bluuebunny/crossref_metadata_2025_split huggingface dataset:
The myths and realities in the management of the Kapenta fishery at Lake Kariba (Zimbabwe)
Authors: Nyikahadzoi Kefasi , Raakjær Jesper 
Published: March 2014

AbstractBiological considerations have dominated the management of the Kapenta fishery since its inception. State fisheries' managers employed the traditional scientific models that proved useful in managing temperate fisheries. This study uses both secondary and primary data to discuss the problems of using scientific models to manage tropical river‐fed lakes. Where fish stock size fluctuates in response to environmental factors such as river flows and lake level (which influence the level of nutrients in the water body), the concepts of maximum sustainable yield (MSY) and maximum economic yield (MEY) become problematic. This study demonstrated that, in an unstable environment, and where the target species is resilient to high levels of fishing effort, biological models lose their predictive power, allowing the state to determine the proportion of the resource to be distributed among its nationals. The redistribution of access rights or fishing licences (as a way of redressing a legacy of an unequal distribution of resources between emerging local entrepreneurs and companies established during the colonial era) is a major management issue in Zimbabwe. This study uses historical appraisal to illustrate how biological growth models failed to determine the optimal level of fishery exploitation upon which informed decisions could be made regarding whether to redistribute fish access rights or to broaden participation (or just recruit more fishers into the industry). This study also investigates tensions between the industry (advocating for broadening of access) and the state (seeking to redistribute existing resource use rights). Each stakeholder group has evoked institutions and discourses supporting their positions in influencing the strategies to eliminate the existing imbalances.
Aspergillus tracheobronchitis in critically ill patients with chronic obstructive pulmonary diseases
Authors: He Hangyong , Jiang Shan , Zhang Li , Sun Bing , Li Fang , Zhan Qingyuan , Wang Chen 
Published: March 2014

SummaryAspergillus tracheobronchitis (ATB) is considered as an unusual form of invasive aspergillosis and has a fatal outcome. There is little current information on several aspects of chronic obstructive pulmonary diseases (COPD) complicated by ATB, the frequency of which is expected to increase in the coming years. In a prospective study of invasive bronchial‐pulmonary aspergillosis (IBPA) in a critically ill COPD population, three proven cases of ATB were identified. The three new cases, combined with eight previously reported cases of COPD with ATB over a 30‐year period (1983–2013), were analysed. Among 153 critically ill COPD patients admitted to the ICU, eight cases were complicated by ATB [23.5% of IBPA (8 of 34); and 5.2% of COPD (8 of 153)], and three cases were finally diagnosed as proven ATB by histopathological findings. Among the three new cases reported and the eight published cases, the overall mortality rate was 72.7% (8 of 11 cases), with a median of 11.5 days (range, 7–27 days) between admission to death. The mortality rate was significantly higher in patients with invasive pulmonary aspergillosis (IPA) [100% (8 of 8 patients)] than in patients without parenchyma invasion [0% (0 of 3 patient), P = 0.006]. Seven patients (77.8%) received systemic corticosteroid therapy and three patients (33.3%) inhaled corticosteroids before diagnosis with ATB. Dyspnoea resistant to corticosteroids (77.8%) was the most frequent symptom. The radiological manifestations progressed rapidly in three patients (75%) who had normal chest X‐rays (CXRs) at admission. Pseudomembranous lesions were the most frequent form (54.5%) observed by bronchoscopy. Aspergillus fumigatus was the most frequently isolated pathogen (40%). ATB is an uncommon cause of exacerbation in approximately 5% of critically ill COPD patients admitted to the ICU, and may progress rapidly to IPA with a high mortality rate. Dyspnoea resistant to corticosteroids and appropriate antibiotics with a negative CXR should raise the suspicion of ATB. Early diagnosis of ATB is based on bronchoscopic examination and proven diagnosis maybe safely established with a bronchial mucous biopsy.
Understanding the genetic control and physiological traits associated with rhizosheath production by barley (Hordeum vulgare)
Authors: George Timothy S. , Brown Lawrie K. , Ramsay Luke , White Philip J. , Newton Adrian C. , Bengough A. Glyn , Russell Joanne , Thomas William T. B. 
Published: March 2014

Summary

There is an urgent need for simple rapid screens of root traits that improve the acquisition of nutrients and water. Temperate cereals produce rhizosheaths of variable weight, a trait first noted on desert species sampled by Tansley over 100 yr ago. This trait is almost certainly important in tolerance to abiotic stress.

