Miracle-dz/UniFAR-FTUs huggingface dataset:
Ecosystem Engineering of Harvester Ants: Effects on Vegetation in a Sagebrush-Steppe Ecosystem

Abstract. Harvester ants are influential in many ecosystems because they distribute and consume seeds, remove vegetation, and redistribute soil particles and nutrients. Understanding the interaction between harvester ants and plant communities is important for management and restoration efforts, particularly in systems altered by fire and invasive species such as the sagebrush-steppe. Our objective was to evaluate how vegetation cover changed as a function of distance from Owyhee harvester ant (Pogonomyrmex salinus) nests within a sagebrush-steppe ecosystem. We sampled 105 harvester ant nests within southern Idaho, USA, that occurred in different habitats: annual grassland, perennial grassland, and native shrubland. The influence of Owyhee harvester ants on vegetation was larger at the edge of ant nests, but the relationship was inconsistent among plant species. Percent cover was positively associated with distance from harvester ant nests for plant species that were considered undesirable food sources and were densely distributed. However, percent cover was negatively associated with distance-from-nests for patchily distributed and desirable plant species. For some plant species, there was no change in cover associated with distance-from-nests. Total vegetation cover was associated with distance-from-nests in the shrubland habitat but not in the 2 grasslands. The dominant plant species in the shrubland habitat was a densely distributed shrub (winterfat, Krascheninnikovia lanata) that was defoliated by harvester ants. Our results suggest that Owyhee harvester ants increase spatial heterogeneity in plant communities through plant clearing, but the direction and magnitude of effect will likely be contingent on the dominant vegetation groups. This information may inform future management and plant restoration efforts in sagebrush-steppe by directly considering the islands of influence associated with harvester ant engineering.
Dose–response of germinating Rudbeckia mollis (Asteraceae) seeds exposed to various thermal scenarios

Abstract Temperature is a key environmental signal regulating germination. A thorough understanding of how seed populations respond to various temperatures can inform end-users regarding effective establishment strategies and forms the basis for questions related to a taxon's thermo-biology. Although abundant information exists regarding germination responses of economically important crops to several temperature scenarios, much less is known concerning the seed biology of wild germplasm. To address this, we examined the germination response of non-dormant Rudbeckia mollis seeds to various doses of constant or simulated seasonal diel temperatures. Germination response was sigmoidal. Seeds of R. mollis were capable of germinating within a few days to high percentages (>95%) at relatively cool constant (15–25°C) or 12-hour alternating (22/11–33/24°C) temperatures, with optimum temperatures for germination occurring at 25°C or 29/19°C. Germination was inhibited as temperatures increased to 30°C or 33/24°C with early and late germinating phenotypes displaying differential responses at these temperatures. No germination occurred at 35°C. Results are discussed in terms of seedling establishment of R. mollis outside its natural range and implications of climate change on germination.
Orientation of Harmonia axyridis ab. spectabilis to plant and prey combinations

Orientation of Harmonia axyridis ab. spectabilis to different plant and prey combinations was investigated with Y olfactometer. Results showed that un-injured Chaenomeles speciosa, Salix matsudana, Populus tomentosa did not produce plant volatiles attractive to H. axyridis, but after being injured by different aphids, they produced plant volatiles attractive to H. axyridis. The choice rates of the female and male ladybeetles for Ch. speciosa were 73.3 and 56.7, for S. matsudana, 71.7 and 73.3, for P. tomentosa, 58.3 and 68.3. Plant volatiles released by Wistaria sinensis repelled the ladybeetles whenever the plant was intact or injured.
Automated analysis of single cell leukemia data

