Establishment of Regional Herbarium Leads to More Than 200 New Flora Atlas Records for New York State

Loss of small herbaria is an unfortunate global trend, and initiation of new collections at small academic institutions is an increasingly rare occurrence. In 2006, a new herbarium was established at the State University of New York College at Plattsburgh. The PLAT herbarium has since grown to more than 7,000 specimens, many of them representative of the flora of northeastern New York (especially Clinton County). Previous to 2006, this region was without a recognized herbarium, the nearest in-state collections being more than 150 miles away. Although botanists have previously worked in the region, relatively few plant species were recorded for Clinton County by the New York Flora Atlas – a resource providing species distribution records based on specimens accessioned in herbarium collections. Given the dearth of available distribution data for Clinton County (including the eastern Adirondack Mountains and the western Lake Champlain valley), this project sought to provide records of previously unreported species by comparing NY Flora Atlas maps with current holdings. 203 species will now be added to the NY Flora Atlas for Clinton County, roughly half of those considered exotic. This exercise has amplified the importance of supporting and maintaining small regional herbaria as repositories of valuable biodiversity information. Likewise, this project also highlights the enduring value of training in floristics and taxonomy.

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47

Genome-wide association studies and candidate gene studies in ulcerative colitis have identified 18 susceptibility loci. We conducted a meta-analysis of six ulcerative colitis genome-wide association study datasets, comprising 6,687 cases and 19,718 controls, and followed up the top association signals in 9,628 cases and 12,917 controls. We identified 29 additional risk loci (P < 5 × 10(-8)), increasing the number of ulcerative colitis-associated loci to 47. After annotating associated regions using GRAIL, expression quantitative trait loci data and correlations with non-synonymous SNPs, we identified many candidate genes that provide potentially important insights into disease pathogenesis, including IL1R2, IL8RA-IL8RB, IL7R, IL12B, DAP, PRDM1, JAK2, IRF5, GNA12 and LSP1. The total number of confirmed inflammatory bowel disease risk loci is now 99, including a minimum of 28 shared association signals between Crohn's disease and ulcerative colitis.

Not in the Legends

In writing “Not in the Legends”, one of the images and concepts which constantly returned was that of pilgrimage. I began to write these poems while studying abroad in London, after having passed the previous semester in France and travelling around Europe. There was something in the repetition of sightseeing— walking six miles in Luxembourg to see the grave of General Patton, taking photographs of the apartment where Sylvia Plath ended her life, bowing before the bones of saints, searching through Père Lachaise for the grave of Théodore Gericault— which struck me as numinous and morbid. At the same time, I came to love living abroad and I grew discontent with both remaining and returning. I wanted the opportunity to live everywhere all the time and not have to choose between home and away. Returning from abroad, I turned my attention to the landscape of my native country. I found in the New England pilgrims a narrative of people who had left their home in search of growth and freedom. In these journeys I began to appreciate the significance of place and tried to understand what it meant to move from one place to another, how one chose a home, and why people searched for meaning in specific locations. The processes of moving from student to worker and from childhood to adulthood have weighed on me. I began to see these transitions towards maturity as travels to a different land. Memory and nostalgia are their own types of pilgrimage in their attempts to return to lost places, as is the reading of literature. These pilgrimages, real and metaphorical, form the thematic core of the collection. I read the work of many poets who came before me, returning to the places where the Canon was forged. Those poets have a large presence in the work I produced. I wondered how I, as a young poet, could earn my own place in the tradition and sought models in much the same way a painter studies the brushstrokes of a master. In the process, I have tried to uncover what it means to be a poet. Is it something like being a saint? Is it something like being a colonist? Or is to be the one who goes in search of saints and colonists? In trying to measure my own life and work based on the precedent, I have questioned what role era and generation have on the formation of identity. I focused my reading heavily on the early years of English poetry, trying to find the essence of the time when the language first achieved the transcendence of verse. In following the development of English poetry through Coleridge, John Berryman, and Allison Titus, I have explored the progression of those basic virtues in changing contexts. Those bearings, applied to my modern context, helped to shape the poetry I produced. Many of the poems in “Not in the Legends” are based on my own personal experience. In my recollections I have tried to interrogate nostalgia rather than falling into mere reminiscence. Rather than allowing myself poems of love and longing, I have tried to find the meaning of those emotions. A dominant conflict exists between adventure and comfort which mirrors the central engagement with the nature of being “here” or “there”. It is found in scenes of domesticity and wilderness as I attempt to understand my own simultaneous desire for both. For example, in “Canned Mangoes…” the intrusion of nature, even in a context as innocuous as a poem by Sir Walter Raleigh, unravels ordinary comforts of the domestic sphere. The character of “The Boy” from Samuel Beckett’s Waiting for Godot proved such an interesting subject for me because he is one who can transcend the normal boundaries of time and place. The title suggests connections to both place and time. “Legends” features the dual meaning of both myths and the keys to maps. To propose something “Not in the Legends” is to find something which has no precedent in our histories and our geographies, something beyond our field of knowledge and wholly new. One possible interpretation I devised was that each new generation lives a novel existence, the future being the true locus of that which is beyond our understanding. The title comes from Keats’ “Hyperion, a Fragment”, and details the aftermath of the Titanomachy. The Titans, having fallen to the Olympians, are a representation of the passing of one generation for the next. Their dejection is expressed by Saturn, who laments: Not in my own sad breast, Which is its own great judge and searcher out, Can I find reason why ye should be thus: Not in the legends of the first of days… (129-132) The emotions of the conquered Titans are unique and without antecedent. They are experiencing feelings which surpass all others in history. In this, they are the equivalent of the poet who feels that his or her own sufferings are special. In contrast are Whitman’s lines from “Song of Myself” which serve as an epigraph to this collection. He contends for a sense of continuity across time, a realization that youth, age, pleasure, and suffering have always existed and will always exist. Whitman finds consolation in this unity, accepting that kinship with past generations is more important that his own individuality. These opposing views offer two methods of presenting the self in history. The instinct of poetry suggests election. The poet writes because he feels his experiences are special, or because he believes he can serve as a synecdoche for everyone. I have fought this instinct by trying to contextualize myself in history. These poems serve as an attempt at prosopography with my own narrative a piece of the whole. Because the earth abides forever, our new stories get printed over the locations of the old and every place becomes a palimpsest of lives and acts. In this collection I have tried to untangle some of those layers, especially my own, to better understand the sprawling legend of history.

