bluuebunny/crossref_metadata_2025 huggingface dataset:
Herpesviral helicase-primase subunit UL8 is inactivated B-family polymerase
Authors: Kazlauskas Darius , Venclovas Česlovas
Published: April 2014

Motivation: Herpesviruses are large DNA viruses causing a variety of diseases in humans and animals. To develop effective treatment, it is important to understand the mechanisms of their replication. One of the components of the herpesviral DNA replication system is a helicase–primase complex, consisting of UL5 (helicase), UL52 (primase) and UL8. UL8 is an essential herpesviral protein involved in multiple protein–protein interactions. Intriguingly, so far no UL8 homologs outside of herpesviruses could be identified. Moreover, nothing is known about its structure or domain organization.

Results: Here, combining sensitive homology detection methods and homology modeling, we found that the UL8 protein family is related to B-family polymerases. In the course of evolution, UL8 has lost the active site and has undergone a reduction of DNA-binding motifs. The loss of active site residues explains the failure to detect any catalytic activity of UL8. A structural model of human herpes virus 1 UL8 constructed as part of the study is consistent with the mutation data targeting its interaction with primase UL52. It also provides a platform for studying multiple interactions that UL8 is involved in. The two other components of helicase–primase complex show evolutionary links with a newly characterized human primase that also has DNA polymerase activity (PrimPol) and the Pif1 helicase, respectively. The role of these enzymes in recovering stalled replication forks suggests mechanistic and functional similarities with herpesviral proteins.

Contact:  venclovas@ibt.lt

Supplementary information:  Supplementary data are available at Bioinformatics online.
DSRC 2—Industry-oriented compression of FASTQ files
Authors: Roguski Łukasz , Deorowicz Sebastian
Published: April 2014

Summary: Modern sequencing platforms produce huge amounts of data. Archiving them raises major problems but is crucial for reproducibility of results, one of the most fundamental principles of science. The widely used gzip compressor, used for reduction of storage and transfer costs, is not a perfect solution, so a few specialized FASTQ compressors were proposed recently. Unfortunately, they are often impractical because of slow processing, lack of support for some variants of FASTQ files or instability. We propose DSRC 2 that offers compression ratios comparable with the best existing solutions, while being a few times faster and more flexible.

Availability and Implementation: DSRC 2 is freely available at http://sun.aei.polsl.pl/dsrc . The package contains command-line compressor, C and Python libraries for easy integration with existing software and technical documentation with examples of usage.

Contact : sebastian.deorowicz@polsl.pl

Supplementary information:  Supplementary data are available at Bioinformatics online
High Mortality Among Human Immunodeficiency Virus (HIV)-Infected Individuals Before Accessing or Linking to HIV Care: A Missing Outcome in the Cascade of Care?
Authors: Krentz Hartmut B. , MacDonald Judy , John Gill M.
Published: April 2014

Background.  The “cascade of care” displays the proportion of individuals who are infected with human immunodeficiency virus (HIV), diagnosed, linked, retained, on antiretroviral treatment, and HIV suppressed. We examined the implications of including death in the use of this cascade for program and public health performance metrics.

Methods.  Individuals newly diagnosed with HIV and living in Calgary between 2006 and 2013 were included. Through linkage with Public Health and death registries, the deaths (ie, all-cause mortality) and their distribution within the cascade were determined. Mortality rates are reported per 100 person-years.

Results.  Estimated new HIV infections were 680 (543 confirmed and 137 unknown cases). Forty-three individuals, after diagnosis, were never referred for HIV care. Despite referral(s), 88 individuals (18%) never attended the clinic for HIV care. Of individuals retained in care, 87% received antiretroviral therapy and 76% achieved viral suppression. Thirty-six deaths were reported (mortality rate, 1.50/100 person-years). One diagnosis was made posthumously. Deaths (20 of 35; 57%) occurred for individuals linked but not retained in care (6.93/100 person-years), and 70% were HIV-related. Mortality rate for patients in care was 0.79/100 person-years. Retained patients with detectable viremia had a death rate of 2.49/100, which contrasted with 0.28/100 person-years in those with suppressed viremia. Eight of these 15 deaths (53%) were HIV-related.

Conclusions.  Over half of deaths occurred in those referred but not effectively linked or retained in HIV care, and these cases may be easily overlooked in standard HIV mortality studies. Inclusion of deaths into the cascade may further enhance its value as a public health metric.
Green Herring Syndrome: Bacterial Infection in Patients With Mucormycosis Cavitary Lung Disease
Authors: Peixoto Driele , Hammond Sarah P. , Issa Nicolas C. , Madan Rachna , Gill Ritu R. , Milner Danny A. , Colson Yolonda L. , Koo Sophia , Baden Lindsey R. , Marty Francisco M.
Published: April 2014

Mucormycosis is a life-threatening fungal disease in patients with hematological malignancies. The diagnosis of pulmonary mucormycosis is particularly challenging. We describe 3 mucormycosis cases with an uncommon presentation in patients whose cavitary lung disease was attributed to well documented bacterial infection, although evolution and reassessment established mucormycosis as the underlying disease.
Multisite Laboratory Evaluation of a Dual Human Immunodeficiency Virus (HIV)/Syphilis Point-of-Care Rapid Test for Simultaneous Detection of HIV and Syphilis Infection
Authors: Bristow Claire C. , Adu-Sarkodie Yaw , Ondondo Raphael O. , Bukusi Elizabeth Anne , Dagnra Claver Anoumou , Oo Khin Yi , Pe Eh Htoo , Khamsay Chanthavysouk , Houng Le Thi , Campuzano Roberto Vázquez , Estes Jason , Klausner Jeffrey D.
Published: April 2014

