Ecology of fishes in Upper Newport Bay, California: seasonal dynamics and community structure

A total of 366 bimonthly (January 1978-January 1979) samples taken with six types of gear (otter trawl, gill net, bag seine, small seine, drop net, square enclosure - all with replication except the gill net) at four stations in upper Newport Bay, California yielded 51,816 fishes belonging to 46 species and weighing over 353 kg. Atherinops affinis (topsmelt) was the most abundant species accounting for 76% of total individuals. Seven species, all of low trophic levels, made up over 97% of the total catch. Mugil cephalus (striped mullet) ranked first in biomass (= 36% of the total) with six species accounting for more than 80% of the total biomass. The largest number of individuals (71%) was collected with the bag seine, the greatest number of species (35) was captured with the otter trawl and the largest percentage of the biomass (56%)was obtained with the gill net. Species richness, number of individuals and biomass were lowest in January (1978 or 1979) or March and highest in July (numbers, biomass) or September (species). Bimonthly diversity (H') values ranged from 0.48 to 2.17 (overall value 1.05) and tended to be inversely related to abundance levels. Species richness was greatest at Station 4 (the lowermost station) and least at Station 1 (the uppermost station). Numbers of individuals and biomass peaked at Station 2 and reached lowest levels at Station 1. Length-frequency analysis of six of the most abundant species indicated utilization of the upper bay by two or more stages in the life history of these species. More than 92,000 eggs belonging to seven taxa and an unknown category and 426 larvae from 20 taxa were collected with a 0.5 m net mounted on an epibenthic sled during the same bimonthly periods and at the same stations as the juvenile/adult samples. Most of the eggs were collected at Station 2 in May with the numbers overwhelmingly dominated by those of Anchoa compressa (deepbody anchovy) (99.7% of total numbers). The most abundant larva was that of Clevelandia ios (arrow goby). Nearly 60% of the total larval catch was made up of members of the family Gobiidae. Larval taxa and individuals were fewest in January (1978). The number of taxa was highest in March, September and January (1979) whereas larval numbers peaked in May. The number of taxa and of individual larvae varied only slightly among the four stations. Asymptotic species accumulation curves indicated adequate sampling of juvenile/adult fishes. Cluster analysis produced eight species groups of resident and periodic species that variously utilize the three main habitats (channel, inshore, pannes) in the upper bay. Species richness and abundance were positively correlated with both temperature and salinity. Temperature, salinity and depth of capture were frequently correlated with individual species abundances and were used in combination to partially explain the spatial utilization of species and species groups. The upper bay fish community is important and worthy of preservation for at least three reasons: 1) it contains species assemblages not duplicated in any other coastal environment; 2) it contains life history stages of a variety of coastal fish species; and 3) it contains large populations of small, low-trophic level species and juveniles of other species which serve as forage for larger, predatory species that are frequently of economic importance. Members of the fish community respond noticeably to altered environmental conditions such as the heavy rainfall (and accompanying low salinity and high turbidity) that occurred during the early months of 1978. The short and long term, as yet often unpredictable, fluctuations in the populations emphasize the need for periodic monitoring and for the development of a mathematical model of the fish community if it is to be thoroughly understood and properly managed. (102pp.

A key to the stromateoid fishes

Originally issued as Reference No. 69-70, series later renamed WHOI-.Our primary purpose in preparing "A Key to the Stromateoid Fishes" is to provide field workers and curators with a convenient and concise aid for the identification of the diverse species in this somewhat difficult group . Secondarily, we hope to present , through the keys , a summary of the present state of our knowledge of these fi.shes, and to indicate areas where further investigation is needed .Supported by the National Science Foundation under Grants GB-7108 and GZ-259

Krotov: A Python implementation of Krotov's method for quantum optimal control

We present a new open-source Python package, krotov, implementing the quantum optimal control method of that name. It allows to determine time-dependent external fields for a wide range of quantum control problems, including state-to-state transfer, quantum gate implementation and optimization towards an arbitrary perfect entangler. Krotov's method compares to other gradient-based optimization methods such as gradient-ascent and guarantees monotonic convergence for approximately time-continuous control fields. The user-friendly interface allows for combination with other Python packages, and thus high-level customization

Intrathecal B-cell activation in LGI1 antibody encephalitis.

