic tubular channels, derived from the nuclear envelope, that extend deep into the nucleoplasm. These channels show cell-type specific morphologies ranging from single short stubs to multiple, complex, branched structures. Some channels transect the nucleus entirely, opening at two separate points on the nuclear surface, while others terminate at or close to nucleoli. These channels are distinct from other topological features of the nuclear envelope, such as lobes or folds.
The channel wall consists of two membranes continuous with the nuclear envelope, studded with features indistinguishable from nuclear pore complexes, and decorated on the nucleoplasmic surface with lamins. The enclosed core is continuous with the cytoplasm, and the lumenal space between the membranes contains soluble ER-resident proteins (protein disulphide isomerase and glucose-6-phosphatase).
Nuclear channels are also found in live cells labeled with the lipophilic dye DiOC6. Time-lapse imaging of DiOC6-labeled cells shows that the channels undergo changes in morphology and spatial distribution within the interphase nucleus on a timescale of minutes.
The presence of a cytoplasmic core and nuclear pore complexes in the channel walls suggests a possible role for these structures in nucleo–cytoplasmic transport. The clear association of a subset of these structures with nucleoli would also be consistent with such a transport role.
High Rates of Actin Filament Turnover in Budding Yeast and Roles for Actin in Establishment and Maintenance of Cell Polarity Revealed Using the Actin Inhibitor Latrunculin-A
Authors: Ayscough Kathryn R. , Stryker Joel , Pokala Navin , Sanders Miranda , Crews Phil , Drubin David G. 
Published: July 2002

We report that the actin assembly inhibitor latrunculin-A (LAT-A) causes complete disruption of the yeast actin cytoskeleton within 2–5 min, suggesting that although yeast are nonmotile, their actin filaments undergo rapid cycles of assembly and disassembly in vivo. Differences in the LAT-A sensitivities of strains carrying mutations in components of the actin cytoskeleton suggest that tropomyosin, fimbrin, capping protein, Sla2p, and Srv2p act to increase actin cytoskeleton stability, while End3p and Sla1p act to decrease stability. Identification of three LAT-A resistant actin mutants demonstrated that in vivo effects of LAT-A are due specifically to impairment of actin function and implicated a region on the three-dimensional actin structure as the LAT-A binding site.
LAT-A was used to determine which of 19 different proteins implicated in cell polarity development require actin to achieve polarized localization. Results show that at least two molecular pathways, one actindependent and the other actin-independent, underlie polarity development. The actin-dependent pathway localizes secretory vesicles and a putative vesicle docking complex to sites of cell surface growth, providing an explanation for the dependence of polarized cell surface growth on actin function. Unexpectedly, several proteins that function with actin during cell polarity development, including an unconventional myosin (Myo2p), calmodulin, and an actin-interacting protein (Bud6/Aip3p), achieved polarized localization by an actin-independent pathway, revealing interdependence among cell polarity pathways. Finally, transient actin depolymerization caused many cells to abandon one bud site or mating projection and to initiate growth at a second site. Thus, actin filaments are also required for maintenance of an axis of cell polarity.
Suppression of Apoptosis by Nitric Oxide via Inhibition of Interleukin-1β–converting Enzyme (ICE)-like and Cysteine Protease Protein (CPP)-32–like Proteases
Authors: Dimmeler Stefanie , Haendeler Judith , Nehls Michael , Zeiher Andreas M. 
Published: July 2002

Physiological levels of shear stress alter the genetic programm of cultured endothelial cells and are associated with reduced cellular turnover rates and formation of atherosclerotic lesions in vivo. To test the hypothesis that shear stress (15 dynes/cm2) interferes with programmed cell death, apoptosis was induced in human umbilical venous cells (HUVEC) by tumor necrosis factor-α (TNF-α). Apoptosis was quantified by ELISA specific for histone-associated DNA-fragments and confirmed by demonstrating the specific pattern of internucleosomal DNA-fragmentation. TNF-α (300 U/ml) mediated increase of DNA-fragmentation was completely abrogated by shear stress (446 ± 121% versus 57 ± 11%, P &lt;0.05). This anti-apoptotic activity of shear stress decreased after pharmacological inhibition of endogenous nitric oxide (NO)-synthase by NG-monomethyl-l-arginine and was completely reproduced by exogenous NO-donors.
The activation of interleukin-1β–converting enzyme (ICE)-like and cysteine protease protein (CPP)-32-like cysteine proteases was required to mediate TNF-α–induced apoptosis of HUVEC. Endothelial-derived nitric oxide (NO) as well as exogenous NO donors inhibited TNF-α–induced cysteine protease activation. Inhibition of CPP-32 enzyme activity was due to specific S-nitrosylation of Cys 163, a functionally essential amino acid conserved among ICE/CPP-32–like proteases. Thus, we propose that shear stress-mediated NO formation interferes with cell death signal transduction and may contribute to endothelial cell integrity by inhibition of apoptosis.
Culture and Consumption: A Theoretical Account of the Structure and Movement of the Cultural Meaning of Consumer Goods
Authors: McCracken Grant 
Published: July 2002

Abstract
Cultural meaning in a consumer society moves ceaselessly from one location to another. In the usual trajectory, cultural meaning moves first from the culturally constituted world to consumer goods and then from these goods to the individual consumer. Several instruments are responsible for this movement: advertising, the fashion system, and four consumption rituals. This article analyzes the movement of cultural meaning theoretically, showing both where cultural meaning is resident in the contemporary North American consumer system and the means by which this meaning is transferred from one location in this system to another.
ASEdb: a database of alanine mutations and their effects on the

free energy of binding in protein interactions
Authors: Thorn Kurt S. , Bogan Andrew A. 
Published: July 2002

Abstract
Summary: The Alanine Scanning Energetics database (ASEdb) is a searchable database of single alanine mutations in protein–protein, protein–nucleic acid, and protein–small molecule interactions for which binding affinities have been experimentally determined. In cases where structures are available, it contains surface areas of the mutated side chain and links to the PDB entries. It is useful for studying the contribution of single amino acids to the energetics of protein interactions, and can be updated by researchers as new data are generated.
Availability: ASEdb is accessible on the Web at http://www.asedb.org
Contact: thorn@itsa.ucsf.edu
* To whom correspondence should be addressed.
Automated ortholog inference from phylogenetic trees and
calculation of orthology reliability
Authors: Storm Christian E. V. , Sonnhammer Erik L. L. 
Published: July 2002

Abstract
Motivation: Orthologous proteins in different species are likely to have similar biochemical function and biological role. When annotating a newly sequenced genome by sequencehomology, the most precise and reliable functional information can thus be derived from orthologs in other species. A standard method of finding orthologs is to compare the sequence tree with the species tree. However, since the topology of phylogenetic tree is not always reliable one might get incorrect assignments.
Results: Here we present a novel method that resolves this problem by analyzing a set of bootstrap trees instead of the optimal tree. The frequency of orthology assignments in the bootstrap trees can be interpreted as a support value for the possible orthology of the sequences. Our method is efficient enough to analyze data in the scale of whole genomes. It is implemented in Java and calculates orthology support levels for all pairwise combinations of homologous sequences of two species. The method was tested on simulated datasets and on real data of homologous proteins.
Availability: Downloadable free of charge from ftp://ftp.cgb.ki.se/pub/prog/orthostrapper/or on request from the authors.
Contact: christian.storm@cgb.ki.se