Making Figures with Inkscape

Submitted by sbrewer on Fri, 09/20/2019 - 11:59

Screencasts for making multipanel scientific figures using Inkscape

Creating Figures: Part 1. Compositing
Creating Figures: Part 2. Labels and Arrows
Creating Figures: Part 3. Document Properties and Exporting

Hints

  • Think ahead of time. What is your figure going to look like? Should you crop imagery ahead of time? Do you need to adjust image or exposure? (Note: Some journals don't allow digital manipulation of imagery). Do this in a bitmap editing program (e.g. GIMP or Photoshop).
  • Do all your work in a folder. Put your image files in there. Save your SVG file in there. Save early and often.

Workflow

  1. Import all your images: Either Link or Embed. Note things can be “above” or “below” others. Click or drag over to select. Hold the “shift” key to select multiple objects.
  2. Composite your images to make your design: Lock proportions to avoid stretching. Turn “snapping” on or off. Set height and width directly to resize. Use Align and Distribute (switch to "relative to first selected").
  3. Construct one label: Consider font and contrast.
  4. Duplicate label to make more: Select label, duplicate object, move. Repeat as necessary.
  5. Finish each label: Replace each letter as necessary. Use Align and Distribute to center. Use align and distribute to put labels at corners of each panel.
  6. Create arrows: Use the Line Tool to draw a straight line segment (click, click-click). Then use Fill and Stroke tool to set the line width and add arrow head to start (or end).
  7. Set the Page Size: Open Document Properties. Resize Page to Drawing. Set background to not be transparent (increase alpha channel to 255).
  8. Export Finished Figure: Export PAGE. Set width to 1200pixels. Save with name “Lastname-Original.png” The resultant PNG file is your finished figure.

Note: Do not share your finished figure or include in your METHODS manuscript until your methods have been followed!

Seaweed. (1hr writing session for missing a day)

Submitted by rbudnick on Sat, 09/21/2019 - 22:59

There are 7 types of popular edible seaweed: Wakame, Kombu, Nori, Dulse, Hijiki, Irish Moss, and Sea Lettuce. Seaweed is a part of the diets of many cultures which border the sea, and is especially popular in Japan. Seaweed has a salty, rich, and savory taste due both to the environment it grows in and amino acids called glutamates which greatly enhance its unique flavors. Often labeled as a super food, seaweed contains a wide variety of minerals (sodium, magnesium, phosphorus, potassium, zinc, iodine, and iron to name a few) and important vitamins including A, C, E, and B12. Seaweed is not only a relatively easy and abundant food to grow, but one which will offer excellent nutritional benefits to those who consume it. 

From an agricultural perspective, the cultivation of edible seaweed is far more environmentally conscious than traditional farming and traditional foods. It can either be maintained and harvested from naturally occurring clusters, or grown in isolated areas specifically for cultivation. No deforestation and fertilization of land is needed to successfully grow seaweed crops. The plant itself is excellent at absorbing CO2, which has continued to build up in the ocean along with increasing acidity. Since seaweed absorbs so much carbon, it can also be used as a carbon donor to other environments which are very carbon poor. Seaweed also has great potential to be used as a biofuel and if brought into the energy industry could provide an extremely environmentally conscious alternative to traditional fuels. 

Currently, Asian-Pacific countries lead the world in agricultural seaweed production, with countries including Australia joining in on the process. If the coastal countries of the would invest in commercial seaweed production, the impact could be drastic. The problem is that not every culture has accepted seaweed into its diet. For most of the eastern world, seaweed is not considered a particularly valuable food source. If cultures and societies could accept seaweed, production would increase dramatically. 

Over the past few years, scientists and farmers alike have become more aware of the positive effect seaweed cultivation has on the environment. As the planet continues to change both on land and in the sea, it is important to do all we can as a species to try and reverse the damage we have caused. Agricultural production of seaweed is just one step in the process. 

