Miracle-dz/UniFAR-FTUs huggingface dataset:
A genetics‐based Universal Community Transfer Function for predicting the impacts of climate change on future communities

Summary Although the genetics of foundation plant species is known to be important drivers of biodiversity and community structure, and climate change is known to have ecological and evolutionary consequences for plants, no studies have integrated these concepts. Here we examine how their combined effects are likely to affect the diversity of future communities. We draw on several complimentary fields (community ecology, landscape genetics and biogeography) to model how climate change will alter productivity of foundation plant species and their associated communities. We focus on three issues: (i) genetic variation of foundation species influences community diversity; (ii) gene-by-environment interactions define associated communities; and (iii) relationships between productivity and species diversity follow predictable patterns. For many foundation species, responses to climate are population specific because populations are often genetically differentiated and locally adapted. Thus, biological models that examine the effects of climate change on species distribution, forest productivity, community structure or function, should incorporate population effects. Our genetics-based Universal Community Transfer Function (UCTF) provides a method to integrate climate-based population differences into community diversity models. Several major findings emerged: (i) using the UCTF, we found that genetics-based differences between populations play an important role in defining future communities. (ii) The shape of the productivity/diversity relationship (e.g. humpbacked versus linear) dramatically affects future communities making it essential to quantify this relationship. (iii) Climate change will impact the community differently at leading, continuous and rear edges of a species' distribution, but diversity at the rear edge will suffer most. Genetics-based approaches are important to understand the ecological and evolutionary consequences of climate change on future communities and ecosystems. Such modelling can assist in identifying populations of foundation species of special value based on their sensitivity to climate change, future biodiversity and potential to support high biodiversity with assisted migration.
Use of Individual Feed Records in a Selection Program for Egg Production Efficiency.I. Heritability of the Residual Component of Feed Efficiency

Abstract The data consists of individual records on feed consumption, body weight, and egg mass from 4909 pedigreed White Leghorns from two separate populations, Q and R. The residual component is defined as the amount of feed consumption remaining after statistical adjustment for body weight and egg mass. The heritability of the residual, as estimated from the sire component of variance, was . 29 ± . 07 in Q and . 15 ± . 06 in R. The moderately high heritability of the residual component, as estimated, suggests that individual feed consumption records will enhance selection for efficiency of egg production.
Tools (Viewer, Library and Validator) that Facilitate Use of the Peptide and Protein Identification Standard Format, Termed mzIdentML

The Proteomics Standards Initiative has recently released the mzIdentML data standard for representing peptide and protein identification results, for example, created by a search engine. When a new standard format is produced, it is important that software tools are available that make it straightforward for laboratory scientists to use it routinely and for bioinformaticians to embed support in their own tools. Here we report the release of several open-source Java-based software packages based on mzIdentML: ProteoIDViewer, mzidLibrary, and mzidValidator. The ProteoIDViewer is a desktop application allowing users to visualize mzIdentML-formatted results originating from any appropriate identification software; it supports visualization of all the features of the mzIdentML format. The mzidLibrary is a software library containing routines for importing data from external search engines, post-processing identification data (such as false discovery rate calculations), combining results from multiple search engines, performing protein inference, setting identification thresholds, and exporting results from mzIdentML to plain text files. The mzidValidator is able to process files and report warnings or errors if files are not correctly formatted or contain some semantic error. We anticipate that these developments will simplify adoption of the new standard in proteomics laboratories and the integration of mzIdentML into other software tools. All three tools are freely available in the public domain.
Detritus in the epilithic algal matrix and its use by coral reef fishes

