bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluating the impact of MEDLINE filters on evidence retrieval: study protocol
Authors: Shariff Salimah Z , Cuerden Meaghan S , Haynes R Brian , McKibbon K Ann , Wilczynski Nancy L , Iansavichus Arthur V , Speechley Mark R , Thind Amardeep , Garg Amit X 
Published: July 2010

Abstract

Background
Rather than searching the entire MEDLINE database, clinicians can perform searches on a filtered set of articles where relevant information is more likely to be found. Members of our team previously developed two types of MEDLINE filters. The 'methods' filters help identify clinical research of high methodological merit. The 'content' filters help identify articles in the discipline of renal medicine. We will now test the utility of these filters for physician MEDLINE searching.

Hypothesis
When a physician searches MEDLINE, we hypothesize the use of filters will increase the number of relevant articles retrieved (increase 'recall,' also called sensitivity) and decrease the number of non-relevant articles retrieved (increase 'precision,' also called positive predictive value), compared to the performance of a physician's search unaided by filters.

Methods
We will survey a random sample of 100 nephrologists in Canada to obtain the MEDLINE search that they would first perform themselves for a focused clinical question. Each question we provide to a nephrologist will be based on the topic of a recently published, well-conducted systematic review. We will examine the performance of a physician's unaided MEDLINE search. We will then apply a total of eight filter combinations to the search (filters used in isolation or in combination). We will calculate the recall and precision of each search. The filter combinations that most improve on unaided physician searches will be identified and characterized.

Discussion
If these filters improve search performance, physicians will be able to search MEDLINE for renal evidence more effectively, in less time, and with less frustration. Additionally, our methodology can be used as a proof of concept for the evaluation of search filters in other disciplines.
X-chromosome terminal deletion in a female with premature ovarian failure: Haploinsufficiency of X-linked genes as a possible explanation
Authors: Ferreira Susana I , Matoso Eunice , Pinto Marta , Almeida Joana , Liehr Thomas , Melo Joana B , Carreira Isabel M 
Published: July 2010

AbstractBackgroundPremature ovarian failure (POF) has repeatedly been associated to X-chromosome deletions.FMR1gene premutation allele's carrier women have an increased risk for POF. We intent to determine the cause of POF in a 29 year old female, evaluating both of these situations.MethodsConcomitant analysis ofFMR1gene CGG repeat number and karyotype revealed an X-chromosome terminal deletion. Fluorescencein situfurther characterized the breakpoint. A methylation assay forFMR1gene allowed to determine its methylation status, and hence, the methylation status of the normal X-chromosome.ResultsWe report a POF patient with a 46,X,del(X)(q26) karyotype and with skewed X-chromosome inactivation of the structural abnormal X-chromosome.ConclusionsDespite the hemizygosity ofFMR1gene, the patient does not present Fragile X syndrome features, since the normal X-chromosome is not subject to methylation. The described deletion supports the hypothesis that haploinsufficiency of X-linked genes can be on the basis of POF, and special attention should be paid to X-linked genes in region Xq28 since they escape inactivation and might have a role in this disorder. A full clinical and cytogenetic characterization of all POF cases is important to highlight a pattern and help to understand which genes are crucial for normal ovarian development.
Changes in expression of oestrogen regulated and proliferation genes with neoadjuvant treatment highlight heterogeneity of clinical resistance to the aromatase inhibitor, letrozole
Authors: Miller William R , Larionov Alexey 
Published: July 2010

Abstract
Introduction
Clinical resistance is a major factor limiting benefits to endocrine therapy. Causes of resistance may be diverse and the mechanism of resistance in individual breast cancers is usually unknown. The present study illustrates how changes in the expression of proliferation and oestrogen-regulated genes occurring during neoadjuvant treatment with the aromatase inhibitor, letrozole, may define distinctive tumour subgroups and suggest different mechanisms of resistance in clinically endocrine resistant breast cancers.

