bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sorting permutations by cut-circularize-linearize-and-paste operations
Authors: Huang Keng-Hsuan , Chen Kun-Tze , Lu Chin Lung 
Published: December 2011

Abstract

Background
Genome rearrangements are studied on the basis of genome-wide analysis of gene orders and important in the evolution of species. In the last two decades, a variety of rearrangement operations, such as reversals, transpositions, block-interchanges, translocations, fusions and fissions, have been proposed to evaluate the differences between gene orders in two or more genomes. Usually, the computational studies of genome rearrangements are formulated as problems of sorting permutations by rearrangement operations.

Result
In this article, we study a sorting problem by cut-circularize-linearize-and-paste (CCLP) operations, which aims to find a minimum number of CCLP operations to sort a signed permutation representing a chromosome. The CCLP is a genome rearrangement operation that cuts a segment out of a chromosome, circularizes the segment into a temporary circle, linearizes the temporary circle as a linear segment, and possibly inverts the linearized segment and pastes it into the remaining chromosome. The CCLP operation can model many well-known rearrangements, such as reversals, transpositions and block-interchanges, and others not reported in the biological literature. In addition, it really occurs in the immune response of higher animals. To distinguish those CCLP operations from the reversal, we call them as non-reversal CCLP operations. In this study, we use permutation groups in algebra to design an O(δn) time algorithm for solving the weighted sorting problem by CCLP operations when the weight ratio between reversals and non-reversal CCLP operations is 1:2, where n is the number of genes in the given chromosome and δ is the number of needed CCLP operations.

Conclusion
The algorithm we propose in this study is very simple so that it can be easily implemented with 1-dimensional arrays and useful in the studies of phylogenetic tree reconstruction and human immune response to tumors.
ApicoAlign: an alignment and sequence search tool for apicomplexan proteins
Authors: Ali Jamshaid , Paila Umadevi , Ranjan Akash 
Published: December 2011

Abstract

Background
Over the recent years, a number of genomes have been successfully sequenced and this was followed by genome annotation projects to help understand the biological capabilities of newly sequenced genomes. To improve the annotation of Plasmodium falciparum proteins, we earlier developed parasite specific matrices (PfSSM) and demonstrated their (Smat80 and PfFSmat60) better performance over standard matrices (BLOSUM and PAM). Here we extend that study to nine apicomplexan species other than P. falciparum and develop a web application ApicoAlign for improving the annotation of apicomplexan proteins.

Results
The SMAT80 and PfFSmat60 matrices perform better for apicomplexan proteins compared to BLOSUM in detecting the orthologs and improving the alignment of these proteins with their potential orthologs respectively. Database searches against non-redundant (nr) database have shown that SMAT80 gives superior performance compared to BLOSUM series in terms of E-values, bit scores, percent identity, alignment length and mismatches for most of the apicomplexan proteins studied here. Using these matrices, we were able to find orthologs for rhomboid proteases of P. berghei, P. falciparum &P. vivax and large subunit of U2 snRNP auxiliary factor of Cryptosporidium parvum in Arabidopsis thaliana. We also show improved pairwise alignments of proteins from Apicomplexa viz. Cryptosporidium parvum and P. falciparum with their orthologs from other species using the PfFSmat60 matrix.

Conclusions
The SMAT80 and PfFSmat60 substitution matrices perform better for apicomplexan proteins compared to BLOSUM series. Since they can be helpful in improving the annotation of apicomplexan genomes and their functional characterization, we have developed a web server ApicoAlign for finding orthologs and aligning apicomplexan proteins.
Genome-scale reconstruction and system level investigation of the metabolic network of Methylobacterium extorquensAM1
Authors: Peyraud Rémi , Schneider Kathrin , Kiefer Patrick , Massou Stéphane , Vorholt Julia A , Portais Jean-Charles 
Published: December 2011

