Miracle-dz/UniFAR-FTUs huggingface dataset:
Specific immunoassays for detection of intact and cleaved forms of the urokinase receptor.

BACKGROUND The cell surface receptor (uPAR) for urokinase plasminogen activator (uPA) is a strong prognostic marker in several types of cancer. uPA cleaves the three-domain protein uPAR(I-III) into two fragments: uPAR(I), which contains domain I; and uPAR(II-III), which contains domains II and III. Established immunoassays measure a combination of uPAR forms. Our aim was to design immunoassays for specific quantification of the individual forms of uPAR. METHODS Using appropriate combinations of epitope-mapped monoclonal antibodies (Mabs) for capture and europium-labeled detection Mabs, we designed two-site sandwich time-resolved fluorescence immunoassays (TR-FIAs): TR-FIA 1 to measure uPAR(I-III) alone; TR-FIA 2 to measure both uPAR(I-III) and uPAR(II-III); and TR-FIA 3 to measure uPAR(I). To avoid detection of uPAR(I-III) in TR-FIA 3, we used a combination of the peptide uPAR antagonist AE120 and a domain I antibody, R3. AE120 blocks the binding of R3 to uPAR(I-III). In contrast, AE120 does not interact with liberated domain I and therefore does not interfere with the binding of R3 to uPAR(I). RESULTS The limits of quantification (CV <20%) determined by adding the proteins to uPAR-depleted plasma were <3 pmol/L in all three assays. The interassay CVs in plasma with added analytes were <11%, and recoveries were between 93% and 105%. Cross-reactivities of purified proteins in the three TR-FIAs were no more than 4%. Studies on chymotrypsin cleavage of uPAR and size-exclusion chromatography of plasma with and without added protein further supported the specificity of the assays. CONCLUSIONS The three novel TR-FIAs accurately quantify uPAR(I-III) alone, uPAR(I-III) together with uPAR(II-III), and uPAR(I), respectively, in biological samples, including plasma, and thus are well suited for studies of the diagnostic and prognostic value of individual uPAR forms in cancer patients.
Zinc Finger Recombinases with Adaptable DNA Sequence Specificity

Site-specific recombinases have become essential tools in genetics and molecular biology for the precise excision or integration of DNA sequences. However, their utility is currently limited to circumstances where the sites recognized by the recombinase enzyme have been introduced into the DNA being manipulated, or natural ‘pseudosites’ are already present. Many new applications would become feasible if recombinase activity could be targeted to chosen sequences in natural genomic DNA. Here we demonstrate efficient site-specific recombination at several sequences taken from a 1.9 kilobasepair locus of biotechnological interest (in the bovine β-casein gene), mediated by zinc finger recombinases (ZFRs), chimaeric enzymes with linked zinc finger (DNA recognition) and recombinase (catalytic) domains. In the "Z-sites" tested here, 22 bp casein gene sequences are flanked by 9 bp motifs recognized by zinc finger domains. Asymmetric Z-sites were recombined by the concomitant action of two ZFRs with different zinc finger DNA-binding specificities, and could be recombined with a heterologous site in the presence of a third recombinase. Our results show that engineered ZFRs may be designed to promote site-specific recombination at many natural DNA sequences.
IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY

