MBLWHOI Library

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For over a century, the MBLWHOI Library has been the intellectual heart of the Woods Hole scientific community. Today the Library is internationally recognized as defining current trends and practices in marine information sciences and bioinformatics.

The Marine Biological Laboratory and the Woods Hole Oceanographic Institution maintain a vital partnership in the day-to-day operation of the MBLWHOI Library. The Library continues to build one of the most unique print and electronic literature collections in the biological, biomedical, ecological, and oceanographic sciences. The Library has broken the physical barriers of the charming village and surrounding waters of Woods Hole, to serve the cutting edge bio information needs of affiliated researchers worldwide, often no more than a single email message away.

In addition to serving MBL and WHOI scientists daily, the staff and resources of the MBLWHOI Library are utilized year round by the distinguished resident research and education programs of the MIT/WHOI Joint Program, the Sea Education Association, NOAA National Marine Fisheries Service, and the United States Geological Survey. The Library also supports a unique summer population of visiting researchers and students from more than 200 institutions worldwide.

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A new framework for quantifying alongshore variability of swash motion using fully convolutional networks

(Elsevier, 2024-05-24) Salatin, Reza ; Chen, Qin ; Raubenheimer, Britt ; Elgar, Steve ; Gorrell, Levi ; Li, Xin

Waves running up and down the beach (‘swash’) at the landward edge of the ocean can cause changes to the beach topology, can erode dunes, and can result in inland flooding. Despite the importance of swash, field observations are difficult to obtain in the thin, bubbly, and potentially sediment laden fluid layers. Here, swash excursions along an Atlantic Ocean beach are estimated with a new framework, V-BeachNet, that uses a fully convolutional network to distinguish between sand and the moving edge of the wave in rapid sequences of images. V-BeachNet is trained with 16 randomly selected and manually segmented images of the swash zone, and is used to estimate swash excursions along 200 m of the shoreline by automatically segmenting four 1-h sequences of images that span a range of incident wave conditions. Data from a scanning lidar system are used to validate the swash estimates along a cross-shore transect within the camera field of view. V-BeachNet estimates of swash spectra, significant wave heights, and wave-driven setup (increases in the mean water level) agree with those estimated from the lidar data.
An Academic Service Learning (AS-L) Activity within an Undergraduate Course in Pharmacology

(Journal of Toxicological Education, 2013) Billack, Blase

Academic service learning (AS-L) is a type of active learning in which a student demonstrates knowledge and understanding through service to the community and reflection. The present report describes an activity in which AS-L was implemented as part of an undergraduate pharmacology course. The course is common to the curricula of the Doctor of Pharmacy, Physician Assistant and Toxicology programs at St. John’s University. In the AS-L project, students were charged to develop a presentation which they would then give to members of the community who were unfamiliar with the presentation topics. Students worked in teams and formed their presentations around discussion topics such as drugs versus natural substances, the medical benefits of drugs, the possible toxicities of drugs both legal and illegal, or the mechanisms by which drugs enter or leave our bodies. The student teams then traveled to various service sites throughout the greater university community with the goal of community outreach through education. In the present report, strengths and limitations of the AS-L project have been noted. The major strength of the project, as indicated from student reflection papers, was that each student in the team became an active learner and the otherwise “passive learning” environment of the classroom became an active one at the service site. All students in the team presented and answered questions. A major limitation of the activity was finding a suitable instrument for the assessment of student learning. Future AS-L courses of this type are anticipated to include pre and post surveys.
Advancing Open Source, Linked Data Solutions for Cross-Repository Discovery and Collaboration

( 2016-05) Raymond, Lisa ; Mickle, Audrey

The MBLWHOI Library collaborated in multi-year NSF EarthCube funded projects, applying semantic technologies to enable knowledge discovery, sharing, and integration
Adventures in Minimal Marc and Bulkimport

( 2009-10-12T17:50:22Z) Rioux, Margaret A.

Method for adding data, such as OCLC numbers or URLs to bibliographic records in an Ex Libris Voyager library system using minimal Marc records and Bulkimport
Agents of Bioterrorism: Curriculum and Pedagogy in an Online Masters Program

(Journal of Toxicological Education, 2013) Page, Eric ; Gray, Joshua P.