AbstractBackgroundMethylotrophic microorganisms are playing a key role in biogeochemical processes - especially the global carbon cycle - and have gained interest for biotechnological purposes. Significant progress was made in the recent years in the biochemistry, genetics, genomics, and physiology of methylotrophic bacteria, showing that methylotrophy is much more widespread and versatile than initially assumed. Despite such progress, system-level description of the methylotrophic metabolism is currently lacking, and much remains to understand regarding the network-scale organization and properties of methylotrophy, and how the methylotrophic capacity emerges from this organization, especially in facultative organisms.ResultsIn this work, we report on the integrated, system-level investigation of the metabolic network of the facultative methylotrophMethylobacterium extorquensAM1, a valuable model of methylotrophic bacteria. The genome-scale metabolic network of the bacterium was reconstructed and contains 1139 reactions and 977 metabolites. The sub-network operating upon methylotrophic growth was identified from bothin silicoand experimental investigations, and13C-fluxomics was applied to measure the distribution of metabolic fluxes under such conditions. The core metabolism has a highly unusual topology, in which the unique enzymes that catalyse the key steps of C1 assimilation are tightly connected by several, large metabolic cycles (serine cycle, ethylmalonyl-CoA pathway, TCA cycle, anaplerotic processes). The entire set of reactions must operate as a unique process to achieve C1 assimilation, but was shown to be structurally fragile based on network analysis. This observation suggests that in nature a strong pressure of selection must exist to maintain the methylotrophic capability. Nevertheless, substantial substrate cycling could be measured within C2/C3/C4 inter-conversions, indicating that the metabolic network is highly versatile around a flexible backbone of central reactions that allows rapid switching to multi-carbon sources.ConclusionsThis work emphasizes that the metabolism ofM. extorquensAM1 is adapted to its lifestyle not only in terms of enzymatic equipment, but also in terms of network-level structure and regulation. It suggests that the metabolism of the bacterium has evolved both structurally and functionally to an efficient but transitory utilization of methanol. Besides, this work provides a basis for metabolic engineering to convert methanol into value-added products.
Working alliance, interpersonal trust and perceived coercion in mental health review hearings
Authors: Donnelly Vidis , Lynch Aideen , Mohan Damian , Kennedy Harry G 
Published: December 2011

Abstract

Background
There is some evidence that when mental health commitment hearings are held in accordance with therapeutic jurisprudence principles they are perceived as less coercive, and more just in their procedures leading to improved treatment adherence and fewer hospital readmissions. This suggests an effect of the hearing on therapeutic relationships. We compared working alliance and interpersonal trust in clinicians and forensic patients, whose continued detentions were reviewed by two different legal review bodies according to their legal category.

Methods
The hearings were rated as positive or negative by patients and treating psychiatrists using the MacArthur scales for perceived coercion, perceived procedural justice (legal and medical) and for the impact of the hearing. We rated Global assessment of Function (GAF), Positive and Negative Symptom Scale (PANSS), Working Alliance Inventory (WAI) and Interpersonal Trust in Physician (ITP) scales six months before the hearing and repeated the WAI and ITP two weeks before and two weeks after the hearing, for 75 of 83 patients in a forensic medium and high secure hospital.

Results
Psychiatrists agreed with patients regarding the rating of hearings. Patients rated civil hearings (MHTs) more negatively than hearings under insanity legislation (MHRBs). Those reviewed by MHTs had lower scores for WAI and ITP. However, post-hearing WAI and ITP scores were not different from baseline and pre-hearing scores. Using the receiver operating characteristic, baseline WAI and ITP scores predicted how patients would rate the hearings, as did baseline GAF and PANSS scores.

