Miracle-dz/UniFAR-FTUs huggingface dataset:
Characterization of genes encoding type 1 fimbriae of Klebsiella pneumoniae, Salmonella typhimurium, and Serratia marcescens

With a minicell system, the organization of genes encoding type 1 fimbriae of Salmonella typhimurium, Klebsiella pneumoniae, and Serratia marcescens was determined. In all cases multiple gene products were necessary for the phenotypic expression of fimbriae; thus fimbrial expression in these strains is similar to that in Escherichia coli. The type 1 fimbrial subunit gene was detected by the ability of its product to react with specific antiserum. At least six genes were found to be involved in the expression of type 1 fimbriae by S. typhimurium, and at least four genes constituted the fimbrial gene cluster of K. pneumoniae. In the case of S. marcescens, a minimum of three detectable polypeptides was required for the production of fimbriae. Also, a gene probe consisting in part of nucleotide sequences from the E. coli fimbrial subunit gene hybridized to a discrete DNA fragment derived from the plasmid encoding K. pneumoniae fimbriae. Such a fragment was assumed to contain a gene encoding the structural component of the type 1 fimbriae. Each of the three cloned systems encoded a number of polypeptides which varied in size; thus, the organization and molecular weight of fimbrial accessory proteins of each genus were not identical.
Hydromagnetic Taylor–Couette flow: wavy modes

We investigate magnetic Taylor–Couette flow in the presence of an imposed axial magnetic field. First we calculate nonlinear steady axisymmetric solutions and determine how their strength depends on the applied magnetic field. Then we perturb these solutions to find the critical Reynolds numbers for the appearance of wavy modes, and the related wave speeds, at increasing magnetic field strength. We find that values of imposed magnetic field which alter only slightly the transition from circular-Couette flow to Taylor-vortex flow, can shift the transition from Taylor-vortex flow to wavy modes by a substantial amount. The results are compared to those for onset in the absence of a magnetic field.
Use Case Elicitation with FrameNet Frames

Natural language-based use cases remains the main means of requirements elicitation and specification, despite the well-known problems that accompany natural language specifications, namely their incompleteness, inconsistency and ambiguity. This paper presents a novel approach for tackling the textual description problems by using FrameNet frames, which are linguistics patterns for concept description. The proposed approach is demonstrated via an explorative example. We show that use of frames in use case-based elicitation has a promise to lead to clearer understanding of the domain concepts covered in a use-case and to help acquire more complete information.
Genetic structure of populations of the threatened eastern massasauga rattlesnake, Sistrurus c. catenatus: evidence from microsatellite DNA markers

Throughout its distribution in North America, the threatened eastern massasauga rattlesnake (Sistrurus c. catenatus) persists in a series of habitat‐isolated disjunct populations of varying size. Here, we use six microsatellite DNA loci to generate information on the degree of genetic differentiation between, and the levels of inbreeding within populations to understand how evolutionary processes operate in these populations and aid the development of conservation plans for this species. Samples were collected from 199 individuals from five populations in Ontario, New York and Ohio. Our results show that all sampled populations: (i) differ significantly in allele frequencies even though some populations are < 50 km apart, and may contain genetically distinct subpopulations < 2 km apart; (ii) have an average of 23% of alleles that are population specific; and (iii) have significant FIS values (mean overall FIS= 0.194) probably due to a combination of Wahlund effects resulting from fine‐scale genetic differentiation within populations and the presence of null alleles. Our results imply that massasauga populations may be genetically structured on an extremely fine scale even within continuous populations, possibly due to limited dispersal. Additional information is needed to determine if dispersal and mating behaviour within populations can account for this structure and whether the observed differentiation is due to random processes such as drift or to local adaptation. From a conservation perspective, our results imply that these massasauga populations should be managed as demographically independent units and that each has high conservation value in terms of containing unique genetic variation.
Experimenting with STA, a tool for automatic analysis of security protocols

We present STA (Symbolic Trace Analyzer), a tool for the analysis of security protocols. STA relies on symbolic techniques that avoid explicit construction of the whole, possibly infinite, state-space of protocols. This results in accurate protocol modeling, increased efficiency and more direct formalization, when compared to finite-state techniques. We illustrate the use of STA by analyzing the well-known asymmetric Needham Schroeder protocol. We discuss the results of this analysis, and contrast them with previous work based on finite-state model checking.
Saving face: Managing rapport in a Problem-Based Learning group

