Expected Performance of the ATLAS Experiment - Detector, Trigger and Physics

A detailed study is presented of the expected performance of the ATLAS detector. The reconstruction of tracks, leptons, photons, missing energy and jets is investigated, together with the performance of b-tagging and the trigger. The physics potential for a variety of interesting physics processes, within the Standard Model and beyond, is examined. The study comprises a series of notes based on simulations of the detector and physics processes, with particular emphasis given to the data expected from the first years of operation of the LHC at CERN.

The secretion of gonadotrophin-releasing hormone by peri-implantation embryos of the rhesus monkey: comparison with the secretion of chorionic gonadotrophin

Chorionic gonadotrophin (CG) is the first clear embryonic signal during early pregnancy in primates. CG has close structural and functional similarities to pituitary luteinizing hormone (LH) which is regulated by gonadotrophin releasing hormone (GnRH). To study the regulatory mechanism of CG secretion in primate embryos, we examined the production and timing of secretion of GnRH in peri-implantation embryos of the rhesus monkey. In-vivo fertilized/developed morulae and early blastocysts, recovered from non-superovulated, naturally-bred rhesus monkeys by non-surgical uterine flushing, were cultured in vitro to hatched, attached and post-attached blastocyst stages using a well-established culture system. We measured GnRH and CG in media samples from cultured embryos with a sensitive radioimmunoassay and bioassay, respectively. The secretion of GnRH (pg/ml; mean +/- SEM) by embryos (n = 20) commenced from low levels (0.32 +/- 0.05) during the pre-hatching blastocyst stage to 0.70 +/- 0.08 at 6-12 days and 1.30 +/- 0.23 at greater than or equal to 13 days of hatched blastocyst attachment and proliferation of trophoblast cells. GnRH concentrations in culture media obtained from embryos (n = 5) that failed to hatch and attach were mostly undetectable (less than or equal to 0.1). Samples that did not contain detectable GnRH failed to show detectable CG. Immunocytochemical studies, using a specific monoclonal anti-GnRH antibody (HU4H) as well as polyclonal antisera (LR-1), revealed that immunopositive GnRH cells were localized in pre-hatching blastocysts (n = 4), in blastocysts (n = 2) after 5-10 days of attachment and in monolayer cultures (n = 4) of well-established embryonic trophoblast cells. GnRH positive staining was seen only in cytotrophoblasts but not in syncytiotrophoblasts. Similarly, cytotrophoblast, but not syncytiotrophoblast, cells of the rhesus placenta were immunopositive. In controls, either in the absence of antibody or in the presence of antibody pre-absorbed with GnRH, these cells failed to show stain. These observations indicate, for the first time, that an immunoreactive GnRH is produced and secreted by blastocysts during the peri-attachment period and by embryo-derived cytotrophoblast cells in the rhesus monkey.

Does Long-Term Macrophyte Management in Lakes Affect Biotic Richness and Diversity?

We hypothesize that the richness and diversity of the biota in Lake Moraine (42°50’47”N, 75°31’39”W) in New York have been negatively impacted by 60 years of macrophyte and algae management to control Eurasian watermilfoil ( Myriophyllum spicatum L.) and associated noxious plants. To test this hypothesis we compare water quality characteristics, richness and selected indicators of plant diversity, zooplankton, benthic macroinvertebrates and fish in Lake Moraine with those in nearby Hatch Lake (42°50’06”N, 75°40’67”W). The latter is of similar size and would be expected to have similar biota, but has not been subjected to management. Measurements of temperature, pH, oxygen, conductivity, Secchi transparency, calcium, total phosphorus and nitrites + nitrates are comparable. Taxa richness and the diversity indices applied to the aquatic macrophytes are similar in both lakes. (PDF has 8 pages.)