The epilithic algal matrix (EAM) is a ubiquitous component of coral reefs and is the primary grazing surface for many reef fishes. Detritus accounts for at least 10% to 78% of all the organic matter present in the EAM, variation being attributed to hydrodynamic forces such as wave energy and biological elements such as algal morphology. When compared with filamentous algae, the other major source of organic matter in the EAM, protein:energy ratios, C:N ratios and total hydrolysable amino acids all suggest that detritus is of higher nutritional value than the algae. Lipid biomarkers indicate that more than 70% of the detritus is derived from the filamentous algae but the addition of bacteria and microalgae add essential nutrients and improve the nutritional value of the detritus. The detritus is typically of an amorphic form with protein:energy ratios which indicate that it is capable of sustaining fish growth. Detritus within the EAM may be derived from dissolved organic matter, which reduces refractory material, enhancing the palatability and digestibility of detritus relative to filamentous algae. Detritus in the EAM may also come from settling material and fish faeces. Studies that quantified the amount of detritus ingested by fishes have identified at least 24 species from five families that predominantly ingest detritus. These species represent some of the most widespread and abundant EAM feeding fishes on coral reefs. It is estimated that detritivorous fishes account for at least 20% of individuals and 40% of the biomass of an EAM-feeding fish assemblage on the Great Barrier Reef. Comparisons of ingested material with the EAM indicate that many of these species selectively feed on detritus, particularly the small, organic rich particles <125 μm. Furthermore, analysis of lipids in body tissues of blennies and assimilation of nutrients from the alimentary canal of scarids and acanthurids provide strong evidence that detritus is assimilated by coral reef fishes. Consequently, a large percentage of EAM-feeding fishes on coral reefs can unequivocally be classified as detritivores. The ingestion and assimilation of detritus by these fishes represents a significant pathway for transferring energy from within the EAM to secondary consumers, making detritivorous fishes a critically important component of coral reef trophodynamics.
Melatonin against Myocardial Ischemia-Reperfusion Injury: A Meta-analysis and Mechanism Insight from Animal Studies

Aims Myocardial reperfusion damage after severe ischemia was an important issue during a clinical practice. However, the exacted pathogenesis involved remained unclear and also lacks effective interventions. Melatonin was identified to exert protective effects for alleviating the myocardial I/R injury. This meta-analysis was determined to evaluate the efficacy of melatonin treatment against reperfusion insult and further summarize potential molecular and cellular mechanisms. Methods and Results 15 eligible studies with 211 animals (108 received melatonin and 103 received vehicle) were included after searching the databases of PubMed, MEDLINE, Embase, and Cochrane. Pretreatment with melatonin was associated with a significant lower infarct size in comparison with vehicle in myocardial I/R damage (WMD: -20.45, 95% CI: -25.43 to -15.47, p < 0.001; I2 = 91.4%, p < 0.001). Evidence from subgroup analyses and sensitivity analysis indicated the robust and consistent cardioprotective effect of melatonin, while the metaregression also did not unmask any significant interactions between the pooled estimates and covariates (i.e., sample size, state, species, study type, route of administration, and duration of reperfusion, along with timing regimen of pretreatment). Accordingly, melatonin evidently increased EF (WMD: 17.19, 95% CI: 11.08 to 23.29, p < 0.001; I2 = 77.0%, p < 0.001) and FS (WMD: 14.18, 95% CI: 11.22 to 17.15, p < 0.001; I2 = 3.5%, p = 0.387) in the setting of reperfusion damage. Conclusions Melatonin preadministration conferred a profound cardioprotection against myocardial I/R injury in preclinical studies.
THE NUCLEOTIDE SEQUENCE OF THE CHROMOSOMAL TETRACYCLINE-RESISTANCE GENE OF BACILLUS SUBTILIS R DIFFERS FROM THAT OF B. SUBTILIS 168 BY FIVE BASE PAIRS