This qualitative study investigated the complex social aspects of communication required for students to participate effectively in Problem-Based Learning and explored how these dynamics are managed. The longitudinal study of a group of first-year undergraduates examined interactions using Rapport Management as a framework to analyse communication with regard to the concepts of face, sociality rights and interactional goals. Problem-Based Learning requires students to engage in potentially face-threatening interactions as they discuss subjects of which they have little prior knowledge, placing them in situations that require negotiation using face-saving strategies in order to meet objectives to share their learning with others. The study described within this article focuses on the key role of the Problem-Based Learning chair and shows how failure by the chair to manage rapport effectively can influence the quality of group learning. The findings suggest that educators need to understand the complex interactional demands students have to face in undertaking Problem-Based Learning and support students to overcome these difficulties considering the three bases of rapport management.
Does Diploidy Increase the Rate of Adaptation ?

Explanations of the evolution of diploidy have focused on the advantages gained from masking del-eterious alleles. Recent theory has shown, however, that masking does not always provide an advantage to diploidy and would never favor diploidy in predominantly asexual organisms. We explore a neglected alternative theory which posits that, by doubling the genome size, diploids double the rate at which favorable mutations arise. Consequently, the rate of adaptation in diploids is presumed to be faster than in haploids. The rate of adaptation, however, depends not only on the rate of appearance of new favorable mutations but also on the rate at which these mutations are incorporated (which depends on the population size and on the dominance of favorable mutations). We show that, in both asexuals and sexuals, doubling the mutation rate via diploidy often does not accelerate the rate of adaptation. Indeed, under-many conditions, diploidy slows adaptation. T HERE has been a great deal of interest recently in the evolutionary advantages of diploidy (KONDRA-Several genetic theories have been offered. Perhaps the most popular emphasizes that diploids enjoy an advantage due to masking the deleterious effects of recessive mutations. This advantage does not, however, confer a higher mean fitness upon diploids at equilibrium since diploids suffer from the load of twice as many deleterious mutations (CROW and KIMURA 1965). Two recent variations on the masking hypothesis appear more promising. First, KONDRASHOV and CROW (1991) have shown that, with truncation selection , the mean fitness of a diploid population can exceed that of a haploid population. Further, PERROT et al. (1991), considering individual-level selection among interbreeding haploids and diploids, showed that an allele increasing the proportion of time spent as a diploid can invade despite a subsequent decrease in mean fitness at equilibrium. Unfortunately, the latter result depends critically on the assumptions of random mating and free recombi-nation between the locus controlling ploidy and the lo-cus under selection. When asexuality, assortative mating , or selfing are common or when recombination is rare, alleles increasing the diploid phase of a life cycle do not invade while those increasing the haploid phase those many organisms having low rates of either recom-bination or outcrossing [ e. q. , many taxa in the chloro-cillariophyta (WETZEL 1983)], the prevalence of diploidy is not satisfactorily explained by the masking hypothesis. Moreover, it is unclear whether diploidy evolved before or after high rates of recombination in the lineage leading to …
α- Versus β-Emitting Radionuclides for Pretargeted Radioimmunotherapy of Carcinoembryonic Antigen–Expressing Human Colon Cancer Xenografts

