National Status and Trends Bioeffects Program: field methods

Environmental quality indicators provide resource managers with information useful to assess coastal condition and scientifically defensible decisions. Since 1984, the National Oceanic and Atmospheric Administration (NOAA), through its National Status and Trends (NS&T) Program, has provided environmental monitoring data on chemical, physical, and biological indicators of coastal environments. The program has two major monitoring components to meet its goals. The Bioeffects Assessments Program evaluates the health of bays, estuaries, and the coastal zone around the nation using the Sediment Quality Triad technique that includes measuring sediment contaminant concentrations, sediment toxicity and benthic community structure. The Mussel Watch Program is responsible for temporal coastal monitoring of contaminant concentrations by quantifying chemicals in bivalve mollusks. The NS&T Program is committed to providing the highest quality data to meet its statutory and scientific responsibilities. Data, metadata and information products are managed within the guidance protocols and standards set forth by NOAA’s Integrated Ocean Observing System (IOOS) and the National Monitoring Network, as recommended by the 2004 Ocean Action Plan. Thus, to meet these data requirements, quality assurance protocols have been an integral part of the NS&T Program since its inception. Documentation of sampling and analytical methods is an essential part of quality assurance practices. A step-by–step summary of the Bioeffects Program’s field standard operation procedures (SOP) are presented in this manual.

峨眉山藏猕猴雄—婴社会行为的补充观察

藏猕猴 (Macaca thibetana) 雄—婴行为的补充数据收集于1997年1～9月、覆盖了整个出生季节和半个交配季节. 分别用1分钟点取样和5分钟事件取样收集雄婴照料(怀抱+接近)和雄—婴—雄三边作用 (triad) 的数据. 焦点动物为两个猴群中的8个婴儿. 数据处理结果表明: ①雄—婴照料集中在4.5～18周龄, 而20周龄内的婴儿平均有7.9％的时间受到雄性照料(雄9.6％, 雌5.6％); ②雄性婴儿较雌性接受的照料偏多, 但同性个体间无差异; ③雄性照料的强度随行为者社会等级的升高而增大;④婴儿介入 triad的频次与其接受照料的强度正相关. 考虑到藏猕猴繁殖单位中非优势雄猴的效配机会极少, 结果③、④支持了先前关于性/新选择介入了藏猕猴猴雄—婴行为进化的结论. 然而, 因为结果②不支持严格的“父—子”照料假设, 这种介入只具有模糊的统计学意义。

Male-infant-male interactions in Tibetan macaques

Event-sampling and scans were used for collecting data on male-infant-male triadic interactions, and their effects on member spacing respectively in a group of Macaca thibetana at Mt. Emei in 1989. The group was partially provisioned by human visitors in seasons other than winter, and could be observed closely. In addition, a stable linear male-hierarchy among five males existed for two years since the end of 1987, providing a good social condition for this topic. The triadic interactions were specific to the birth season, and recognized as three types being on a continuum functionally changing from passive ''agonistic buffering'' (4.8%) to active spatial cohesion, which resulted in a significant decline of intermale distances. Positive correlations were documented between the triad initiation rate and the number of females in consort with the males in the mating season (MS), and between the triad reception rate and the number of infants in proximity to the males in the MS when maternal care was significantly reduced. Thus the male's mating effort and kin/sexual selection may deeply be involved in the triad of this species. Considering that the two triad-species, M. sylvanus and M. thibetana, had different levels of paternity, but shared similar foraging conditions, and showed similar intensities of male-infant caretaking, the triad was very likely a byproduct of male-infant caretaking, which was probably shaped to compensate heavy maternal investment to young offspring in harsh conditions. Accordingly, the long-term arguments about the triad in M. sylvanus can be united to a model of the way in which ''male-infant caretaking'' hypothesis works ultimately, and ''regulating social relations'' hypothesis does proximately.