We have previously cloned in Escherichia coli a 4.5-kbp HindIII DNA fragment carrying tetracycline-resistance (Tcr) determinant (named tetBS908) from the Bacillus subtilis GSY908 (168 strain) chromosome (8) using plasmid vector pLS353 (S). tetBS908 consisted of 1,347 by encoding 458 amino-acid residues initiating from a GTG colon preceded by a ribosome-binding site (RBS-2). Upstream from tetBS908 there exists a short open reading frame (leader peptide) consisting of 20 amino acids initiating from an ATG colon preceded by its own RBS (RBS-1) (7) (see Fig. 1). The 4.5-kbp sequence carrying tetBS908 was localized to the replication origin region of the chromosome (1). B. subtilis 168 derivatives RM 125, 1012 and KS 162 also carry the 4.5-kbp HindIII sequence (1). The nucleotide sequence (3,070 bp) of the tet gene and flanking regions of the 4.5kbp fragment of the 1012 chromosome agreed perfectly with those of the GSY908 (1). Southern-blot analysis of the HindIII-digested chromosomal DNAs of B. subtilis W23, B. subtilis R, two B. subtilis var. natto strains and six other Bacillus strains using the 4.5-kbp Hin dIII fragment of the GSY908 chromosome as a probe revealed that only B. subtilis R chromosome carries a 3.6-kbp HindIII sequence that can hybridize to the probe (1). An attempt has been made in the present study to determine the nucleotide sequence of the 3.6-kbp HindIII fragment and compare it with that of the GSY908 chromosome. Cloning and sequencing of the 3.6-kbp HindIII fragment were performed according to the methods previously reported (7, 8). The results showed that the
Emotion detection through biomedical signals: a pilot study

Emotions are affective states accompanied by physiological reactions that affect cognition processes such as decision making, perception, and learning. Emotion detection can be helpful in fields like education, sports and accident prevention. In this pilot study, we used biosensors to measure heart rate and galvanic skin response of twenty-eight volunteers (fourteen male, fourteen female). They were asked to watch video clips to elicit two target emotions: amusement and anger. The purpose of this study was to determine the relationship between mean values of biosignals and emotional states (including amusement, anger and neutral state). From the analysis of variance, Fisher least significant difference and Multiple Range test, it was observed that emotions elicited with video clips influence mean values and other features of physiological signals with a confidence level of 90%.
Monosomes and their Influence on Meiosis in ‘Holdfast’ (Triticum aestivum L.)

Like ‘Chinese Spring’, ‘Holdfast’ is a hexaploid wheat (2n=42), and can be used in building a set of monosomic lines just as conveniently, for meiosis in it is not as stable as is to be expected in a stable commercial variety. Monosomics are regularly thrown out as a result of meiotic instability and as such several lines can be built up within comparatively a short time. In this paper eleven apparently different monosomic lines have been studied cytologically. The morphological features of the individual monosomes have been described and an attempt has been made to compare and identify these with the chromosomes in ‘Chinese Spring’. Meiotic irregularities have been described in these monosomic lines and at first appear substantial and significant but when they are assessed against the background of ‘Holdfast’ these irregularities no longer seem to be of much significance. However, it may be said that all these monosomic lines are not similar in the type and to the extent to which they exhibit aberrant features in meiosis. Some lines produce appreciably more aberrant features than others whereas some seem to be even more regular than the parent variety itself.
Actualización en cardiopatía isquémica 2005

En este articulo se revisan los principales avances publicados o comunicados durante el ano 2005 en la fisiopatologia, la prevencion secundaria, el pronostico y el tratamiento de los sindromes coronarios agudos con y sin elevacion del segmento ST, asi como las nuevas guias de practica clinica.
The Mechanochemistry of Cardiac Muscle

The utilization of creatine phosphate (CP) and adenosine triphosphate (ATP) was studied in the iodoacetate (IAA) and nitrogen (N2)-treated cat papillary muscle. Under these conditions the net production of ATP does not occur, and the net utilization of ATP is reflected in a fall in CP concentration. The rate of energy utilization of the IAA-N2-treated cat papillary muscle resting without tension was 0.68 µmole CP/g/min. This rate was increased to 1.07 µmole/g/min when muscles were passively stretched with 2 g of tension. In a series of isometrically contracting muscles CP utilization was found to be proportional to the number of activations and the summated contractile element work. These rates of CP utilization were 0.083 µmole/g/activation and 0.0059 µmole/g-cm of work. The calculated mechanochemical coupling efficiency was 33%.
The Use of Pledges to Build and Sustain Commitment in Distribution Channels