Acute myeloid leukemia (AML) is a high grade malignancy of non-lymphoid cells of the hematopoietic system. AML is a heterogeneous disease, and numerous attempts have been made to risk-stratify AML so that appropriate treatment can be o↵ered. Single cell analysis methods could provide insights into the biology of AML leading to risk-stratified and functionally tailored treatments and hence improved outcomes. Recent advances in flow cytometry allow the simultaneous measurement of up to 17 antibody markers per cell for up to millions of cells, and it is performed routinely during AML clinical workup. However, despite vast amounts of flow cytometry data being gathered, comprehensive, objective and automated studies of this data have not been undertaken. Another method, strand-seq, elucidates template strand inheritance in single cells, with a range of potential applications, none of which had been automated when this thesis work commenced. I have developed bioinformatic methods enabling research into AML using both these types of data. I present flowBin, a method for faithfully recombining multitube flow cytometry data. I present flowType-DP, a new version of flowType, able to process flow cytometry and other single cell data having more than 12 markers (including flowBin output). I demonstrate the application of flowBin to AML data, for digitally isolating abnormal cells, and classifying AML patients. I also use flowBin in conjunction with flowType to find cell types associated with clinically relevant gene mutations in AML. I present BAIT, a software package for accurately detecting sister chromatid exchanges in strand-seq data. I present functionality to place unbridged contigs in late-build genomes into their correct location, and have, with collaborators, published the corrected locations of more than half the unplaced contigs in the current build of the mouse genome. I present contiBAIT, a software package for assembling early-build genomes which consist entirely of unanchored, unbridged contigs. ContiBAIT has the potential to dramatically improve the quality of many model organism genomes at low cost. These developments enable rapid, automated, objective and reproducible deep profiling of AML flow cytometry data, subclonal cell analysis of AML cytogenetics, and improvements to model organisms used in AML research.
Two-Exon Skipping Due to a Point Mutation in p67-phox-Deficient Chronic Granulomatous Disease

HRONIC GRANULOMATOUS disease (CGD) is a rare inherited disorder whereby phagocytes cannot generate superoxide anion and its derivatives to other active oxygen species that may be used for killing infectious agents. Patients with this disease have recurrent, life-threatening infections with catalase-positive bacteria and fungi. ’ The superoxide generating system in phagocytes and B lymphocytes’ consists of a membrane-bound catalytic component, cytochrome bSs8, and cytosolic components that seem to be required for activation of the system. A functionally active enzyme complex is formed on stimulation of macrophages or neutrophils by assembly of the necessary components on the plasma membrane. This complex carries an electron from reduced form of nicotinamide-adenine dinucleotide phosphate to molecular oxygen to form superoxide anion, which is then released to the outside of the cells or inside the phagosomes.3 The catalytic component, cytochrome bSs8, is composed of two subunits, gp91- and p22-phox (phagocyte oxidase). Cytosolic components include p47- and p67-phox and a small guanosine-triphosphate binding protein Ra~-p21. ‘“~ These five proteins were shown to be sufficient to support superoxide-generation in a cell free ~ystem. ~. ~ Any defect in the four “phox” proteins causes CGD, which occurs either as an X-linked or an autosomal di~order. ~ The gene responsible for the former type of CGD codes for gp91-phox and genes responsible for the latter for p22-, p47-, and p67-phox. The mRNAs that code for allphox proteins have been cloned and sequenced and the genomic organizations rep~rted. ~”~ It is known that p67-phox deficiency is rare in the United States,” Europe,*’ and Japan (manuscript in preparation). Mutations that cause this type of CGD are heterogeneous,’ in contrast to the cases in p47-phox deficiency, the majority of which seem to be accounted for by a common dinucleotide deleti~n,’~~~~ although some patients were heterozygous for this deletion and had a second missense rnutaion in the other allelle. ’33’5 We found a homozygous AG dinucleotide insertion in one patient with p67-phox deficiency, which would bring about a frame shift into mRNA resulting in an early stop codon.26 de Boer et alZ7 reported that a mutation resulting in a nonconservative amino acid change in p67-phox
Assessment of genetic purity of four rice cultivars using microsatellite and ISSR markers

Summary The estimation of rice seed purity is conventionally done by a grow-out-test (GOT). As well as other issues, the time required for GOT is a major limitation. In this study, DNA-based microsatellite and ISSR markers were used to establish fingerprints of four rice varieties and used for assessment of genetic purity. A total of 160 alleles were obtained using 23 microsatellite primer pairs for four rice varieties. Six microsatellite markers (RM 247, RM 303, RM 164, RM 108, RM 72 and RM 19) and eight ISSR markers (UBC 842, UBC 810, UBC 812, UBC 834, UBC 808, UBC 873, UBC 841 and ISSR 2) were found to be the most informative primer sets. These primers sets were used for seed purity analysis of all four varieties. Genetic purity based on a set of three markers revealed that all the tagged plants identified as off-types on the basis of morphological traits were confirmed by the molecular marker in seed samples of the four rice varieties.
Quantifying ocular morphologies in extant primates for reliable interspecific comparisons