Neuron Staining Techniques

Submitted by semans on Sat, 09/21/2019 - 10:56

The lack of neuron staining techniques prior to the Nissl stain and the Golgi stain. Though Nissl’s technique came first, it only revealed neurons’ endoplasmic reticulum and parts of the cell body. It was only until Camillo Golgi developed his staining method, first known as the “black reaction”, that neurons as a whole were revealed. This was a groundbreaking technique that led to decade long debates about the nature of the nervous system, especially as to whether neurons were contiguous or separate. Since then, staining techniques have evolved to allow imaging of anything from axonal networks to individual neuropeptides. The Weigert-Weil stain enables us to visualise the myelin sheath of axons, giving us the opportunity to observe how connections are established throughout the brain. Modern techniques like in-situ hybridization (ISH) allow us to see which genes are expressed in a sample of neurons. The first step in ISH involves binding a labelled mRNA strand complementary to the mRNA produced by the gene of interest. The second step involves the introduction of a primary antibody with a variable region keyed to the mRNA label binds to the mRNA strand. The final step is injection of fluorescently labelled secondary antibodies with variable regions that recognize the species-specific heavy chain of the primary antibodies, and then imaging the cells with the appropriate wavelength of light. This technique allows scientists to know which neurons are expressing the gene of interest. Another modern staining method called immunohistochemistry (IHC) is also an antibody stain that uses fluorescently labelled antibodies to visualise certain molecules. However, as opposed to ISH, IHC reveals the presence of proteins such as neuropeptides, which can also be indicative of neuronal function.

Draft#10

Submitted by ashorey on Fri, 09/20/2019 - 23:16

Today I would like to remark at the incredible burst of knowledge that occured in the scientific field with the technological revolution. I learned today that the scientist that discovered tubulin is still alive today. That put in perspective to me that so much of what we currently accept as common knowledge in almost all scientific fields are relatively recent discoveries and theories. The growth of technology and advanced methods of experimenting and researching all sprung up in a short hundred years of human history. What amazes me the most is the ability of the science community to adapt and accept the new findings as they accumulate so quickly. The fact that our classes are making common knowledge of things discovered within 20 years is remarkable to me and speaks volumes about the ability of education. I also now ponder that is this is only the beginning of the technological revolution and realization of what that means for science, how much can the future hold? Are we just on the brink on a never-before-phathomed amount of things there are to learn about life and organisms and evolution? I think the answer to the question can only be yes, and that is exciting and terrifying. 

Methods Draft

Submitted by nskinner on Fri, 09/20/2019 - 19:58

Phytophagy is the act of consuming plants. This can be done in many ways and evidence of this is all around us. Right here on campus at the University of Massachusetts, phytophagy is present in the form of insects consuming leaves. On a warm sunny day in fall around 4:00pm on a Friday I left the BCRC room in Morrill Science Center III south by taking a right down the hallway. At the end of the hallway I took a left and then a left again through a big heavy door into the stair well that has the walls painted with various themes of science. I walked to the bottom of the stair well and opened the door to a new hallway where I took a left. I went through a set of doors, down a short set of stairs and through the last set of doors finally stepping outside. I walked down the side walk to the left and then went down the first set of stairs on the right. I walked down the short set of stairs and crossed the crosswalk located at the bottom of the stairs. I was sure to look both ways before crossing the street and made sure no cars where coming. Once across the street I walked across the east lawn heading towards the library tower. At the edge of the campus pond there are two granite benches. The bench on the left is located between two trees. The tree on the right in-between the two benches has a small shoot growing from the base f the adult tree. Halfway up this shoot is a leaf that has three large wholes in the center of the leaf almost in a clover shape. It also has two smaller holes towards the apice of the leaf one on each side of the main venation of the leaf. On the left side of the leaf there is a series of holes in what looks like a “cancer ribbon” shape. In my left hand I held the leaf and a ruler on the inches side to show that the leaf is approximately 2 inches long which is approximately 5 centimeters. I held the leaf and measured it with the stem to the left and the apice to the right. I took the picture with my phone.

Swamp Sparrow Perfect Paragraph

Submitted by nskinner on Fri, 09/20/2019 - 19:36

The Melospiza georgiana, more commonly known as the swamp sparrow, resides in sedge swamps that include cat tails, tussocks and various shrubs. Swamp sparrows eat insects and seeds and can be found foraging on mud at the edge of the water, as well as flying from shrub to shrub; often shrubs are no more than 1.5-2 meters high. They can be found in New England year-round and breeding occurs sometime between April and June.