Commitment in channel relationships is modeled as a function of (1) each party's perception of the other party's commitment, (2) self-reported and perceived pledges (idiosyncratic investments and contractual terms) made by each party, and (3) other factors such as communication level, reputation, and relationship history. A dyadic model represented by a simultaneous equation system is estimated with data from 378 pairs of manufacturers and industrial distributors. The results indicate that one type of pledge, idiosyncratic investments, has a strong effect on the commitment of both parties to the relationship. In addition, each party's commitment is affected by the perceived commitment of the other party. Finally, idiosyncratic investments signal commitment, affecting each party's perceptions of the other party's commitment.
Statins in primary and secondary prevention: what should the target LDL cholesterol value be?

‹nsandaki tüm organ sistemlerinin fonksiyonunda önemli rol oynayan kolesterol, Bat› dünyas›ndaki tüm ölümlerin üçte birinden fazlas›n›n nedeni olan koroner kalp hastal›¤› patogenezindeki önemli unsurlardan biridir. Yüz y›la yak›n bir süre içinde elde edilen epidemiyolojik ve deneysel veriler, bir kolesterol tafl›y›c› protein olan düflük yo¤unluklu lipoproteinin (LDL) aterosklerozla olan iliflkisini kuflkuya yer b›rakmayacak netlikte ortaya koymufltur. Art›k pandemik hale gelen aterosklerotik hastal›klarla mücadelenin önemli bir unsuru olan kolesterol düflürücü tedaviler günümüz kardiyovasküler t›bb›n›n en önemli u¤rafl›lar›ndan birini oluflturmaktad›r.
Book Reviews

The purpose of this book is to outline the varied knowledge sources available to participants in understanding discourse. "Specifically," van Dijk and Kintsch state, "we attempt to sketch the way knowledge is used in discourse comprehension" (pp. ix-x). The word strategies, a plural form, signals the multifaceted nature of van Dijk and Kintsch's analyses. Through a model of discourse processing, the authors bring coherence to diverse comprehension studies by indicating the specific aspect of discourse processing addressed in each study. They also note conflicting results, which are often explained by attention to a facet of the model not originally considered in the experimental design. The numerous missing links in our knowledge of discourse processes are highlighted. This is a book for researchers in the field of discourse understanding. It is not easy reading, but it is requisite reading for any who hope to either understand or to add to the literature in the field. Van Dijk and Kintsch provide a further statement of their goal for the book in the last paragraph.
Modification of the Sodium Hexametaphosphate Extraction‐Precipitation Technique of Rapeseed Protein Concentrate Preparation

A previously reported method of preparing rapeseed protein concentrate (RC) involving 2% sodium hexametaphosphate (SHMP) was modified to reduce SHMP lost in the effluent, to produce a product with higher protein, lower phosphorous content and improved color close to that of rapeseed flour and promine D. Addition of 0.25% Na2S2O5 to the 0.25% SHMP extractant improved color but had little effect on flavor. Except for nitrogen solubility, whippaachieved the first two objectives. Double washing of precipitate with 50% alcohol or precipitation in 15 or 30% alcohol yielded RC with color close to that of rapeseed flour and promine D. Addition of 0.25% Na2S2O5 to the 0.25% SHMP extractant improved color but had little effect on flavor. Except for nitrogen solubility, whippability and viscosity, the functional properties and chemical scores of the improved RC's were similar to the control RC (2% SHMP).
Biology of mycorrhizal associations of epacrids (Ericaceae).