Cross-examining evidence from comparative morphology has become a way to support specific hypotheses in social cognition. In particular, ocular morphology has been compared across extant primate species in order to argue that humans present a unique morphology that enables also an uniquely human array of socio-cognitive functions—including a crucial role in the acquisition and practice of linguistic abilities. Even though some of these comparisons have relied on quantifiable dimensions of ocular morphology, other aspects of the comparison have been established qualitatively, based on subjective ratings. In this article, I present a new method that intends to restrain the focus of attention to one specific perceptual aspect of ocular morphology—namely, the contrast between scleral and iridal colors, as it is thought to enable (or ease) gaze following from other individuals. The method also allows for more reliable comparisons across extant primate species, as it relies on quantifiable measurements. I exemplify the potential of this method with a three-fold comparison of three great ape species ( Pongo pygmaeus , Pongo abelii , and Homo sapiens ).
High sensitivity, high resolution physical mapping by fluorescence in situ hybridization on to individual straightened DNA molecules

High resolution physical mapping of clonal DNA fragments with kilobase (kb) resolution can now be performed rapidly by fluorescence in situ hybridization (FISH) onto individual DNA molecules (DNA fibers). We developed a sensitive procedure termed 'quantitative DNA fiber mapping' which consists of three steps: preparation of DNA fibers, hybridization of non-isotopically labeled probes and determination of the relative mapping position by fluorescence image analysis. The DNA fibers are produced by binding linearized DNA molecules with one or both ends to a solid substrate followed by homogeneous stretching of the molecule by the action of a receding meniscus during drying ('molecular combing'). In a slight variation of this protocol, we deposit circular DNA molecules. Substrates for DNA immobilization are glass slides, coverslips or thin sheets of mica derivatized with amino-silane. Probes are prepared to counterstain the DNA fibers, from the clones to be mapped and for specific landmarks along linear or circular DNA molecules such as cloning vector sequences. Following hybridization and immunocytochemical detection of bound probes, images are analysed and relative distances are recorded for map assembly. Here, we describe our experience with substrate preparation, molecular combing and mapping of cloned or enzymatically synthesized probes ranging in size from 1.2 kb to 100 kb along DNA molecules that are between 17 kb and 1200 kb in size.
Transcriptional Activity of Full-Length and Truncated Metallothionein Promoters of Crassostrea hongkongensis in Response to Metal Stress

ABSTRACT A 717-bp 5′-flanking regulatory sequence of the metallothionein gene in Crassostrea hongkongensis (ChMT) was isolated using anchored polymerase chain reaction. Several regulatory elements embedded in the flanking sequence, including the central promoter region, five putative metal-responsive elements (MRE), and an octamer-binding site (OBS), were analyzed using online prediction software. Then, the effects of element-based promoter truncations in the upstream regulatory region of ChMT on the metal stress response were examined. The expression levels of the promoters of various lengths were determined individually using a luciferase reporter gene in HEK293T cells. Transfection assays revealed that MRE1- and MRE5-containing DNA fragments inhibited transcription, whereas MRE4-containing DNA sequences activated promoter expression under both metal-stressed and unstressed conditions. A 39-bp DNA fragment containing the OBS was shown to respond positively to metal stress induced by cadmium and copper, but not to mercury. MRE2- and MRE3-containing DNA fragments comprised a portion of the central promoter region, the loss of which resulted in a significant reduction in promoter activity. Interestingly, the loss of promoter activity due to MRE3 deletion could be rescued by copper-induced stress. This study demonstrates the importance of MRE and additional regulatory elements in the regulation of ChMT promoter expression in response to metal stress.
Growth Rate and Temperature Responses in Bryophytes: I. An Investigation of Brachythecium Rutabulum