Molecular modeling on some human interleukins sharing gamma c of interleukin-2 receptor, and structure-function relationships

Five models for human interleukin-7 (HIL-7), HIL-9, HIL-13, HIL-15 and HIL-17 have been generated by SYBYL software package. The primary models were optimized using molecular dynamics and molecular mechanics methods. The final models were optimized using a steepest descent algorithm and a subsequent conjugate gradient method. The complexes with these interleukins and the common gamma chain of interleukin-2 receptor (IL-2R) were constructed and subjected to energy minimization. We found residues, such as Gln127 and Tyr103, of the common gamma chain of IL-2R are very important. Other residues, e.g. Lys70, Asn128 and Glu162, are also significant. Four hydrophobic grooves and two hydrophilic sites converge at the active site triad of the gamma chain. The binding sites of these interleukins interaction with the common gamma chain exist in the first helical and/or the fourth helical domains. Therefore, we conclude that these interleukins binds to the common gamma chain of IL-2R by the first and the fourth helix domain. Especially at the binding sites of some residues (lysine, arginine, asparagine, glutamic acid and aspartic acid), with a discontinuous region of the common gamma chain of IL-2R, termed the interleukins binding sites (103-210). The study of these sites can be important for the development of new drugs. (C) 2000 Elsevier Science B.V. All rights reserved.

峨眉山藏猕猴部分雄-婴社会行为的补充观察

藏猕猴（Macaca thibetana）雄-婴行为补充数据收集于整个出生季节和交配季节初期(1997年1-9月)。针对两个猴群中的8个婴猴，1分钟点取样和5分钟事件取样法分别用来收集照料行为（怀抱+接近）、阴部探查和雄-婴-雄三边作用（triad）。婴猴4.5-18周龄受到群内成年雄性的照料，20周龄内有7.9%时间受到成年雄猴照料(雄婴：9.57%对雌：5.56%)；照料在行为者和接受者之间分布均无差异的结果倾向于支持生态环境决定说。婴猴3.9-14.6周龄接受成年雄性阴部探查，20周龄内雄性婴儿接受的探查频率高于雌性婴儿（0.92次/小时对0.03次/小时），探查在行为者和接受者之间的分布均有差异。探查比照料开始早且持续期短，可能是成年雄性对婴儿的识别和接受。照料婴猴多的成年雄性在triad中使用婴猴也多；雄性婴儿接受照料多，在triad中被使用也多；此结果支持“Triad是雄-婴照料的副产物”假说。

A clip domain serine protease (cSP) from the Chinese mitten crab Eriocheir sinensis: cDNA characterization and mRNA expression

Clip domain serine protease (cSP), characterized by conserved clip domains, is a new serine protease family identified mainly in arthropod, and plays important roles in development and immunity. In the present study, the full-length cDNA of a cSP (designated EscSP) was cloned from Chinese mitten crab Eriocheir sinensis by expressed sequence tags (ESTs) and PCR techniques. The 1380 bp EscSP cDNA contained a 1152 bp open reading frame (ORF) encoding a putative cSP of 383 amino acids, a 5'-untranslated region (UTR) of 54 bp, and a 3'-UTR of 174 bp. Multiple sequence alignment presented twelve conserved cysteine residues and a canonical catalytic triad (His(185), Asp(235) and Ser(332)) critical for the fundamental structure and function of EscSP. Two types of cSP domains, the clip domain and tryp_spc domain, were identified in the deduced amino acids sequence of EscSP. The conservation characteristics and similarities with previously known cSPs indicated that EscSP was a member of the large cSP family. The mRNA expression of EscSP in different tissues and the temporal expression in haemocytes challenged by Listonella anguillarum were measured by real-time RT-PCR. EscSP mRNA transcripts could be detected in all examined tissues, and were higher expressed in muscle than that in hepatopancreas. gill, gonad, haemocytes and heart. The EscSP mRNA expression in haemocytes was up-regulated after L anguillarum challenge and peaked at 2 h (4.96 fold, P < 0.05) and 12 h (9.90 fold, P < 0.05). Its expression pattern was similar to prophenoloxidase (EsproPO), one of the components of crab proPO system found in our previous report. These results implied that EscSP was involved in the processes of host-pathogen interaction probably as one of the proPO system members. (C) 2009 Elsevier Ltd. All rights reserved.