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease

Crohn's disease and ulcerative colitis, the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry, with rising prevalence in other populations. Genome-wide association studies and subsequent meta-analyses of these two diseases as separate phenotypes have implicated previously unsuspected mechanisms, such as autophagy, in their pathogenesis and showed that some IBD loci are shared with other inflammatory diseases. Here we expand on the knowledge of relevant pathways by undertaking a meta-analysis of Crohn's disease and ulcerative colitis genome-wide association scans, followed by extensive validation of significant findings, with a combined total of more than 75,000 cases and controls. We identify 71 new associations, for a total of 163 IBD loci, that meet genome-wide significance thresholds. Most loci contribute to both phenotypes, and both directional (consistently favouring one allele over the course of human history) and balancing (favouring the retention of both alleles within populations) selection effects are evident. Many IBD loci are also implicated in other immune-mediated disorders, most notably with ankylosing spondylitis and psoriasis. We also observe considerable overlap between susceptibility loci for IBD and mycobacterial infection. Gene co-expression network analysis emphasizes this relationship, with pathways shared between host responses to mycobacteria and those predisposing to IBD.

Effects of non-ionic iodinated contrast media on patient heart rate and pressures during intra-cardiac or intra-arterial injection

PURPOSE: To compare the effects on heart rate (HR), on left ventricular (LV) or arterial pressures, and the general safety of a non-ionic low-osmolar contrast medium (CM) and a non-ionic iso-osmolar CM in patients undergoing cardiac angiography (CA) or peripheral intra-arterial digital subtraction angiography (IA-DSA). MATERIALS AND METHODS: Two double-blind, randomized studies were conducted in 216 patients who underwent CA (n=120) or peripheral IA-DSA (n=96). Patients referred for CA received a low-osmolar monomeric CM (iomeprol-350, n=60) or an iso-osmolar dimeric CM (iodixanol-320; n=60). HR and LV peak systolic and end-diastolic pressures were determined before and after the first injection during left and right coronary arteriography and left ventriculography. Monitoring for all types of adverse event (AE) was performed for 24 h following the procedure. t-tests were performed to compare CM for effects on HR. Patients referred for IA-DSA received iomeprol-300 (n=49) or iodixanol-320 (n=47). HR and arterial blood pressure (BP) were evaluated before and after the first 4 injections. Monitoring for AE was performed for 4 h following the procedure. Repeated-measures ANOVA was used to compare mean HR changes across the first 4 injections, whereas changes after the first injection were compared using t-tests. RESULTS: No significant differences were noted between iomeprol and iodixanol in terms of mean changes in HR during left coronary arteriography (p=0.8), right coronary arteriography (p=0.9), and left ventriculography (p=0.8). In patients undergoing IA-DSA, no differences between CM were noted for effects on mean HR after the first injection (p=0.6) or across the first 4 injections (p=0.2). No significant differences (p>0.05) were noted in terms of effects on arterial BP in either study or on LV pressures in patients undergoing CA. Non-serious AE considered possibly CM-related (primarily headache and events affecting the cardiovascular and digestive systems) were reported more frequently by patients undergoing CA and more frequently after iodixanol (14/60 [23.3%] and 2/47 [4.3%]; CA and IA-DSA, respectively) than iomeprol (10/60 [16.7%] and 1/49 [2%], respectively). CONCLUSIONS: Iomeprol and iodixanol are safe and have equally negligible effects on HR and LV pressures or arterial BP during and after selective intra-cardiac injection and peripheral IA-DSA. CLINICAL APPLICATION: Iomeprol and iodixanol are safe and equally well tolerated with regard to cardiac rhythm and clinical preference should be based on diagnostic image quality alone.

Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes

Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.

Study of water use and supply in the district of Independencia, Peru

