Miracle-dz/UniFAR-FTUs huggingface dataset:
In Situ Hybridization to Metaphase Chromosomes and Interphase Nuclei

In situ hybridization is used to determine the chromosomal map location and the relative order of genes and DNA sequences within a chromosomal band. It can also be used to detect aneuploidy, gene amplification, and subtle chromosomal rearrangements. Fluorescence in situ hybridization (FISH), probably the most widely used method, is described in the first basic protocol. Two support protocols are provided to amplify weak fluorescent signals obtained in FISH. Nonisotopic probes can also be detected by enzymatic reactions using horseradish peroxidase or alkaline phosphatase, as described in alternate protocols. Nonisotopic labeling of DNA probes by nick translation is described in a support protocol. The order of closely spaced FISH probes along chromosomes in interphase nuclei can be determined. A basic protocol for isotopic in situ hybridization (IISH) with 3H is provided followed by a support protocol for preparation of autoradiographic emulsion.
Does resource availability affect host manipulation? – an experimental test with Schistocephalus solidus

Host manipulation is a common strategy of parasites employed to increase their fitness by changing the phenotype of their hosts. Whether host manipulation might be affected by environmental factors such as resource availability, has received little attention. We experimentally infected laboratory-bred copepods with the cestode Schistocephalus solidus, submitted infected and uninfected copepods to either a high or a low food treatment, and measured their behaviour. Infection reduced host activity and speed in both feeding treatments. However, the difference between the infected and uninfected copepods was smaller under low food conditions, because uninfected, but not infected, copepods moved slower under these conditions. We suggest that these differences are mediated by the physical condition of copepods rather than changes in how strongly the parasite manipulated host behaviour. Additionally, we measured three fitness-relevant traits (growth, development and infection rate in the next host) of the parasite to identify potential trade-offs with host manipulation. The largest parasites in copepods appeared the least manipulative, i.e. their hosts showed the smallest behavioural alterations, but this may again reflect variation in copepod condition, rather than life history trade-offs between parasite growth and host manipulation. Our results point to the possibility that parasite transmission depends on environmental conditions.
Recent trends in soil fertility across the farms of East Gippsland

Current data are needed to manage our soil resources but there are few recent purpose-built surveys of soil fertility, a critical asset for natural resources management. Instead, data collected for other purposes are re-used as has been the case in our area of interest here: managing the threat of soil erosion on farm land in East Gippsland. The dynamic nature of soil fertility challenges this approach, so we conducted a new survey using 234 paddocks selected at random. These new data were compared to re-purposed legacy data. Plant tissue samples from a selected subset were used to assess micronutrients. Separately, 27 paddocks that had been sampled during 1975–89 were re-tested to examine temporal changes. We concluded that many paddocks are now strongly or very strongly acidic and deficient in molybdenum (Mo) and boron (B). More specifically, those under dairying, cropping and horticulture are likely to have adequate phosphorus (P) while those grazed for meat and wool are likely to be deficient in P. We concluded that grazing enterprises need to either re-adopt soil testing and fertiliser treatment or adopt management practices suitable for acid soils deficient in P, Mo and B, if their paddocks are to support sustainable productive agriculture. Data from the re-tested paddocks suggest that, in general, many were once less acidic, highlighting the difficulties in using legacy data. Also, contrasts in soil pH and available P between paddocks under different management regimes, highlighted the difficulties in using re-purposed data. We concluded that a statistically designed survey is a preferable basis for natural resource management.
Defensive responding on the MMPI-2 in family custody and access evaluations