A novel serine protease with clip domain from scallop Chlamys farreri

The serine proteases with clip domain are involved in various innate immune functions in invertebrate such as antimicrobial activity, cell adhesion, pattern recognition and regulation of the prophenoloxidase system. A serine protease with clip-domain cDNA (Cf SP) was obtained by Expressed sequence taggings (ESTs) method and rapid amplification of cDNA ends (RACE). The Cf SP full-length cDNA was of 1,152 bp, including a 5'-terminal untranslated region (UTR) of 63 bp, a 3'-terminal UTR of 81 bp with a canonical polyadenylation signal sequence AATAAA and a poly(A) tail, and an open reading frame of 1,008 bp encoding a polypeptide of 336 amino acids with a putative signal peptide of 19 amino acids. The deduced amino acid sequence of Cf SP contained an amino-terminal clip domain with three disulfide bonds formed six conserved Cys residues, a carboxyl-terminal trypsin-like domain with the conserved His-Asp-Ser catalytic triad, and a low complexity linker sequence. The Cf SP was strongly expressed in hemocytes and the mRNA expression of Cf SP was up-regulated and increased 3.2-fold and 2.6-fold at 16 h after injection of Vibrio anguillarum and Micrococcus luteus. The results suggested that Cf SP gene might be involved in immune response of Gram-negative and Gram-positive microbial infection in scallop.

Molecular cloning and characterization of a serine proteinase homolog prophenoloxidase-activating factor in the swimming crab Portunus trituberculatus

Serine proteinase homologues (SPHs), as one of prophenoloxiase-activating factors (PPAFs), play critical roles in innate immunity of crabs. Based on an EST from the eyestalk full length cDNA library, the complete cDNA (designated as PtSPH) and genomic DNA of SPH from the swimming crab Portunus trituberculatus were cloned in this study. The estimated molecular weight of mature PtSPH (354 amino acids) was 38.7 kDa and its isoelectric point was 5.08. Multiple sequence alignment revealed that PtSPH lacked a catalytic residue with a substitution of Ser in the active site triad to Gly. Phylogenetic analysis indicated PtSPH together with PPAFs of Callinectes sapidus (AAS60227), Eriocheir sinensis (ACU65942), Penaeus monodon (ABE03741, ACP19563) and Pacifastacus leniusculus (ACB41380), formed a distinct cluster which only included clip-SPHs. As the first analyzed genomic structure of PPAFs in crustaceans, two introns were found in the open reading frame region of this gene. The mRNA transcripts of PtSPH could be detected in all the examined tissues, and were higher expressed in the eyestalk than that in gill, hepatopancreas, haemocytes and muscle. Accompanied with the change in phenoloxidase (PO) activity and total haemocyte counts, the temporal expression of PtSPH gene in haemocytes after Vibrio alginolyticus challenge demonstrated a clear time-dependent expression pattern with two peaks within the experimental period of 32 h. These findings suggest that PtSPH is involved in the antibacterial defense mechanism of Portunus tritubercualtus crab. (C) 2010 Elsevier Ltd. All rights reserved.

Learning from triads: training undergraduates in counselling skills

Background: Research has shown that counselling skills training in undergraduate programmes is effective. However, there is potential that premature intimacy and disclosures during triad work may impact on relationships which must be maintained out-with the counselling component of the course. Little research has examined individual pedagogical practices within training. Aim: The aim of this research was to explore the experience of the practical skills training component of a counselling course for a cohort of undergraduate students, and the impact of this learning experience. The objective being an evaluation of the use of this approach for this group and of the impact of personal sharing within cohorts of undergraduates. Method: Semi-structured interviews focusing on the experience of skills training and self-disclosure during training were carried out on 12 undergraduates taking counselling skills modules as part of their BSc Psychology and Counselling degree. Thematic analysis was carried out on the interview transcripts. Results: As a result of engagement in skills training and acting as ‘clients’ for one another, individuals perceived the formation of a positive group identity with implicit ‘rules’, but also an impact of training on relationships within the group which relied on the ability to maintain boundaries and personal identities with peers, and this influenced the learning experience. The ability to manage their engagement on the programme was dependent on ongoing support and guidance from tutors. Discussion: While this pedagogical approach appears appropriate for facilitating learning and potentially provides a rich learning journey for undergraduate students, tutors must act proactively to ensure a safe learning environment.