Methods
Postmenopausal women with large primary oestrogen-receptor (ER)-rich breast cancers were treated neoadjuvantly with letrozole (2.5 mg daily) for three months. Clinical response was determined by ultrasound changes in tumour volume. Tumour ribonucleic acid (RNA) from biopsies taken before, after 14 days and after three months of treatment was hybridized on Affymetrix U133A chips. Changes in expression of KIAA0101, TFF3, SERPINA3, IRS-1 and TFF1 were taken as markers of oestrogen regulation and those in CDC2, CKS-2, Cyclin B1, Thymidine Synthetase and PCNA as markers of proliferation.

Results
Fifteen tumours with < 50% volume reduction over three months of treatment were classified as being clinically non-responsive. Gene expression changes after 14 days of treatment with letrozole revealed different patterns of change in oestrogen regulated and proliferation genes in individual resistant tumours. Tumours could be separated into three different subgroups as follows: i) nine cases in which both proliferation and oestrogen signalling signatures were generally reduced on treatment (ii) four cases in which both signatures were generally unaffected or increased with treatment and (iii) two cases in which expression of the majority of oestrogen-regulated genes decreased whereas proliferation genes remained unchanged or increased. In 14 out of 15 tumours, RNA profiles were also available after three months of treatment. Patterns of change observed after 14 days were maintained or accentuated at three months in nine tumours but changes in patterns were apparent in the remaining five cancers.

Conclusions
Different dynamic patterns of expression of oestrogen-regulated and proliferation genes were observed in tumours clinically resistant to neoadjuvant letrozole, thus illustrating heterogeneity of resistance and discriminating molecular sub-classes of resistant tumours. Molecular phenotyping might help to direct circumventing therapy suggesting the targeting of specific pathways in different tumour subtypes.
Capacity to Consent to Research Participation in Adults With Malignant Glioma
Authors: Marson Daniel C. , Martin Roy C. , Triebel Kristen L. , Nabors Louis B. 
Published: July 2010

Purpose To investigate research consent capacity (RCC) in patients with malignant gliomas (MGs) and identify cognitive abilities and clinical factors associated with RCC in MG. Patients and Methods Participants were 22 healthy controls and 26 patients with diagnosed and histologically verified MG. All patients with MG were receiving various combinations of treatment (surgery, radiation, chemotherapy, medication). Both groups were administered a neurocognitive test battery and a standardized RCC measure (Capacity to Consent to Research Instrument [CCRI]). Capacity performance was evaluated across four core consent abilities (choice, appreciation, reasoning, understanding), and categorical capacity impairment ratings (no impairment, mild/moderate impairment, severe impairment) were also identified for individual patients with MG. Stepwise regression analyses identified cognitive predictors of CCRI performance in the MG group. Results The MG patient group performed significantly below the control group on the three clinically relevant consent standards (appreciation, reasoning, and understanding). Patients with MG performed equivalently to controls in evidencing a simple research participation choice. Approximately one third of patients with MG showed compromised impairment ratings (mild/moderate impairment or severe impairment) on the three consent abilities. Cognitive measures of phonemic and semantic word fluency predicted performance on the consent standards. Steroid treatment and anticonvulsant use were related to poorer CCRI performance. Conclusion A substantial portion of patients with MG after diagnosis show impairments in research consent capacity. Word fluency measures reflecting expressive language and executive function abilities are strongly associated with these consent impairments. This study highlights the importance of careful attention to consent issues when enrolling patients with MG in clinical trials and other research studies.
Time to Activate Lung Cancer Clinical Trials and Patient Enrollment: A Representative Comparison Study Between Two Academic Centers Across the Atlantic
Authors: Wang-Gillam Andrea , Williams Kristina , Novello Silvia , Gao Feng , Scagliotti Giorgio V. , Govindan Ramaswamy 
Published: July 2010

