semans's blog

Sound perception and production in birds, especially oscines, has been the subject of much research. Birds’ singing and song learning systems have been studied from perspectives ranging from mechanical through neurological to social and adaptive. Mechanically speaking, birds produce song via the syrinx, an analog to the human larynx. Found at the entrance of the bronchioles, the syrinx is a group of connective tissues, cartilage rings, and membranes that vibrate in concert to produce sound. Sound itself comes not from the vibration of the medial tympaniform membranes but from connective tissue at the end of each bronchus that sticks into the syringeal lumen. From a neurological point of view, bird song perception, production, and learning originates in a series of neuronal nuclei heretofore referred to as the song pathway. Perception of song begins in auditory field L in conjunction with the NCM and CMM areas. These signals are then passed through the HVC, area X, LMAN, and DLM which all have song selective neurons that discriminate between different song types. Song production also comes from the song pathway and uses the same nuclei. Firstly, main auditory field L projects to both the HVC and RA, and the HVC itself projects to the RA. Secondly, from the RA is a projection to nXIIts, from which there is direct innervation of the syrinx, and thus, song production. Song learning also takes place in the song pathway, though this is less well understood and seems to have to do with the expression of immediate early genes (IEGs) such as ZENK in different neuronal nuclei depending on the acoustic environment.

A recent study by The New England Journal of Medicine has shown that public research institutes have had increased contribution to drug discovery. Since the dawn of biotechnology, it has generally been the case that public research institutions perform the basic research necessary to understand disease mechanisms while corporate research has been focused on developing drugs to treat diseases. However, after two acts passed in the mid 1980s, federally funded institutions and laboratories were granted the possibility to both freely publish their inventions in the scientific literature and convert them into intellectual property for commercialization. With a decade of delay, this change was reflected in the percentage of FDA approved drugs originating in the public sector. Between 1981 and 1999, only 7.6% of the FDA approved biological molecules came from non-industry sources. Whereas, between 1998 and 2007, 24.1% of the FDA approved biological molecules came from public research institutions. Lastly, the study suggests that public sector research aims to discover drugs that are expected to have a large clinical impact.

Building the Figure

    I created a Google Slides presentation with a blank template. I changed the size of the slide by going to the File tab, scrolling down to Page Setup, choosing the Custom option, and making the slide 15.15 x 7.85 in. I added the “close-up”, “contextual”, and “sylvan_map” images to the slide. I cropped the “sylvan_map” image to include only the map up until right hand most edge of Parking Lot 44. By right clicking the “sylvan_map” image and going to Format options, and opening the Size & Rotation dropdown menu, I scaled the image to 9.84 x 7.95 in. Using the same method, I scaled both the “close-up” and “contextual” images to 5.31 x 3.92 in. I placed the “sylvan_map” image flush against the right side of the slide. I placed the “close-up” image above the “contextual” image, and fitted them in the remaining space, flush against the left side of the slide.

Self care: 575 min

I woke up and took a shower for 5 minutes. I made and drank a protein shake for 5 minutes. I made and drank my coffee over 10 minutes. I acquired a coffee from the cafeteria and drank it over about 15 minutes. I had dinner which took 10 minutes. I brushed my teeth for 5 minutes. I read my book for 75 minutes. I slept for 450 minutes.

Homework: 440 min

Class: 330 min

Travel: 50 min

Using a laptop, a folder called “Figure” was created on the desktop. The “Detailed Campus Map” PDF was downloaded from https://www.umass.edu/visitorsctr/campusmaps and saved to the “Figure” folder as “campus_map”. The “campus_map” PDF was uploaded to https://www.pdf2go.com/split-pdf where the legend page was deleted and the map page re-downloaded. The map page was saved to the “Figure” folder under the name “campus_map”. A copy of the map file was made and named “sylvan_map”. The “sylvan_map” file was uploaded to https://pdfresizer.com/crop and cropped such that the “Sylvan Residential Area” text appeared in the centre. Additionally, the cropped image’s margin included: the grey area below the “Sylvan Residential Area” text; the part of Eastman Lane leading past North Apartments A & B and up to the Sylvan area; most of North A and some of North B; parking lot 44 to the right of the Sylvan area; and both parking lots numbered 47 next to Cashin and behind MacNamara. The file was then saved to the “Figure” folder as “sylvan_map_resize”. Both the “campus_map” file and “sylvan_map_resize” file were converted to PNG format at https://pdf2png.com/, redownloaded, and saved to the “Figure” folder. The close-up and contextual pictures were downloaded from email and saved to the “Figure” folder as “close-up” and “contextual”, respectively.

The pictures were all taken at 8:45AM on a sunny, windless day. First, a pen was held next to the subject. Then, a smartphone camera with flash turned off was aimed at the specimen, such that the camera was held flat and pointed directly at the specimen without angling the camera. Then, with the pen slightly offset, hand holding the pen out of shot, and the subject at the centre of the shot, several pictures were taken. The images were then self-emailed.

At 9:00AM a picture contextualizing the phytophagy was taken. The picture was taken from the path next to the divot and about ten metres down from the pedestrian crossing. The shot was taken from eye level, pointing the smartphone camera directly towards the hillock, and placing the specimen’s location more or less centrally in the picture. The bottom two thirds of the shot were made up of hillside and the top third was forest, including the subject of the close-up image. The images were then self-emailed.

The methods section of the leaf-mining paper is divided into three subheadings, each describing a different part of experimental data collection. The leaf-mining paper’s results section is divided into four subheadings, each explaining a different part of the data collected. The second section of the slime-mold paper describes the reasons for which the experimental subject was chosen, serving a similar purpose to the leaf-mining paper’s introduction. In the slime-mold paper, the third and fourth sections serve as a combined methods and results section. These parts of the paper both describing how the experiments were carried out and the results thereof. 

The discussion portion of the leaf-mining paper is subdivided under three headings and details the implications of the study as well as plausible avenues of future investigation. The fifth section of the slime mold paper takes a step back from the experiment and instead describes why the subject of the study was chosen as it applies to another field. The final section of the slime mold paper bears similarities to the discussion portion of the leaf-mining paper, as it too describes the implications of the research and areas of future inquiry. 

The documents both start with the title of the paper in bold followed by the names of the authors. The slime mold paper labels the abstract as such while the leaf-mining paper does not, though both abstracts are found at the start of each paper. The leaf-mining paper is structured like classic primary literature, featuring level 1 headings for the introduction, methods, results, discussion, and references sections, as well as various level 2 headings within each section. However, the slime mold paper is organized by topic using only level 1 headers. 

The abstracts of both papers are short paragraphs describing the object of and reason for the study. The introduction to the leaf-mining paper opens with an explanation as to why the subject of the study was chosen, followed by a series of explanatory paragraphs concerning the reasons for the study. The first section of the slime mold paper describes the conceptual question at hand and addresses the reason for the study.

The object is a stem ending in three glossy, green leaves featuring some red-brown splotches. The stem is a matte, reddish-brown colour covered in fuzzy, white hairs. The leaves have similar hair extending out from their contours, though individual hairs are thicker, sparser and have a yellow tinge. The leaves are somewhat opaque, their yellow-green vein systems letting through the most light and creating a scale-like pattern on each leaf. Each leaf is shaped like an extended, rounded V, topped with a series of nubs that build symmetrically into a point. From the middle leaf's top to the stem's end the object is 7.7 cm long. Though waxy on top, the leaves are matte underneath, paler in colour, and rougher in texture.