The objective of this study was to examine defensive underreporting on the Minnesota Multiphasic Personality Inventory-2 (MMPI-2) with a sample of parents involved in custody dispute litigation. With a composite score derived from 2 nontraditional validity indicators-the Wiggins Social Desirability scale (WSD) and the Superlative scale (S), which had previously been identified as the best predictors of fake-good responding, 74% of litigants were identified as underreporting compared with 52% identified using traditional Lie (L) and Correction (K) scale criterion. Litigants identified as underreporters, whether using either the WSD-S criterion or the L-K criterion, had clinical scale profiles that were similar to those identified as nonunderreporters. The outcome of this study suggests that the WSD and S scales are perhaps more useful in the identification of defensive underreporting than the L and K scales.
Thermodynamics of One-Dimensional Solvable Models: Free energy and correlation functions of the XY model

Part I. Thermodynamics of Non-Interacting Systems and Ground States on Interacting Systems: 1. Free energy and correlation functions of XY models 2. Systems with delta-function potential 3. Isotropic Heisenberg model 4. XXZ model 5. XYZ and eight-vertex models 6. Hubbard model Part II. Finite Temperature Integral Equations for Un-Nested Systems: 7. Repulsive delta-function bosons 8. Thermodynamics of the XXX chain 9. Thermodynamics of the XXZ model 10. Thermodynamics of the XYZ model 11. Low-temperature thermodynamics Part III. Finite Temperature Integral Equations for Nested Systems: 12. S=1/2 fermions with repulsive potential in the continuum 13. S=1/2 fermions with an attractive potential 14. Thermodynamics of the Hubbard model Part IV. Quantum Transfer Matrix and Recent Developments: 15. Transfer matrix and correlation length 16. The spin 1/2 XXZ model in a magnetic field 17. The XYZ model with no magnetic field 18. Recent developments and related topics.
Ovoviviparity and genital evolution: a lesson from an earwig species with coercive traumatic mating and accidental breakage of elongated intromittent organs

Ovoviviparity or viviparity has evolved independently in animals and involves adaptations in females to accommodate developing embryos for a prolonged duration in their bodies, a condition which has likely to have influenced the evolution of the male genitalia. We aimed to ascertain whether the elongated male genitalia of the ovoviviparous free-living earwig species Marava arachidis (Dermaptera: Spongiphoridae) delivers sperm directly to the female ovaries where fertilization occurs. Males mated coercively with females by grabbing the female antenna with their mouth parts. Although females resisted the mating attempts, pairs mated 3.3 times on average over 15 h. The elongated intromittent organ, known as a virga, was inserted into the long-tubed spermatheca during insemination. Surgical ectomy of the spermatheca confirmed that sperm migrated from here to the ovaries with a variable delay. A pair of sclerites in the male genitalia frequently inflicted wounds near the spermathecal opening, while the single, thin virga sometimes broke off during mating. However, unlike earwigs bearing a ‘spare’ virga, damage was restricted to the tip of the virga, without which the males could still inseminate the females. We discuss the evolution of the genitalia in this insect in the light of sexual selection and sexual conflict over mating and fertilization.
Cross-Cultural Validation of the English Chronic Pain Myth Scale in Emergency Nurses

Background Utilization of the emergency department (ED) by patients seeking relief from chronic pain (CP) has increased. These patients often face stigmatization, and the ED is no exception. The French-Canadian Chronic Pain Myth Scale (CPMS) was developed to evaluate common societal misconceptions about CP including among healthcare providers. To our knowledge, no tool of this nature is available in English. Objectives This study thus aimed at determining to what extent a new English adaptation of the CPMS could provide valid scores among US emergency nurses. The internal consistency, construct validity, and internal structure of the translated scale were thus examined. Methods After careful translation of the scale, the English CPMS was administered to 482 emergency nurses and its validity was explored through a web-based cross-sectional study. Results Acceptable reliability (α > 0.7) was reported for the first and third subscales. The second subscale's reliability coefficient was below the cutoff (α=0.67) but is still considered adequate. As expected, statistically significant differences were found between nurses suffering from CP vs nurses not suffering from CP, supporting the construct validity of the scale. After exploratory factor analysis, similar internal structure was found supporting the 3-factorial nature of the original CPMS. Conclusion Our results provide support for the preliminary validity of the English CPMS to measure knowledge, beliefs, and attitudes towards CP among emergency nurses in the United States.
Allergen Immunotherapy in Children User’s Guide