Egg production, spawning biomass and factors influencing recruitment of striped bass in the Potomac River and the upper Chesapeake Bay

Ichthyoplankton surveys in the Potomac River and Upper Chesapeake Bay were carried out in 1989 to estimate striped bass egg productions, age specific spawning biomasses of adult females, cohort-specific larval growth and mortality rates, and hatch dates of 8.0 mm larvae survivors. Possible consequences to recruitment of environmental factors were examined in 1989 and for data collected in 1987-1988. The temporal and spatial occurrences and distributions of eggs and larvae In both spawning areas are described and discussed in relation to environmental factors (temperature, rainfall, river discharge, pH, conductivity, zooplankton abundances) (PDF contains 319 pages)

Spawning, egg development, and early life history dynamics of arrowtooth flounder (Atheresthes stomias) in the Gulf of Alaska

Arrowtooth flounder (Atheresthes stomias) has the highest biomass of any groundfish species in the Gulf of Alaska, is a voracious predator of age 1 walleye pollock (Theragra chalcogramma), and is a major component in the diet of Steller sea lions (Eumetopias jubatus). Owing to its ecological importance in the Gulf of Alaska and the limited information available on its reproduction, interest has intensified in describing its spawning and early life history. A study was undertaken in late January–February 2001–2003 in the Gulf of Alaska to obtain information on adult spawning location, depth distribution, and sexual maturity, and to obtain fertilized eggs for laboratory studies. Adults were found 200–600 m deep east of Kodiak Island over the outer continental shelf and upper slope, and southwest along the shelf break to the Shumagin Islands. Most ripe females (oocytes extruded with light pressure) were found at 400 m and most ripe males (milt extruded with light pressure) were found at depths ≥450 m. Eggs were fertilized and incubated in the laboratory at 3.0°, 4.5°, and 6.0°C. Eggs were reared to hatching, but larvae did not survive long enough to complete yolk absorption and develop pigment. Eggs were staged according to morphological hallmarks and incubation data were used to produce a stage duration table and a regression model to estimate egg age based on water temperature and developmental stage. Arrowtooth flounder eggs (1.58–1.98 mm in diameter) were collected in ichthyoplankton surveys along the continental shelf edge, primarily at depths ≥400 m. Early-stage eggs were found in tows that sampled to depths of ≥450 m. Larvae, which hatch between 3.9 and 4.8 mm standard length, increased in abundance with depth. Observations on arrowtooth flounder eggs and early-stage larvae were used to complete the description of the published partial developmental series.(PDF file contains 34 pages.)

Marine Ranching: Proceedings of the Eighteenth U.S.-Japan Meeting on Aquaculture Port Ludlow, Washington, 18-19 September 1989

Female reproduction in penaeid shrimp is carefully regulated by several different endocrine factors. Their precise modes of action have not yet been fully elucidated. Three endocrine factors, each representing a different chemical class of hormones, have been investigated in the penaeid shrimp Sicyonia ingentis in our laboratory: ecdysteroids, vitellogenesis-inhibiting hormone (VIH) , and methyl farnesoate (MF). Ecdysteroids (the steroid molting hormones of arthropods; predominantly 20-hydroxyecdysone), are initially present in low levels (<10 ng/mg) in shrimp embryos. As development of the embryos nears time of hatch, the ecdysteroid levels increase to approximately 150 ng/ mg, indicating that they may be of embryonic origin and involved in embryonic development. An assay was developed for shrimp VIH, which presumably is a protein. Delay of onset of the next reproductive cycle was observed following injection of sinus gland extracts into shrimp that had previously had their eyestalks removed. A photoaffinity analog was synthesized for the putative shrimp reproductive hormone MF-a terpenoid. This analog, farnesyl diazomethyl ketone (FDK) , was used to demonstrate the presence of specific binding proteins for MF in shrimp hemolymph. (PDF file contains 136 pages.)