 Male swamp sparrows singing attracts females to mate. Males will attract a mate to a territory that to which he claims. The male will chase out any intruding males within his territory, often with the help of his female. During the spring months, swamp sparrows can be observed gathering materials for nest making, copulating, and foraging within their territories. Swamp sparrows tend to build their nests off the ground in a low growth shrub. They cover their nest with grasses to camouflage it. With the nest being a little higher than ground level, there’s plenty of room for the water level in the swamp to rise and fall as precipitation occurs. Swamp sparrows usually lay between 4-5 eggs in a nest. Only females incubate the eggs while the male brings food to the female.

After the eggs have hatched, usually after 12-13 days of incubating, both males and females will feed the young. The young are altricial, meaning they are extremely vulnerable, unable to walk, fly or feed themselves. The young may leave the nest after about 10-13 days after hatching. Swamp sparrows may have up to two broods during a season.

Perfect Paragraph 3

Submitted by dfmiller on Fri, 09/20/2019 - 17:49

The pursuit of green energy is a necessity to combat climate change; this much is certain. However, the way we are approaching this transition to renewable energy needs to be reevaluated. Green initiatives across the world tout wind, solar, and a distancing from fossil fuel-based energy production as goals not only in their respective countries, but globally. One green source of energy seems to be missing from this conversation, and that is nuclear. Nuclear energy has become unfavorable in the eyes of climate activists for several reasons, mainly their association to nuclear weapons and the possibility of meltdowns. What these activists have not been studying, however, is new progress in liquid fluoride thorium reactors (LFTR). These reactors are meltdown-resistant via new safety features. LFTRs feature a dump tank sealed off by a salt plug that melts in the case of an emergency. These reactors also cannot meltdown, since the core reaction is already in the molten state. Obtaining weapons-grade uranium from an LFTR is difficult, since these products are in solution with molten salt in the reactor. In addition, these reactors do not produce as much long-lived nuclear waste as traditional uranium-based reactors. Nuclear energy is the only real, efficient solution to our energy crisis, and therefore deserves a front and center place in global discussion.

Neurobiology History Perfect Paragraph

Submitted by semans on Fri, 09/20/2019 - 16:35

The history of neurology is a fragmented one fraught with disagreements, propositions, and rebuttals, often taking two steps forward and one step back. The earliest evidence of brain surgery dates back to prehistoric skulls with the marks of trepanation and subsequent recovery. Many millennia later in 400BCE, the Ancient Greeks discovered the separation between the central nervous system (CNS) and peripheral nervous system (PNS), though opinions were split as to the function of the brain. Two hundred years later, Galen of Ancient Rome found cerebrospinal fluid (CSF) in sheep skulls and, in the current of the bodily humours popular at the time, concluded that it was this liquid that gave rise to the conscious mind. Records of brain research in the Occident end there for nearly 1700 years, until the 16th century. During the Renaissance, Leonardo da Vinci restarts the study of brain anatomy and makes detailed drawings of the brain and its ventricles. In the mid-1500s, Andreas Vesalius dissects the bodies of executed prisoners and refutes Galen’s hypothesis that CSF is the seat of consciousness, claiming that the brain matter gives rise to the mind. However, in the 1600s, Descartes counters Vesalius’ theory in saying that the mind and brain are separate entities, thus giving birth to Dualism. This idea wouldn’t last long in the field of neurology as Willis and Wren’s study of brain anatomy led them to the same conclusion as Vesalius, brain matter not CSF holds human consciousness. Many small discoveries over the next centuries resulted in the discovery that nerves communicate via electricity and that different parts of the brain are responsible for different functions. The functional unit of the brain, the neuron, was only discovered in the 1900s when they were stained by Camillo Golgi. For decades Golgi and his colleague Santiago Ramon y Cajal would debate neuronal function. Golgi favoured the idea that neurons formed a contiguous system while Cajal hypothesized that neurons were separable, discrete units. Finally, as we approach the 21st century, the advent of the electron microscope vindicated Cajal’s theory. Neurons are in fact the basic unit of the brain and, though separate, they communicate via synapses.

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