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D10. Links and References - Biology

D10.  Links and References - Biology


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Photosynthesis - ASU

Photosynthesis on the Web - 2002

  1. Current Opinion in Chemical Biology (2012) 16, 11–18. DOI 10.1016/j.cbpa.2012.03.003
  2. Nature (2011) 473, 55,-61.
  3. Journal of Biophysical Chemistry (2012) 3, 111-126. doi:10.4236/jbpc.2012.32013
  4. Coordination Chemistry Reviews (2012) 256, 2445– 2452
  5. Sessions, A. et al. The Continuing Puzzle of the Great Oxidation Event. Currrent Biology, 19, R567–R574 (2009)
  6. Alper, J. Water Splitting Goes Au Naturel. Science, 299, pg 1686 (2003)
  7. Demming-Adams, B. & Adams, W. Antioxidants in photosynthesis and human nutrition. Science. 298, pg 2149 (2002)
  8. Jordan et al. 3D Structure of Cyanobacterial Photosystem I (shows how chlorophylls use solar energy to transport electrons) Nature. 411. pg 896, 909 ((2001)
  9. Balabin and Onuchic. Exploiting thermal motion in electron transfer (combined molecular dynamics, quantum mechanics to study e transfer in photosynthetic reaction center) Science. 290. pg 61, 114 (2000)
  10. Dismukes. Photosynthesis: Splitting Water. 292. pg 447 (2001)

Contributors

  • Prof. Henry Jakubowski (College of St. Benedict/St. John's University)

D10. Links and References - Biology

In working with spreadsheets, you need to know about relative vs. absolute cell references.

Here is the issue: when you COPY A FORMULA that contains cell references, what happens to the cell references?

Usually the CELL REFERENCES will CHANGE! If you copy a formula 2 rows to the right, then the cell references in the formula will shift 2 cells to the right. If you copy a formula 3 rows down and 1 row left, then the cell references in the formula will shift 3 rows down and 1 row left. These are called "relative" cell references, since they change relative to where you copy the formula.

If you do not want cell references to change when you copy a formula, then make those cell references absolute cell references. Place a "$" before the column letter if you want that to always stay the same. Place a "$" before a row number if you want that to always stay the same. For example, "$C$3" refers to cell C3, and "$C$3" will work exactly the same as "C3", expect when you copy the formula. Note: when entering formulas you can use the F4 key right after entering a cell reference to toggle among the different relative/absolute versions of that cell address.

The trick in creating spreadsheets is deciding before you copy a formula what cell references in the formula you want to be relative and what you want to be absolute. If some cell references refer to input cells in the spreadsheet, you usually want those cells to be absolute.

The article below gives further instruction in absolute vs. relative cell references.

Excel uses two types of cell references to create formulas. Each has its own purpose. Read on to determine which type of cell reference to use for your formula.

This is the most widely used type of cell reference in formulas. Relative cell references are basic cell references that adjust and change when copied or when using AutoFill.

=SUM(B5:B8), as shown below, changes to =SUM(C5:C8) when copied across to the next cell.

Situations arise in which the cell reference must remain the same when copied or when using AutoFill. Dollar signs are used to hold a column and/or row reference constant.

In the example below, when calculating commissions for sales staff, you would not want cell B10 to change when copying the formula down. You want both the column and the row to remain the same to refer to that exact cell. By using $B$10 in the formula, neither changes when copied.

A more complicated example:

Let's pretend that you need to calculate the prices of items in stock with two different price discounts. Take a look at the worksheet below.

Examine the formula in cell E4. By making the first cell reference $C4, you keep the column from changing when copied across, but allow the row to change when copying down to accommodate the prices of the different items going down. By making the last cell reference A$12, you keep the row number from changing when copied down, but allow the column to change and reflect discount B when copied across. Confused? Check out the graphics below and the cell results.

