Epistemic and methodological iteration in scientific research

A number of scholars have recently drawn attention to the importance of iteration in scientific research. This paper builds on these previous discussions by drawing a distinction between epistemic and methodological forms of iteration and by clarifying the relationships between them. As defined here, epistemic iteration involves progressive alterations to scientific knowledge claims, whereas methodological iteration refers to an interplay between different modes of research practice. While distinct, these two forms of iteration are related in important ways. Contemporary research on the biological effects of nanomaterials illustrates that methodological iteration can help to “initiate,” “equip,” and “stimulate” epistemic iteration.     

Approaches to Improving Consistency of Interval Fuzzy Preference Relations

This article introduces a consistency index for measuring the consistency level of an interval fuzzy preference relation（IFPR）.An approach is then proposed to construct an additive consistent IFPR from a given inconsistent IFPR.By using a weighted averaging method combining the original IFPR and the constructed consistent IFPR,a formula is put forward to repair an inconsistent IFPR to generate an IFPR with acceptable consistency.An iterative algorithm is subsequently developed to rectify an inconsistent IFPR and derive one with acceptable consistency and weak transitivity.The proposed approaches can not only improve consistency of IFPRs but also preserve the initial interval uncertainty information as much as possible.Numerical examples are presented to illustrate how to apply the proposed approaches.     

Functional genomics reveal that the serine synthesis pathway is essential in breast cancer

Cancer cells adapt their metabolic processes to drive macromolecular biosynthesis for rapid cell growth and proliferation. RNA interference (RNAi)-based loss-of-function screening has proven powerful for the identification of new and interesting cancer targets, and recent studies have used this technology in vivo to identify novel tumour suppressor genes. Here we developed a method for identifying novel cancer targets via negative-selection RNAi screening using a human breast cancer xenograft model at an orthotopic site in the mouse. Using this method, we screened a set of metabolic genes associated with aggressive breast cancer and stemness to identify those required for in vivo tumorigenesis. Among the genes identified, phosphoglycerate dehydrogenase (PHGDH) is in a genomic region of recurrent copy number gain in breast cancer and PHGDH protein levels are elevated in 70% of oestrogen receptor (ER)-negative breast cancers. PHGDH catalyses the first step in the serine biosynthesis pathway, and breast cancer cells with high PHGDH expression have increased serine synthesis flux. Suppression of PHGDH in cell lines with elevated PHGDH expression, but not in those without, causes a strong decrease in cell proliferation and a reduction in serine synthesis. We find that PHGDH suppression does not affect intracellular serine levels, but causes a drop in the levels of α-ketoglutarate, another output of the pathway and a tricarboxylic acid (TCA) cycle intermediate. In cells with high PHGDH expression, the serine synthesis pathway contributes approximately 50% of the total anaplerotic flux of glutamine into the TCA cycle. These results reveal that certain breast cancers are dependent upon increased serine pathway flux caused by PHGDH overexpression and demonstrate the utility of in vivo negative-selection RNAi screens for finding potential anticancer targets.     

Black hole growth in the early Universe is self-regulated and largely hidden from view

The formation of the first massive objects in the infant Universe remains impossible to observe directly and yet it sets the stage for the subsequent evolution of galaxies. Although some black holes with masses more than 10(9) times that of the Sun have been detected in luminous quasars less than one billion years after the Big Bang, these individual extreme objects have limited utility in constraining the channels of formation of the earliest black holes; this is because the initial conditions of black hole seed properties are quickly erased during the growth process. Here we report a measurement of the amount of black hole growth in galaxies at redshift z = 6-8 (0.95-0.7 billion years after the Big Bang), based on optimally stacked, archival X-ray observations. Our results imply that black holes grow in tandem with their host galaxies throughout cosmic history, starting from the earliest times. We find that most copiously accreting black holes at these epochs are buried in significant amounts of gas and dust that absorb most radiation except for the highest-energy X-rays. This suggests that black holes grew significantly more during these early bursts than was previously thought, but because of the obscuration of their ultraviolet emission they did not contribute to the re-ionization of the Universe.     

Habitat use by breeding male sage grouse: a management approach

Radio telemetry was used to study habitat use of breeding male sage grouse ( Centrocercus urophasianus ) at a lek in northeastern Utah during 1983 and 1984. Objectives were to determine if grouse day-use areas differed significantly in sagebrush characteristics from adjacent nonuse areas and to establish a simplified method for use by land managers in identifying grouse use areas. We determined that male grouse used areas of greatest sagebrush height and cover. Our methods provide a means for land managers to identify habitat associated with a lek that is suitable for male sage grouse day use in the event sagebrush alteration is planned within 3 km of a lek.     

Spreads versus professional forecasters as predictors of future output change

We examine whether real output forecasts obtained from the Survey of Professional Forecasters efficiently embody information in the term structure spread. To this end, we employ revised data as well as real‐time vintage data, and we also allow for the possible impact of asymmetric loss functions. Assuming quadratic loss, our results suggest that the term structure spread does contain information useful for forecasting not reflected in the survey forecasts, at least over the longest forecast horizon. However, if we allow agents' loss functions to become more negatively skewed with the forecast horizon, then we cannot reject the rationality of the survey forecasts. Copyright © 2009 John Wiley & Sons, Ltd.     

Chilli anthracnose disease caused by Colletotrichum species

Anthracnose disease is one of the major economic constraints to chilli production worldwide, especially in tropical and subtropical regions. Accurate taxonomic information is necessary for effective disease control management. In the Colletotrichum patho-system, different Colletotrichum species can be associated with anthracnose of the same host. Little information is known concerning the interactions of the species associated with the chilli anthracnose although several Colletotrichum species have been reported as causal agents of chilli anthracnose disease worldwide. The ambiguous taxonomic status of Colletotrichum species has resulted in inaccurate identification which may cause practical problems in plant breeding and disease management. Although the management and control of anthracnose disease are still being extensively researched, commercial cultivars of Capsicum annuum that are resistant to the pathogens that cause chilli anthracnose have not yet been developed. This paper reviews the causal agents of chilli anthracnose, the disease cycle, conventional methods in identification of the pathogen and molecular approaches that have been used for the identification of Colletotrichum species. Pathogenetic variation and population structure of the causal agents of chilli anthracnose along with the current taxonomic status of Colletotrichum species are discussed. Future developments leading to the disease management strategies are suggested.