Background.  Recently, test developers have created rapid point-of-care tests that can simultaneously detect multiple infections within the same specimen using a single device. The SD BIOLINE Duo HIV/Syphilis rapid point-of-care test uses a solid-phase immunochromatographic assay to detect immunoglobulin (Ig)G, IgM, and IgA antibodies to human immunodeficiency virus (HIV)-specific antigens (HIV-1 gp41, sub O, HIV-2 gp36) and recombinant Treponema pallidum antigen (17 kDa) in human serum. This study was a multisite laboratory-based evaluation of the performance of SD BIOLINE HIV/Syphilis Duo test using previously characterized sera in 6 countries.

Methods.  Laboratories in Ghana, Mexico, Laos, Togo, Kenya, and Myanmar participated in the evaluation during 2012–2013. Each site characterized sera using T pallidum particle agglutination assay or T pallidum hemagglutination assay and HIV enzyme immunoassay, Western blot, and/or HIV antibody rapid tests. Those gold standard test results were compared with SD BIOLINE Duo test results. We calculated the sensitivity and specificity of test performance and used the exact binomial method to calculate 95% confidence intervals (CIs).

Results.  The sensitivity and specificity for the HIV antibody test component (n = 2336) were estimated at 99.91% (95% CI, 99.51% and 100%) and 99.67% (95% CI, 99.16% and 99.91%), respectively. For the T pallidum test component (n = 2059), the sensitivity and specificity were estimated at 99.67% (95% CI, 98.82% and 99.96%) and 99.72% (95% CI, 99.29% and 99.92%), respectively.

Conclusions.  The sensitivity and specificity of the SD BIOLINE HIV/Syphilis Duo test were consistently high across sera specimens from 6 countries around the world. Dual rapid tests should be considered for improved HIV and syphilis screening coverage.
Safety Profile of the Merck Human Immunodeficiency Virus-1 Clade B gag DNA Plasmid Vaccine With and Without Adjuvants
Authors: Quirk Erin K. , Brown Elizabeth L. , Leavitt Randi Y. , Mogg Robin , Mehrotra Devan V. , Evans Robert K. , DiNubile Mark J. , Robertson Michael N.
Published: April 2014

The immunogenicity results from 3 phase I trials of the Merck DNA human immunodeficiency virus (HIV) vaccine have previously been reported. Because preventive DNA vaccine strategies continue to be leveraged for diverse infections, the safety and tolerability results from these studies can inform the field moving forward, particularly regarding adverse reactions and adjuvants. No serious vaccine-related adverse events were reported during the 3-dose priming phase. Pain at the injection site was more common with adjuvanted formulations than with the phosphate-buffered saline diluent alone. Febrile reactions were usually low grade. Although the AlPO4 or CRL1005 adjuvants used in these studies did not significantly enhance the immunogenicity of the DNA vaccine, adverse events were numerically more common with adjuvanted formulations than without adjuvants.
Genome-Wide Association Study of Human Immunodeficiency Virus (HIV)-1 Coreceptor Usage in Treatment-Naive Patients from An AIDS Clinical Trials Group Study
Authors: Henrich Timothy J. , McLaren Paul J. , Rao Suhas S. P. , Lin Nina H. , Hanhauser Emily , Giguel Francoise , Gulick Roy M. , Ribaudo Heather , de Bakker Paul I. W. , Kuritzkes Daniel R.
Published: April 2014

Objectives.  We conducted a genome-wide association study to explore whether common host genetic variants (>5% frequency) were associated with presence of virus able to use CXCR4 for entry.

Methods.  Phenotypic determination of human immunodeficiency virus (HIV)-1 coreceptor usage was performed on pretreatment plasma HIV-1 samples from treatment-naive participants in AIDS Clinical Trials Group A5095, a study of initial antiretroviral regimens. Associations between genome-wide single-nucleotide polymorphisms (SNPs), CCR5 Δ32 genotype, and human leukocyte antigen (HLA) class I alleles and viral coreceptor usage were explored.

Results.  Viral phenotypes were obtained from 593 patients with available genome-wide SNP data. Forty-four percent of subjects had virus capable of using CXCR4 for entry as determined by phenotyping. Overall, no associations, including those between polymorphisms in genes encoding viral coreceptors and their promoter regions or in HLA genes previously associated with HIV-1 disease progression, passed the statistical threshold for genome-wide significance (P < 5.0 × 10−8) in any comparison. However, the presence of viruses able to use CXCR4 for entry was marginally associated with the CCR5 Δ32 genotype in the nongenome-wide analysis.

Conclusions.  No human genetic variants were significantly associated with virus able to use CXCR4 for entry at the genome-wide level. Although the sample size had limited power to definitively exclude genetic associations, these results suggest that host genetic factors, including those that influence coreceptor expression or the immune pressures leading to viral envelope diversity, are either rare or have only modest effects in determining HIV-1 coreceptor usage.
Urinalysis in Acute Care of Adults: Pitfalls in Testing and Interpreting Results
Authors: Pallin Daniel J. , Ronan Clare , Montazeri Kamaneh , Wai Katherine , Gold Allen , Parmar Siddharth , Schuur Jeremiah D.
Published: April 2014

Background.  Rapid urine tests for infection (urinalysis, dipstick) have low up-front costs. However, many false positives occur, with important downstream consequences, including unnecessary antibiotics. We studied indications, collection technique, and results of urinalyses in acute care.