Here, we screened association genetics populations of barley for rhizosheath weight and derived quantitative trait loci (QTLs) and candidate genes. We assessed whether rhizosheath weight was correlated with plant performance and phosphate uptake under combined drought and phosphorus deficiency. Rhizosheath weight was investigated in relation to root hair length, and under both laboratory and field conditions.

Our data demonstrated that rhizosheath weight was correlated with phosphate uptake under dry conditions and that the differences in rhizosheath weight between genotypes were maintained in the field. Rhizosheath weight also varied significantly within barley populations, was correlated with root hair length and was associated with a genetic locus (QTL) on chromosome 2H. Putative candidate genes were identified.

Rhizosheath weight is easy and rapid to measure, and is associated with relatively high heritability. The breeding of cereal genotypes for beneficial rhizosheath characteristics is achievable and could contribute to agricultural sustainability in nutrient‐ and water‐stressed environments.
The Priority of the Now
Authors: Baron Sam 
Published: March 2014

AbstractThis article motivates and develops a new theory of time: priority presentism. Priority presentism is the view according to which (i) only present entities exist fundamentally and (ii) past and future entities exist, but they are grounded in the present. The articulation of priority presentism is an exercise in applied grounding: it draws on concepts from the recent literature on ontological dependence and applies those concepts in a new way, to the philosophy of time. The result, as I will argue, is an attractive position that can do much of the same work in satisfying our intuitions about time as presentism, but without the ontological cost.
Managing Mismatch Between Belief and Behavior
Authors: Tumulty Maura 
Published: March 2014

AbstractOur behavior doesn't always match the beliefs attributed to us, and sometimes the mismatch raises questions about what our beliefs actually are. I compare two approaches to such cases, and argue in favor of the one which allows some belief‐attributions to lack a determinate truth‐value. That approach avoids an inappropriate assumption about cognitive activity: namely, that whenever we fail in performing one cognitive activity, there is a distinct cognitive activity at which we succeed. The indeterminacy‐allowing approach also meshes well with an attractive view of folk‐psychology: that ascriptions can help shape the attitudes they report.
On What We are and How We Persist
Authors: Langford Simon 
Published: March 2014

AbstractThis article defends novel approaches to what we are and how we persist. First it is claimed that we have disjunctive persistence conditions: we can persist by way of either biological continuity or psychological continuity. Then it is claimed that we are neither human beings nor persons essentially. Rather, we are essentially bio‐psycho‐continuers, a concept to be explained along the way. A variety of objections are considered and found wanting.
Experiences of self‐practice/self‐reflection in cognitive behavioural therapy: A meta‐synthesis of qualitative studies
Authors: Gale Corinne , Schröder Thomas 
Published: March 2014

BackgroundSelf‐practice/self‐reflection is a valuable training strategy which involves therapists applying therapeutic techniques to themselves, and reflecting on the process.PurposeTo undertake a meta‐synthesis of qualitative studies exploring therapists' experiences of self‐practice/self‐reflection in cognitive behavioural therapy (CBT). This would integrate, and interpret, the current literature in order to develop a new understanding, and contribute to the development of CBT training programmes.MethodsThe meta‐synthesis encompassed three distinct phases: undertaking a comprehensive and systematic literature search; critically appraising the papers; and synthesising the data using the meta‐ethnographic method.ResultsThe literature search identified 378 papers, ten met the criteria for inclusion. After critical appraisal, all were included in the synthesis. The synthesis identified 14 constructs, which fell into three broad categories: ‘experience of self‐practice/self‐reflection’; ‘outcomes of self‐practice/self‐reflection’; and ‘implications for training’. This synthesis found that self‐practice allows therapists to put themselves into their clients' shoes, experiencing the benefits that therapy can bring but also the problems that clients can run in to. This experience increases therapists' empathy for their clients, allowing them to draw on their own experiences in therapy. As a result, therapists tend to feel both more confident in themselves and more competent as a therapist. The self‐practice/self‐reflection process was facilitated by reflective writing and working with others, particularly peers.ConclusionsSelf‐practice/self‐reflection is a valuable training strategy in CBT, which has a range of beneficial outcomes. It can also be used as a means of continuing personal and professional development.Practitioner points

Self‐practice of CBT techniques, and reflecting on the process, can be a useful training strategy and helpful for ongoing development

Therapists could consider developing a ‘self‐case’ study, rather than using the exercises as one‐off techniques, recording reflections in writing, and sharing reflections with peers.