Development of hexagrammids (Pisces: Scorpaeniformes) in the northeastern Pacific Ocean

Larvae of Oxylebius pictus, Zaniolepis sp., Ophiodon elongatus, Hexagrommos stelleri, H. decagrammus, H. lagocephalus, H. octogrammus, and Pleurogrammus monopterygius are described and illustrated from field collections which were supplemented by laboratory reared specimens of some species. Larvae hatch at a rather large size (3-9 mm), are heavily pigmented, and undergo direct development to an epipelagic prejuvenile stage. Larvae or the five genera are separable on the basis of body shape, pigmentation, and meristic characters. Larvae or the four species of Hexagrammos, which are quite similar in appearance, are separable on the basis of a combination of several pigmentation characters. Developmental evidence indicates that Oxylebius and Zaniolepis are similar to each other and are more similar to presumed primitive coUids than the other included genera. Ophiodon is dissimilar to the other four genera. Pleurogrammus and Hexagrommos have similar appearing larvae. Among the species of Hexagrammos a progression or increasing larval pigmentation can be seen from H. stelleri to H. decagrammus, H. lagocephalus, and H. octogrammus. (PDF file contains 50 pages.)

Mortality, growth and growth rate variability of striped bass larvae in Chesapeake Subestuaries

In this report we develop age-length keys and derive age-frequency data. We estimate striped bass and white perch mortality and growth rates, based on the otolith-aging analysis. We also report on hatch-date frequencies of striped bass and white perch larvae, and we discuss environmental effects on recruitment potential.

Factors influencing the start of development in Daphnia pulex winter eggs [Translation from: Biological Reviews Vol. 13, 24-26, 1951]

The winter eggs of Daphnia pulex, after passing safely through the winter , develop and hatch in the spring, multiplying by themselves, while some males emerging among them with the changes in environment produce fertile eggs, which are universally known as winter eggs . This study researches the factors governing the development of winter eggs through experiments.

The effects of temperature on hatching and survival of northern rock sole larvae (Lepidopsetta polyxystra)

Northern rock sole (Lepidopsetta polyxystra) is a commercially important flatfish in Alaska and was recently classified as a distinct species from southern rock sole (L. bilineata). Taxonomic and vital rate data for northern rock sole are still not fully described, notably at early egg and larval stages. In this study, we provide new taxonomic descriptions of late-stage eggs and newly hatched larvae, as well as temperature-response models of hatching (timing, duration, success), and larval size-at-hatch and posthatch survival at four temperatures (2°, 5°, 9°, and 12°C). Time-to-first-hatch, hatch cycle duration, and overall hatching success showed a negative relationship with temperature. Early hatching larvae within each temperature treatment were smaller and had larger yolk sacs, but larvae incubated at higher temperatures (9° and 12°C) had the largest yolk reserves overall. Despite having smaller yolks, size-at-hatch and the maximum size achieved during the hatching cycle was highest for larvae reared at cold temperatures (2° and 5°C), indicating that endogenous reserves are more efficiently used for growth at these temperatures. In addition, larvae reared at high temperatures died more rapidly in the absence of food despite having more yolk reserves than cold-incubated larvae. Overall, northern rock sole eggs and larvae display early life history traits consistent with coldwater adaptation for winter spawning in the North Pacific.

All their eggs in one basket: a rocky reef nursery for the longnose skate (Raja rhina Jordan & Gilbert, 1880) in the southern California Bight

Skates (family Rajidae) are oviparous and lay tough, thick-walled eggs. At least some skate species lay their eggs in spatially restricted nursery grounds where embryos develop and hatch (Hitz, 1964; Hoff, 2007). After hatching, neonates may quickly leave the nursery grounds (Hoff, 2007). Egg densities in these small areas may be quite high. As an example, in the eastern Bering Sea, a site <2 km2 harbored eggs of Alaska skate (Bathyraja parmifera) exceeding 500,000/km2. All skate nursery grounds have been identified over soft sea floors (Lucifora and García, 2004; Hoff, 2007).