Methods.  This research was a prospective observational study of a convenience sample of emergency department (ED) patients who had urinalysis performed between June 1, 2012 and February 15, 2013 at an urban teaching hospital. Analyses were conducted via t tests, χ2 tests, and multivariable logistic regression.

Results.  Of 195 cases included in the study, the median age was 56 and 70% of participants were female. There were specific symptoms or signs of urinary tract infection (UTI) in 74 cases (38%; 95% confidence interval [CI], 31%–45%), nonspecific symptoms or signs in 83 cases (43%; 95% CI, 36%–50%), and no symptoms or signs of UTI in 38 cases (19%; 95% CI, 14%–25%). The median age was 51 (specific symptoms), 58 (nonspecific symptoms), and 61 (no symptoms), respectively (P = .005). Of 137 patients who produced the specimen without assistance, 78 (57%; 95% CI, 48%–65%) received no instructions on urine collection. Correct midstream clean-catch technique was used in 8 of 137 cases (6%). Presence of symptoms or signs was not associated with a new antibiotic prescription, but positive urinalysis (OR, 4.9; 95% CI, 1.7–14) and positive urine culture (OR, 3.6; 95% CI, 1.1–12) were. Of 36 patients receiving antibiotics, 10 (28%; 95% CI, 13%–43%) had no symptoms or nonspecific symptoms.

Conclusion.  In this sample at an urban teaching hospital ED, urine testing was not driven by symptoms. Improving practice may lower costs, improve efficiency of care, decrease unnecessary data that can distract providers and impair patient safety, decrease misdiagnosis, and decrease unnecessary antibiotics.
Spinal and Paraspinal Fungal Infections Associated With Contaminated Methylprednisolone Injections
Authors: Moudgal Varsha , Singal Bonita , Kauffman Carol A. , Brodkey Jason A. , Malani Anurag N. , Olmsted Russell N. , Kasotakis Michael J. , Koch Spencer R. , Kaakaji Rami , Nyaku Mawuli , Neelakanta Anupama , Valenstein Paul , Winter Suzanne , Otto Michael , Jagarlamudi Rajasekhar , Kerr Lisa , Czerwinski Jennifer , Vandenberg David , Sutton Suzanne R. , Murphy Holly , Halasyamani Lakshmi K.
Published: April 2014

Background.  A nationwide outbreak of fungal infections was traced to injection of Exserohilum-contaminated methylprednisolone. We describe our experience with patients who developed spinal or paraspinal infection after injection of contaminated methylprednisolone.

Methods.  Data were assembled from the Michigan Department of Community Health, electronic medical records, and magnetic resonance imaging (MRI) reports.

Results.  Of 544 patients who received an epidural injection from a contaminated lot of methylprednisolone at a pain clinic in southeastern Michigan, 153 (28%) were diagnosed at our institution with probable or confirmed spinal or paraspinal fungal infection at the injection site. Forty-one patients had both meningitis and spinal or paraspinal infection, and 112 had only spinal or paraspinal infection. Magnetic resonance imaging abnormalities included abscess, phlegmon, arachnoiditis, and osteomyelitis. Surgical debridement in 116 patients revealed epidural phlegmon and epidural abscess most often. Among 26 patients with an abnormal MRI but with no increase or change in chronic pain, 19 (73%) had infection identified at surgery. Fungal infection was confirmed in 78 patients (51%) by finding hyphae in tissues, positive polymerase chain reaction, or culture. Initial therapy was voriconazole plus liposomal amphotericin B in 115 patients (75%) and voriconazole alone in 38 patients (25%). As of January 31, 2014, 20 patients remained on an azole agent. Five patients died of infection.

Conclusions.  We report on 153 patients who had spinal or paraspinal fungal infection at the site of epidural injection of contaminated methylprednisolone. One hundred sixteen (76%) underwent operative debridement in addition to treatment with antifungal agents.
Innate Immune Responses after Resection for Lung Cancer via Video-Assisted Thoracoscopic Surgery and Thoracotomy
Authors: Jones Richard O. , Anderson Niall H. , Murchison John T. , Brittan Mairi , Simon Ellis J. , Casali Gianluca , Simpson A. John , Walker William S.
Published: April 2014

Objective

Innate immune responses to pulmonary resection may be critical in the pathogenesis of important postoperative pulmonary complications and potentially longer-term survival. We sought to compare innate immunity of patients undergoing major pulmonary resection for bronchogenic carcinoma via video-assisted thoracoscopic surgery (VATS) and thoracotomy.

Methods

Bronchoalveolar lavage was conducted in the contralateral lung before staging bronchoscopy and mediastinoscopy and immediately after lung resection. Blood and exhaled nitric oxide were sampled preoperatively and at 6, 24, and 48 hours postoperatively.

Results

Forty patients were included (26 VATS and 14 thoracotomy). There was a lower systemic cytokine response from lung resection undertaken by VATS compared with thoracotomy [interleukin 6 (IL-6), analysis of variance (ANOVA) P = 0.026; IL-8, ANOVA P = 0.018; and IL-10, ANOVA P = 0.047]. The VATS patients had higher perioperative serum albumin levels (ANOVA P = 0.001). Lower levels of IL-10 were produced by lipopolysaccharide-stimulated blood monocytes from the VATS patients compared with the thoracotomy patients at 6 hours postoperatively (geometric mean ratio, 1.16; 95% confidence interval, 1.08–1.33; P = 0.011). No statistically significant differences in the neutrophil phagocytic capacity, overall leukocyte count, or differential leukocyte count were found between the surgical groups (ANOVA P > 0.05). No statistically significant differences in bronchoalveolar lavage fluid parameters were found. Exhaled nitric oxide levels fell postoperatively, which reached statistical significance at 48 hours (geometric mean ratio, 1.2; 95% confidence interval, 1.02–1.46; P = 0.029). There were no significant differences found between the surgical groups (ANOVA P = 0.331).