Self‐practice/self‐reflection can be particularly helpful for increasing empathy for clients, highlighting the difficulties they may encounter.
Preliminary Ultrasonication Affects the Rate of the Bacteriorhodopsin Bleaching and the Effectiveness of the Reconstitution Process in Bacterioopsin
Authors: Druzhko Anna B. , Pirutin Sergey K. 
Published: March 2014

AbstractThe formation process of polymer films based on bacteriorhodopsin (BR) analogs requests a high amount of BR samples one time only. The common technique for apomembrane formation (preparation of bacterioopsin, BO) is not designed to be operated with high concentrations and high volumes of BR, so the use of this technique results in a low rate of BR bleaching. To accelerate the process of BR bleaching preliminary sonication was used. It was used just as preliminary sonication before bleaching of BR samples, so also sonication was used before reconstitution of resulted BO samples. These modifications of the common technique lead to an acceleration of BR bleaching and an increase in effectiveness of reconstitution of BO in comparison with the nonmodified technique. The quantitative results of sonication's effect on the bleaching acceleration and the effectiveness of reconstitution are different depending on the BR strains.
Validity of Birth Certificate‐Derived Maternal Weight Data
Authors: Bodnar Lisa M. , Abrams Barbara , Bertolet Marnie , Gernand Alison D. , Parisi Sara M. , Himes Katherine P. , Lash Timothy L. 
Published: March 2014

AbstractBackgroundStudies using vital records‐based maternal weight data have become more common, but the validity of these data is uncertain.MethodsWe evaluated the accuracy of prepregnancy body mass index (BMI) and gestational weight gain (GWG) reported on birth certificates using medical record data in 1204 births at a teaching hospital in Pennsylvania from 2003 to 2010. Deliveries at this hospital were representative of births statewide with respect to BMI, GWG, race/ethnicity, and preterm birth. Forty‐eight strata were created by simultaneous stratification on prepregnancy BMI (underweight, normal weight/overweight, obese class 1, obese classes 2 and 3), GWG (<20th, 20–80th, >80th percentile), race/ethnicity (non‐Hispanic white, non‐Hispanic black), and gestational age (term, preterm).ResultsThe agreement of birth certificate‐derived prepregnancy BMI category with medical record BMI category was highest in the normal weight/overweight and obese class 2 and 3 groups. Agreement varied from 52% to 100% across racial/ethnic and gestational age strata. GWG category from the birth registry agreed with medical records for 41–83% of deliveries, and agreement tended to be the poorest for very low and very high GWG. The misclassification of GWG was driven by errors in reported prepregnancy weight rather than maternal weight at delivery, and its magnitude depended on prepregnancy BMI category and gestational age at delivery.ConclusionsMaternal weight data, particularly at the extremes, are poorly reported on birth certificates. Investigators should devote resources to well‐designed validation studies, the results of which can be used to adjust for measurement errors by bias analysis.
The Activation and Inactivation of Mature CD4 T cells: A Case for Peripheral Self–Nonself Discrimination
Authors: Bretscher P. A. 
Published: March 2014

AbstractThe establishment of central tolerance to most self‐antigens results in a repertoire of mature peripheral lymphocytes specific for foreign and peripheral self‐antigens. The framework that single, mature lymphocytes are inactivated by antigen, whereas their activation requires lymphocyte cooperation, accounts for diverse observations and incorporates a mechanism of peripheral tolerance. This framework accounts for the generalizations that the sustained activation by antigen of most B cells and CD8 T cells requires CD4 T helper cells; in the absence of CD4 T cells, antigen can inactivate these B cells and CD8 T cells. In this sense, CD4 T cells are the guardians of the fate of most B cells and CD8 T cells when they encounter antigen. I argue here that the single‐lymphocyte/multiple‐lymphocyte framework for the inactivation/activation of lymphocytes also applies to CD4 T cells. I consider within this framework a model for the activation/inactivation of CD4 T cells that is consistent with the large majority of contemporary observations, including significant clinical observations. I outline the grounds why I feel this model is more plausible than the contemporary and predominant pathogen‐associated molecular pattern (PAMP) and Danger Models for CD4 T cell activation. These models are based upon what I consider the radical premise that self–nonself discrimination does not exist at the level of mature CD4 T cells. I explain why I feel this feature renders the PAMP and Danger Models somewhat implausible. The model I propose, in contrast, is conservative in that it embodies such a process of self–nonself discrimination.
The CXCR4 and adhesion molecule expression of CD34+ hematopoietic cells mobilized by “on‐demand” addition of plerixafor to granulocyte–colony‐stimulating factor
Authors: Girbl Tamara , Lunzer Verena , Greil Richard , Namberger Konrad , Hartmann Tanja Nicole 
Published: March 2014