Effects of Spring Temperatures on the Strength of Selection on Timing of Reproduction in a Long-Distance Migratory Bird

Climate change has differentially affected the timing of seasonal events for interacting trophic levels, and this has often led to increased selection on seasonal timing. Yet, the environmental variables driving this selection have rarely been identified, limiting our ability to predict future ecological impacts of climate change. Using a dataset spanning 31 years from a natural population of pied flycatchers (Ficedula hypoleuca), we show that directional selection on timing of reproduction intensified in the first two decades (1980-2000) but weakened during the last decade (2001-2010). Against expectation, this pattern could not be explained by the temporal variation in the phenological mismatch with food abundance. We therefore explored an alternative hypothesis that selection on timing was affected by conditions individuals experience when arriving in spring at the breeding grounds: arriving early in cold conditions may reduce survival. First, we show that in female recruits, spring arrival date in the first breeding year correlates positively with hatch date; hence, early-hatched individuals experience colder conditions at arrival than late-hatched individuals. Second, we show that when temperatures at arrival in the recruitment year were high, early-hatched young had a higher recruitment probability than when temperatures were low. We interpret this as a potential cost of arriving early in colder years, and climate warming may have reduced this cost. We thus show that higher temperatures in the arrival year of recruits were associated with stronger selection for early reproduction in the years these birds were born. As arrival temperatures in the beginning of the study increased, but recently declined again, directional selection on timing of reproduction showed a nonlinear change. We demonstrate that environmental conditions with a lag of up to two years can alter selection on phenological traits in natural populations, something that has important implications for our understanding of how climate can alter patterns of selection in natural populations.

Três datas: entre nascer e morrer, O guardador de rebanhos

O presente trabalho objetiva o exercício de criação em torno do dia 8 de março de 1914, dito como triunfal pelo poeta Fernando Pessoa, nos momentos que antecedem a escrita do poema O guardador de rebanhos, de autoria do heterônimo Alberto Caeiro. A partir de versos do poema intenta-se uma construção ficcional fincada em um estado onírico que é canal para os fluxos de criação, preparação para o que vai eclodir: um poema potente que emerge do mistério da heteronímia, renúncia do poeta à sua voz para dar lugar ao OUTRO que dele difere, porém dele surge, nele mora. Há no espaço ficcional a ideia de inscrever a data de 8 de março de 1914 como um terceiro marco na biografia do poeta que negou ter biografia, apenas nascimento e morte como limites entre os quais a vida correu como obra, como fazer poesia. A data que dá carne ao poema é ficção dentro da ficção, contraponto de guerra em meio à luz da poesia que nasce como tarefa heroica de enfrentamento diante dos perigos do mundo. O trabalho pretende chegar mais perto de uma verdade que só através da ficção pode ser tocada: sentir o fluxo de um dia no processo de criação do poeta, ser livre como ele, na ousadia de recriar o momento da escrita do poema em 1914

Menhaden: The Resource, The Industry, and a Management History

PREFACE: Four species of menhaden, Brevoortia spp., are found along the Atlantic and Gulf of Mexico coasts of the United States. The Atlantic menhaden, B. tyrannus, is found from Nova Scotia, Can., to West Palm Beach, Fla.; the yellowfin menhaden, B. smithi, is found from Cape Lookout, N. C., to the Mississippi River Delta, La.;the Gulf menhaden, B. patronus, is found from Cape Sable, Fla., to Veracruz, Mex.; and the finescale menhaden, B. gunteri, is found from the Mississippi River Delta, La., to Campeche, Mex. Menhaden are euryhaline species that inhabit coastal and inland tidal waters. Spawning occurs principally at sea (in northern areas some spawning occurs in bays and sounds). Eggs hatch at sea and the larvae are moved to estuaries by ocean currents where they metamorphose and develop as juveniles.

Cheshire stillwaters. Summary results of September 1998

This is the Cheshire stillwaters. Summary results of September 1998 from the Environment Agency, 1998. In May 1997, a Stillwaters meeting was held to discuss the way forward in stillwaters monitoring. It decided upon the establishment of a three year rolling programme, in which three stillwaters would be monitored three times a year, every third year. Oak Mere, Tatton Park Mere and Hatch Mere were surveyed between the 29th - 30th September as part of the three year rolling programme. Betley Mere, Petty Pool, Scotman's Flash and Pearson's Flash were also surveyed. Surveys also included algal and zooplankton samples, which are to be analysed by APEM and presented in the end of year report. The section on results contains information about water column profile; and nutrients (chlorophyll a; Phaeophytin; Nitrate and Nitrite; Ammonia; ortho-Phosphate; Silicate; and total Phosphorus).