Miracle-dz/UniFAR-FTUs huggingface dataset:
Use of component analysis in QTL mapping of complex crop traits : A case study on yield in barley

Genes contributing to the quantitative variation of a complex crop trait can be numerous. However, using existing approaches, the number of quantitative trait loci (QTL) detected for a trait is limited. Therefore, rather than looking for QTL for a complex trait itself, determining QTL for underlying component traits might give more information. In this study the potential of component analysis in QTL mapping of complex traits was examined using grain yield in spring barley as an example. Grain yield was divided into three components: number of spikes/m2, number of kernels/spike, and 1000-kernel weight. These traits were measured for individuals of a recombinant inbred-line population in field trials conducted over 2 years. By the use of an approximate multiple QTL model, one to eight QTL were detected for each trait in a year. Some QTL were mapped to similar positions in both years. Almost all QTL for yield were found at the position of or in close proximity to QTL for its component traits. A number of QTL for component traits were not detected when yield itself was subjected to QTL analysis. However, relative to the QTL for yield itself, all component-trait QTL did not explain the variation in yield better. The results in relation to the potential of using component analysis in studying complex crop traits are discussed.
Chrysomya albiceps (Wiedemann) and Hemilucilia segmentaria (Fabricius) (Diptera, Calliphoridae) used to estimate the postmortem interval in a forensic case in Minas Gerais, Brazil

ABSTRACT. Chrysomya albiceps (Wiedemann) and Hemilucilia segmentaria (Fabricius) (Diptera, Calliphoridae) used to estimate the postmortem interval in a forensic case in Minas Gerais, Brazil. The corpse of a man was found in a Brazilian highland savanna (cerrado) in the state of Minas Gerais. Fly larvae were collected at the crime scene and arrived at the laboratory three days afterwards. From the eight pre-pupae, seven adults of Chrysomya albiceps (Wiedemann, 1819) emerged and, from the two larvae, two adults of Hemilucilia segmentaria (Fabricius, 1805) were obtained. As necrophagous insects use corpses as a feeding resource, their development rate can be used as a tool to estimate the postmortem interval. The post-embryonary development stage of the immature collected on the body was estimated as the difference between the total development time and the time required for them to become adults in the lab. The estimated age of the maggots from both species and the minimum postmortem interval were four days. This is the first time that H. segmentaria is used to estimate the postmortem interval in a forensic case.
Avian Communal Roosting: Implications of Diurnal Activity Centers

Most current explanations of avian communal roosting focus on benefits derived at the roost itself and assume that the roost is the individual's base of operation. A very different view of communal roosting emerges when the birds are marked individually. A recent radiotelemetric study of communally roosting European starlings (Sturnus vulgaris) revealed that individuals are far more faithful to their diurnal activity centers (DAC's) than to their roosts (Morrison and Caccamise 1985). Studies of other communally roosting species have suggested that DAC's are probably not unique to starlings. The finding that at least some communally roosting species have DAC's has important implications for both foraging-based and predation-based interpretations of communal roosting. Our studies of starlings suggest that foraging factors were of primary importance in the evolution of both DAC's and communal roosting. Foraging daily on a familiar DAC may have benefits similar to those of holding a territory. Furthermore, DAC-based birds should forage away from the DAC only when the food intake rate in the supplemental feeding area (SFA) more than compensates for the cost of commuting to that SFA. And finally, although DAC-based birds probably join small communal roosts near their DAC's to reduce the risk of nocturnal predation, they join much larger, more distant roosting groups primarily to reduce commuting costs to supplemental feeding areas. We hypothesize that major communal roosts may simply be aggregations of individuals roosting as close as possible to especially rich feeding areas. Our patch-sitting hypothesis generates predictions that clearly distinguish it from other foraging-based hypotheses. We encourage researchers to look for DAC-based behavior in other species and to consider a DAC-based perspective when formulating and testing hypotheses about communal roosting.
Restoration of a Danish headwater stream: short-term changes in plant species abundance and composition

