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71. Shakespeare and Company Project Dataset: Lending Library Members, Books, Events

Author(s):
Kotin, Joshua; Koeser, Rebecca Sutton; Adair, Carl; Alagappan, Serena; Bauer, Jean; Browne, Oliver J.; Budak, Nick; Calver, Harriet; Chow, Jin; Davis, Ian; Doroudian, Gissoo; Engel, Currie; Green, Elspeth; Hicks, Benjamin; Joelson, Madeleine E.; Kelly, Carolyn; Krolewski, Sara; Li, Xinyi; Maag, Ellie; Mahoney, Cate; McCarthy, Jesse D.; Naydan, Mary; Ruehl, Isabel; Thode, Sylvie; VanSant, Camey; Wulfman, Clifford E.
Abstract:
The Shakespeare and Company Project makes three datasets available to download in CSV and JSON formats. The datasets provide information about lending library members; the books that circulated in the lending library; and lending library events, including borrows, purchases, memberships, and renewals. The datasets may be used individually or in combination site URLs are consistent identifiers across all three. The DOIs for each dataset are as follows: Members (https://doi.org/10.34770/ht30-g395); Books (https://doi.org/10.34770/g467-3w07); Events (https://doi.org/10.34770/2r93-0t85).
Type:
Dataset
Issue Date:
July 2020

72. A dual-mechanism antibiotic kills Gram-negative bacteria and avoids drug resistance

Author(s):
Martin, James K; Sheehan, Joseph P; Bratton, Benjamin P; Moore, Gabriel M; Mateus, André; Li, Sophia Hsin-Jung; Kim, Hahn; Rabinowitz, Joshua D; Typas, Athanasios; Savitski, Mikhail M; Wilson, Maxwell Z; Gitai, Zemer
Abstract:
The rise of antibiotic resistance and declining discovery of new antibiotics have created a global health crisis. Of particular concern, no new antibiotic classes have been approved for treating Gram-negative pathogens in decades. Here, we characterize a compound, SCH-79797, that kills both Gram-negative and Gram-positive bacteria through a unique dual-targeting mechanism of action (MoA) with undetectably-low resistance frequencies. To characterize its MoA, we combined quantitative imaging, proteomic, genetic, metabolomic, and cell-based assays. This pipeline demonstrates that SCH-79797 has two independent cellular targets, folate metabolism and bacterial membrane integrity, and outperforms combination treatments in killing MRSA persisters. Building on the molecular core of SCH-79797, we developed a derivative, Irresistin-16, with increased potency and showed its efficacy against Neisseria gonorrheae in a mouse vaginal infection model. This promising antibiotic lead suggests that combining multiple MoAs onto a single chemical scaffold may be an underappreciated approach to targeting challenging bacterial pathogens.
Type:
Dataset
Issue Date:
20 May 2020

73. Data from a flume experiment of passive scalar diffusion within vegetation canopies using laser-induced fluorescence

Author(s):
Ghannam, Khaled; Poggi, Davide; Katul, Gabriel; Bou-Zeid, Elie
Abstract:
This dataset is a sequence of laser-induced fluorescence images of a dye injected in a channel flow with canopy-like stainless steel rods simulating a vegetation canopy stand. The data is acquired close to the channel bottom at z/h=0.2, where z is the height referenced to the channel bed and h is the canopy height. The dataset provides spatial distribution of scalar concentration in a plane parallel to the channel bed. The data has been used (but the data itself has not been published or available to the public) in previous work. The references are: Ghannam, K., Poggi, D., Porporato, A., & Katul, G. (2015). The spatio-temporal statistical structure and ergodic behaviour of scalar turbulence within a rod canopy. Boundary-Layer Meteorology,157(3), 447–460. Ghannam, K, Poggi, D., Bou-Zeid, E., Katul, G. (2020). Inverse cascade evidenced by information entropy of passive scalars in submerged canopy flows. Geophysical Research Letters (accepted).
Type:
Dataset
Issue Date:
22 April 2020

74. Visual Analogy Extrapolation Challenge (VAEC)

Author(s):
Webb, Taylor; Dulberg, Zachary; Frankland, Steven; Petrov, Alexander; O'Reilly, Randall; Cohen, Jonathan
Abstract:
Extrapolation -- the ability to make inferences that go beyond the scope of one's experiences -- is a hallmark of human intelligence. By contrast, the generalization exhibited by contemporary neural network algorithms is largely limited to interpolation between data points in their training corpora. In this paper, we consider the challenge of learning representations that support extrapolation. We introduce a novel visual analogy benchmark that allows the graded evaluation of extrapolation as a function of distance from the convex domain defined by the training data. We also introduce a simple technique, context normalization, that encourages representations that emphasize the relations between objects. We find that this technique enables a significant improvement in the ability to extrapolate, considerably outperforming a number of competitive techniques.
Type:
Dataset and Image
Issue Date:
2020