Team-teaching for inclusive learning: Purposes, practices and perceptions of a team-teaching initiative in Irish post-primary schools

Background. Schools unequivocally privilege solo-teaching. This research seeks to enhance our understanding of team-teaching by examining how two teachers, working in the same classroom at the same time, might or might not contribute to the promotion of inclusive learning. There are well-established policy statements that encourage change and moves towards the use of team-teaching to promote greater inclusion of students with special educational needs in mainstream schools and mainstream classrooms. What is not so well established is the practice of team-teaching in post-primary settings, with little research conducted to date on how it can be initiated and sustained, and a dearth of knowledge on how it impacts upon the students and teachers involved. Research questions and aims. In light of the paucity and inconclusive nature of the research on team-teaching to date (Hattie, 2009), the orientating question in this study asks ‘To what extent, can the introduction of a formal team-teaching initiative enhance the quality of inclusive student learning and teachers’ learning at post-primary level?’ The framing of this question emerges from ongoing political, legal and educational efforts to promote inclusive education. The study has three main aims. The first aim of this study is to gather and represent the voices and experiences of those most closely involved in the introduction of team-teaching; students, teachers, principals and administrators. The second aim is to generate a theory-informed understanding of such collaborative practices and how they may best be implemented in the future. The third aim is to advance our understandings regarding the day-to-day, and moment-to-moment interactions, between teachers and students which enable or inhibit inclusive learning. Sample. In total, 20 team-teaching dyads were formed across seven project schools. The study participants were from two of the seven project schools, Ash and Oak. It involved eight teachers and 53 students, whose age ranged from 12-16 years old, with 4 teachers forming two dyads per school. In Oak there was a class of first years (n=11) with one dyad and a class of transition year students (n=24) with the other dyad. In Ash one class group (n=18) had two dyads. The subjects in which the dyads engaged were English and Mathematics. Method. This research adopted an interpretive paradigm. The duration of the fieldwork was from April 2007 to June 2008. Research methodologies included semi-structured interviews (n=44), classroom observation (n=20), attendance at monthly teacher meetings (n=6), questionnaires and other data gathering practices which included school documentation, assessment findings and joint examination of student work samples (n=4). Results. Team-teaching involves changing normative practices, and involves placing both demands and opportunities before those who occupy classrooms (teachers and students) and before those who determine who should occupy these classrooms (principals and district administrators). This research shows how team-teaching has the potential to promote inclusive learning, and when implemented appropriately, can impact positively upon the learning experiences of both teachers and students. The results are outlined in two chapters. In chapter four, Social Capital Theory is used in framing the data, the change process of bonding, bridging and linking, and in capturing what the collaborative action of team-teaching means, asks and offers teachers; within classes, between classes, between schools and within the wider educational community. In chapter five, Positioning Theory deductively assists in revealing the moment-to-moment, dynamic and inclusive learning opportunities, that are made available to students through team-teaching. In this chapter a number of vignettes are chosen to illustrate such learning opportunities. These two theories help to reveal the counter-narrative that team-teaching offers, regarding how both teachers and students teach and learn. This counter-narrative can extend beyond the field of special education and include alternatives to the manner in which professional development is understood, implemented, and sustained in schools and classrooms. Team-teaching repositions teachers and students to engage with one another in an atmosphere that capitalises upon and builds relational trust and shared cognition. However, as this research study has found, it is wise that the purposes, processes and perceptions of team-teaching are clear to all so that team-teaching can be undertaken by those who are increasingly consciously competent and not merely accidentally adequate. Conclusions. The findings are discussed in the context of the promotion of effective inclusive practices in mainstream settings. I believe that such promotion requires more nuanced understandings of what is being asked of, and offered to, teachers and students. Team-teaching has, and I argue will increasingly have, its place in the repertoire of responses that support effective inclusive learning. To capture and extend such practice requires theoretical frameworks that facilitate iterative journeys between research, policy and practice. Research to date on team-teaching has been too focused on outcomes over short timeframes and not focused enough on the process that is team-teaching. As a consequence team-teaching has been under-used, under-valued, under-theorised and generally not very well understood. Moving from classroom to staff room and district board room, theoretical frameworks used in this research help to travel with, and understand, the initiation, engagement and early consequences of team-teaching within and across the educational landscape. Therefore, conclusions from this study have implications for the triad of research, practice and policy development where efforts to change normative practices can be matched by understandings associated with what it means to try something new/anew, and what it means to say it made a positive difference.