Conclusions

Overall, a trend toward greater proinflammatory and anti-inflammatory responses is seen with lung resection performed via thoracotomy compared with VATS.
Exact Reconstruction of Gene Regulatory Networks using Compressive Sensing
Authors: Chang Young Hwan , Gray Joe W. , Tomlin Claire J.
Published: April 2014

Background: We consider the problem of reconstructing a gene regulatory network structure from limited time series gene expression data, without any a priori knowledge of connectivity. We assume that the network is sparse, meaning the connectivity among genes is much less than full connectivity. We develop a method for network reconstruction based on compressive sensing, which takes advantage of the network's sparseness. Results: For the case in which all genes are accessible for measurement, and there is no measurement noise, we show that our method can be used to exactly reconstruct the network. For the more general problem, in which hidden genes exist and all measurements are contaminated by noise, we show that our method leads to reliable reconstruction. In both cases, coherence of the model is used to assess the ability to reconstruct the network and to design new experiments. For each problem, a set of numerical examples is presented. Conclusions: The method provides a guarantee on how well the inferred graph structure represents the underlying system, reveals deficiencies in the data and model, and suggests experimental directions to remedy the deficiencies.
Severed stems of Amaranthus palmeri are capable of regrowth and seed production in Gossypium hirsutum
Authors: Sosnoskie L.M. , Webster T.M. , Grey T.L. , Culpepper A.S.
Published: April 2014

Field studies were conducted to evaluate the capacity of Amaranthus palmeri to grow and reproduce following incomplete physical control in Gossypium hirsutum fields. A. palmeri plants that emerged simultaneously with a G. hirsutum crop were selected for use. Treatments included severing the main stem of flowering plants at heights of 0, 3 and 15 cm above the soil level. A non‐cut/intact control, in which the apical meristem was not removed, was also included. Six weeks after treatment, intact A. palmeri plants had grown to a mean height of 210 cm (SE = 38) and produced 477 408 (SE = 81 250) seeds per plant. Thirty‐five percent of the A. palmeri plants cut back to a height of 15 cm above the soil level did not recover from the treatment; survivors regrew to a mean height of 102 cm (51% reduction, compared to intact plants) and produced 116 000 seeds per plant (73% reduction). A. palmeri plants cut to 3 cm above the soil level had a mortality rate of 64%, an 82% reduction in final plant height, and produced 28 000 seeds per plant. When stems were severed at the soil surface, plant mortality was 95%; final plant height and seed production of survivors were reduced by 95 and 99%, respectively, relative to the control. G. hirsutum seeded yields exceeded 3 t ha−1 when A. palmeri plants were cut back to at least 15 cm, whereas yield was reduced 50% in the control treatment, where A. palmeri growth was not interrupted by cutting. In conclusion, while there is immediate benefit of removing A. palmeri plants in terms of G. hirsutum yield, incomplete stem removal can have multi‐season implications. Results demonstrate that severely pruned A. palmeri plants can resume growth, reach reproductive maturity and produce viable seed, which have the potential to repopulate soil seedbanks.
Transcobalamin II (TCN2 67A>G and TCN2 776C>G) and Transcobalamin II Receptor (TCblR 1104C>T) Polymorphisms in Korean Patients with Idiopathic Recurrent Spontaneous Abortion
Authors: Kim Hyun Seok , Lee Bo Eun , Jeon Young Joo , Rah HyungChul , Lee Woo Sik , Shin Ji Eun , Choi Dong Hee , Kim Nam Keun
Published: April 2014

Problem

The transcobalamin II (TCN2) 776C>G polymorphism has been reported to be a genetic risk factor for idiopathic recurrent spontaneous abortion (RSA). However, the sample size in previous studies was small, and other TCN2 polymorphisms have not been studied. Moreover, the TCN2 67A>G and 776C>G polymorphisms, and the transcobalamin II receptor (TCblR/CD320) 1104C>T polymorphism, have demonstrated associations with immune responses.

Method of study

Three hundred and seventy‐eight RSA patients who had at least two consecutive spontaneous abortions were enrolled. Two hundred and seven control subjects were collected from a convenience sample. Polymerase chain reaction and restriction fragment length polymorphism analysis were performed to identify the TCN2 67A>G and 776C>G polymorphisms, and the TCblR 1104C>T polymorphism.

Results

RSA patients showed significantly different frequencies of the TCN2 67AG+GG genotypes compared with control subjects.