Pretargeted radioimmunotherapy (PRIT) with the β-emitting radionuclide 177Lu is an attractive approach to treat carcinoembryonic antigen (CEA)–expressing tumors. The therapeutic efficacy of PRIT might be improved using α-emitting radionuclides such as 213Bi. Herein, we report and compare the tumor-targeting properties and therapeutic efficacy of 213Bi and 177Lu for PRIT of CEA-expressing xenografts, using the bispecific monoclonal antibody TF2 (anti-CEA × anti–histamine-succinyl-glycine [HSG]) and the di-HSG-DOTA peptide IMP288. Methods: The in vitro binding characteristics of 213Bi-IMP288 were compared with those of 177Lu-IMP288. Tumor targeting of 213Bi-IMP288 and 177Lu-IMP288 was studied in mice bearing subcutaneous LS174T tumors that were pretargeted with TF2. Finally, the effect of 213Bi-IMP288 (6, 12, or 17 MBq) and 177Lu-IMP288 (60 MBq) on tumor growth and survival was assessed. Toxicity was determined by monitoring body weight, analyzing blood samples for hematologic and renal toxicity (hemoglobin, leukocytes, platelets, creatinine), and immunohistochemical analysis of the kidneys. Results: The in vitro binding characteristics of 213Bi-IMP288 (dissociation constant, 0.45 ± 0.20 nM) to TF2-pretargeted LS174T cells were similar to those of 177Lu-IMP288 (dissociation constant, 0.53 ± 0.12 nM). In vivo accumulation of 213Bi-IMP288 in LS174T tumors was observed as early as 15 min after injection (9.2 ± 2.0 percentage injected dose [%ID]/g). 213Bi-IMP288 cleared rapidly from the circulation; at 30 min after injection, the blood levels were 0.44 ± 0.28 %ID/g. Uptake in normal tissues was low, except for the kidneys, where uptake was 1.8 ± 1.1 %ID/g at 30 min after injection. The biodistribution of 213Bi-IMP288 was comparable to that of 177Lu-IMP288. Mice treated with a single dose of 213Bi-IMP288 or 177Lu-IMP288 showed significant inhibition of tumor growth. Median survival for the groups treated with phosphate-buffered saline, 6 MBq 213Bi-IMP288, 12 MBq 213Bi-IMP288, and 60 MBq 177Lu-IMP288 was 22, 31, 45, and 42 d, respectively. Mice receiving 17 MBq 213Bi-IMP288 showed significant weight loss, resulting in a median survival of only 24 d. No changes in hemoglobin, platelets, or leukocytes were observed in the treatment groups. However, immunohistochemical analysis of the kidneys of mice treated with 17 or 12 MBq 213Bi-IMP288 showed signs of tubular damage, indicating nephrotoxicity. Conclusion: To our knowledge, this study shows for the first time that PRIT with TF2 and 213Bi-IMP288 is feasible and at least as effective as 177Lu-IMP288. However, at higher doses, kidney toxicity was observed. Future studies are warranted to determine the optimal dosing schedule to improve therapeutic efficacy while reducing renal toxicity.
A Colorectal Cancer Susceptibility New Variant at 4q26 in the Spanish Population Identified by Genome-Wide Association Analysis

Background Non-hereditary colorectal cancer (CRC) is a complex disorder resulting from the combination of genetic and non-genetic factors. Genome–wide association studies (GWAS) are useful for identifying such genetic susceptibility factors. However, the single loci so far associated with CRC only represent a fraction of the genetic risk for CRC development in the general population. Therefore, many other genetic risk variants alone and in combination must still remain to be discovered. The aim of this work was to search for genetic risk factors for CRC, by performing single-locus and two-locus GWAS in the Spanish population. Results A total of 801 controls and 500 CRC cases were included in the discovery GWAS dataset. 77 single nucleotide polymorphisms (SNP)s from single-locus and 243 SNPs from two-locus association analyses were selected for replication in 423 additional CRC cases and 1382 controls. In the meta-analysis, one SNP, rs3987 at 4q26, reached GWAS significant p-value (p = 4.02×10−8), and one SNP pair, rs1100508 CG and rs8111948 AA, showed a trend for two-locus association (p = 4.35×10−11). Additionally, our GWAS confirmed the previously reported association with CRC of five SNPs located at 3q36.2 (rs10936599), 8q24 (rs10505477), 8q24.21(rs6983267), 11q13.4 (rs3824999) and 14q22.2 (rs4444235). Conclusions Our GWAS for CRC patients from Spain confirmed some previously reported associations for CRC and yielded a novel candidate risk SNP, located at 4q26. Epistasis analyses also yielded several novel candidate susceptibility pairs that need to be validated in independent analyses.
Climate Response to External Sources of Freshwater: North Atlantic versus the Southern Ocean