(1) The growth of the perennial pleurocarpous moss Brach 'thecium rutabulum under controlled conditions of temperature, irradiance, moisture and inorganic nutrient supply was analysed. (2) Over a period of 30 days, the species maintained exponential growth and attained a relative growth rate of 0 071 day-'-a value exceeding the reported maxima for seedlings of ten vascular plant species. (3) In a temperature gradient, maxima in relative growth rate, shoot length and leaf area occurred at about 19 IC but at 5 ? C the reduction in relative growth rate was less than 40%. (4) The comparatively high relative growth rate of B. rutabulum is consistent with the large amplitude of seasonal change in biomass and rapid turnover of shoots observed under natural conditions. The capacity to grow at low temperature may be related to the tendency of the species to exploit the cool conditions of spring and autumn and may also explain the ability of the species to co-exist with productive vascular plants.
A Cavernicolous Form of the Poeciliid Fish Poecilia sphenops from Tabasco, Mexico

LADIGES, W. 1958. Der malaiische Gurami Spaerichthys osphromenoides Canestrini. D. Aquar. u. Terr. Z. 11:3-7. MAGOUN, H. W. 1958. The waking brain. Thomas, Springfield, Ill. 138 p. MORRIS, D. 1958. The reproductive behaviour of the ten-spined stickleback (Pygosteus pungitius L.). Behaviour Suppl. 6:1-154. MORRIS, R. W. 1956. Clasping mechanism of the cottid fish Oligocottus snyderi Greeley. Pacif. Sci. 10:314-7. NIEUWENHUIZEN, A. V. D. 1958. Badis badis (Hamilton). D. Aquar. u. Terr. Z. 11:35962.
Three lernaeid copepods parasitic on South Indian fishes.

The three lernaeids described here belong to the genus Lerneaenicus. W\ilson (1917) listed twelve species of this genus. Six more, (L. cerberus Leigh Sharpe, 1927; L. hemirharnphi Kirtisinghe, 1932; L. gnavius Leigh Sharpe, 1934; L. gnathoricus Leigh Sharpe, 1934; L. seeri Kirtisinghe, 1934; L. savori Yamaguti, 1939) as well as a new variety L. sardinae var longicornis Boudoin, 1918, have been added since. In the present paper, L. hemirhamphi Kirtisinghe, is described more fully than before and a brief note on its anatomy is added. The other two lernaeids, L. nemipteri and L. stromatei are new species which are described below.
Droplet size spectra generated in turbulent pipe flow of dilute liquid/liquid dispersions

Experiments were carried out with water dispersed in hydrocarbons at various flow rates. The measured size spectra can be well represented by either an upper limit log-probability function or a Rosin-Rammler type of equation with constant parameters and only one variable, the maximum drop diameter dmax or d95. The latter can be predicted satisfactorily by a correlation based on the Hinze/Kolmogorov model of droplet breakup.
Changes in sugar and starch concentrations in parsnip (Pastinaca sativa L.) during root growth and development and in cold storage

Summary Low-temperature sweetening of parsnip (Pastinaca sativa L.) roots, which may occur both pre-harvest and post-harvest, is a well-known phenomenon, but is poorly understood. ‘White King’ parsnip roots were analysed over two seasons (2008 and 2009) during field growth and over six months cold storage at 1ºC for their dry matter content, as well as their starch, sucrose, glucose, fructose, and malto-oligosaccharide (MOS) concentrations and for their changes in amylolytic enzyme activities (2009 only). In 2008, when the air temperature fell below 5ºC for 12 d in the last 8 weeks before harvest, the concentration of starch decreased significantly (P ≤ 0.05) and the concentration of total sugar increased significantly. In 2009, when temperatures did not fall below 5°C during the last 8 weeks before harvest, the concentrations of starch (339 + 17 mg g–1 DW) and total sugars (168 + 12 mg g–1 DW) did not change significantly. However, in both years, during 24 weeks in cold storage at 1ºC, starch levels were almost completely depleted, whereas sucrose concentrations and, to a lesser extent, MOS concentrations increased at least two-fold. Glucose and fructose concentrations also increased significantly during 24 weeks in cold storage, but to a much lower level than sucrose or MOS. Total amylolytic activity and α-amylase activity doubled during the first 8 weeks in cold storage, whereas β-amylase activity did not change significantly. As products of α-amylase activity, changes in MOS concentration paralleled the changes in α-amylase activity. The accumulation of sucrose and MOS may raise the culinary quality of cold-stored parsnip.
The New Economics: For Industry, Government, Education