1. This paper describes the short-term effects (2 years) of stream restoration on vascular plant communities in a 1.4 km upper reach of the River Gudena, Denmark. The effects of restoration were assessed in terms of the abundance and composition of plant species in the stream, on the banks and in the stream valley. 2. Total species richness was similar before and after restoration, and comprised approximately 150 species representing 12% of the entire Danish vascular plant flora. 3. In the stream, total plant cover had not recovered to pre-restoration levels 2 years after restoration. Cover by submerged, amphibious and terrestrial species growing submerged decreased, as did the number of amphibious and terrestrial species growing submerged. 4. On the banks, total plant cover almost attained pre-restoration levels the second year after restoration. The plant communities changed from dominance by non-riparian species to more diverse communities with a greater number and increased cover of riparian gramineous species requiring a higher soil moisture content. 5. In the valley, the plant communities only changed slightly after restoration, although growth of riparian species was enhanced on the southern side of the stream. Copyright © 2000 John Wiley & Sons, Ltd.
Effects of Suture Type and Patterns on Surgical Wound Healing in Rainbow Trout

Abstract In two separate experiments we investigated the effects of different types of suture material and patterns on wound healing in rainbow trout Oncorhynchus mykiss with and without transmitter implants. We used absorbable and nonabsorbable monofilament and braided silk sutures in simple interrupted and vertical mattress patterns to close 3-cm incisions on rainbow trout. Braided silk sutures and vertical mattress suture patterns caused significantly more tissue inflammation (P < 0.05) as shown by macroscopic analysis. However, there were no significant differences in the histology or strength of the wounds related to the type of suture material or the type of suture pattern used. Dummy radio transmitters compounded the inflammatory effect silk had on healing incisions compared with inflammation without transmitters.
Sediment Organic Matter and its Nutritional Quality: A Short-Term Experiment with Two Exotic Bivalve Species

This study was aimed to investigate the role of two exotic bivalves (Ruditapes philippinarum and Museulista senhousia) on the trophic enrichment and the nutritional quality of sediments from the Sacca di Goro (northern Adriatic Sea) through manipulative experiments. The concentrations of sedimentary total organic matter. biopolymeric carbon, carbohydrates. proteins, lipids. and chlorophyll-a were determined through a 64 days-long period. The experimental setup consisted in three replicated treatments (R. philippinarum. M. senhousia and simply sand). with treatments and time as fixed factors. All the biochemical classes showed wide fluctuation, and significant differences among treatments were detected during the experimental period. Both bivalve species played a role in sediment enrichment process. At the end of the experimental period, proteins represented the main biochemical class of organic compounds in the treatments with bivalves (48.5 and 44.5% of the biopolymeric fraction in the M. senhousia and R. philippinarum treatments, respectively), while in the control treatment they were only 32.7%. The accumulation ofproteic nitrogen increased the nutritional quality of the sedimentary organic matter. Moreover. the presence of M. senhousia also enhanced the accumulation of microphytobenthic carbon.
Interaction between sites of magnesium absorption in the digestive tract of the sheep

The effect of magnesium chloride infusion to different sites in the gastrointestinal tract of sheep upon the net absorption of magnesium from different regions of the digestive tract has been examined. Four Merino wethers were each prepared with cannulas sited in the rumen, in the duodenum adjacent to the pylorus and in the terminal ileum. The basal diet provided 18.45 mmoles magnesium/ day and an additional 65 mmoles magnesium/day as magnesium chloride was continuously infused into (A) the rumen, (B) the rumen and duodenum in equal portions, (C) the duodenum and (D) the terminal ileuni. A continuous infusion of Cr-EDTA to the ruinen enabled digcsta and magnesium flow rates to be estimated from digesta samples obtained from the intestinal cannulas at 4 hr intervals over 3 days. For treatments A, B, C and D respectively, the mean net absorption of magnesium (mmoles/day) from the rumen was 20.4, 11.4, 1.4 and 3.4; from the small intestine –0.5, 1.7, –5.1 and –9.8; from the large intestine 4.6, 2.2, 12.7 and 12.3; and from the total gastrointestinal tract 24.6, 15.4, 9.1 and 4.9. In each case the effect of treatment was significant. The total net absorption of magnesium caudal to the pylorus was unaffected by treatment. Plasma magnesium levels were reduced during post-ruminal infusion of magnesium, but these changes were not obviously linked to the changed net absorption from the intestinal segments. The urinary and faecal excretion of magnesium, but not the magnesium balance, was strongly related to the total net absorption of magnesium. The results emphasize the major contribution of the stomach to the gastrointestinal net absorption of magnesium and show that although the amount absorbed from this region may influence separately the net absorption from the large and small intestine, it does not appear to influence the overall intestinal net absorption of magnesium.
Factors Relating to Development of Spontaneous Oxidized Flavor in Raw Milk