Allergen immunotherapy is a cornerstone in the treatment of allergic children. The clinical efficiency relies on a well‐defined immunologic mechanism promoting regulatory T cells and downplaying the immune response induced by allergens. Clinical indications have been well documented for respiratory allergy in the presence of rhinitis and/or allergic asthma, to pollens and dust mites. Patients who have had an anaphylactic reaction to hymenoptera venom are also good candidates for allergen immunotherapy. Administration of allergen is currently mostly either by subcutaneous injections or by sublingual administration. Both methods have been extensively studied and have pros and cons. Specifically in children, the choice of the method of administration according to the patient's profile is important. Although allergen immunotherapy is widely used, there is a need for improvement. More particularly, biomarkers for prediction of the success of the treatments are needed. The strength and efficiency of the immune response may also be boosted by the use of better adjuvants. Finally, novel formulations might be more efficient and might improve the patient's adherence to the treatment. This user's guide reviews current knowledge and aims to provide clinical guidance to healthcare professionals taking care of children undergoing allergen immunotherapy.
nfsim: Untested code is buggy code

The netﬁlter simulation environment ( nfsim ) allows netﬁlter developers to build, run, and test their code without having to touch a real network, or having superuser privileges. On top of this, we have built a regression testsuite for netﬁlter and iptables. Nfsim provides an emulated kernel environment in userspace, with a simulated IPv4 stack, as well as enhanced versions of standard kernel primitives such as locking and a proc ﬁlesys-tem. The kernel code is imported into the nfsim environment, and run as a userspace application with a scriptable command-line interface which can load and unload modules, add a route, inject packets, run iptables, control time, inspect /proc , and so forth.
Characterisation of two Plasmodium falciparum cell cycle related kinases and the effect of kinase inhibitors on the parasite

Drug resistant malaria caused by Plasmodium falciparum remains a major health issue in under-developed countries. The Plasmodium genome project provides the facility to search for and identify novel drug targets. The regulation of the unique P. falciparum cell cycle remains poorly understood and a better understanding of the enzymes involved in this process may reveal parasite selective drug targets. Protein kinases are important in the control of the cell cycle and in signal transduction processes and are frequently deregulated in human disease. Recently inhibitors selective for specific kinases have been introduced to treat cancer. The objective of this study was to identify Plasmodium protein kinases that may be involved in the regulation of the cell cycle and to evaluate purine derivatives as potential antimalarial compounds. Two genes potentially involved in the cell cycle were identified with a homology-based approach using data provided by the Plasmodium genome project. A putative homologue of cyclin G associated kinase (PfcGAK) and a NIMA related kinase (Pfnek-3) were identified. P. falciparum DNA was used to amplify the genes coding for the two kinases by PCR, and this DNA was cloned into expression vectors. The respective proteins were isolated and tested for in vitro kinase activity. The effect of purine inhibitors on P. falciparum survival was assessed by the H-hypoxanthine incorporation assay. Both recombinant PfcGAK and Pfnek-3 were found to phosphorylate casein in vitro. PfcGAK displays structural features that indicate that the protein may be bound to membranes and is likely to be regulated by site-specific phosphorylation. PfcGAK has a unique nanomeric repetitive sequence that is rich in potential serine/threonine phospho-rylation sites. Pfnek-3 has a potential Pexel export sequence, which indicates that the protein is transported to the parasitophorous vacuole and functions outside the parasite. A large number of purine related compounds (565) were screened for anti-malarial activity from which 19 compounds were selected for further analysis. There was considerable variation in the sensitivity of P. falciparum to the different inhibitors with a number of purines showing sub-micromolar activity against the parasite. Structure activity analysis showed that certain
Two new paraclupeid fi shes (Clupeomorpha: Ellimmichthyiformes) from the Upper Cretaceous of Morocco