Epacrids, a group of southern hemisphere plants formerly considered members of the separate family Epacridaceae, are in fact most closely allied to the Vaccinioid tribe (Ericaceae). Epacrids and other extant ericoid mycorrhiza-forming plants appear to have a monophyletic origin. In common with many Ericaceae they form ericoid mycorrhizas. ITS sequence data indicate that the fungi forming ericoid mycorrhizas with epacrids and other extant Ericaceae are broadly similar, belonging to a poorly defined group of ascomycetes with phylogenetic affinities to Helotiales. The basic development and structure of ericoid mycorrhizal infections in epacrids is similar to other Ericaceae. However, data are limited on the structure and physiology of both hair roots and ericoid mycorrhizas for all Ericaceae. Relatively little is known about the functional significance of ericoid mycorrhizas in epacrids in southern hemisphere habitats that are often poor in organic matter accumulation. However the abilities of fungal endophytes of epacrids to utilize organic N and P substrates equal those of endophytes from northern hemisphere heathland plant hosts. Investigations using 15 N/13 C-labelled organic N substrates suggest that mycorrhizal endophytes are important, at least, to the N nutrition of their epacrid hosts in some habitats. Contents Summary 305 I. Epacrid plant hosts 306 II. Evolution of ericoid mycorrhizas in epacrids 306 III. Epacrid hair roots and their mycorrhizal associations 307 IV. Seasonality and incidence of mycorrhizal infection 310 V. Structure and development of mycorrhizal associations 311 VI. Nature of the mycorrhizal fungal endophytes 315 VII. Community and population biology of mycorrhizal endophytes 318 VIII. Functional aspects of mycorrhizas in epacrids 319 IX. Conclusions 322 Acknowledgements 322 References 322.
The Past, Present and Future Role of Limnology in Freshwater Fisheries Science

Limnology has greatly influenced the field of freshwater fisheries science, particularly fisheries biology. However, both fields became increasingly disconnected during the 20th century, when major research traditions within limnology became more tightly focused and humans, even fish, were externalized. A paradigm shift occurring within freshwater fisheries science today is redefining research questions and approaches and is further challenging the role of limnology within fisheries science. Modern fisheries science has become a multidisciplinary, interdisciplinary and sometimes transdisciplinary endeavour that melds the social with the natural sciences to understand fisheries as social-ecological systems. Limnology remains important to capture some of the dynamics inherent in social-ecological fisheries systems, but becomes one of the many necessary scientific disciplines of fisheries science, rather than the primary supporting science that it used to be. To improve scholarly communication between limnologists and freshwater fisheries scientists, major shifts in perspective are needed. It is hardly understandable why fish are only regarded as a component of the aquatic ecosystem or a means for biomanipulation in modern textbooks on limnology or limno-ecology, while the fisheries science as a natural component of theoretical and applied limnology in the spirit of Thienemann is not mentioned in the table of contents! H. -J. Elster, 1993 (translated from German) (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
Single-plant selection at ultra-low density to improve stability of a bread wheat cultivar

The goal of the study was to assess within bread wheat (Triticum aestivum L.) cultivar variation through honeycomb selection, under the ultra-low density (ULD) of 1.2 plants/m 2 . Divergent selection of individual plants characterized as providing high (H) and low (L) yield led to 10 H and 10 L first generation families, respectively. Further selection of high yielding plants within H families resulted in 20 second generation families. Progeny evaluation was conducted in two locations, under ULD and the typical crop density (TCD) of 500 plants/m 2 . Six of the first generation families were also tested, in two locations for two years, across four densities (100, 300, 500, and 700 plants/m 2 ). Intra-cultivar selection improved yield potential per plant (i.e., expressed under low competition conditions), and there was an indication of overall crop yield potential improvement (i.e., maximum yield per unit area). Compared to the original cultivar at ULD conditions, five of the H first generation and 15 of the second generation families had significantly higher grain yield per plant (by 18 to 53%). Two of the H first generation and four of the second generation families significantly outperformed the original cultivar by 17 to 22% under TCD. Experimentation across the four densities showed that derived families exhibited less density dependence than their original cultivar, a determinant parameter for stability of performance. Results constituted evidence of low densities being more suitable for breeder's seed maintenance, so that any existing or newly developed variation is beneficially exploited.