Abstract Factors affecting spontaneous oxidation in 1198 raw milk samples collected from 137 herds were determined. Milk was examined organoleptically for oxidized flavor 48h after collection on a 0 (none) to 4 (pronounced) scale. The mean concentration of copper was 48 μ g/kg and of tocopherol 25.6 μ g/kg lipid. Copper and tocopherol concentrations were correlated with oxidized flavor score and together accounted for 15.1% of its variation. Variables of herd were breed of cow, age of cow, and percent of herd in first 60, second 60, and more than 120 days of lactation. No correlations were significant between breed or age of cow and oxidized flavor score. The percent of herd in the first 60 days of lactation was correlated with oxidized flavor score but accounted for only 3.9% of the variability. Variables of management were age, type, and amount of hay fed, type and amount of concentrate fed, and production of milk and milk fat. No correlations between type or amount of feed and oxidized flavor score were significant. Production both of milk and milk fat was correlated with oxidized flavor score but accounted for only . 40 and . 03% of the variability.
Interferon‐γ differentially regulates TGF‐β1 and TGF‐β2 expression in human retinal pigment epithelial cells through JAK‐STAT pathway

Retinal pigment epithelium (RPE) and transforming growth factor‐β (TGF‐β) have been shown to be involved in various retinal diseases. We have studied the role of inflammatory cytokines on the expression and secretion of TGF‐β in human RPE cells (HRPE). Confluent cultures of HRPE derived from donor eyes were used. RT‐PCR analyses showed that TNF‐α and IL‐1β increased the mRNA levels of both TGF‐β1 and TGF‐β2. IFN‐γ enhanced constitutively expressed, as well as, TNF‐α‐and IL‐1β‐induced TGF‐β1 mRNA levels but decreased TGF‐β2 mRNA. The effects of these cytokines on TGF‐β1 and TGF‐β2 secretion correlated with the mRNA levels. TGF‐β1 was always produced as the latent form while 21–31% of TGF‐β2 was in the active form. IFN‐γ reduced the production of active form of TGF‐β2 to 4–9%. TGF‐β3 secretion was not detectable under any of the conditions. The Real‐Time PCR analysis of TGF‐β mRNAs confirmed the observed results. The TGF‐β1 and TGF‐β2 secretion was induced by TGF‐β2 and TGF‐β1, respectively. Under these conditions, the contrasting effects of IFN‐γ on TGF‐β1 and TGF‐β2 secretion were also observed. JAK inhibitor selectively inhibited IFN‐γ induced TGF‐β1 secretion and mRNA levels while reversing the inhibitory effects of IFN‐γ on TGF‐β2. Analyses of transcription factor activity strongly indicated the role of STAT‐1 but not NFκB, C‐Myc, C‐Jun, SP‐1, MEF‐2. Our data demonstrate that IFN‐γ differentially regulates constitutively expressed, as well as, cytokine‐induced TGF‐β1 and TGF‐β2 mRNA levels and secretion of TGF‐βs by HRPE. J. Cell. Physiol. 210: 192–200, 2007. © 2006 Wiley‐Liss, Inc.
How accurate are the marker orders in crop linkage maps generated from large marker datasets