Conclusions
There was no evidence that positively perceived hearings improved WAI or ITP, but some evidence showed that negatively perceived hearings worsened them. Concentrating on functional recovery and symptom remission remains the best strategy for improved therapeutic relationships.
Detection of patients with acute kidney injury by the clinical laboratory using rises in serum creatinine: comparison of proposed definitions and a laboratory delta check
Authors: Garner Ashley E , Lewington Andrew J P , Barth Julian H 
Published: December 2011

Background Timely detection of acute kidney injury (AKI) in hospital patients has been hampered by the multiple definitions of AKI and difficulties applying their criteria. A laboratory delta check may provide an effective means of detecting patients developing AKI. This study compared three of the proposed AKI definitions and a delta check to detect AKI using serum creatinine results of hospital inpatients. Methods Serum creatinine results for 2822 inpatients were gathered retrospectively from the clinical biochemistry database. All serum creatinine results within 30 d of admission were included for each patient and assessed for AKI according to four criteria: Risk, Injury, Failure (RIFLE), Acute Kidney Injury Network (AKIN), Waikar & Bonventre or a delta check (increase of >26 μmol/L between two successive values). Results A total of 149 (11.3%) patients were defined as having AKI by at least one of the four criteria. Different populations of patients were identified by each criterion. The number of patients identified and the incidence of AKI were as follows: RIFLE 94 (7.1%), AKIN 125 (9.5%), Waikar & Bonventre 100 (7.6%) and delta check 146 (11.1%). The delta check detected 132 (98%) of all 135 cases detected by the other three criteria. A further 14 patients were detected solely by the delta check. Conclusions The different definitions proposed for AKI detect different populations of patients. A laboratory delta check detected 98% of all the patients identified by AKIN, RIFLE and Waikar & Bonventre combined and could therefore provide a practical way of detecting AKI patients.
In Situ Measurement of Compression Set in Building Sealants During Outdoor Aging
Authors: Schueneman Gregory T. , Hunt Christopher G. , Lacher Steven , White Christopher C. , Hunston Donald L. 
Published: December 2011

Abstract
The durability of sealants is dictated by many factors such as joint design, surface preparation, application, formulation, joint movement, and weather. Among these factors the link between formulation (material behavior) and weathering durability is difficult to assess in short term tests. We attempt to address this challenge by monitoring changes in apparent modulus during exposure to outdoor weathering and cyclic strain. This is accomplished via custom built systems that apply cyclic strain to 16 samples simultaneously viaprograms that simulate wood (cold compression) and concrete/metal (hot compression) construction materials. A key finding of the research presented here is that changes in apparent modulus are primarily driven by underlying changes in the compression set, a potentially critical contributor to stress in structures during rapid temperature changes. Detection of the compression set is made possible by the in situ material property assessments used in this research. Aging tests that rely on offline evaluation of property changes may miss or underestimate this effect on the sealant’s stiffness due to time delay and/or losing track of the original zero stress–zero strain state.
Kombination von Prozessanalysentechnik und Softsensoren zur Online-Berechnung erweiterter Prozesskenngrößen und -informationen
Authors: Kleinert Tobias , Mühlbeyer Sandra , Schladt Markus , Schocker Alexander 
Published: December 2011

Zusammenfassung
Softsensoren bieten eine attraktive Option, schwer messbare Prozessinformationen indirekt aus konventionellen Messgrößen (Druck, Temperatur und Durchfluss) online zu berechnen. Durch Kombination mit Prozessanalysentechnik, die spezifische physiko-chemische Informationen liefert, lässt sich der Anwendungsbereich von Softsensoren und Prozessanalytik deutlich erweitern. Mit der Online-Berechnung einer Katalysatoraktivität und eines Verkokungsgrades wird der Einsatz von Softsensoren in der industriellen Praxis bei BASF demonstriert. Das zukünftige Potential für Softsensoren in der Prozessanalytik wird anhand der überarbeiteten Technologie-Roadmap “Prozesssensoren 2015+” diskutiert.
The Genetic Consequences of Spatially Varying Selection in the Panmictic American Eel (Anguilla rostrata)
Authors: Gagnaire Pierre-Alexandre , Normandeau Eric , Côté Caroline , Møller Hansen Michael , Bernatchez Louis 
Published: December 2011