The Agents of Bioterrorism course (BSBD 640, University of Maryland University College) is a graduate level course created in response to an elevated need for scientists working in the field of medical countermeasures to biological and chemical weapons in the years following 9/11. Students read and evaluate assigned current primary literature articles investigating medical countermeasures at each stage of development. In addition, students learn concepts of risk assessment, comparing and ranking several agents of terror. Student learning is assessed through a variety of assignments. A term paper focuses on a lesser known weapon of terror, with students recommending the best countermeasure in development and delivering a risk assessment comparing their agent to other major weapons of terror discussed throughout the semester. Similarly, a group project on an assigned major weapon of terror (anthrax, plague, smallpox, vesicants, or nerve agent) focuses more heavily on evaluating primary literature and concluding which countermeasure(s) in development are the best. Students complete the course with a fundamental understanding of the mechanism of action of many biological agents, information literacy for the medical literature available at PubMed and the primary scientific literature, and a basic understanding of the role of the government in biodefense research. This paper describes the pedagogical approaches used to teach this course and how they might be adopted for other courses.
The Alvin Bibliography: from paper to on-line access

(IAMSLIC, 1994) Berteaux, Susan S.
Ameripathidae, a new family of antipatharian corals (Cnidaria, Anthozoa, Hexacorallia, Antipatharia)

(Pensoft Publishers, 2024-05-31) Horowitz, Jeremy ; Opresko, Dennis M. ; Herrera, Santiago ; Hansel, Colleen M. ; Quattrini, Andrea M.

A new family of antipatharian corals, Ameripathidae (Cnidaria: Anthozoa: Antipatharia), is established for Ameripathes pseudomyriophylla Opresko & Horowitz, gen. et sp. nov. The new family resembles Myriopathidae and Stylopathidae in terms of the morphology of the polyps and tentacles and the pinnulate branching of the corallum. Phylogenetic analysis using a genomic data set of 741 conserved element loci indicates that the new family is sister to a clade containing the Myriopathidae, Stylopathidae, Antipathidae, and Aphanipathidae.
Anatomie menschlicher Embryonen. I. Embryonen des ersten Monats

(Verlag von F. C. W. Vogel, 1880) His, Wilhelm
An annotated list of the vascular plants growing without cultivation in the Town of Falmouth (Barnstable Co.), Massachusetts

( 2009-02-27T17:09:04Z) Backus, Richard H. ; Polloni, Pamela T.
An Arctic ecosystem : the coastal tundra at Barrow, Alaska

(Dowden, Hutchinson & Ross, Inc., 1980) Brown, Jerry ; Miller, Philip C. ; Tieszen, Larry L. ; Bunnell, Fred

From the Foreward: This book is one of a series of volumes reporting results of research by U. S. scientists participating in the International Biological Program (IBP). As one of the 58 nations taking part in the IBP during the period July 1967 to June 1974 , the United States organized a number of large, multidisciplinary studies pertinent to the central IBP theme of "the biological basis of productivity and human welfare."
Argon and the pathophysiology of pulmonary oxygen toxicity