ObjectiveTo study intrathecal B-cell activity in leucine-rich, glioma-inactivated 1 (LGI1) antibody encephalitis. In patients with LGI1 antibodies, the lack of CSF lymphocytosis or oligoclonal bands and serum-predominant LGI1 antibodies suggests a peripherally initiated immune response. However, it is unknown whether B cells within the CNS contribute to the ongoing pathogenesis of LGI1 antibody encephalitis.MethodsPaired CSF and peripheral blood (PB) mononuclear cells were collected from 6 patients with LGI1 antibody encephalitis and 2 patients with other neurologic diseases. Deep B-cell immune repertoire sequencing was performed on immunoglobulin heavy chain transcripts from CSF B cells and sorted PB B-cell subsets. In addition, LGI1 antibody levels were determined in CSF and PB.ResultsSerum LGI1 antibody titers were on average 127-fold higher than CSF LGI1 antibody titers. Yet, deep B-cell repertoire analysis demonstrated a restricted CSF repertoire with frequent extensive clusters of clonally related B cells connected to mature PB B cells. These clusters showed intensive mutational activity of CSF B cells, providing strong evidence for an independent CNS-based antigen-driven response in patients with LGI1 antibody encephalitis but not in controls.ConclusionsOur results demonstrate that intrathecal immunoglobulin repertoire expansion is a feature of LGI1 antibody encephalitis and suggests a need for CNS-penetrant therapies

A key to the stromateoid fishes

This second edition of "A Key to the Stromateoid Fishes" is a partially up-dated version of the original (W.H.O.I. Ref. No. 69-70, September 1969).Our primary purpose in preparing "A Key to the Stromateoid Fishes" is to provide field workers and curators with a convenient and concise aid for the identification of the diverse species in this somewhat difficult group. Secondarily, we hope to present, through the keys, a summary of the present state of our knowledge of these fishes, and to indicate areas where further investigation is needed. The keys which compose this handbook have been derived from several sources. Some are slightly modified from already published or about-to-be-published sources. Others form a part of manuscripts in preparation. A third group of keys has been constructed from published species descriptions and our own often meagre data. The keys are intended primarily for larger specimens. Small stromateoids are particularly confusing, and it is not our purpose to treat them here. The well-known and marked allometric growth in stromateoids remains a problem, and those who use these keys should be aware that the body proportions of very large and/or very small specimens can fall well outside the limits here set. We expect and hope for corrections and improvements to the keys, and have left them double-spaced so comments may be written in by users. We have not attempted to settle nomenclatural problems, but have used the oldest name we know of when a choice is necessary. Neither have we gone into the problem of synonymy to any great extent. In some cases we have approached this problem by including two names under one couplet in a key. The choice of which name to employ is thus passed on to the user.Prepared for the National Science Foundation under Grants GA-31365X, GB-710B, and GZ-259

Biomimetic mono- and dinuclear Ni(I) and Ni(II) complexes studied by X-ray absorption and emission spectroscopy and quantum chemical calculations

Five biomimetic mono- or dinuclear nickel complexes featuring Ni(I) or Ni(II) sites were studied by X-ray absorption and emission spectroscopy and DFT calculations. Ni K-edge XANES spectra and Kβ main and satellite emission lines were collected on powder samples. The pre-edge absorption transitions (core-to-valence excitation) and Kβ2,5 emission transitions (valence-to-core decay) were calculated using DFT (TPSSh/TZVP) on crystal structures. This yielded theoretical ctv and vtc spectra in near-quantitative agreement with the experiment, showing the adequacy of the DFT approach for electronic structure description, emphasizing the sensitivity of the XAS/XES spectra for ligation/redox changes at nickel, and revealing the configuration of unoccupied and occupied valence levels, as well as the spin-coupling modes in the dinuclear complexes. XAS/XES-DFT is valuable for molecular and electronic structure analysis of synthetic complexes and of nickel centers in H2 or COx converting metalloenzymes.Peer Reviewe

Monitoring retinal changes with optical coherence tomography predicts neuronal loss in experimental autoimmune encephalomyelitis.

BACKGROUND:Retinal optical coherence tomography (OCT) is a clinical and research tool in multiple sclerosis, where it has shown significant retinal nerve fiber (RNFL) and ganglion cell (RGC) layer thinning, while postmortem studies have reported RGC loss. Although retinal pathology in experimental autoimmune encephalomyelitis (EAE) has been described, comparative OCT studies among EAE models are scarce. Furthermore, the best practices for the implementation of OCT in the EAE lab, especially with afoveate animals like rodents, remain undefined. We aimed to describe the dynamics of retinal injury in different mouse EAE models and outline the optimal experimental conditions, scan protocols, and analysis methods, comparing these to histology to confirm the pathological underpinnings. METHODS:Using spectral-domain OCT, we analyzed the test-retest and the inter-rater reliability of volume, peripapillary, and combined horizontal and vertical line scans. We then monitored the thickness of the retinal layers in different EAE models: in wild-type (WT) C57Bl/6J mice immunized with myelin oligodendrocyte glycoprotein peptide (MOG35-55) or with bovine myelin basic protein (MBP), in TCR2D2 mice immunized with MOG35-55, and in SJL/J mice immunized with myelin proteolipid lipoprotein (PLP139-151). Strain-matched control mice were sham-immunized. RGC density was counted on retinal flatmounts at the end of each experiment. RESULTS:Volume scans centered on the optic disc showed the best reliability. Retinal changes during EAE were localized in the inner retinal layers (IRLs, the combination of the RNFL and the ganglion cell plus the inner plexiform layers). In WT, MOG35-55 EAE, progressive thinning of IRL started rapidly after EAE onset, with 1/3 of total loss occurring during the initial 2 months. IRL thinning was associated with the degree of RGC loss and the severity of EAE. Sham-immunized SJL/J mice showed progressive IRL atrophy, which was accentuated in PLP-immunized mice. MOG35-55-immunized TCR2D2 mice showed severe EAE and retinal thinning. MBP immunization led to very mild disease without significant retinopathy. CONCLUSIONS:Retinal neuroaxonal damage develops quickly during EAE. Changes in retinal thickness mirror neuronal loss and clinical severity. Monitoring of the IRL thickness after immunization against MOG35-55 in C57Bl/6J mice seems the most convenient model to study retinal neurodegeneration in EAE