Abstract The response of an atmosphere–ocean general circulation model (AOGCM) to perturbations of freshwater fluxes across the sea surface in the North Atlantic and Southern Ocean is investigated. The purpose of this study is to investigate aspects of the so-called bipolar seesaw where one hemisphere warms and the other cools and vice versa due to changes in the ocean meridional overturning. The experimental design is idealized where 1 Sv (1 Sv ≡ 106 m3 s−1) of freshwater is added to the ocean surface for 100 model years and then removed. In one case, the freshwater perturbation is located in the Atlantic Ocean from 50° to 70°N. In the second case, it is located south of 60°S in the Southern Ocean. In the case where the North Atlantic surface waters are freshened, the Atlantic thermohaline circulation (THC) and associated northward oceanic heat transport weaken. In the Antarctic surface freshening case, the Atlantic THC is mainly unchanged with a slight weakening toward the end of the integration. This w.
The von Hippel-Lindau Chuvash mutation in mice causes carotid-body hyperplasia and enhanced ventilatory sensitivity to hypoxia

The hypoxia-inducible factor (HIF) family of transcription factors coordinates diverse cellular and systemic responses to hypoxia. Chuvash polycythemia (CP) is an autosomal recessive disorder in humans in which there is impaired oxygen-dependent degradation of HIF, resulting in long-term systemic elevation of HIF levels at normal oxygen tensions. CP patients demonstrate the characteristic features of ventilatory acclimatization to hypoxia, namely, an elevated baseline ventilation and enhanced acute hypoxic ventilatory response (AHVR). We investigated the ventilatory and carotid-body phenotype of a mouse model of CP, using whole-body plethysmography, immunohistochemistry, and electron microscopy. In keeping with studies in humans, CP mice had elevated ventilation in euoxia and a significantly exaggerated AHVR when exposed to 10% oxygen, with or without the addition of 3% carbon dioxide. Carotid-body immunohistochemistry demonstrated marked hyperplasia of the oxygen-sensing type I cells, and the cells themselves appeared enlarged with more prominent nuclei. This hypertrophy was confirmed by electron microscopy, which also revealed that the type I cells contained an increased number of mitochondria, enlarged dense-cored vesicles, and markedly expanded rough endoplasmic reticulum. The morphological and ultrastructural changes seen in the CP mouse carotid body are strikingly similar to those observed in animals exposed to chronic hypoxia. Our study demonstrates that the HIF pathway plays a major role, not only in regulating both euoxic ventilatory control and the sensitivity of the response to hypoxia, but also in determining the morphology of the carotid body.
Epidemiology of sexually transmitted infections in rural southwestern Haiti: the Grand'Anse Women's Health Study.

The study attempts to define socioeconomic, clinical, and laboratory correlates in vaginitis and other sexually transmitted infections in rural southwestern Haiti. A convenience sample of subjects recruited from a rural women's health clinic and attending an established clinic at the Haitian Health Foundation (HHF) clinic was studied. A standardized history and physical examination, including speculum examination, and collection of blood, urine, and vaginal swabs were obtained from the women at the rural clinic. Additional vaginal swab samples only for Nucleic Acid Amplification Test (NAAT) testing were obtained from women at the HHF clinic in Jérémie. Laboratory results from Leon subjects were positive for Gardnerella vaginalis in 41% (41 of 100), Trichomonas vaginalis in 13.5% (14 of 104), Candida sp. in 9% (9 of 100), Mycoplasma genitalium in 6.7% (7 of 104), Chlamydia trachomatis in 1.9% (2 of 104), and Neisseria gonorrhea in 1% (1 of 104) of patients. Human immunodeficiency virus (HIV) antibody tests were negative in 100% (103 of 103) of patients, and syphilis antibody testing was positive for treponemal antibodies in 7.7% (8 of 104) patients. For subjects from the HHF, 19.9% were positive for T. vaginalis, 11.9% were positive for C. trachomatis, 10.1% were positive for M. genitalium, and 4.1% were positive for N. gonorrhea. Infections with G. vaginalis, T. vaginalis, and Candida were the most common. N. gonorrhea, C. trachomatis, Candida sp. , T. vaginalis, and M. genitalium infections were associated with younger age (less than 31 years old).
Sports Type Classification Using Signature Heatmaps

Automatic classification of activities in a sports arena is important in order to analyse and optimise the use of the arenas. In this work we classify five sports types based only on occupancy heatmaps produced from position data. Due to privacy issues we use thermal imaging for detecting people and then calculate their positions on the court using homography. Heatmaps are produced by summarising Gaussian distributions respresenting people over 10-minute periods. Before classification the heatmaps are projected to a low-dimensional discriminative space using the principle of Fisherfaces. Our result using two weeks of video are very promising with a correct classification of 90.76 %.
User subjectivity in Monte Carlo modeling of pesticide exposure