( 2011-05-23) Shanklin, D. Radford

Molecular interaction can be determined from biological experiments. In the case of dynamics at the atmosphere-lung interface the physicochemical and atomic attributes of inhalant gases has significant biological and pathogenetic consequences. Hyaline membrane disease (HMD) is a common and sometimes lethal disorder, especially in premature newborns. Current therapy includes artificial ventilation and increased oxygen in the inspired air, despite evidence the lesions can be induced by oxygen enrichment [Lab.Invest. 21 439, 19691. Bilateral cervical vagotomy (BCV) is a standard method of inducing ventilatory distress which leads to HMD [J Exp.Med. 66:397, 1937; Biol.Neonat. 6:340, 1964; Biol. Neonat. 1 1 :6 I. 19671. The lungs of post-vagotomy newborn rabbits show the lesions of HMD in extent directly proportionate to the percentage of oxygen in polybaric (0.2 - 3.0 Atm.Abs) mixtures with nitrogen. Avery [Pediatrics 32:801, 19631 found that lesions of HMD did not form at very low levels of oxygen (3-4% in nitrogen] in various newborn animals. suggesting that inhalant hypoxia was not a pathogenetic factorper se. The observation of lung injury proportionate to oxygen percentage indicates the physiological axiom of gas effects by their partial pressure is an artefact of sea level gas dynamics. The toxic effect of oxygen can be viewed as nitrogen lack. Some lung injury does occur when only 3 and 7 per cent oxygen in nitrogen is used, suggesting rather a specific oxygen effect. When nitrogen is replaced by hydrogen, helium. neon, argon, or sulfur hexafluoride, the extent of lesions often increases, indicating again a fundamental oxygen-nitrogen interaction. Low level studies with hydrogen and argon are especially instructive with and without BCV: (1) extremely long survival without BCV in oxygen-argon at 3% and 7 %; (2) significant but less enhancement of survival in 3% oxygen-hydrogen; (3) no distinction in survival after BCV for 3% oxygen in nitrogen or hydrogen; (4) a pattern of lesion formation in the alternative gas mixtures which suggests nitrogen has a partially protective effect along with its stochastic competition for a conlmon oxygen-nitrogen receptor or transmembrane port; and (5) generally, the mammalian lung is well adapted by evolution to current atmospheric composition but at the price of more inhaled oxygen than is required for cellular function [Perspect.Biol.Med. 13:80, 19691, allowing for toxic effects. The distinctions amongst these gases in the biologic sense are due to differences in their mass, moiloatomic or diatomic structure: possibly viscosity in air passageway flow, inherent energy state, and at low levcls, in the electron saturation of the outer atomic shell. Unbuffered oxygen enrichment of air for ventilatory support is fundamentally injurious; hydrogen has obvious risks in a clinical setting but argon, which is abundant, non-flammable, and relatively non-toxic, may be the diluent gas of choice for ventilatory support.
Atlantic Ocean atlas of temperature and salinity profiles and data from the International Geophysical Year of 1957-1958

(Woods Hole Oceanographic Institution, 1960) Fuglister, Frederick C.

From the Preface: Within the framework of the observational program in physical oceanography which was executed during the International Geophysical Year of 1957-58, the WOODS HOLE OCEANOGRAPHIC INSTITUTION, Woods Hole, Massachusetts, in partial association with the NATIONAL INSTITUTE OF OCEANOGRAPHY, England, performed a methodical oceanographic survey covering most of the Atlantic Ocean. Supplemented with similar observations made in the western North Atlantic just prior to the IGY, the data obtained constitute a comprehensive new body of information pertaining to the circulation of the entire Atlantic. To summarize many of the observations in a particularly useful and efficient manner, as well as to perform a fundamental analysis upon them, the following atlas of Atlantic thermohaline structure has been prepared. Although distributions of other properties measured on these cruises might also have been depicted in this volume, it was felt that a more coherent and serviceable atlas would be produced if attention were concentrated exclusively upon temperature and salinity; the measurements of these two variables, moreover, are of consistent quality, since they were all made by a single small research group employing the same techniques and equipment throughout the survey period.
Axonal maintenance, glia, exosomes, and heat shock proteins

(F1000 Research, 2016-02-22) Tytell, Michael ; Lasek, Raymond J. ; Gainer, Harold

Of all cellular specializations, the axon is especially distinctive because it is a narrow cylinder of specialized cytoplasm called axoplasm with a length that may be orders of magnitude greater than the diameter of the cell body from which it originates. Thus, the volume of axoplasm can be much greater than the cytoplasm in the cell body. This fact raises a logistical problem with regard to axonal maintenance. Many of the components of axoplasm, such as soluble proteins and cytoskeleton, are slowly transported, taking weeks to months to travel the length of axons longer than a few millimeters after being synthesized in the cell body. Furthermore, this slow rate of supply suggests that the axon itself might not have the capacity to respond fast enough to compensate for damage to transported macromolecules. Such damage is likely in view of the mechanical fragility of an axon, especially those innervating the limbs, as rapid limb motion with high impact, like running, subjects the axons in the limbs to considerable mechanical force. Some researchers have suggested that local, intra-axonal protein synthesis is the answer to this problem. However, the translational state of axonal RNAs remains controversial. We suggest that glial cells, which envelop all axons, whether myelinated or not, are the local sources of replacement and repair macromolecules for long axons. The plausibility of this hypothesis is reinforced by reviewing several decades of work on glia-axon macromolecular transfer, together with recent investigations of exosomes and other extracellular vesicles, as vehicles for the transmission of membrane and cytoplasmic components from one cell to another.
Basin-dependent response of Northern Hemisphere winter blocking frequency to CO2 removal