Conclusion

The TCN2 67G allele is a possible risk factor for idiopathic RSA.
A pilot study of cerebral tissue oxygenation and postoperative cognitive dysfunction among patients undergoing coronary artery bypass grafting randomised to surgery with or without cardiopulmonary bypass*
Authors: Kok W. F. , van Harten A. E. , Koene B. M. J. A. , Mariani M. A. , Koerts J. , Tucha O. , Absalom A. R. , Scheeren T. W. L.
Published: April 2014

Coronary artery bypass surgery, performed with or without cardiopulmonary bypass, is frequently followed by postoperative cognitive decline. Near‐infrared spectroscopy is commonly used to assess cerebral tissue oxygenation, especially during cardiac surgery. Recent studies have suggested an association between cerebral desaturation and postoperative cognitive dysfunction. We therefore studied cerebral oxygen desaturation, defined as area under the cerebral oxygenation curve < 40% of > 10 min.%, with respect to cognitive performance at 4 days (early) and 3 months (late) postoperatively, compared with baseline, using a computerised cognitive test battery. We included 60 patients, of mean (SD) age 62.8 (9.4) years, scheduled for elective coronary artery bypass grafting, who were randomly allocated to surgery with or without cardiopulmonary bypass. Cerebral desaturation occurred in only three patients and there was no difference in cerebral oxygenation between the two groups at any time. Among patients who received cardiopulmonary bypass, 18 (62%) had early cognitive decline, compared with 16 (53%) in the group without cardiopulmonary bypass (p = 0.50). Three months after surgery, 11 patients (39%) in the cardiopulmonary bypass group displayed cognitive dysfunction, compared with four (14%) in the non‐cardiopulmonary bypass group (p = 0.03). The use of cardiopulmonary bypass was identified as an independent risk factor for the development of late cognitive dysfunction (OR 6.4 (95% CI 1.2–33.0) p = 0.027. In conclusion, although cerebral oxygen desaturation was rare in our population, postoperative cognitive decline was common in both groups, suggesting that factors other than hypoxic neuronal injury are responsible.
The α3β4* nicotinic ACh receptor subtype mediates physical dependence to morphine: mouse and human studies
Authors: Muldoon P P , Jackson K J , Perez E , Harenza J L , Molas S , Rais B , Anwar H , Zaveri N T , Maldonado R , Maskos U , McIntosh J M , Dierssen M , Miles M F , Chen X , De Biasi M , Damaj M I
Published: April 2014

Background and Purpose

Recent data have indicated that α3β4* neuronal nicotinic (n) ACh receptors may play a role in morphine dependence. Here we investigated if nACh receptors modulate morphine physical withdrawal.

Experimental Approaches

To assess the role of α3β4* nACh receptors in morphine withdrawal, we used a genetic correlation approach using publically available datasets within the GeneNetwork web resource, genetic knockout and pharmacological tools. Male and female European‐American (n = 2772) and African‐American (n = 1309) subjects from the Study of Addiction: Genetics and Environment dataset were assessed for possible associations of polymorphisms in the 15q25 gene cluster and opioid dependence.

Key Results

BXD recombinant mouse lines demonstrated an increased expression of α3, β4 and α5 nACh receptor mRNA in the forebrain and midbrain, which significantly correlated with increased defecation in mice undergoing morphine withdrawal. Mice overexpressing the gene cluster CHRNA5/A3/B4 exhibited increased somatic signs of withdrawal. Furthermore, α5 and β4 nACh receptor knockout mice expressed decreased somatic withdrawal signs compared with their wild‐type counterparts. Moreover, selective α3β4* nACh receptor antagonists, α‐conotoxin AuIB and AT‐1001, attenuated somatic signs of morphine withdrawal in a dose‐related manner. In addition, two human datasets revealed a protective role for variants in the CHRNA3 gene, which codes for the α3 nACh receptor subunit, in opioid dependence and withdrawal. In contrast, we found that the α4β2* nACh receptor subtype is not involved in morphine somatic withdrawal signs.

Conclusion and Implications

Overall, our findings suggest an important role for the α3β4* nACh receptor subtype in morphine physical dependence.
Growth of Social Competence During the Preschool Years: A 3‐Year Longitudinal Study
Authors: Santos António J. , Vaughn Brian E. , Peceguina Inês , Daniel João R. , Shin Nana
Published: April 2014

This study examined the stability and growth over a 3‐year period of individual differences in preschool children's social competence, which was assessed in three domains: social engagement/motivation, profiles of behavior and personality attributes characteristic of socially competent young children, and peer acceptance. A total of 255 children (126 girls and 129 boys) participated in this study. Growth curve analyses demonstrated both stability and change with regard to social competence over early childhood. Social competence measures and latent variables were invariant over this time period, individual differences in social competence were largely stable from year to year, and significant increases over time were observed for the domain most closely reflective of specific personal attributes skills.
Self‐cleaning Bombyx mori silk: room‐temperature preparation of anatase nano‐TiO2 by the sol–gel method and its application
Authors: Zheng Chenghui , Qi Zhenming , Shen Wenchao , Chen Guoqiang
Published: April 2014

The aim of this work was to obtain anatase nano‐TiO2 by the sol–gel method at room temperature and to achieve self‐cleaning Bombyx mori silk fabrics. Nano‐TiO2 sols based on an aqueous system and an ethanol system were prepared separately by the sol–gel method using tetrabutyl orthotitanate as a precursor at room temperature. Particle size analyses showed that nano‐TiO2 particles in an aqueous system were much bigger and more variant than those in ethanol. X‐ray diffraction patterns revealed a pure anatase phase of nano‐TiO2 in an aqueous system. Crystalline transformation of TiO2 from anatase to rutile by photoradiation at ambient temperature was also proved. Thermogravimetric and differential scanning calorimetric analyses confirmed the phase transformation of nano‐TiO2. A scanning electron microscope equipped with an energy‐dispersive spectrometer was used to investigate the surface morphology and elements of Bombyx mori silk fabrics. The contact angles with water, the kinetics of photocatalytic degradation of Methylene Blue, and decontamination of red‐wine‐stained fabrics under ultraviolet radiation demonstrated that the fabrics had good self‐cleaning properties and photoinduced hydrophilicity.
My Sisters Will Not Speak: Boas, Hunt, and the Ethnographic Silencing of First Nations Women
Authors: Bruchac Margaret M.
Published: April 2014