Purpose Activation of clinical trials is a lengthy process. We studied the procedures and time required to activate lung cancer clinical trials in a US academic center compared with a European center. Methods A retrospective review was performed of all thoracic oncology therapeutic trials submitted for regulatory review between 2001 and 2008 at Washington University School of Medicine (WUSM; St Louis, MO) and the University of Torino (UT; Torino, Italy). A process map was drafted by both institutions to establish the order of required events. Results We reviewed 137 therapeutic thoracic oncology trials from WUSM (n = 83) and UT (n = 54). The median times from submission to opening a trial were 163 days for WUSM and 112.5 days for UT (P = .048). The median times for regulatory approval were 75 days for WUSM and 31 days for UT (P < .001). The difference is more pronounced in a homogeneous subset of phase II, industrial-sponsored trials for the median calendar time from submission to opening a trial (239.5 days for WUSM v 112.5 days for UT; P < .001) and time for regulatory approval (99 days for WUSM v 13.5 days for UT; P < .001). The median number of patients accrued at WUSM was 7.4 patients per study compared with an average of 37 patients per study at UT. The proportion of trials that enrolled 20 patients or more represented 22.2% of trials at UT but only 1.1% of trials at WUSM. Conclusion It takes additional steps and significantly longer time to activate a therapeutic thoracic clinical trial at a representative US site (WUSM) compared with a European site (UT).
Nuclear rDNA sequences of Wittrockiella amphibia (Collins) comb. nov. (Cladophorales, Chlorophyta) and morphological characterization of the mat-like growth form
Authors: Boedeker Christian , Hansen Gayle I. 
Published: July 2010

Abstract

Cladophora amphibia was found in Yaquina Bay (Oregon, USA) for the first time since the type collection from California in 1903. Vegetative plants were buried in the top centimeter of intertidal mud, partially covered by mats of Rhizoclonium and Chaetomorpha. Cladophora amphibia plants had densely pigmented upright branches penetrating the mud surface and overlying algal mats. Morphological and habitat characteristics of C. amphibia strongly overlap with those of Wittrockiella paradoxa, and molecular sequences of ribosomal genes, including the variable internally transcribed spacer 2 (ITS2) region, indicate very high genetic similarity between these two taxa. The seven point mutations in the ITS2 DNA sequences are regarded as low intraspecific variation. Since C. amphibia had been described earlier, W. paradoxa becomes a taxonomic synonym of C. amphibia, and the new binomial Wittrockiella amphibia (Collins) comb. nov. is required. As previously reported for W. paradoxa, the studied Pacific plants were “cladophoroid” in form (upright, branched thalli with cylindrical cells), in contrast to the stunted and poorly branched “rhizoidal” plants mainly found in Europe. The heterotrichous mode of growth is further characterized.
Maternal Prenatal Anxiety and Stress Predict Infant Illnesses and Health Complaints
Authors: Beijers Roseriet , Jansen Jarno , Riksen-Walraven Marianne , de Weerth Carolina 
Published: July 2010

OBJECTIVES:
Evidence from both animals and humans suggests that maternal prenatal anxiety and stress can have adverse consequences on the offspring's development. Animal models also show that prenatal stress has programming effects on the physical health of the offspring, such as immune functioning. In human studies, however, physical health outcomes are often restricted to birth complications; studies on the effects of acquiring illnesses are scarce. This study aimed to examine whether maternal prenatal anxiety and stress, measured both by self-report and by cortisol physiology, are related to more infant illnesses and antibiotic use during the first year of life.

METHODS:
Participants in the study were 174 mothers with normal pregnancies and term deliveries (71 firstborns; 91 boys). The mothers filled out third-trimester questionnaires on general and pregnancy-specific anxiety and stress and provided saliva samples for circadian cortisol. Information on infant illnesses and antibiotic use was obtained through monthly maternal interviews across the infant's first year of life.

RESULTS:
Hierarchical multiple regressions showed that, even after controlling for many relevant confounders, prenatal anxiety and stress predicted a considerable amount of variance in infant illnesses and antibiotic use: 9.3% for respiratory, 10.7% for general, 8.9% for skin, and 7.6% for antibiotic use. Digestive illnesses were not related to prenatal anxiety and stress.