(Nature Research, 2024-05-23) Hwang, Jaeyoung ; Son, Seok-Woo ; Martineau, Patrick ; Sung, Mi-Kyung ; Barriopedro, David ; An, Soon-Il ; Yeh, Sang-Wook ; Min, Seung-Ki ; Kug, Jong-Seong ; Shin, Jongsoo

Atmospheric blocking has been identified as one of the key elements of the extratropical atmospheric variabilities, controlling extreme weather events in mid-latitudes. Future projections indicate that Northern Hemisphere winter blocking frequency may decrease as CO2 concentrations increase. Here, we show that such changes may not be reversed when CO2 concentrations return to the current levels. Blocking frequency instead exhibits basin-dependent changes in response to CO2 removal. While the North Atlantic blocking frequency recovers gradually from the CO2-induced eastward shift, the North Pacific blocking frequency under the CO2 removal remains lower than its initial state. These basin-dependent blocking frequency changes result from background flow changes and their interactions with high-frequency eddies. Both high-frequency eddy and background flow changes determine North Atlantic blocking changes, whereas high-frequency eddy changes dominate the slow recovery of North Pacific blocking. Our results indicate that blocking-related extreme events in the Northern Hemisphere winter may not monotonically respond to CO2 removal.
Best practices for Core Argo floats—Part 2: Physical handling, deployment and metadata considerations

(Frontiers Media, 2024-04-03) Morris, Tamaryn ; Scanderbeg, Megan ; West-Mack, Deborah ; Gourcuff, Claire ; Poffa, Noe ; Udaya Bhaskar, T. V. S. ; Hanstein, Craig ; Diggs, Steve ; Talley, Lynne D. ; Turpin, Victor ; Liu, Zenghong ; Owens, Breck

Following on from Part 1: Best Practices for Core Argo floats - Getting started and data considerations, we present Part 2: Best Practices for Core Argo floats in terms of physical handling and deployments and recommended metadata parameters. The objective is to encourage new and developing scientists, research teams and institutions to contribute to the OneArgo Program through increased deployments regionally, specifically to the Core Argo mission. Only by leveraging sustained contributions of current Core Argo float groups with new and emerging Argo teams and users, can the OneArgo initiative be realized. This paper makes involvement with the Core Argo mission smoother by providing a framework endorsed by a wide community for these observations.
The Biodiversity Heritage Library : advancing metadata practices in a collaborative digital library

(Taylor & Francis, 2010-04) Pilsk, Suzanne C. ; Person, Matthew A. ; deVeer, Joseph M. ; Furfey, John F. ; Kalfatovic, Martin R.

The Biodiversity Heritage Library is an open access digital library of taxonomic literature, forming a single point of access to this collection for use by a worldwide audience of professional taxonomists, as well as “citizen scientists.” A successful mass-scanning digitization program, one that creates functional and findable digital objects, requires thoughtful metadata work flow that parallels the work flow of the physical items from shelf to scanner. This article examines the needs of users of taxonomic literature, specifically in relation to the transformation of traditional library material to digital form. It details the issues that arise in determining scanning priorities, avoiding duplication of scanning across the founding 12 natural history and botanical garden library collections, and the problems related to the complexity of serials, monographs, and series. Highlighted are the tools, procedures, and methodology for addressing the details of a mass-scanning operation. Specifically, keeping a steady flow of material, creation of page level metadata, and building services on top of data and metadata that meet the needs of the targeted communities. The replication of the BHL model across a number of related projects in China, Brazil, and Australia are documented as evidence of the success of the BHL mass-scanning project plan.
Building repositories: why DSpace?