Marker ordering during linkage map construction is a critical component of QTL mapping research. In recent years, high-throughput genotyping methods have become widely used, and these methods may generate hundreds of markers for a single mapping population. This poses problems for linkage analysis software because the number of possible marker orders increases exponentially as the number of markers increases. In this paper, we tested the accuracy of linkage analyses on simulated recombinant inbred line data using the commonly used Map Manager QTX (Manly et al. 2001: Mammalian Genome 12, 930-932) software and RECORD (Van Os et al. 2005: Theoretical and Applied Genetics 112, 30-40). Accuracy was measured by calculating two scores: % correct marker positions, and a novel, weighted rank-based score derived from the sum of absolute values of true minus observed marker ranks divided by the total number of markers. The accuracy of maps generated using Map Manager QTX was considerably lower than those generated using RECORD. Differences in linkage maps were often observed when marker ordering was performed several times using the identical dataset. In order to test the effect of reducing marker numbers on the stability of marker order, we pruned marker datasets focusing on regions consisting of tightly linked clusters of markers, which included redundant markers. Marker pruning improved the accuracy and stability of linkage maps because a single unambiguous marker order was produced that was consistent across replications of analysis. Marker pruning was also applied to a real barley mapping population and QTL analysis was performed using different map versions produced by the different programs. While some QTLs were identified with both map versions, there were large differences in QTL mapping results. Differences included maximum LOD and R-2 values at QTL peaks and map positions, thus highlighting the importance of marker order for QTL mapping
DEGRADATION CHARACTERISTICS AND TANNIN BIOASSAY OF SOME BROWSE FORAGE FROM KENYA HARVESTED DURING THE DRY SEASON

The potential nutritional value of six species of browse forage from Kenya harvested during the dry season were evaluated by chemical composition, in sacco dry matter (DM) degradation and in vitro gas production technique. The effect of tannins on the rumen fermentation of the forage was evaluated using polyethylene glycol (PEG) in an in vitro study. The chemical composition of the species of browse forage differed significantly (P < 0.05). The content of organic matter ranged from 846.7 to 946.5 g/kg DM. The forage had a high crude protein content (155.5-280.9 g/kg DM) and variable content of neutral detergent fiber (NDF, 236.2-682.8 g/kg DM). The content of total extractable tannins was generally low (0.6- 38.5 g/kg DM). At 24 h of incubation, the in sacco DM disappearance ranged from 31.2% to 84.2%. The effective DM degradability also ranged from 29.7 to 73.5%. The gas production after 96 h incubation ranged from 17.5 to 44.2 mL/ 200 mg DM. Use of PEG indicated that tannins had an inhibitory effect on rumen microbial fermentation and this is depen- dant upon the amount and activity of the tannins present. The estimated in vitro organic matter digestibility and metab- olizable energy also increased numerically with the PEG addition. The result of this study indicates that such species of browse forage have the potential to be used as feed supplements for ruminants, especially during the dry season.
Analysing 157 learning designs using learning analytic approaches as a means to evaluate the impact of pedagogical decision making

Educators need to change their practice to adapt to a shifting educational context. By visualising learning design decisions, this article highlights the need to capture educators' “tacit” knowledge relating to course material, activity types and workload, through employing learning analytics methods in order to analyse the learning designs of courses taken by 60,000+ students, common pedagogical patterns are identified. When analysing 157 learning designs using a taxonomy of seven different learning activities, we found that the majority of educators used two types of learning activities most widely, namely assimilative activities (reading, watching videos and listening to audio) and assessment activities. Surprisingly, educators do not choose different activity types based upon function (eg, replace one type of student-activating activity by another), but patterns can be seen where educators combine assimilative, productive and assessment activities or assimilative, finding and handling information and communication tasks. While educators rely heavily on assimilative and assessment activities, no positive correlation was found between any of the seven learning design activity types and student outcomes. Our initial findings suggest that student outcomes are negatively correlated with a high proportion of assimilative activities. Further studies are needed to establish whether particular learning design decisions are related to student outcomes and whether these findings can be replicated in different research settings.
Antigenic and genetic relationships between European very virulent infectious bursal disease viruses and an early West African isolate

The antigenic and genetic relationships between very virulent (vv) infectious bursal disease viruses (IBDV) from different countries were investigated. Antigenic characterization was performed using an antigencapture ELISA based on a panel of seven neutralizing monoclonal antibodies (Mabs), which probe at least three VP2-located antigenic domains. All these domains are reactive in the Faragher 52/70 (F52/70) reference strain for European classical serotype 1 IBDV. Genomic characterization was achieved by reverse transcription, amplification and direct sequencing of a genome fragment encoding the VP2 variable domain. Eleven vv isolates from France were compared to the British, Dutch and Belgian UK661, DV86 and 849VB viruses, and to an early vv isolate obtained from the Ivory Coast in 1988. All viruses exhibited antigenic profiles characterized by no binding of Mabs 3 and 4. Lack of binding of Mabs 3 and 4 might thus be helpful for differentiating classical and vvIBDVs. None of the non-French strains resemb.
Tests of Microchannel Plate (MCP) Detector Response to MeV Electrons in Support of Juno, JUICE, and Europa Mission UVS Instrument Investigations