Abstract
Our understanding of the genetic basis of local adaptation has recently benefited from the increased power to identify functional variants associated with environmental variables at the genome scale. However, it often remains challenging to determine whether locally adaptive alleles are actively maintained at intermediate frequencies by spatially varying selection. Here, we evaluate the extent to which this particular type of balancing selection explains the retention of adaptive genetic variation in the extreme situation of perfect panmixia, using the American eel (Anguilla rostrata) as a model. We first conducted a genome scan between two samples from opposite ends of a latitudinal environmental gradient using 454 sequencing of individually tagged cDNA libraries. Candidate SNPs were then genotyped in 992 individuals from 16 sampling sites at different life stages of the same cohort (including larvae from the Sargasso Sea, glass eels, and 1-year-old individuals) as well as in glass eels of the following cohort. Evidence for spatially varying selection was found at 13 loci showing correlations between allele frequencies and environmental variables across the entire species range. Simulations under a multiple-niche Levene’s model using estimated relative fitness values among genotypes rarely predicted a stable polymorphic equilibrium at these loci. Our results suggest that some genetic-by-environment interactions detected in our study arise during the progress toward fixation of a globally advantageous allele with spatially variable effects on fitness.
Lack of Oral Health Care for Adults in Harlem: A Hidden Crisis
Authors: Zabos Georgina P. , Northridge Mary E. , Ro Marguerite J. , Trinh Chau , Vaughan Roger , Howard Joyce Moon , Lamster Ira , Bassett Mary T. , Cohall Alwyn T. 
Published: December 2011

Objectives. Profound and growing disparities exist in oral health among certain US populations. We sought here to determine the prevalence of oral health complaints among Harlem adults by measures of social class, as well as their access to oral health care. Methods. A population-based survey of adults in Central Harlem was conducted from 1992 to 1994. Two questions on oral health were included: whether participants had experienced problems with their teeth or gums during the past 12 months and, if so, whether they had seen a dentist. Results. Of 50 health conditions queried about, problems with teeth or gums were the chief complaint among participants (30%). Those more likely to report oral health problems than other participants had annual household incomes of less than $9000 (36%), were unemployed (34%), and lacked health insurance (34%). The privately insured were almost twice as likely to have seen a dentist for oral health problems (87%) than were the uninsured (48%). Conclusions. There is an urgent need to provide oral health services for adults in Harlem. Integrating oral health into comprehensive primary care is one promising mechanism.
Public Conceptions of Serious Mental Illness and Substance Abuse, Their Causes and Treatments: Findings from the 1996 General Social Survey
Authors: Kuppin Sara , Carpiano Richard M. 
Published: December 2011

Objectives. We examined the degree to which lay beliefs about the causes of disorders may predict beliefs about what constitutes appropriate treatment. Methods. We analyzed randomized vignette data from the MacArthur Mental Health Module of the 1996 General Social Survey (n=1010). Results. Beliefs in biological causes (i.e., chemical imbalance, genes) were significantly associated with the endorsement of professional, biologically focused treatments (e.g., prescription medication, psychiatrists, and mental hospital admissions). Belief that the way a person was raised was the cause of a condition was the only nonbiologically based causal belief associated with any treatment recommendations (talking to a clergy member). Conclusions. Lay beliefs about the biological versus nonbiological causes of mental and substance abuse disorders are related to beliefs regarding appropriate treatment. We suggest areas for further research with regard to better understanding this relationship in an effort to construct effective messages promoting treatment for mental health and substance abuse disorders.
Health Policy and the Coloring of an American Male Crisis: A Perspective on Community-Based Health Services
Authors: Smith Amos L. 
Published: December 2011

Health services at the community level are organized and financed in such a way that men need access but encounter barriers to care such as poor service design, lack of insurance, and the absence of health literacy. Community health delivery systems may not be appropriate, effective, fit, or able to meet the needs they are charged to fill. Community-based health services, including health departments, are underfunded, understaffed, and unable to carry out their mission in a way that protects the health of the community. The current design for funding and delivering health care services excludes poor men, particularly men of color. Improving the health of men requires modifications in the way health care is financed, delivered, and managed.
National Health Insurance or Incremental Reform: Aim High, or at Our Feet?
Authors: Himmelstein David U. , Woolhandler Steffie 
Published: December 2011