BackgroundGranulocyte–colony‐stimulating factor (G‐CSF) is routinely used for mobilization of hematopoietic stem and progenitor cells preceding autologous transplantation after high‐dose chemotherapy in hematologic malignancies. However, due to high mobilization failure rates, alternative mobilization strategies are required.Study Design and MethodsPatients who poorly mobilized CD34+ hematopoietic cells (HCs) with G‐CSF additionally received the CXCR4 antagonist plerixafor. The phenotype of CD34+ HCs collected after this plerixafor‐induced “rescue” mobilization, in regard to adhesion molecule and CD133, CD34, and CD38 expression in comparison to CD34+ HCs collected after traditional G‐CSF administration in good mobilizers, was analyzed flow cytometrically. To confirm previous studies in our patient cohort, the efficiency of mobilization and subsequent engraftment after this “on‐demand” plerixafor mobilization were analyzed.ResultsPronounced mobilization occurred after plerixafor administration in poor mobilizers, resulting in similar CD34+ cell yields as obtained by G‐CSF in good mobilizers, whereby plerixafor increased the content of primitive CD133+/CD34+/CD38– cells. The surface expression profiles of the marrow homing and retention receptors CXCR4, VLA‐4, LFA‐1, and CD44 on mobilized CD34+ cells and hematopoietic recovery after transplantation were similar in patients receiving G‐CSF plus plerixafor or G‐CSF. Unexpectedly, the expression levels of respective adhesion receptors were not related to mobilization efficiency or engraftment.ConclusionThe results show that CD34+ HCs collected by plerixafor‐induced rescue mobilization are qualitatively equivalent to CD34+ HCs collected after traditional G‐CSF mobilization in good mobilizers, in regard to their adhesive phenotype and engraftment potential. Thereby, plerixafor facilitates the treatment of poor mobilizers with autologous HC transplantation after high‐dose chemotherapy.
Full-Genome Sequences of Influenza H3N2 Virus Strains Isolated from Finnish Patients during the 2012-2013 Epidemic Season
Authors: Lakspere Triin , Kallio-Kokko Hannimari , Kantele Anu , Mattila Pirkko , Almusa Henrikki , Kainov Denis , Kakkola Laura 
Published: March 2014

ABSTRACT
Here, we sequenced 10 influenza A(H3N2) virus genomes isolated from Finnish patients diagnosed with flu-like illness during the 2012-2013 influenza season. The alignment showed a high number of amino acid substitutions (238 in total) in only 10 samples, proving that a high mutation rate exists in seasonal influenza A viruses.
Genome Sequence of Proteus mirabilis Clinical Isolate C05028
Authors: Shi Xiaolu , Zhu Yuanfang , Li Yinghui , Jiang Min , Lin Yiman , Qiu Yaqun , Chen Qiongcheng , Yuan Yanting , Ni Peixiang , Hu Qinghua , Huang Shenghe 
Published: March 2014

ABSTRACT

Genomic DNA of
Proteus mirabilis
C05028 was sequenced by an Illumina HiSeq platform and was assembled to 39 scaffolds with a total length of 3.8 Mb. Next, open reading frames (ORFs) were identified and were annotated by the KEGG, COG, and NR databases. Finally, we found special virulence factors only existing in
P. mirabilis
C05028.
Draft Genome Sequence of Actinomadura madurae LIID-AJ290, Isolated from a Human Mycetoma Case
Authors: Vera-Cabrera Lucio , Ortiz-Lopez Rocio , Elizondo-González Ramiro , Campos-Rivera Mayra Paola , Gallardo-Rocha Anabel , Molina-Torres Carmen Amelia , Ocampo-Candiani Jorge 
Published: March 2014

ABSTRACT

Here we present the draft genome sequence of a member of the
Thermomonosporaceae
,
Actinomadura madurae
LIID-AJ290, isolated from a human case of mycetoma. The assembly contains 10,308,866 bp. This is to our knowledge the first reported genome of a human-pathogenic
Actinomadura
species.
Genome Sequences of Rhinovirus B Isolates from Wisconsin Pediatric Respiratory Studies
Authors: Liggett Stephen B. , Bochkov Yury A. , Pappas Tressa , Lemanske Robert F. , Gern James E. , Sengamalay Naomi , Zhao Xuechu , Su Qi , Fraser Claire M. , Palmenberg Ann C. 
Published: March 2014