Now, you might be thinking, why not just use 10% and 15% in the actual formulas? Wouldn't that be easier? Yes, if you are sure the discount percentages will never change - which is highly unlikely. It's more likely that eventually those percentages will need to be adjusted. By referencing the cells containing 10% and 15% and not the actual numbers, when the percentage changes all you need to do is change the percentage one time in cell A12 and/or B12 instead of rebuilding all of your formulas. Excel would automatically update the discount prices to reflect your discount percentage change.

Summary of absolute cell reference uses:

Relative & Absolute Cell References
$A1 Allows the row reference to change, but not the column reference.
A$1 Allows the column reference to change, but not the row reference.
$A$1 Allows neither the column nor the row reference to change.

There is a shortcut for placing absolute cell references in your formulas!

When you are typing your formula, after you type a cell reference - press the F4 key. Excel automatically makes the cell reference absolute! By continuing to press F4 , Excel will cycle through all of the absolute reference possibilities. For example, in the first absolute cell reference formula in this tutorial, =B4*$B$10, I could have typed, =B4*B10, then pressed the F4 key to change B10 to $B$10. Continuing to press F4 would have resulted in B$10, then $B10, and finally B10. Pressing F4 changes only the cell reference directly to the left of your insertion point.

I hope this tutorial has made these cell reference types "absolutely" clear!


Reference Examples

More than 100 reference examples and their corresponding in-text citations are presented in the seventh edition Publication Manual. Examples of the most common works that writers cite are provided on this page additional examples are available in the Publication Manual.

To find the reference example you need, first select a category (e.g., periodicals) and then choose the appropriate type of work (e.g., journal article) and follow the relevant example.

When selecting a category, use the webpages and websites category only when a work does not fit better within another category. For example, a report from a government website would use the reports category, whereas a page on a government website that is not a report or other work would use the webpages and websites category.

Also note that print and electronic references are largely the same. For example, to cite both print books and ebooks, use the books and reference works category and then choose the appropriate type of work (i.e., book) and follow the relevant example (e.g., whole authored book).

Reference examples are covered in Chapter 10 of the APA Publication Manual, Seventh Edition


The Rationale for the GRC

The availability of a high quality human genome assembly has revolutionized biomedical research. Genomics has now entered the realm of clinical genetics, with many groups using either whole genome sequencing [1],[2] or whole exome sequencing [3] to identify variants underlying diseases and informing treatment options [4]. Advances in technology have increased the number of sequenced human genomes however, de novo assembly of next generation sequencing reads is still problematic. The alignment of sequencing reads from these new genomes to a high quality reference genome remains a critical aspect of data interpretation [5].

While the human reference assembly is the highest quality mammalian assembly available, it is not without shortcomings. The “finished” assembly [6] contained over 300 gaps in the euchromatic portion of the genome, tiling path errors and regions represented by uncommon alleles. Furthermore, assessment of genome-wide variation revealed regions of the genome with complex, structurally diverse, allelic representations [7]–[9] that were insufficiently represented in the reference genome. Other analyses identified sequences that failed to align to the reference assembly either because the reference assembly contained a valid deletion allele or underrepresented multi-copy genes [10]–[13]. The Genome Reference Consortium (GRC) was formed to address these issues.

The GRC (the GRC consists of The Genome Institute at Washington University, The Wellcome Trust Sanger Institute, The European Bioinformatics Institute, and The National Center for Biotechnology Information) is an international consortium with expertise in genome mapping, sequencing, and informatics. The goal of the GRC is to provide high quality genome assemblies that will allow a user to place any sequence greater than 500 bp into a chromosome context. While this report focuses largely on recent GRC advances concerning the human reference assembly, the GRC is also responsible for the mouse and zebrafish reference assemblies. Continued improvement of the human reference assembly is critical as we move towards an era of clinical and personal genomics. The reference genomes of mouse and zebrafish are similarly critical in light of their importance as model organisms and the significant investments made in creating community resources such as gene knockout collections.


Morphogenesis

Our editors will review what you’ve submitted and determine whether to revise the article.

Morphogenesis, the shaping of an organism by embryological processes of differentiation of cells, tissues, and organs and the development of organ systems according to the genetic “blueprint” of the potential organism and environmental conditions.