First Nations women were instrumental to the collecting of Northwest Coast Indigenous culture, yet their voices are nearly invisible in the published record. The contributions of George Hunt, the Tlingit/British culture broker who collaborated with anthropologist Franz Boas, overshadow the intellectual influence of his mother, Anislaga Mary Ebbetts, his sisters, and particularly his Kwakwaka'wakw wives, Lucy Homikanis and Tsukwani Francine ‘Nakwaxda'xw. In his correspondence with Boas, Hunt admitted his dependence upon high‐status Indigenous women, and he gave his female relatives visual prominence in film, photographs, and staged performances, but their voices are largely absent from anthropological texts. Hunt faced many unexpected challenges (disease, death, arrest, financial hardship, and the suspicions of his neighbors), yet he consistently placed Boas' demands, perspectives, and editorial choices foremost. The resulting cultural representations marginalized the influence of the First Nations women who had been integral to their creation.
Ornithologists in Olman: Epistemological Ecologies in the Field and the Museum
Authors: Kett Robert J.
Published: April 2014

This article examines scientific activities surrounding a series of excavations of Olmec archaeological sites in the 1930s and 1940s. These excavations were the first to concertedly explore areas of Tabasco and Veracruz, Mexico that would come to be called Olman. These sites were the locus of various collecting activities including the unearthing of monuments and systematic studies of stratigraphies and ceramic sequences, as well as the gathering of ornithological specimens from an underexplored region. Through publications inNational Geographicmagazine and elsewhere, scientists would introduce Olman to wider scientific and popular audiences. This article explores this history in order to understand scientists’ attempts to make sense of a new region as they documented the Olmec and Olman's fauna. These collaborative scientific practices underline the need for ecological attention to how disciplinary knowledge‐making practices interact during field research, an argument that is extended in a consideration of museum collections architectures.
Life Histories and Dynamic Objects: The Klasies River Mouth Collection
Authors: Pyne Lydia
Published: April 2014

Klasies River Mouth, a Middle Stone Age archaeological site along the southern coast of South Africa, has long held an iconic status within the field of archaeology, for many reasons. In the four decades since its original excavation, the site's artifact collection has demonstrated dynamic characteristics as the artifacts are analyzed, interpreted, and reinterpreted. The site and its collection became a standard (both scientifically and culturally) for comparing other Middle Stone Age sites. The collection, however, does more than just provide a comparative sample for archaeologists. The collection is a way to trace identity and shifting methodological and theoretical paradigms for Pleistocene archaeology. The life history of Klasies River Mouth pairs the physical materiality of the collection with its subsequent cultural (and disciplinary) cachet.
Returning the tataayiyam honuuka' (Ancestors) to the Correct Home: The Importance of Background Investigations for NAGPRA Claims
Authors: Martinez Desireé R. , Teeter Wendy G. , Kennedy‐Richardson Karimah
Published: April 2014

The Native American Graves Protection and Repatriation Act (NAGPRA) claims process can be frustrating for Native American communities due to hindrances such as the lack of provenience and provenance of collections. Through historic research on and preliminary analysis of Santa Catalina Island archaeological collections assembled by Ralph Glidden and held by museums across the United States, the authors have discovered that much of the documented provenience and provenance information is missing, wrong, or at best more complicated than previously thought. The authors assert that background research of collections is imperative to ensure that ancestral remains are returned to the appropriate lineal descendants or Native American descendant community. Further, the Glidden collections show that disputed provenience and provenance information has massive implications for NAGPRA claims made by non‐federally recognized tribes, such as the Gabrielino/Tongva, the Indigenous inhabitants of Santa Catalina and the Los Angeles Basin.
When Remains are “Lost”: Thoughts on Collections, Repatriation, and Research in American Physical Anthropology
Authors: Kakaliouras Ann M.
Published: April 2014

Repatriation has been a practical reality for physical anthropology since the passage of NAGPRA in 1990. Even so, discourse in the professional literature regarding what to do about the loss of human skeletal remains has largely been limited to the development of standards for osteological data collection. This article explores the concept of “loss” in physical anthropology in the context of repatriation, reviews the history of how physical anthropologists have conceptually approached skeletal collections housed in museums and universities, and examines alternative ways in which physical anthropologists may pursue research on collections of human remains, beyond their use in the reconstruction of past human behavior and population adaptations. By moving beyond a unitary idea about the use—and loss—of human skeletal remains, physical anthropologists may be able to foster more productive partnerships with descendant communities.
Lost in Museums: The Ethical Dimensions of Historical Practices of Anthropological Specimen Exchange
Authors: Nichols Catherine A.
Published: April 2014

The exchange of anthropological objects by museums in the nineteenth and twentieth centuries involved circulation of Indigenous material culture and human remains beyond the institution in which collections were originally accessioned. This paper traces the biography of a Hopi sacred object collected by the Bureau of American Ethnology in 1879 from the Smithsonian Institution to the Musée d'Ethnographie du Trocadéro in 1885 in order to highlight the ethical implications of how historical practices of specimen exchange affect knowledge about and contemporary access to museum objects. Analysis of specimen exchange emphasizes how the aims and actions of curators contribute to the dynamic nature of museum collections.
Contemporary Museum Policies and the Ethics of Accepting Human Remains
Authors: Edgar Heather J.H. , Rautman Anna L.M.
Published: April 2014