The d i s s e r t a t i o n r e a p p r a i s e s Thomas Dekker's dramatic achievement through an examination of h i s c o n t r i b u t i o n to the development of Elizabethan-Jacobean domestic drama. Dekker's a l t e r a t i o n s and m o d i f i c a t i o n s of two e s s e n t i a l f e a t u r e s o f e a r l y E n g l i s h domestic drama—the h o m i l e t i c p a t t e r n of s i n , punishment, and repentance, which the genre i n h e r i t e d from the m o r a l i t y t r a d i t i o n , and the g l o r i f i c a t i o n of the c u l t o f d o m e s t i c i t y — a t t e s t to a complex moral and dramatic v i s i o n which c r i t i c s have g e n e r a l l y ignored. In P a t i e n t G r i s s i l , h i s e a r l i e s t extant domestic p l a y , which p o r t r a y s a m b i v a l e n t l y the v i c i s s i t u d e s of m a r i t a l and f a m i l y l i f e , Dekker combines an a l l e g o r i c a l s u p e r s t r u c t u r e with a r e a l i s t i c s e t t i n g . The t e n s i o n between h o m i l e t i c and r e a l i s t i c impulses i s a l s o at the he a r t o f The Honest Whore. In Part I, although Dekker prov i d e s a trenchant p o r t r a i t of the a f f l i c t e d domus, the p l a y ' s s a t i r i c a l tone c l a s h e s oddly with the h o m i l e t i c schemes. In Part I I , however, the marriage code i s presented amid i n t r i c a t e p l o t t i n g and a complex e t h i c a l d esign i n which orthodox h o m i l e t i c paradigms such as the p a t i e n t wife, the t e s t i n g o f the wife ' s v i r t u e , and the p r o d i g a l husband's r e f o r m a t i o n are c o n s i s t e n t l y undermined through i r o n y and paradox. Taken as a whole, these three p l a y s r e v e a l Dekker's growing c y n i c i s m toward the t i d y moral and dramatic schemes of t h e i r analogues, and of the
Genetic Analysis of Feline Caliciviruses Associated with a Hemorrhagic-Like Disease

Feline calicivirus (FCV) is 1 of the most common causes of upper respiratory tract disease in cats. Other disease syndromes associated with FCV infection have been reported. Recently, calicivirus infection associated with a hemorrhagic-like disease leading to significant mortality in cats has been reported. The clinical signs are similar to those observed with the calicivirus of rabbit hemorrhagic disease. This study characterized 2 FCV isolates associated with hemorrhagic-like disease. Nucleotide sequencing of the complete genome has been done for these 2 isolates as well as for 4 additional isolates representing other disease syndromes. Previously reported sequence data for the entire genome of classical FCV (6 isolates) and a portion of the capsid gene for hemorrhagic-like FCV (3 isolates), isolated in different regions of United States were used in the genetic analysis. Sequence data were used to determine relationships among the isolates and any correlation with phenotype. Nucleotide sequence comparisons of the entire genome and individual open reading frames revealed high homology among all isolates. Data suggest that the virulence may have genetic determinants on the basis of phylogenetic clustering of the isolates associated with hemorrhagic-like disease.
Premorbid predictors of chronic fatigue.

CONTEXT Chronic fatigue syndrome is a disabling problem characterized by persistent fatigue lasting at least 6 months with a number of ancillary symptoms. Although the etiology of chronic fatiguing illness is unknown, some evidence suggests that stress may confer increased risk for development of the disorder. Moreover, subjects with chronic fatiguing illness may have distinctive personality traits, although this finding could reflect confounding by other mechanisms. OBJECTIVE To assess the prospective association of premorbid self-reported stress and personality with chronic fatigue-like illness. DESIGN Prospective nested case-control study in a population-based sample. SETTING General community. PARTICIPANTS From the Swedish Twin Registry, 19,192 twins born between January 1, 1935, and December 31, 1958. MAIN OUTCOME MEASURES Information about current chronic fatiguing illnesses was obtained from computer-assisted telephone interviews conducted between 1998 and 2002. Self-reported stress (based on a single question) and personality scales (emotional instability and extraversion in the Eysenck Personality Inventory) were measured from 1972 to 1973 by a mailed questionnaire. Relative risks were estimated with case-control analyses (matched for age and sex) and co-twin control analyses (comparing discordant pairs). RESULTS Higher emotional instability and self-reported stress in the premorbid period were associated with higher risk for chronic fatigue-like illness in matched case-control analyses (odds ratios, 1.72 and 1.64, respectively). In co-twin control analyses, relative risk of emotional instability decreased to 1.02 whereas that of stress increased considerably to 5.81. There was no association between extraversion and fatigue. CONCLUSIONS Elevated premorbid stress is a significant risk factor for chronic fatigue-like illness, the effect of which may be buffered by genetic influences. Emotional instability assessed 25 years earlier is associated with chronic fatigue through genetic mechanisms contributing to both personality style and expression of the disorder. These findings suggest plausible mechanisms for chronic fatiguing illness.
Elements Explaining Learning Clinical Reasoning Using Simulation Games