( 2007-10-25) Devenish, Ann

This presentation looked at the process of selecting a software platform for hosting the Woods Hole Open Access Server (WHOAS), an institutional repository serving the Woods Hole (MA) science community.
Building research networks to support campus programs [poster]

( 2012-04-04) Furfey, John F. ; Devenish, Ann ; Hurter, Colleen ; Stafford, Nancy

This poster focuses on the methods, tools and outcomes involved in creating two targeted research networks to support large, long-running research programs in the Woods Hole scientific community.
Calcareous nannoplankton biocoenosis : sediment trap studies in the equatorial Atlantic, central Pacific, and Panama Basin

(Woods Hole Oceanographic Institution, 1991) Steinmetz, John C. ; Honjo, Susumu

Sediment traps deployed on three moored vertical arrays collected particles at various depths in the equatorial Atlantic (Station E), central Pacific (Station P1), and in the Panama Basin (Station PB1). The calcareous nannoplankton from the <63 μm size fraction were studied in order to characterize the flux of coccospheres and coccoliths, the taxa present, and their condition of preservation throughout the water column. The average calculated flux of coccospheres ranged from a low value of 24 coccospheres/m2/day in the central Pacific, to an intermediate value of 4725 in the equatorial Atlantic, to a high of 8030 in the Panama Basin. In general, the coccosphere flux decreased with depth at all three sites. Coccolith fluxes and flux profiles were significantly different at each of the three sites. At Station E, the flux decreased regularly with depth but increased sharply at the lowermost trap (724 m above the bottom). The average flux for the entire column was 316 x 106 coccoliths/m2/day. At Station P1, the flux was low in the shallowest two traps and increased markedly in the three deepest traps. This increase is due mainly to a suspected Umbilcosphaera sibogae bloom which occurred shortly before the traps were deployed in September 1978. The highest coccolith flux was recorded in the Station PB1 traps averaging 910 x 10 6 coccoliths/m2/day. The flux profile at this station was essentially constant in the shallowest four traps and decreased almost 59% in the lowermost two traps. The average coccolith carbonate fluxes for the entire columns for the Stations E, P1, and PB1 are, respectively, 2.53, 2.68, and 7.28 mg/m2/day. These fluxes represent minimum values, since coccospheres and coccoliths were also contained in fecal pellets and other particles larger than the size fraction studied (<63 μm). Scanning electron microscopic examination of the trap samples revealed 56 species belonging to 33 genera of calcareous nannoplankton. Three new species are described and illustrated: Alsphaera spatula n. sp., Umbilcosphaera calvata n. sp., ari;d Umbilcosphaera scituloma n. sp. A census of taxa present, including their relative frequency and state of preservation, is presented together with a photographic atlas of the taxa. Station E is the most diverse with 50 species, and is the best preserved of the three sites. Station PBi the least diverse with 26 more poorly preserved species. In general, the best preserved specimens were observed in the shallowest sample at each of the three sites; diversity and state of preservation diminished with increasing depth.
Cellular magnesium acquisition : an anomaly in embryonic cation homeostasis

( 2007-03-14) Shanklin, D. Radford

The intracellular dominance of magnesium ion makes clinical assessment difficult despite the critical role of Mg++ in many key functions of cells and enzymes. There is general consensus that serum Mg++ levels are not representative of the growing number of conditions for which magnesium is known to be important. There is no consensus method or sample source for testing for clinical purposes. High intracellular Mg++ in vertebrate embryos results in part from interactions of cations which influence cell membrane transport systems. These are functionally competent from the earliest stages, at least transiently held over from the unfertilized ovum. Kinetic studies with radiotracer cations, osmolar variations, media lacking one or more of the four biological cations, Na+, Mg++, K+, and Ca++, and metabolic poison 0.05 mEq/L NaF, demonstrated: (1) all four cations influence the behavior of the others, and (2) energy is required for uptake and efflux on different time scales, some against gradient. Na+ uptake is energy dependent against an efflux gradient. The rate of K+ loss is equal with or without fluoride, suggesting a lack of an energy requirement at these stages. Ca++ efflux took twice as long in the presence of fluoride, likely due in part to intracellular binding. Mg++ is anomalous in that early teleost vertebrate embryos have an intracellular content exceeding the surrounding sea water, an isolated unaffected yolk compartment, and a clear requirement for energy for both uptake and efflux. The physiological, pathological, and therapeutic roles of magnesium are poorly understood. This will change: (1) when 28Mg is once again generally available at a reasonable cost for both basic research and clinical assessment, and (2) when serum or plasma levels are determined simultaneously with intracellular values, preferably as part of complete four cation profiles. Atomic absorption spectrophotometry, energy-dispersive x-ray analysis, and inductively coupled plasma emission spectroscopy on sublingual mucosal and peripheral blood samples are potential methods of value for coordinated assessments.

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