Plant morphogenesis is brought about chiefly through differential growth. Permanent embryonic tissue results in a morphogenetic potential that varies greatly with the environment and continues to produce new organs throughout the life of the plant. Animal morphogenesis is accomplished by growth and by cell movement. A fixed pattern is established early the organism is determined as to shape, size, and organ complement. Once organs are formed, no new ones (with few exceptions) are produced. See also histogenesis organogenesis.

This article was most recently revised and updated by Robert Lewis, Assistant Editor.


Interleukin-10 and the interleukin-10 receptor

Interleukin-10 (IL-10), first recognized for its ability to inhibit activation and effector function of T cells, monocytes, and macrophages, is a multifunctional cytokine with diverse effects on most hemopoietic cell types. The principal routine function of IL-10 appears to be to limit and ultimately terminate inflammatory responses. In addition to these activities, IL-10 regulates growth and/or differentiation of B cells, NK cells, cytotoxic and helper T cells, mast cells, granulocytes, dendritic cells, keratinocytes, and endothelial cells. IL-10 plays a key role in differentiation and function of a newly appreciated type of T cell, the T regulatory cell, which may figure prominently in control of immune responses and tolerance in vivo. Uniquely among hemopoietic cytokines, IL-10 has closely related homologs in several virus genomes, which testify to its crucial role in regulating immune and inflammatory responses. This review highlights findings that have advanced our understanding of IL-10 and its receptor, as well as its in vivo function in health and disease.


An integrated pan-tropical biomass map using multiple reference datasets

We combined two existing datasets of vegetation aboveground biomass (AGB) (Proceedings of the National Academy of Sciences of the United States of America, 108, 2011, 9899 Nature Climate Change, 2, 2012, 182) into a pan-tropical AGB map at 1-km resolution using an independent reference dataset of field observations and locally calibrated high-resolution biomass maps, harmonized and upscaled to 14 477 1-km AGB estimates. Our data fusion approach uses bias removal and weighted linear averaging that incorporates and spatializes the biomass patterns indicated by the reference data. The method was applied independently in areas (strata) with homogeneous error patterns of the input (Saatchi and Baccini) maps, which were estimated from the reference data and additional covariates. Based on the fused map, we estimated AGB stock for the tropics (23.4 N–23.4 S) of 375 Pg dry mass, 9–18% lower than the Saatchi and Baccini estimates. The fused map also showed differing spatial patterns of AGB over large areas, with higher AGB density in the dense forest areas in the Congo basin, Eastern Amazon and South-East Asia, and lower values in Central America and in most dry vegetation areas of Africa than either of the input maps. The validation exercise, based on 2118 estimates from the reference dataset not used in the fusion process, showed that the fused map had a RMSE 15–21% lower than that of the input maps and, most importantly, nearly unbiased estimates (mean bias 5 Mg dry mass ha −1 vs. 21 and 28 Mg ha −1 for the input maps). The fusion method can be applied at any scale including the policy-relevant national level, where it can provide improved biomass estimates by integrating existing regional biomass maps as input maps and additional, country-specific reference datasets.

Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.


Citations and References

In your lab reports you will typically use information from sources such as your textbook, lab manual, a reference book, and articles published in a science or engineering journal. When you use information from sources, you need to tell the readers where the information came from and where the readers can locate the sources. This is what citations and references are for.

A citation tells the readers where the information came from. In your writing, you cite or refer to the source of information.

A reference gives the readers details about the source so that they have a good understanding of what kind of source it is and could find the source themselves if necessary. The references are typically listed at the end of the lab report.

There are many different forms of documentation (systems of citation and reference), varying across academic fields. You may be familiar with MLA (Modern Language Association) used in English or CBE (Council of Biological Editors) used in the life sciences. But even within academic fields there are different forms because different scholarly journals specify a system to be used in those journals.

Smart Advice: Find out what form of documentation is appropriate to use in your class before you write your first report. The best place to look is the lab manual. If you don't see the form of documentation given there, then ask the lab instructor or the professor of the lecture section.