Towards enhanced divine-human-earth relations: a Christian-Buddhist contribution

The central claim of the dissertation is that lesser known and somewhat neglected, yet influential thinkers, within classical religious traditions have something worthwhile to contribute to the kind of ethos we should adopt in the face of the world’s various environmental crises. Moreover an exploration of such perspectives is best done in dialogue, particularly between Eastern and Western thought. I examine this claim primarily through a dialogue between the Christian philosopher John Scottus Eriugena and the Japanese Buddhist philosopher Kūkai (Kōbō Daishi). This dialogue, framed by the triad of divine-human-earth relations, primarily emphasises the oneness of all reality, and it finds expression in Eriugena’s concept of natura or phusis and Kūkai’s central teaching that the phenomenal world is the cosmic Buddha Dainichi. By highlighting this focus, I contribute to the existing academic field of ecology and religion on the subject of holism. However, I go beyond the materialist focus that generally marks such ecological holism within that field, offering instead a more metaphysical approach. This is indicated through my use of the concept of ‘immanental transcendence’ to describe Eriugena’s and Kūkai’s dynamic, numinous and mysterious notion of reality, as well as my exploration of Eriugena’s concept of theophany and Kūkai’s notion of kaji. I further explore how both philosophers highlight the human role in the process of reaching enlightenment—understood as attaining union with the whole. In that regard, I note significant differences in their positions: in particular, I note that Kūkai’s emphasis on bodily practices contrasts with Eriugena’s more conceptual approach. Finally to bolster my claim, I examine some ecologically oriented understandings of contemporary phenomenological approaches found particularly in the work of Jean-Luc Marion and to a lesser extent Merleau-Ponty, arguing that these reflect notions of reality and of the human role similar to those of the medieval philosophers.

Relating sardine recruitment in the Northern Benguela to satellite-derived sea surface height using a neural network pattern recognition approach

Processes of enrichment, concentration and retention are thought to be important for the successful recruitment of small pelagic fish in upwelling areas, but are difficult to measure. In this study, a novel approach is used to examine the role of spatio-temporal oceanographic variability on recruitment success of the Northern Benguela sardine Sardinops sagax. This approach applies a neural network pattern recognition technique, called a self-organising map (SOM), to a seven-year time series of satellite-derived sea level data. The Northern Benguela is characterised by quasi-perennial upwelling of cold, nutrient-rich water and is influenced by intrusions of warm, nutrient-poor Angola Current water from the north. In this paper, these processes are categorised in terms of their influence on recruitment success through the key ocean triad mechanisms of enrichment, concentration and retention. Moderate upwelling is seen as favourable for recruitment, whereas strong upwelling, weak upwelling and Angola Current intrusion appear detrimental to recruitment success. The SOM was used to identify characteristic patterns from sea level difference data and these were interpreted with the aid of sea surface temperature data. We found that the major oceanographic processes of upwelling and Angola Current intrusion dominated these patterns, allowing them to be partitioned into those representing recruitment favourable conditions and those representing adverse conditions for recruitment. A marginally significant relationship was found between the index of sardine recruitment and the frequency of recruitment favourable conditions (r super(2) = 0.61, p = 0.068, n = 6). Because larvae are vulnerable to environmental influences for a period of at least 50 days after spawning, the SOM was then used to identify windows of persistent favourable conditions lasting longer than 50 days, termed recruitment favourable periods (RFPs). The occurrence of RFPs was compared with back-calculated spawning dates for each cohort. Finally, a comparison of RFPs with the time of spawning and the index of recruitment showed that in years where there were 50 or more days of favourable conditions following spawning, good recruitment followed (Mann-Whitney U-test: p = 0.064, n = 6). These results show the value of the SOM technique for describing spatio-temporal variability in oceanographic processes. Variability in these processes appears to be an important factor influencing recruitment in the Northern Benguela sardine, although the available data time series is currently too short to be conclusive. Nonetheless, the analysis of satellite data, using a neural network pattern-recognition approach, provides a useful framework for investigating fisheries recruitment problems.