76. Distinct cytoskeletal proteins define zones of enhanced cell wall synthesis in Helicobacter pylori

Author(s):
Taylor, Jenny A.; Bratton, Benjamin P.; Sichel, Sophie R.; Blair, Kris M.; Jacobs, Holly M.; DeMeester, Kristen E.; Kuru, Erkin; Gray, Joe; Biboy, Jacob; VanNieuwenhze, Michael S.; Vollmer, Waldemar; Grimes, Catherine L.; Shaevitz, Joshua W.; Salama, Nina R.
Abstract:
Helical cell shape is necessary for efficient stomach colonization by Helicobacter pylori, but the molecular mechanisms for generating helical shape remain unclear. We show that the helical centerline pitch and radius of wild-type H. pylori cells dictate surface curvatures of considerably higher positive and negative Gaussian curvatures than those present in straight- or curved-rod bacteria. Quantitative 3D microscopy analysis of short pulses with either N-acetylmuramic acid or D-alanine metabolic probes showed that cell wall growth is enhanced at both sidewall curvature extremes. Immunofluorescence revealed MreB is most abundant at negative Gaussian curvature, while the bactofilin CcmA is most abundant at positive Gaussian curvature. Strains expressing CcmA variants with altered polymerization properties lose helical shape and associated positive Gaussian curvatures. We thus propose a model where CcmA and MreB promote PG synthesis at positive and negative Gaussian curvatures, respectively, and that this patterning is one mechanism necessary for maintaining helical shape.
Type:
Dataset and Image
Issue Date:
April 2019

77. Climate Impacts from Large Volcanic Eruptions in a High-resolution Climate Model: the Importance of Forcing Structure

Author(s):
Yang, Wenchang; Vecchi, Gabriel; Fueglistaler, Stephan; Horowitz, Larry; Luet, David; Muñoz, Ángel; Paynter, David; Underwood, Seth
Abstract:
Explosive volcanic eruptions have large climate impacts, and can serve as observable tests of the climatic response to radiative forcing. Using a high resolution climate model, we contrast the climate responses to Pinatubo, with symmetric forcing, and those to Santa Maria and Agung, which had meridionally asymmetric forcing. Although Pinatubo had larger global-mean forcing, asymmetric forcing strongly shifts the latitude of tropical rainfall features, leading to larger local precipitation/TC changes. For example, North Atlantic TC activity over is enhanced/reduced by SH-forcing (Agung)/NH-forcing (Santa Maria), but changes little in response to the Pinatubo forcing. Moreover, the transient climate sensitivity estimated from the response to Santa Maria is 20% larger than that from Pinatubo or Agung. This spread in climatic impacts of volcanoes needs to be considered when evaluating the role of volcanoes in global and regional climate, and serves to contextualize the well-observed response to Pinatubo.
Type:
Dataset
Issue Date:
2019

79. Sound velocities in shock-synthesized stishovite to 72 GPa

Author(s):
Berryman, Eleanor J.; Winey, J. M.; Gupta, Yogendra M.; Duffy, Thomas S.
Abstract:
Stishovite (rutile-type SiO2) is the archetype of dense silicates and may occur in post-garnet eclogitic rocks at lower-mantle conditions. Sound velocities in stishovite are fundamental to understanding its mechanical and thermodynamic behavior at high pressure and temperature. Here, we use plate-impact experiments combined with velocity interferometry to determine the stress, density, and longitudinal sound speed in stishovite formed during shock compression of fused silica at 44 GPa and above. The measured sound speeds range from 12.3(8) km/s at 43.8(8) GPa to 9.8(4) km/s at 72.7(11) GPa. The decrease observed at 64 GPa reacts a decrease in the shear modulus of stishovite, likely due to the onset of melting. By 72 GPa, the measured sound speed agrees with the theoretical bulk sound speed indicating loss of all shear stiffness due to complete melting. Our sound velocity results provide direct evidence for shock-induced melting, in agreement with previous pyrometry data.
Type:
Dataset
Issue Date:
2019

80. Fast animal pose estimation using deep neural networks

Author(s):
Pereira, Talmo D.; Aldarondo, Diego E.; Willmore, Lindsay; Kislin, Mikhail; Wang, Samuel S.-H.; Murthy, Mala; Shaevitz, Joshua W.
Abstract:
Recent work quantifying postural dynamics has attempted to define the repertoire of behaviors performed by an animal. However, a major drawback to these techniques has been their reliance on dimensionality reduction of images which destroys information about which parts of the body are used in each behavior. To address this issue, we introduce a deep learning-based method for pose estimation, LEAP (LEAP Estimates Animal Pose). LEAP automatically predicts the positions of animal body parts using a deep convolutional neural network with as little as 10 frames of labeled data for training. This framework consists of a graphical interface for interactive labeling of body parts and software for training the network and fast prediction on new data (1 hr to train, 185 Hz predictions). We validate LEAP using videos of freely behaving fruit flies (Drosophila melanogaster) and track 32 distinct points on the body to fully describe the pose of the head, body, wings, and legs with an error rate of <3% of the animal's body length. We recapitulate a number of reported findings on insect gait dynamics and show LEAP's applicability as the first step in unsupervised behavioral classification. Finally, we extend the method to more challenging imaging situations (pairs of flies moving on a mesh-like background) and movies from freely moving mice (Mus musculus) where we track the full conformation of the head, body, and limbs.
Type:
Dataset
Issue Date:
30 May 2018

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