Single-payer national health insurance could cover the uninsured and upgrade coverage for most Americans without increasing costs; savings on insurance overhead and other bureaucracy would fully offset the costs of improved care. In contrast, proposed incremental reforms are projected to cover a fraction of the uninsured, at great cost. Moreover, even these projections are suspect; reforms of the past quarter century have not stemmed the erosion of coverage. Despite incrementalists’ claims of pragmatism, they have proven unable to shepherd meaningful reform through the political system. While national health insurance is often dismissed as ultra left by the policy community, it is dead center in public opinion. Polls have consistently shown that at least 40%, and perhaps 60%, of Americans favor such reform.
E-Commerce and Privacy: Exploring What We Know and Opportunities for Future Discovery
Authors: Boritz J. Efrim , No Won Gyun 
Published: December 2011

ABSTRACT
Electronic commerce (e-commerce) has a built-in trade-off between the necessity of providing at least some personal information to consummate an online transaction and the risk of negative consequences from providing such information. This requirement and the increased sophistication of companies' personal information gathering have made e-commerce privacy a critical issue and have spawned a broad research literature that is reviewed in this paper. Key research issues and findings are organized, using a framework defined by four key stakeholder groups—companies, customers, privacy solution providers (PSPs), and governments—as well as the interactions among them. The review indicates that the published research on e-commerce privacy peaked in the early 2000s; thus, it has not addressed many of the technological advances and other relevant developments of the past decade. Potential research opportunities for researchers in Management Information Systems (MIS) and Accounting Information Systems (AIS) include: company privacy strategies, operations, disclosures, and compliance practices; customer privacy concerns arising from company practices such as Internet activity tracking, physical location tracking, personal information gathering by social networks, and information exchanges in cloud computing environments; privacy-enhancing technologies, controls, and assurance practices developed by PSPs; and privacy regulations relating to various industries, countries, and cultures. More use of experimental and archival research is encouraged.
IT Capability and a Firm's Ability to Recover from Losses: Evidence from the Economic Downturn of the Early 2000s
Authors: Chen Changling , Lim Jee-Hae , Stratopoulos Theophanis C. 
Published: December 2011

ABSTRACT
Prior literature shows that during an economic downturn firms have difficulty sustaining superior performance, and a larger percentage of firms report losses. Motivated by this literature, we explore the role of sustainability of organizational IT capability (ITC) on a firm's performance during an economic downturn. Specifically, we examine how ITC sustainability contributes to a firm's ability to recover from losses. ITC sustainability reflects a firm's ability to resist competitors' attempts to imitate or improve on its ITC. We use ITC sustainability to classify firms as sustainable (Systematic ITC), as non-sustainable (Occasional ITC), and as having no ITC (Non-ITC). Using a sample of large U.S. firms during the economic downturn of the early 2000s, we show that Systematic ITC firms achieve higher levels of firm-specific abnormal earnings and are capable of faster recovery when compared to all competitors (Occasional ITC and Non-ITC firms) and competitors with only Occasional ITC.
The Business Value of IT: A Synthesis and Framework of Archival Research
Authors: Masli Adi , Richardson Vernon J. , Sanchez Juan Manuel , Smith Rodney E. 
Published: December 2011

ABSTRACT
This paper synthesizes recent empirical archival research investigating the link between information technology investment and business value. It examines (1) financial and nonfinancial measures to represent different elements of business value, (2) IT investment measures and links with firm performance, (3) IT and business complementarities that affect firm performance, and (4) the impact of business context and IT alignment with business strategy on resulting performance. The review of prior research is guided by a balanced scorecard framework that places IT in a business context and highlights the role of potential drivers and contextual factors that impact the association between IT and firm value. The paper concludes by proposing several broad avenues of future research that may be of particular interest to archival accounting information systems researchers.