Characterization of bafinivirus main protease autoprocessing activities

The production of functional nidovirus replication-transcription complexes involves extensive proteolytic processing by virus-encoded proteases. In this study, we characterized the viral main protease (Mpro) of the type species, White bream virus (WBV), of the newly established genus Bafinivirus (order Nidovirales, family Coronaviridae, subfamily Torovirinae). Comparative sequence analysis and mutagenesis data confirmed that the WBV Mpro is a picornavirus 3C-like serine protease that uses a Ser-His-Asp catalytic triad embedded in a predicted two-ß-barrel fold, which is extended by a third domain at its C terminus. Bacterially expressed WBV Mpro autocatalytically released itself from flanking sequences and was able to mediate proteolytic processing in trans. Using N-terminal sequencing of autoproteolytic processing products we tentatively identified Gln?(Ala, Thr) as a substrate consensus sequence. Mutagenesis data provided evidence to suggest that two conserved His and Thr residues are part of the S1 subsite of the enzyme's substrate-binding pocket. Interestingly, we observed two N-proximal and two C-proximal autoprocessing sites in the bacterial expression system. The detection of two major forms of Mpro, resulting from processing at two different N-proximal and one C-proximal site, in WBV-infected epithelioma papulosum cyprini cells confirmed the biological relevance of the biochemical data obtained in heterologous expression systems. To our knowledge, the use of alternative Mpro autoprocessing sites has not been described previously for other nidovirus Mpro domains. The data presented in this study lend further support to our previous conclusion that bafiniviruses represent a distinct group of viruses that significantly diverged from other phylogenetic clusters of the order Nidovirales.

The structure of the Beck Hopelessness Scale: A confirmatory factor analysis in UK students

The aim of this paper was to confirm the factor structure of the 20-item Beck Hopelessness Scale in a non-clinical population. Previous research has highlighted a lack of clarity in its construct validity with regards to this population.

Based on previous factor analytic findings from both clinical and non-clinical studies, 13 separate confirmatory factor models were specified and estimated using LISREL 8.72 to test the one, two and three-factor models.

Psychology and medical students at Queen's University, Belfast (n = 581) completed both the BHS and the Beck Depression Inventory (BDI).

All models showed reasonable fit, but only one, a four-item single-factor model demonstrated a nonsignificant chi-squared statistic. These four items can be used to derive a Short-Form BHS (SBHS) in which increasing scores (0-4) corresponded with increasing scores in the BDI. The four items were also drawn from all three of Beck's proposed triad, and included both positively and negatively scored items.

This study in a UK undergraduate non-clinical population suggests that the BHS best measures a one-factor model of hopelessness. It appears that a shorter four-item scale can also measure this one-factor model. (C) 2011 Elsevier Ltd. All rights reserved.

Design considerations for the autism spectrum disorder-friendly Key Stage 1 classroom

There is a growing consensus that an appropriate classroom environment will aid the performance of the pupil with autism spectrum disorder (ASD). There are, however, very few design guidelines available when considering ASD and the school environment. Such guidelines that do exist tend only to be in general terms. Therefore, this article seeks to highlight design considerations specifically for the ASD-friendly Key Stage 1 (age five to eight) classroom. It will first highlight some of the challenges for those with autism spectrum disorder in a school environment and the triad of challenges faced by architects and designers when considering ASD-friendly classroom design. It will then go on to describe the findings and results of a two-year study carried out in conjunction with the ASD teaching staff of Northern Ireland's Southern Education and Library Board. These consist of 16 specific design considerations for the Key Stage 1 ASD-friendly classroom applicable to all classrooms for pupils between five and eight years of age.