The Maxwell Museum of Anthropology has a policy of accepting all offered human remains into its collections. These remains come from law enforcement agencies and private persons. By accepting Native American and other human remains, the museum assumes all associated legal, ethical, and financial obligations, including complying with NAGPRA regulations and state laws regarding archaeological human remains. However, many museums are ill equipped to accept responsibility for—or have policies against—accepting human remains. There are costs and benefits associated with accepting human remains and associated objects that each museum must consider. We explain the perspective of the Maxwell Museum in its continuing policy of accepting human remains and NAGPRA objects, and explore the consequences of that decision. We also present the results of a survey concerning museums' policies on and experiences with accepting new collections of human remains and artifacts.
Collecting Human Subjects: Ethics and the Archive in the History of Science and the Historical Life Sciences
Authors: Radin Joanna
Published: April 2014

Anthropological collectors have long engaged in “salvage”—the attempt to metaphorically freeze those artifacts, traditions, and languages in danger of disappearing. Beginning in the 1960s, in an effort to establish global baselines of biological variation, biological anthropologists and human geneticists emphasized the importance of salvaging blood samples from Indigenous peoples whose survival they considered to be endangered by the corrosive forces of modernity. This paper focuses on the collection practices of Jonathan Friedlaender, who was a Ph.D. student in biological anthropology at Harvard when he took his first blood samples in 1966. Eventually, Friedlaender began to salvage materials from his own career, assembling an archive that would ultimately be deposited at the American Philosophical Society in Philadelphia. The archive would become part of a “collection of anthropologists,” out of which current and future historians might seek to make sense of the collections they made of other people.
Large Scale Collections of Biological Material and Ethical First Principles
Authors: Turner Trudy R.
Published: April 2014

Collecting and storing research materials is within the purview of all anthropologists. The establishment of collections, especially the large new biobanks of biological materials, requires an examination of the ways in which ethical first principles of autonomy, beneficence, and justice integrate with the goals and scientific aims of the collection. This article presents an example of the establishment of a repository of material for vervet monkeys (Chlorocebus sensu lato) and the ways in which informed consent, ownership of materials, and data sharing were considered in the establishment of the repository. Concepts of stewardship, derived from museum studies, are provided as an example of the way in which collections are currently regarded and maintained.
Predicting mortality in people with Type 2 diabetes mellitus after major complications: a study using Swedish National Diabetes Register data
Authors: Kelly P. J. , Clarke P. M. , Hayes A. J. , Gerdtham U.‐G. , Cederholm J. , Nilsson P. , Eliasson B. , Gudbjornsdottir S.
Published: April 2014

Aim

To predict mortality risk and life expectancy for patients with Type 2 diabetes after a major diabetes‐related complication.

Methods

The study sample, taken from the Swedish National Diabetes Register, consisted of 20 836 people with Type 2 diabetes who had their first major complication (myocardial infarction, stroke, heart failure, amputation or renal failure) between January 2001 and December 2007. A Gompertz proportional hazards model was derived which determined significant risk factors associated with mortality and was used to estimate life expectancies.

Results

Risk of death changed over time according to type of complication, with myocardial infarction initally having the highest initial risk of death, but after the first month, the risk was higher for heart failure, renal failure and amputation. Other factors that increased the risk of death were male gender (hazard ratio 1.06, 95% CI 1.02–1.12), longer duration of diabetes (hazard ratio 1.07 per 10 years, 95% CI 1.04–1.10), smoking (hazard ratio 1.51, 95% CI 1.40–1.63) and macroalbuminuria (hazard ratio 1.14, 95% CI 1.06–1.22). Low BMI, low systolic blood pressure and low estimated GFR also increased mortality risk. Life expectancy was highest after a stroke, myocardial infarction or heart failure, lower after amputation and lowest after renal failure. Smoking and poor renal function were the risk factors which had the largest impact on reducing life expectancy.

Conclusions

Risk of death and life expectancy differs substantially among the major complications of diabetes, and factors significantly increasing risk included smoking, low estimated GFR and albuminuria.
Comparison of different aspects of BMI history to identify undiagnosed diabetes in Japanese men and women: Toranomon Hospital Health Management Center Study 12 (TOPICS 12)
Authors: Yoshizawa S. , Heianza Y. , Arase Y. , Saito K. , Hsieh S. D. , Tsuji H. , Hanyu O. , Suzuki A. , Tanaka S. , Kodama S. , Shimano H. , Hara S. , Sone H.
Published: April 2014

Aims

To examine current BMI and various aspects of BMI history as pre‐screening tools for undiagnosed diabetes in Japanese individuals.

Methods

This cross‐sectional study included 16 226 men and 7026 women aged 30–75 years without a self‐reported history of clinician‐diagnosed diabetes. We estimated the probability of having undiagnosed diabetes (fasting glucose ≥ 7.0 mmol/l and/or HbA1c ≥ 48 mmol⁄mol (≥ 6.5%) for the following variables: current BMI, BMI in the early 20s (BMI20y), lifetime maximum BMI (BMImax), change between BMI in the early 20s and current BMI (ΔBMI20y−cur), change between BMI in the early 20s and maximum BMI (ΔBMI20y−max), and change between lifetime maximum and current BMI (ΔBMImax−cur).