A collection of fossil fishes from the Akrabou Formation of Morocco has provided a number of new species, including three members of the Ellimmichthyiformes. Two of these are here described in one genus and placed in the family Paraclupeidae. One, named here Thorectichthys marocensis gen. et sp. nov., is represented by numerous fairly well preserved specimens, but the second species, T. rhadinus sp. nov., is represented by only three specimens, which are not well preserved. The third ellimmichthyiform from the Akrabou Formation, also represented by three specimens, is a member of the family Sorbinichthyidae. The Ellimmichthyiformes include species that have been found in a diversity of freshwater as well as estuarine or marginal marine habitats, from South and North America, the Mediterranean region and Asia. The Ellimmichthyiformes range from Neocomian (early Early Cretaceous) through Eocene in age, with the Moroccan material being probably early Turonian or possibly late Cenomanian in age, and from normal-salinity marine waters. The new paraclupeids, as well as a number of other recently described ellimmichthyiforms, are included in a new analysis of relationships based on previously documented osteological characters. The analysis indicates that the new genus Thorectichthys is sister to a clade containing Ellimma, Ellimmichthys, Rhombichthys, Paraclupea, Tycheroichthys, and Triplomystus.
Reply [to “Comment on “Dynamics and energetics of bubble growth in magmas: Analytical formulation and numerical modeling” by A. A. Proussevitch and D. L. Sahagian”]

The authors would like to begin by expressing sincere gratitude to Flavio Dobran for his most comprehensive and detailed review of our paper [Proussevitch and Sahagian, 1998]. It is seldom that a reviewer succeeds in following every detail of a complex formulation and identifying inconsistencies or other errors. In the case of this paper, we agreed with many of his suggestions, each of which led to an improvement or clarification in the paper before it was published. There were two issues, mentioned in his comment [Dobran, this issue], which unfortunately leaked through the process. Both were caused by missing symbols in the notation of the internal formulation in Appendix A. Fortunately, neither type of missing printed symbol led to any carry through or error in the formulation itself. The first missing symbol is a 3 in equations (A1), (B5), (B6b), (B12c), and (B12e) as is pointed out by Dobran [this issue], but it is also missing elsewhere (equations (B2a), (B4), and (B7)). It showed on the monitor, but the printer failed to print it (and we all failed to notice until Dobran pointed it out in his commen0. However, this first missing symbol is relatively obvious, so it should not terribly confuse the reader. The second missing symbol is much more subtle and Jeads to a misleading notation inconsistency between equations (A3)-(A5) and equation (A6). The missing symbol is an apostrophe on the total stress tensor x' in equation (A6). This must not be confused with the viscous stress x in equations (A3)-(A5). Because of this missing apostrophe, one is led to believe that equation (A6) referred to the viscous stress rather than to the total stress, in which case, Dobran [this issue] is quite correct in insisting that the -p term should be removed. However, equation (A6) involves the total stress, which must include the -p term. We did not make this sufficiently clear, and indeed, with the missing apostrophe, misunderstanding is not surprising. In his thorough and accurate way, Dobran found a way to alter our formulation to make it correct in his comment, on the assumption that we were concerned with viscous stress in equation (A6). In his comment, Dobran uses o for stress, but in the paper, o was already used for surface tension [see Proussevitch and Sahagian, 1998, Table A1]. The discussion in Appendix A should have read as follows:
Protein Databases on the Internet

This unit provides a starting point for readers to explore the potential of protein databases on the Internet. Databases for different aspects of proteins are discussed, with the focus on sequence, structure, and family. The strengths and weaknesses of the databases are addressed. From hundreds of on‐line protein databases, several major databases are discussed as examples to illustrate their features and how they can be used effectively. Most other protein databases can be explored in a similar way.
Depth Map Refinement using Segment Plane Estimation