Peru is a developing country with abundant fresh water resources, yet the lack of infrastructure leaves much of the population without access to safe water for domestic uses. The author of this report was a Peace Corps Volunteer in the sector of water & sanitation in the district of Independencia, Ica, Peru. Independencia is located in the arid coastal region of the country, receiving on average 15 mm of rain annually. The water source for this district comes from the Pisco River, originating in the Andean highlands and outflowing into the Pacific Ocean near the town of Pisco, Peru. The objectives of this report are to assess the water supply and sanitation practices, model the existing water distribution system, and make recommendations for future expansion of the distribution system in the district of Independencia, Peru. The assessment of water supply will be based on the results from community surveys done in the district of Independencia, water quality testing done by a detachment of the U.S. Navy, as well as on the results of a hydraulic model built in EPANET 2.0 to represent the distribution system. Sanitation practice assessments will be based on the surveys as well as observations from the author while living in Peru. Recommendations for system expansions will be made based on results from the EPANET model and the municipality’s technical report for the existing distribution system. Household water use and sanitation surveys were conducted with 84 families in the district revealing that upwards of 85% store their domestic water in regularly washed containers with lids. Over 80% of those surveyed are drinking water that is treated, mostly boiled. Of those surveyed, over 95% reported washing their hands and over 60% mentioned at least one critical time for hand washing when asked for specific instances. From the surveys, it was also discovered that over 80% of houses are properly disposing of excrement, in either latrines or septic tanks. There were 43 families interviewed with children five years of age or under, and just over 18% reported the child had a case of diarrhea within the last month at the time of the interview. Finally, from the surveys it was calculated that the average water use per person per day is about 22 liters. Water quality testing carried out by a detachment of the U.S. Navy revealed that the water intended for consumption in the houses surveyed was not suitable for consumption, with a median E. coli most probable number of 47/100 ml for the 61 houses sampled. The median total coliforms was 3,000 colony forming units per 100 ml. EPANET was used to simulate the water delivery system and evaluate its performance. EPANET is designed for continuous water delivery systems, assuming all pipes are always flowing full. To account for the intermittent nature of the system, multiple EPANET network models were created to simulate how water is routed to the different parts of the system throughout the day. The models were created from interviews with the water technicians and a map of the system created using handheld GPS units. The purpose is to analyze the performance of the water system that services approximately 13,276 people in the district of Independencia, Peru, as well as provide recommendations for future growth and improvement of the service level. Performance evaluation of the existing system is based on meeting 25 liters per person per day while maintaining positive pressure at all nodes in the network. The future performance is based on meeting a minimum pressure of 20 psi in the main line, as proposed by Chase (2000). The EPANET model results yield an average nodal pressure for all communities of 71 psi, with a range from 1.3 – 160 psi. Thus, if the current water delivery schedule obtained from the local municipality is followed, all communities should have sufficient pressure to deliver 25 l/p/d, with the exception of Los Rosales, which can only supply 3.25 l/p/d. However, if the line to Los Rosales were increased from one to four inches, the system could supply this community with 25 l/p/d. The district of Independencia could greatly benefit from increasing the service level to 24-hour water delivery and a minimum of 50 l/p/d, so that communities without reliable access due to insufficient pressure would become equal beneficiaries of this invaluable resource. To evaluate the feasibility of this, EPANET was used to model the system with a range of population growth rates, system lifetimes, and demands. In order to meet a minimum pressure of 20 psi in the main line, the 6-inch diameter main line must be increased and approximately two miles of trench must be excavated up to 30 feet deep. The sections of the main line that must be excavated are mile 0-1 and 1.5-2.5, and the first 3.4 miles of the main line must be increased from 6 to 16 inches, contracting to 10 inches for the remaining 5.8 miles. Doing this would allow 24-hour water delivery and provide 50 l/p/d for a range of population growth rates and system lifetimes. It is expected that improving the water delivery service would reduce the morbidity and mortality from diarrheal diseases by decreasing the recontamination of the water due to transport and household storage, as well as by maintaining continuous pressure in the system to prevent infiltration of contaminated groundwater. However, this expansion must be carefully planned so as not to affect aquatic ecosystems or other districts utilizing water from the Pisco River. It is recommended that stream gaging of the Pisco River and precipitation monitoring of the surrounding watershed is initiated in order to begin a hydrological study that would be integrated into the district’s water resource planning. It is also recommended that the district begin routine water quality testing, with the results available to the public.