More smart advice: If you can't find out from the lab manual or the teacher what form of documentation you should use, or if you are told to choose one on your own, find out what scholarly journal is appropriate to the field you are studying and use it as a guide to documentation. Find a recent copy of journal in the library or online. It will say what form that it uses (in the "guide to authors"). But you can also determine what to do by looking at how the citations and references are done in an article in the journal.

Generally speaking, there are three basic systems of documentation in science and engineering: the name-and-year system, the alphabet-number system, and the citation-order system. If your teacher says to use one of these systems, you can use the following brief descriptions to guide you in documenting sources:

The name-and-year system.

Citations: When you cite the source of information in the report, you give the names of the authors and the date of publication.

Jenkins and Busher (1979) report that beavers eat several kinds of herbaceous plants as well as the leaves, twigs, and bark of most species of woody plants that grow near water.

Beavers have been shown to be discriminate eaters of hardwoods (Crawford, Hooper, and Harlow 1976).

References: The sources are listed at the end of the report in alphabetical order according to the last name of the first author, as in the following book and article.

Crawford, H.S., R.G. Hooper, and R.F Harlow. 1976. Woody Plants Selected by Beavers in the Appalachian and Valley Province. Upper Darby, PA: U.S. Department of Agriculture.

Jenkins, S.H., and P.E. Busher. 1979. Castor canadensis. Mammalian Species. 120:1-8.

The alphabet-number system.

Citations: When you cite the source of information in the report, you give a number in parentheses that corresponds to the number of the source in the alphabetical listing in the "References."

Jenkins and Busher report that beavers eat several kinds of herbaceous plants as well as the leaves, twigs, and bark of most species of woody plants that grow near water (4).

Beavers have been shown to be discriminate eaters of hardwoods (3).

References: The sources are listed in alphabetical order and numbered accordingly, as in the following book and article.

The Citation-Order System (typically used in engineering--IEEE documentation).

Citations: When you cite the sources of information in the report, you give a number in brackets that corresponds to the number of the source listed in the order in which they appear in the report, the source listed first as [1], the next source [2], etc.

Jenkins and Busher report that beavers eat several kinds of herbaceous plants as well as the leaves, twigs, and bark of most species of woody plants that grow near water [1].

Beavers have been shown to be discriminate eaters of hardwoods [2].

References: The sources are listed in the order in which they are cited in the report, as in the following book and article.

Documentation on the Internet:

Help for using the documentation system of the Council of Biological Editors (for life sciences). The source is the Writing Center at the University of Wisconsin.

Help for using the documentation system of the American Chemical Society (for chemistry classes). The source is the Lehigh University Library.

© Copyright NC State University 2004
Sponsored and funded by National Science Foundation
(DUE-9950405 and DUE-0231086)


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Use cell references in a formula

When you create a simple formula or a formula by that uses a function, you can refer to data in worksheet cells by including cell references in the formula arguments. For example, when you enter or select the cell reference A2, the formula uses the value of that cell to calculate the result. You can also reference a range of cells.

For more information about cell references, see Create or change a cell reference. For more information about formulas in general, see Overview of formulas.

Click the cell in which you want to enter the formula.

In the formula bar , type = (equal sign).

Do one of the following, select the cell that contains the value you want or type its cell reference.

You can refer to a single cell, a range of cells, a location in another worksheet, or a location in another workbook.

When selecting a range of cells, you can drag the border of the cell selection to move the selection, or drag the corner of the border to expand the selection.

1. The first cell reference is B3, the color is blue, and the cell range has a blue border with square corners.

2. The second cell reference is C3, the color is green, and the cell range has a green border with square corners.

Note: If there is no square corner on a color-coded border, the reference is to a named range.

Tip: You can also enter a reference to a named cell or range. For more information, see Define and use names in formulas.


Watch the video: RETHINK EDUCATION: The Biology of Learning Featuring Dr. Andrew Huberman (September 2022).


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