Europa Mission UVS Instrument Investigations. K. D. Retherford M.W. Davis, T. K. Greathouse, R. M. Monreal, R. C. Blase, U. Raut, A. J. Steffl, C. M. Cooke, O. Siegmund, and G. R. Gladstone, Southwest Research Institute, 6220 Culebra Road, San Antonio, TX 78238, Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, MA 02139, Sensor Sciences, 3333 Vincent Road, Ste. 103, Pleasant Hill, CA 94523.
Plant defense against fall armyworm in micro‐sympatric maize (Zea mays ssp. mays) and Balsas teosinte (Zea mays ssp. parviglumis)

Maize [Zea mays L. ssp. mays (Poaceae)] was domesticated from Balsas teosinte (Zea mays ssp. parviglumis Iltis & Doebley) in present‐day Mexico. Fall armyworm, Spodoptera frugiperda JE Smith (Lepidoptera: Noctuidae), is among the most important pests of maize in Mexico and Central America. We compared the strength of plant defenses against fall armyworm between micro‐sympatric landrace maize and Balsas teosinte in the field and laboratory. The field comparison, conducted in Mexico, consisted of comparing the frequency of fall armyworm infestation between young maize and Balsas teosinte plants in dryland agricultural fields in which Balsas teosinte grew as a weed. The laboratory comparison contrasted the performance of fall armyworm larvae provided a diet of leaf tissue excised from maize or Balsas teosinte plants that were intact or had been primed by larval feeding. In the field, maize plants were more frequently infested with fall armyworm than Balsas teosinte plants: over 3 years and three fields, maize was infested at a ca. 1.8‐fold greater rate than Balsas teosinte. In the laboratory, larval growth, but not survivorship, was differently affected by feeding on maize vs. Balsas teosinte, and on primed vs. intact plants. Specifically, survivorship was ca. 98%, and did not differ between maize and Balsas teosinte, nor between primed and intact plants. Larvae grew less on intact vs. primed maize, and similarly on intact vs. primed Balsas teosinte; overall, growth was 1.2‐fold greater on maize compared to Balsas teosinte, and on primed compared to intact plants. Parallel observations showed that the differences in growth could not be attributed to the amount of leaf tissue consumed by larvae. We discuss our results in relation to differences in the strength of plant defenses between crops and their ancestors, the relevance of unmanaged Balsas teosinte introgression in the context of fall armyworm defenses in maize, and whether greater growth of larvae on primed vs. intact plants signifies herbivore offense.
Quantitative chromosome mapping of small plant chromosomes by improved imaging on CHIAS II

Improved imaging procedures were developed and employed for the construction of a quantitative chromosome map based on condensation pattern. The condensa-tion pattern is uneven condensation along a chromosomal axis resulting from differential condensation of chromatin fibers at prometaphase appearing commonly in small plant chromosomes, represented by the genus Brassica. Brassica chromosomes have distinct condensation patterns at the prometaphase stage. The procedures for quantitative mapping are divided into six parts: (i) capture of images, (ii) adjustment of light distortion, (iii) measurements of an image parameter, CP, or density profiles and length of chromosomal arms, (iv) gray value adjustments between homologous chromosomes, (v) adjustment of chromosomal lengths and obtaining the standard CP, or graygram, and (vi) thresholding graygram for a quantitative chromosome map or an idiogram. The quantitative chromosome map shows well the characteristics of the Brassica chromosomes. The series of imaging procedures enable construction of quantitative chromosome maps and can be employed for a wide range of species having various chromosome numbers. The quantitative chromosome map constructed by the improved imaging currently developed is an aid to cytogenetical and genome analysis of plant species.