AN ASSESSMENT OF BALLAST SOURCE'S QUALITY AND LOCATIONS WITH RESPECT TO MDOT'S UPGRADE OF THE WOLVERINE RAILROAD LINE FOR HIGH SPEED RAIL USEAGE

The Michigan Department of Transportation is evaluating upgrading their portion of the Wolverine Line between Chicago and Detroit to accommodate high speed rail. This will entail upgrading the track to allow trains to run at speeds in excess of 110 miles per hour (mph). An important component of this upgrade will be to assess the requirement for ballast material for high speed rail. In the event that the existing ballast materials do not meet specifications for higher speed train, additional ballast will be required. The purpose of this study, therefore, is to investigate the current MDOT railroad ballast quality specifications and compare them to both the national and international specifications for use on high speed rail lines. The study found that while MDOT has quality specifications for railroad ballast it does not have any for high speed rail. In addition, the American Railway Engineering and Maintenance-of-Way Association (AREMA), while also having specifications for railroad ballast, does not have specific specifications for high speed rail lines. The AREMA aggregate specifications for ballast include the following tests: (1) LA Abrasion, (2) Percent Moisture Absorption, (3) Flat and Elongated Particles, (4) Sulfate Soundness test. Internationally, some countries do require a highly standard for high speed rail such as the Los Angeles (LA) Abrasion test, which is uses a higher standard performance and the Micro Duval test, which is used to determine the maximum speed that a high speed can operate at. Since there are no existing MDOT ballast specification for high speed rail, it is assumed that aggregate ballast specifications for the Wolverine Line will use the higher international specifications. The Wolverine line, however, is located in southern Michigan is a region of sedimentary rocks which generally do not meet the existing MDOT ballast specifications. The investigation found that there were only 12 quarries in the Michigan that meet the MDOT specification. Of these 12 quarries, six were igneous or metamorphic rock quarries, while six were carbonate quarries. Of the six carbonate quarries four were locate in the Lower Peninsula and two in the Upper Peninsula. Two of the carbonate quarries were located in near proximity to the Wolverine Line, while the remaining quarries were at a significant haulage distance. In either case, the cost of haulage becomes an important consideration. In this regard, four of the quarries were located with lake terminals allowing water transportation to down state ports. The Upper Peninsula also has a significant amount of metal based mining in both igneous and metamorphic rock that generate significant amount of waste rock that could be used as a ballast material. The main drawback, however, is the distance to the Wolverine rail line. One potential source is the Cliffs Natural Resources that operates two large surface mines in the Marquette area with rail and water transportation to both Lake Superior and Lake Michigan. Both mines mine rock with a very high compressive strength far in excess of most ballast materials used in the United States and would make an excellent ballast materials. Discussions with Cliffs, however, indicated that due to environmental concerns that they would most likely not be interested in producing a ballast material. In the United States carbonate aggregates, while used for ballast, many times don't meet the ballast specifications in addition to the problem of particle degradation that can lead to fouling and cementation issues. Thus, many carbonate aggregate quarries in close proximity to railroads are not used. Since Michigan has a significant amount of carbonate quarries, the research also investigated using the dynamic properties of aggregate as a possible additional test for aggregate ballast quality. The dynamic strength of a material can be assessed using a split Hopkinson Pressure Bar (SHPB). The SHPB has been traditionally used to assess the dynamic properties of metal but over the past 20 years it is now being used to assess the dynamic properties of brittle materials such as ceramics and rock. In addition, the wear properties of metals have been related to their dynamic properties. Wear or breakdown of railroad ballast materials is one of the main problems with ballast material due to the dynamic loading generated by trains and which will be significantly higher for high speed rails. Previous research has indicated that the Port Inland quarry along Lake Michigan in the Southern Upper Peninsula has significant dynamic properties that might make it potentially useable as an aggregate for high speed rail. The dynamic strength testing conducted in this research indicate that the Port Inland limestone in fact has a dynamic strength close to igneous rocks and much higher than other carbonate rocks in the Great Lakes region. It is recommended that further research be conducted to investigate the Port Inland limestone as a high speed ballast material.