A Case Report of Cognitive Processing Therapy Delivered over a Single Week.

Although evidence-based treatments for posttraumatic stress disorder (PTSD), such as Cognitive Processing Therapy (CPT), have been developed and widely disseminated, the rate of veterans engaging in and completing these therapies is low. Alternative methods of delivery may be needed to help overcome key barriers to treatment. Delivering evidence-based therapies intensively may address practical barriers to treatment attendance as well as problems with avoidance. This report details the case of a combat veteran who received 10 sessions of Cognitive Processing Therapy delivered twice per day over a single, five-day work week (CPT-5). Post-treatment, the veteran reported large and clinically meaningful decreases in PTSD and depression symptom severity as well as in guilt cognitions, which is a purported mechanism of successful treatment. These effects persisted six weeks after treatment ended. Despite the intensive nature of the treatment, the veteran found CPT-5 tolerable and could cite many benefits to completing therapy in one work week. In conclusion, CPT-5 holds promise as a way to efficiently deliver an evidence-based therapy that is both clinically effective and acceptable to patients, although more rigorous clinical trials are needed to test this treatment delivery format

In situ observation of stress relaxation in epitaxial graphene

Upon cooling, branched line defects develop in epitaxial graphene grown at high temperature on Pt(111) and Ir(111). Using atomically resolved scanning tunneling microscopy we demonstrate that these defects are wrinkles in the graphene layer, i.e. stripes of partially delaminated graphene. With low energy electron microscopy (LEEM) we investigate the wrinkling phenomenon in situ. Upon temperature cycling we observe hysteresis in the appearance and disappearance of the wrinkles. Simultaneously with wrinkle formation a change in bright field imaging intensity of adjacent areas and a shift in the moire spot positions for micro diffraction of such areas takes place. The stress relieved by wrinkle formation results from the mismatch in thermal expansion coefficients of graphene and the substrate. A simple one-dimensional model taking into account the energies related to strain, delamination and bending of graphene is in qualitative agreement with our observations.Comment: Supplementary information: S1: Photo electron emission microscopy and LEEM measurements of rotational domains, STM data of a delaminated bulge around a dislocation. S2: Movie with increasing brightness upon wrinkle formation as in figure 4. v2: Major revision including new experimental dat

Laboratory and tentative interstellar detection of trans-methyl formate using the publicly available Green Bank Telescope PRIMOS survey

The rotational spectrum of the higher-energy trans conformational isomer of methyl formate has been assigned for the first time using several pulsed-jet Fourier transform microwave spectrometers in the 6-60 GHz frequency range. This species has also been sought toward the Sagittarius B2(N) molecular cloud using the publicly available PRIMOS survey from the Green Bank Telescope. We detect seven absorption features in the survey that coincide with laboratory transitions of trans-methyl formate, from which we derive a column density of 3.1 (+2.6, -1.2) \times 10^13 cm-2 and a rotational temperature of 7.6 \pm 1.5 K. This excitation temperature is significantly lower than that of the more stable cis conformer in the same source but is consistent with that of other complex molecular species recently detected in Sgr B2(N). The difference in the rotational temperatures of the two conformers suggests that they have different spatial distributions in this source. As the abundance of trans-methyl formate is far higher than would be expected if the cis and trans conformers are in thermodynamic equilibrium, processes that could preferentially form trans-methyl formate in this region are discussed. We also discuss measurements that could be performed to make this detection more certain. This manuscript demonstrates how publicly available broadband radio astronomical surveys of chemically rich molecular clouds can be used in conjunction with laboratory rotational spectroscopy to search for new molecules in the interstellar medium.Comment: 40 pages, 7 figures, 4 tables; accepted for publication in Ap