Monte Carlo techniques are increasingly used in pesticide exposure modeling to evaluate the uncertainty in predictions arising from uncertainty in input parameters and to estimate the confidence that should be assigned to the modeling results. The approach typically involves running a deterministic model repeatedly for a large number of input values sampled from statistical distributions. In the present study, six modelers made choices regarding the type and parameterization of distributions assigned to degradation and sorption data for an example pesticide, the correlation between the parameters, the tool and method used for sampling, and the number of samples generated. A leaching assessment was carried out using a single model and scenario and all data for sorption and degradation generated by the six modelers. The distributions of sampled parameters differed between the modelers, and the agreement with the measured data was variable. Large differences were found between the upper percentiles of simulated concentrations in leachate. The probability of exceeding 0.1 μg/L ranged from 0 to 35.7%. The present study demonstrated that subjective choices made in Monte Carlo modeling introduce variability into probabilistic modeling and that the results need to be interpreted with care.
A Subunit of Eukaryotic Translation Initiation Factor 2α-Phosphatase (CreP/PPP1R15B) Regulates Membrane Traffic*

Background: The constitutive reverter of eIF2α phosphorylation (CReP/PPP1r15B) targets the catalytic subunit of protein phosphatase 1 (PP1c) to p-eIF2α to promote translation initiation. Results: CReP associates with membranes and regulates membrane traffic in a PP1c-independent manner. Conclusion: CReP is co-opted by the traffic machinery. Significance: The data reveal a novel link between the molecular machineries regulating translation and traffic. The constitutive reverter of eIF2α phosphorylation (CReP)/PPP1r15B targets the catalytic subunit of protein phosphatase 1 (PP1c) to phosphorylated eIF2α (p-eIF2α) to promote its dephosphorylation and translation initiation. Here, we report a novel role and mode of action of CReP. We found that CReP regulates uptake of the pore-forming Staphylococcus aureus α-toxin by epithelial cells. This function was independent of PP1c and translation, although p-eIF2α was involved. The latter accumulated at sites of toxin attack and appeared conjointly with α-toxin in early endosomes. CReP localized to membranes, interacted with phosphomimetic eIF2α, and, upon overexpression, induced and decorated a population of intracellular vesicles, characterized by accumulation of N-(lissamine rhodamine B sulfonyl)phosphatidylethanolamine (N-Rh-PE), a lipid marker of exosomes and intralumenal vesicles of multivesicular bodies. By truncation analysis, we delineated the CReP vesicle induction/association region, which comprises an amphipathic α-helix and is distinct from the PP1c interaction domain. CReP was also required for exocytosis from erythroleukemia cells and thus appears to play a broader role in membrane traffic. In summary, the mammalian traffic machinery co-opts p-eIF2α and CReP, regulators of translation initiation.
FPGA test time reduction through a novel interconnect testing scheme

As device densities increase, testing cost is becoming a larger portion of the overall FPGA manufacturing cost. We present an approach to speed up testing FPGA interconnect by reconfiguring it during the test. Simple additions are made to create feedback shift register structures, which considerably reduce the number of test configurations for the switching matrix interconnect. This new testing architecture reduces switching matrix test time by 66% and the diagnosis time by 72%. The additions are transparent to the users both in terms of speed and functionality.
Effects of a 12-Week Pilates Course on Lower Limb Muscle Strength and Trunk Flexibility in Women Living in the Community

Researchers in Taiwan studying regular adult physical activity found that among married women aged 26 to 55 years, 56% participated in physical activity, and that the convenience and safety of the activity were major factors contributing to their willingness to exercise. Muscle weakness and poor trunk flexibility are closely related to some chronic diseases in women. In this cross-sectional survey, we used the Polestar Pilates™ method to explore the effects of a 12-week Pilates course on the physical fitness of women living in the community. Fifty-three members of the experimental group (mean age: 42.30±9.97) and 43 of the control group (mean age: 41.23±9.83) were included. We confirm that a convenient Pilates exercise intervention can significantly improve muscle strength and trunk flexibility in women. Our findings serve as an important reference for health authorities in Taiwan and provide higher awareness of women's health and physical fitness, which can help prevent chronic and cardiovascular diseases.