CONCLUSIONS:
Although replication is warranted, to our knowledge, this is the first evidence linking maternal prenatal anxiety and stress to infant illnesses and antibiotic use early in life.
Agricultural Chemicals in Relation to Environmental Quality: Chemical Fertilizers, Present and Future
Authors: Nelson L. B. 
Published: July 2010

AbstractUnfertilized soils no longer can provide the food necessary to meet the needs of expanding populations, Fertilizer use has increased dramatically in recent years; however, intensity of use varies greatly in different parts of the world, in various sections of the USA, and with the kind of crop grown. In the USA, fertilizers have accounted for over 50% of the increase in crop production since 1940, and farmers have substituted fertilizers for land and other inputs. However, considerable controversy has developed in recent years over the role of fertilizers in pollution of natural waters. Increased nitrate and phosphate levels in waters are cited by ecologists as proof of contamination by fertilizers, but this is contested by many agriculturists. Examination by competent reviewers of the limited data available so far indicates that losses of fertilizer nutrients into surface and groundwaters may be minimal under most situations. Should situations be found where fertilizers do contribute appreciably to water pollution, corrective steps may have to be taken. There are a number of ways to minimize losses without sacrificing the important benefits gained from fertilizers. These include carefully tailoring rates and times of nitrogen application to better fit the needs of the growing crop, greater care in irrigation, use of slow‐release nitrogen fertilizers, and wider application of selected soil conservation practices to control surface losses of both nitrates and phosphates.
Chemical Weed Control in the Seventies
Authors: Day Boysie E. 
Published: July 2010

AbstractHerbicides constitute the most widely‐used and rapidly‐growing category of pesticides. They are widely used in industrial land management as well as in agriculture. Herbicides replace a wide range of more expensive or more hazardous weed control practices. The technology now exists for a doubling of the beneficial uses of herbicides during the decade of the 1970's. Shortage of trained personnel and insufficient diffusion of knowledge are currently the limitation on the further use of chemical weed control. Present herbicides, although effective, are far from ideal. However, the outlook for the discovery of more effective and safer herbicides is excellent. The principal limitations to further development of chemical weed control procedures are social and legal rather than technological. The use of herbicides and other agricultural chemicals is increasingly reviewed by the public as offensive, immoral, or dangerous. These views lead to political action in the form of restrictive, and often irrational, regulation. It is upon the resolution of social conflicts, more than on technical matters, that the future of herbicides depends.
Fungicides and Nematicides: Their Role Now and in the Future
Authors: Torgeson D. C. 
Published: July 2010

AbstractA great number of fungicides and nematicides effective in preventing losses from fungi and nematodes attacking plants have been developed. The first developed and most widely used nematicides are volatile and phytotoxic, which require that they be applied to the soil in advance of planting. More recently, less volatile and less phytotoxic nematicides have been developed which can be applied to living plants. The ideal nematicide would be systemic in plants and selectively toxic or repellent to nematodes. Although inorganic copper and sulfur fungicides are still in use, a wide variety of organic fungicides effective for the control of many of the major plant disease fungi have been developed. More recently a number of systemic fungicides have been discovered which are probably indicative of the type of fungicides that will be used in future years. Better fungicides and nematicides are needed not only as replacements for many of those now in use but also for the control of plant parasitic fungi and nematodes not effectively or economically controlled with existing materials. The high cost of developing new pesticides is, however, a deterrent in obtaining such materials.
Physical Methods of Pest Control
Authors: Osmun John V. 
Published: July 2010

AbstractPhysical approaches to control are discussed including those direct or indirect measures which either destroy the insect, disrupt normal physiological activity by means other than chemical, or modify the environment to a degree that is unacceptable or unbearable to the insect. A recognition of specific ecological factors and tolerance thresholds are prerequisites to utilization of physical controls. Temperature survival limits are discussed together with the more subtle use of radiofrequency energy. Manipulation of the environment to alter normally expected humidity patterns is an acceptable approach in the case of certain household, forest, and agricultural pests. Radiant energy, in the example of light traps, incorporates approaches in which traps are used alone, in combination with pheromones, and integrated with both chemical and biological methods. Especially encouraging for night nuisance pests is the use of insect‐free lighting. Infrared, reflected light, and light amplification are discussed. The general prospects for use of sounds are cautiously hopeful as are techniques employing the manipulation of the environmental atmosphere. We are entering an era when systems approaches to pest management will necessitate the integration of a number of methods. The utilization of physical approaches as restraining agents is viewed with moderate optimism.
A Directed Ecosystem Approach to Pest Control and Environmental Quality
Authors: Hanson A. A. 
Published: July 2010