The Aplitic Body Bordering Roosevelt Drive South of Butte, Montana

The area studied consists of a large body of aplite situated 12 miles south of Butte. It extends eastward almost to the Butte-Pipestone road, southward to Lime Kiln Hill and westward a distance of 3000 feet. The petrographic work was supplemented by a map of the area. Special attention was given to those frequent "Limonite Specks" found in the aplite.

A Bentonite Deposit near Warm Springs, Montana

This report deals with a bentonite deposit recently developed, approximately seven miles northeast of Warm Springs, Montana. A group of claims have been staked on the deposit and are owned by the Lincoln Mining Company of Anaconda, Montana. The company also has several claims prospected for silver one mile from its present site of operations, but the silver prospects have failed to produce. The bentonite deposit was discovered incidentally during the course of other development work, and at present two adits have been driven into the side of a mountain, each crosscutting a vein-like mass of bentonite varying from two to three feet in width.

The Calcite Veins of the Livingston Formation

An interesting group of calcite veins occur near Livingston Montana in a zone about eight miles wide and forty miles long in the edge of the Plains region of Montana in front of the Main ranges. The zone extends from the Boulder River south of Big Timber, through Springdale and Hunters Hot Springs, to Potter's Basin just north of Wilsall in Park County. The group of veins is particularly interesting because they cut relatively flat lying strata, suggest a structural relation­ship to one another, and they are nearly pure calcite. The present investigation was to determine the position of the calcite veins by plotting them on a base map of the district. In addition, it was planned to determine the mineralogy end origin of the veins and their structural and stratigraphical relationship to the rocks of the Livingston formation which they cut.

Leaching Copper Minerals in the Butte District

The history of mining in Butte is woven about three of our principal metals. The gold placers first attracted the attention of miners in 1863, and reached their peak production in 1867. Silver was the second metal mined, and this operation required the erection of large mills with a consequent increase in mining activity that made the district a prominent producer. Although the presence of copper in the silver ore had been known, the credit for the first development of the copper veins is due Senator W. A. Clark. The original Colusa, Mining Chief, and Gambetta claims were developed to 1872. The ore was freighted by wagon trains 400 miles to Corrine, Utah, thence by rail eastward, some of it going to Swansea, Wales. The cooper production of the "richest hill on earth" has mounted to ten billion pounds.

Geology and Ore Deposits of the Butte-Highland Gold Mine.

The Butte-Highland mine is situated at the head of Basin Creek, in the Highland mining district, Silver Bow County, about 14 miles south of Butte. The tunnel portal and present surface plant are at an elevation of about 7350 feet above sea level, facing westward across the head of Basin Creek valley. The "ghost" mining town of Highland lies a mile to the east, near the forks of Fish Creek. Access to the mine is obtained at present from Beaudine's siding, 12 miles west. The property may also be reached, with difficulty, over poor roads from Limekiln hill, or from Moose Creek.

The General Geology of the Cardwell Mining District

The Cardwell Mining District is part of the greater Whitehall Mining District. The district is situated about four miles to the east and northeast of Whitehall in the southern end of the Bull Mountains which are near the Continental Divide. The first reported production was in 1896 after the dis­covery of the Mayflower Mine. Mining has been carried on in­termittently and on a small scale since that time.