Depth map is the most common way of expressing 3D space in immersive media. In this paper, we propose a post-processing method to improve the quality of depth map. In proposed method, a depth map is divided into segments, and the plane of each segment estimated using RANSAC. In order to increase the accuracy of the RANSAC process, we apply matching reliability of each pixel in depth map as a weighting factor.
Characterization of the non-structural proteins of adeno-associated virus (AAV) and minute virus of canine (MVC)

x Chapter I . 1 Literature review . 1 Biology of Parvoviridae . 2 General Introduction to AAV . 5 Transcription profile of AAV2 . 9 Transcription profile of AAV5 relative to AAV2 . 12 Adenovirus helper gene products required for productive AAV infection . 15 The roles of E1b 55k and E4orf6 in AAV biology . 19 Ubiquitin, different forms of protein ubiquitination and the ubiquitin proteasome pathway (UPP) . 26 Introduction to Bocaviruses . 41 Transcription profile of MVC. 45 Parvovirus RNA processing strategies to access capsid transcripts . 53
Characterization of Recombinant Proteins

Once a protein has been purified, it is necessary to characterize the protein preparation. The initial and most fundamental analyses performed are checks of purity and of biological or enzymatic activity. Indeed, to purify a protein in the first place a specific assay for the protein must be available, and limited purity determinations are usually made en route to the finished product by SDS-PAGE monitoring of the sample at different purification stages. The first unit of this chapter (UNIT 7.1) provides an overview of the approaches and methods used for more detailed characterization of recombinant proteins. It should be noted that none of the techniques or methods mentioned are used uniquely for recombinant proteins, and protocols dealing with some of the methods are included elsewhere in this book. However, the emphasis of the discussion in UNIT 7.1 (and of the protocols which will appear in future updates) is on addressing the detection and determination of the most pertinent sources of contamination and heterogeneity commonly associated with proteins isolated from recombinant sources.
A Multi-band Microstrip Planar Inverted-F Antenna for Wireless Applications

A new multi-band planar inverted-F antenna (PIFA) is presented for wireless applications‎. ‎PIFA is‎ ‎designed in two stages‎. ‎First‎, ‎the antenna consists of a radiating plate injected with a slot and it is shorted to ground plane with two shorting walls‎. ‎The structure covers three bands‎. ‎A small and narrow slot on the ground plane is embedded to afford increasing the bandwidths of the antenna at the resonance frequencies and improve radiation patterns at the second resonance frequency‎, ‎thereby giving a more omnidirectional pattern‎. ‎Second‎, ‎a parasitic element is used at the antenna to design a quad-band PIFA antenna‎. ‎Moreover‎, ‎an L-shaped slot is embedded on the radiating plate to improve the reflection coefficient at the third resonance frequency‎. ‎The antenna is optimized to operate at 1.1 GHz‎, ‎2.4 GHz‎, ‎3.6 GHz and 5.3 GHz bands‎. ‎It can be used both indoor and outdoor wireless video‎, ‎wireless cameras and wireless security applications at the 1.1 GHz band‎, ‎Bluetooth‎, ‎Wi-Fi and Wireless Local Area Network (WLAN) at the 2.42 GHz band‎, ‎Microwave Access (m-WiMAX) at the 3.6 GHz band‎, ‎and WLAN at the 5.3 GHz‎ . ‎The antenna is simulated and fed through a coaxial cable connected to the feeding strip; then it is fabricated and measured‎. ‎The total antenna volume of the proposed design is 90×42×7.5 mm2‎.
Measuring Protein‐Protein Interactions by Equilibrium Sedimentation

This commentary unit provides a basic introduction to the principles and practice of sedimentaiton equilibrium analytical ultracentrifugation for the study of reversible protein interactions. Equilibrium sedimentation is one of the most effective methods for the detection and characterization of protein interactions and can be applied to the measurement of self association, heterologous association, binding stoichiometry, and the determination of association constants. The unit includes an extensive discussion of the instrumentation required to carry out equilibrium analytical ultracentrifugation and to perform data analysis. A strategic planning section gives the reader several experimental scenarios and conditions for using equilibrium sedimentation.