ABSTRACT
Nearly full-length RNA genome sequences for 39 rhinovirus B isolates (RV-B), representing 13 different genotypes, were resolved as part of ongoing studies at the University of Wisconsin that attempt to link rhinovirus (RV) diversity and respiratory disease in infants.
Draft Genome Sequence of Cytophaga fermentans JCM 21142
T
, a Facultative Anaerobe Isolated from Marine Mud
Authors: Starns David , Oshima Kenshiro , Suda Wataru , Iino Takao , Yuki Masahiro , Inoue Jun-Ichi , Kitamura Keiko , Iida Toshiya , Darby Alistair , Hattori Masahira , Ohkuma Moriya 
Published: March 2014

ABSTRACT

Cytophaga fermentans
strain JCM 21142
T
is a marine-dwelling facultative anaerobe. The draft genome sequence of this strain revealed its diverse chemoorganotrophic potential, which makes it capable of metabolizing various polysaccharide substrates. The genome data will facilitate further studies on its taxonomic reclassification, its metabolism, and the mechanisms pertaining to bacterial gliding.
Genome Sequence of the Octopine-Type Agrobacterium tumefaciens Strain Ach5
Authors: Henkel Christiaan V. , den Dulk-Ras Amke , Zhang Xiaorong , Hooykaas Paul J. J. 
Published: March 2014

ABSTRACT

We have sequenced the complete genome of the plant pathogen
Agrobacterium tumefaciens
strain LBA4213, a derivative of the wild-type strain
A. tumefaciens
Ach5 and the ancestor of
A. tumefaciens
strain LBA4404 used in genetic engineering. The genome consists of a circular chromosome and a linear chromosome, as well as a megaplasmid and a tumor-inducing plasmid.
Draft Genome Sequences of Two
Lactobacillus
Strains,
L. farraginis
JCM 14108
T
and
L. composti
JCM 14202
T
, Isolated from Compost of Distilled Shōchū Residue
Authors: Yuki Masahiro , Oshima Kenshiro , Suda Wataru , Kitahara Maki , Kitamura Keiko , Iida Toshiya , Hattori Masahira , Ohkuma Moriya 
Published: March 2014

ABSTRACT

Here, we report the draft genome sequences of two type strains of
Lactobacillus
,
Lactobacillus farraginis
JCM 14108
T
and
Lactobacillus composti
JCM 14202
T
, isolated from the compost of distilled shōchū residue. Their genome information will be useful for studies of ecological and physiological functions of these
Lactobacillus
species.
An observational study of giant cell interstitial pneumonia and lung fibrosis in hard metal lung disease
Authors: Tanaka Junichi , Moriyama Hiroshi , Terada Masaki , Takada Toshinori , Suzuki Eiichi , Narita Ichiei , Kawabata Yoshinori , Yamaguchi Tetsuo , Hebisawa Akira , Sakai Fumikazu , Arakawa Hiroaki 
Published: March 2014

BackgroundHard metal lung disease has various pathological patterns including giant cell interstitial pneumonia (GIP) and usual interstitial pneumonia (UIP). Although the UIP pattern is considered the prominent feature in advanced disease, it is unknown whether GIP finally progresses to the UIP pattern.ObjectivesTo clarify clinical, pathological and elemental differences between the GIP and UIP patterns in hard metal lung disease.MethodsA cross-sectional study of patients from 17 institutes participating in the 10th annual meeting of the Tokyo Research Group for Diffuse Parenchymal Lung Diseases, 2009. Nineteen patients (seven female) diagnosed with hard metal lung disease by the presence of tungsten in lung specimens were studied.ResultsFourteen cases were pathologically diagnosed as GIP or centrilobular inflammation/fibrosing. The other five cases were the UIP pattern or upper lobe fibrosis. Elemental analyses of lung specimens of GIP showed tungsten throughout the centrilobular fibrotic areas. In the UIP pattern, tungsten was detected in the periarteriolar area with subpleural fibrosis, but no association with centrilobular fibrosis or inflammatory cell infiltration. The GIP group was younger (43.1 vs 58.6 years), with shorter exposure duration (73 vs 285 months; p<0.01), lower serum KL-6 (398 vs 710 U/mL) and higher lymphocyte percentage in bronchoalveolar lavage fluid (31.5% vs 3.22%; p<0.05) than the fibrosis group.ConclusionsThe UIP pattern or upper lobe fibrosis is remarkably different from GIP in distribution of hard metal elements, associated interstitial inflammation and fibrosis, and clinical features. In hard metal lung disease, the UIP pattern or upper lobe fibrosis may not be an advanced form of GIP.