AbstractProblems and opportunities in integrated pest control programs are outlined with primary emphasis on agronomic inputs; basic ecological concepts are reviewed in the context of the disturbed environments in which crops are grown for food and fiber. Particular attention is given to the interrelationship of crop management and plant breeding with other biological control measures, such as exclusion and the use of predators and parasites. The origin of environmental concerns is reviewed together with possible approaches that will aid in solving complex pest control problems. Recognition is given to the need for utilizing existing information on biological control, improving the effectiveness of agricultural chemicals, developing new approaches and improving existing methods of biological pest control, and integrating all components into systems for individual crops and cropping systems.
The Effects of Urbanization on Water Quality
Authors: McGriff E. Corbin 
Published: July 2010

AbstractThis paper attempts to summarize existing knowledge of the effects of urbanization on hydrologic factors and their ultimate effect on water quality. Urbanization has the greatest effect on the hydrology of an area which ultimately results in the degradation of the quality of both surface and ground water. Urbanization increases the sediment load carried by streams, decreases ground water recharge, promotes eutrophication, and causes temperature variation in streams, all of which tend to alter water quality.
Interface Between Man and His Forest Environment
Authors: Arnold R. Keith 
Published: July 2010

AbstractForest environments, covering one‐third of our nation, have multiple uses and benefits of increasing value to our growing population. In addition to the well‐known uses for wood, water, wildlife, range, and recreation, our forests enhance man's general welfare. Among other benefits, forest environments provide shelter from climatic extremes, screens to hide unpleasant views, interesting and pleasing landscapes, and biological air conditioning. Everyone receives these benefits whether he lives near the forest or in a crowded city. While these benefits are sizable today, they can be increased substantially in the future. Environmental forestry offers service, production, and enjoyment for mankind.Scientists, the citizenry, and legislators shape the practices and standards that professional foresters follow in managing and protecting forest environments. Environmental forestry, because it is more than production forestry, provides new challenges for research. More interdisciplinary attention must be given to environmental impacts of production programs in forests. Ways must be found to augment multiple outputs from forests. Managers of forest environments need new value systems and decision‐making procedures. A new Pinchot Institute of Environmental Forestry Research exemplifies a cooperative, multidisciplinary approach to solving current problems of environmental forestry. Through forestry research we can find better ways to manage and protect forest environments for the future of all Americans.
Research Natural Areas: Contributors to Environmental Quality Programs
Authors: Franklin Jerry F. , Jenkins Robert E. , Romancier Robert M. 
Published: July 2010

AbstractResearch programs on environmental quality will require studies of conditions in natural environments. Numerous protected natural ecosystems, known as Research Natural Areas, are available for such studies. The Research Natural Area concept and history and scope of present programs are outlined. These tracts are particularly valuable sites for baseline and monitoring programs, for ecosystem studies, as in situ preserves of gene pools, and for selected educational purposes.
Effect of Lime on Lead Uptake by Five Plant Species
Authors: Cox W. J. , Rains D. W. 
Published: July 2010

AbstractLiming at 0, 2.2, and 4.4 tons/hectare (0, 1, and 2 English tons/acre) was tested as a means of reducing Pb uptake by five species from two Pb contaminated soils. The soils represent the 0‐ to 10‐ and 10‐ to 30‐cm horizons of Los Osos clay loam (a Typic Argixeroll) and contained 94 ± 18 and 32 ± 7 ppm Pb, respectively. There was no effect of lime on yield, but Pb concentrations in tops were reduced. At all times of harvest and lime rates the Pb concentration followed the series Glycine max L. ≫ Trifolium subterraneum L. > Zea mays L. = Avena sativa L. = Triticum aestivum L.