Results

The prevalence of undiagnosed diabetes was 3.3% (771/23252) among participants. BMImax, ΔBMI20y–max and current BMI (1‐sd increments) were more strongly associated with diabetes than the other factors (multivariate odds ratio 1.58 [95% CI 1.47–1.70] in men and 1.65 [95% CI 1.43–1.90] in women for BMImax; multivariate odds ratio 1.47 [95% CI 1.37–1.58] in men and 1.61 [95% CI 1.41–1.84] in women for ΔBMI20y–max; multivariate odds ratio 1.47 [95% CI 1.36–1.58] in men and 1.63 [95% CI 1.40‐1.89] in women for current BMI). The probability of having diabetes was markedly higher in those with both the highest tertile of BMImax and greatest ΔBMI20y‐max; however, a substantially lower likelihood of diabetes was observed among individuals with the lowest and middle tertiles of current BMI (< 24.62 kg/m2 in men and < 22.54 kg/m2 in women).

Conclusions

Lifetime maximum BMI and BMI changes from early adulthood were strongly associated with undiagnosed diabetes. Adding BMI history to people's current BMI would improve the identification of individuals with a markedly higher probability of having undiagnosed diabetes.
The Context of Social Capital: A Comparison of Rural and Urban Entrepreneurs in Uganda
Authors: Rooks Gerrit , Klyver Kim , Sserwanga Arthur
Published: April 2014

Classical network theory states that social networks are a form of capital because they provide access to resources. In this article, we propose that network effects differ between collectivistic and individualistic contexts. In a collectivistic context, resource sharing will be “value based.” It is expected that members of a group support each other and share resources. In contrast, in an individualistic context, resource sharing will be more often based on reciprocity and trust. Hence, we hypothesized that networks will be more beneficial in individual contexts compared with collectivistic context. We found partial support for our hypotheses.
Abundance–occupancy relationships of larval black flies (Diptera: Simuliidae) in temperate Nearctic streams
Authors: McCreadie John W. , Adler Peter H.
Published: April 2014

This study examines abundance–occupancy relationships of larval black flies in temperate streams of the south‐eastern United States. It is the first study of abundance–occupancy relationships in lotic macro‐invertebrate assemblages to focus on a single family. We address the following questions: (i) Do larval black flies show a strong inter‐specific abundance–occupancy relationship? (ii) Do widespread and abundant species demonstrate greater niche breadth (NB) or niche position (NP) than do species with limited distributions and low local abundances? (iii) Does the abundance–occupancy relationship change between habitat generalists and specialists?

Species abundance was measured as the total mean relative abundance over all sites. Three measures of occupancy were used: occurrence (number of sites occupied), latitudinal extent of occupancy, and longitudinal extent of occupancy. Niche‐based indices (breadth and position) were expressed as multivariate indices of habitat variables, reflecting variation in the niche of a species, as opposed to a simple range.

Non‐ecological factors (sampling, analytical artefacts, phylogenetic non‐independence) accounted for our results and, accordingly, we focus on ecological explanations of inter‐specific abundance–occupancy relationships, grounded in niche and meta‐population theory. When occupancy was measured as the number of sites at which a species occurred, a strong inter‐specific abundance–occupancy relationship was found. Niche‐based indices did not have a significant influence on shaping this relationship. When occupancy was measured as geographic extent, the abundance–occupancy relationship was weak or non‐significant, although niche‐based indices had a significant effect on occupancy. No evidence supported the notion that meta‐population dynamics influence abundance–occupancy relationships. Abundance–occupancy relationship is a summation of individual species traits, a point that often receives little attention.
A nurse–family partnership intervention to increase the self‐efficacy of family caregivers and reduce catheter‐associated urinary tract infection in catheterized patients
Authors: Lee Kwo‐Chen , Chao Yann‐Fen C , Wang Yueh‐Mien , Lin Pi‐Chu
Published: April 2014

The purpose of this study was to evaluate the effects of a nurse–family partnership model on the self‐efficacy of family caregivers (FCs) and the incidence of catheter‐associated urinary tract infection (CAUTI) among patients. A randomized controlled study was conducted. We recruited 61 patients and their FCs, who were randomly divided into an experimental group (n = 30) and a control group (n = 31). In the experimental group, the main caregivers comprised a nurse–family partnership, whereas the control participants received routine care. The findings were as follows: (i) the incidence of CAUTI was lower in the experimental group than in the control group (20% vs. 38.8%), but the difference was not statistically significant; and (ii) no significant difference emerged for reported Caregiver Self‐Efficacy Score between the two groups. The nursing team and FCs must become partners in cooperative caregiving to enhance the quality of patient care.
Invisible Disabilities: Unique Challenges for Employees and Organizations
Authors: Santuzzi Alecia M. , Waltz Pamela R. , Finkelstein Lisa M. , Rupp Deborah E.
Published: April 2014

Workers with invisible disabilities encounter unique challenges compared to workers with other concealable identities and even workers with visible disabilities. These challenges occur not only in the decisions of whether to disclose the invisible disability in the workplace but also in the detection and acceptance of having a disability to disclose. Disclosure of disabilities in the workplace likely has implications for the individual worker's health, social relationships, and work performance as well as for an employing organization's outcomes. We argue that current legislation and policies might not be sensitive to the unique experiences and disclosure decisions faced by workers with invisible disabilities. We invite researchers and practitioners to consider adjustments to current legislation and workplace practices in order for employing organizations to account for the unique challenges facing workers with invisible disabilities and fully accommodate those workers.