A new edition of a book that details the system of transformation underlying the 14 Points for Management presented in Deming's Out of the Crisis. It would be better if everyone would work together as a system, with the aim for everybody to win. What we need is cooperation and transformation to a new style of management. from The New Economics for Industry, Government, Education In this book, W. Edwards Deming details the system of transformation that underlies the 14 Points for Management presented in Out of the Crisis. The Deming System of Profound Knowledge, as it is called, consists of four parts: appreciation for a system, knowledge about variation, theory of knowledge, and psychology. Describing the prevailing management style as a prison, Deming shows applying the System of Profound Knowledge increases productivity, quality, and people's joy in work and joy in learning. Another outcome is short-term and long-term success in the market. Indicative of Deming's philosophy is his advice to abolish performance reviews on the job, to look deeper than spreadsheets for opportunities, and even to rethink how we teach and manage our schools. Moreover, Deming's method enables organizations to make accurate predictions, which is a valuable tool in today's uncertain economic climate. This third edition features a new chapter (written by business consultant and Deming expert Kelly L. Allan) that explains the relevance of Deming's management method, and case studies from organizations that have adopted Deming's System of Profound Knowledge, and offers guidance on how organizations can effectively ? do Deming.
Optimum conditions of UV ray irradiation for genetic inactivation of loach eggs

Optimum conditions of ultraviolet (UV) ray irradiation for genetic inactivation of eggs were examined to develop simple and easy techniques to induce androgenesis in the loach , Misgurnus anguillicaudatus, since ionizing radiation such as gamma-or X-ray, which has been used generally for fish androgenesis, gives technical problems of safety and the need for special facilities . In the first and second experiments, unfertilized eggs were exposed to UV rays from two sources, germicidal lamps affixed to the ceiling and below, at dosages from 1875 to 15000 erg/mm2. While in the third experiment, eggs being shaken in a micro mixer were irradiated with UV rays from ceiling lamps at dosages between 4200 and 21000 erg/mm2. Most embryos developing after fertilization with normal spermatozoa showed abnormal morphology and a haploid number of chromosomes (n=25) in all the experiments, indicating successful induction of androgenesis. Occurrence of some aneuploids and diploids suggests the necessity of further improvement for homogeneity of treatment.
Influence of Local Pressures on Maldivian Coral Reef Resilience Following Repeated Bleaching Events, and Recovery Perspectives

Two severe heat waves triggered coral bleaching and mass mortality in the Maldives in 1998 and 2016. Analysis of live coral cover data from 1997 to 2019 in shallow (5 m depth) reefs of the Maldives showed that the 1998 heat wave caused more than 90% of coral mortality leaving only 6.8 ± 0.3% of survived corals in all the shallow reefs investigated. No significant difference in coral mortality was observed among atolls with different levels of human pressure. Maldivian reefs needed 16 years to recover to the pre-bleaching hard coral cover values. The 2016 heat wave affected all reefs investigated, but reefs in atolls with higher human pressure showed greater coral mortality than reefs in atolls with lower human pressure. Additionally, exposed (ocean) reefs showed lower coral mortality than those in sheltered (lagoon) reefs. The reduced coral mortality in 2016 as compared to 1998 may provide some support to the Adaptive Bleaching Hypothesis (ABH) in shallow Maldivian reefs, but intensity and duration of the two heat waves were different. Analysis of coral cover data collected along depth profiles on the ocean sides of atolls, from 10 to 50 m, allowed the comparison of coral mortality at different depths to discuss the Deep Refuge Hypothesis (DRH). In the upper mesophotic zone (i.e., between 30 and 50 m), coral mortality after bleaching was negligible. However, live coral cover did not exceed 15%, a value lower than coral survival in shallow reefs. Low cover values of corals surviving in the mesophotic reefs suggest that their role as refuge or seed banks for the future recovery of some species in shallow-water reefs of the Maldives may be small. The repeatedly high coral mortality after bleaching events and the long recovery period, especially in sites with human pressure, suggest that the foreseen increased frequency of bleaching events would jeopardize the future of Maldivian reefs, and ask for reducing local pressures to improve their resilience.