This article presents the findings on which elements in a game-based simulation affect learning clinical reasoning in nursing education. By using engaging gaming elements in virtual simulations and integrating the clinical reasoning process into game mechanics, games can enhance learning clinical reasoning and offer meaningful learning experiences. The study was designed to explore how nursing students experience gaming and learning when playing a simulation game, as well as which gaming elements explain learning clinical reasoning. The data was collected by questionnaire from nursing students (N = 166) in autumn 2014 over thirteen gaming sessions. The findings showed that usability, application of nursing knowledge, and exploration have the most impact on learning clinical reasoning when playing simulation games. Findings also revealed that authentic patient-related experiences, feedback, and reflection have an indirect effect on learning clinical reasoning. Based on these results, more efficient simulation games to improve clinical reasoning may be developed.
A Predominant-F0 Estimation Method for Real-world Musical Audio Signals: MAP Estimation for Incorporating Prior Knowledge about F0s and Tone Models

In this paper we describe a robust method, called PreFEst, for estimating the fundamental frequency (F0) of melody and bass lines in monaural audio signals containing sounds of various instruments. Most previous F0-estimation methods have difficulty dealing with such complex audio signals because they are designed for mixtures of only a few sounds. Without assuming the number of sound sources, PreFEst can obtain the most predominant F0 — corresponding to the melody or bass line — supported by harmonics within an intentionally-limited frequency range. It estimates the relative dominance of every possible F0 (represented as a probability density function of the F0) and the shape of harmonic-structure tone models by using the MAP (MaximumA Posteriori Probability) estimation considering their prior distribution. Experimental results showed that a real-time system implementing this method is robust enough to detect the melody and bass lines in compact-disc recordings.
Huntington's Chorea in the West of Scotland

There have been relatively few studies of Huntington's Chorea in Britain. They include those of Curran (1930), Critchley (1934), Spillane and Phillips (1937), Minski and Gutt- mann (1938), Bickford and Ellison (1953), Pleydell (1954), Lyon (1962), Heathfield (1967), and Oliver (1970). Julia Bell's (1934) monograph was primarily a review of the literature, but included cases previously reported in this country and the results of her own observations.
The effects of physical activity, education, and body mass index on the aging brain

Normal human aging is accompanied by progressive brain tissue loss and cognitive decline; however, several factors are thought to influence brain aging. We applied tensor‐based morphometry to high‐resolution brain MRI scans to determine whether educational level or physical activity was associated with brain tissue volumes in the elderly, particularly in regions susceptible to age‐related atrophy. We mapped the 3D profile of brain volume differences in 226 healthy elderly subjects (130F/96M; 77.9 ± 3.6 SD years) from the Cardiovascular Health Study‐Cognition Study. Statistical maps revealed the 3D profile of brain regions whose volumes were associated with educational level and physical activity (based on leisure‐time energy expenditure). After controlling for age, sex, and physical activity, higher educational levels were associated with ∼2–3% greater tissue volumes, on average, in the temporal lobe gray matter. After controlling for age, sex, and education, greater physical activity was associated with ∼2–2.5% greater average tissue volumes in the white matter of the corona radiata extending into the parietal‐occipital junction. Body mass index (BMI) was highly correlated with both education and physical activity, so we examined BMI as a contributing factor by including physical activity, education, and BMI in the same model; only BMI effects remained significant. This is one of the largest MRI studies of factors influencing structural brain aging, and BMI may be a key factor explaining the observed relationship between education, physical activity, and brain structure. Independent contributions to brain structure could not be teased apart as all these factors were highly correlated with one another. Hum Brain Mapp, 2010. © 2010 Wiley‐Liss, Inc.
Transcriptome analysis of the murine forelimb and hindlimb autopod

To gain insight into the coordination of gene expression profiles during forelimb and hindlimb differentiation, a transcriptome analysis of mouse embryonic autopod tissues was performed using Affymetrix Murine Gene Chips (MOE‐430). Forty‐four transcripts with expression differences higher than 2‐fold (T test, P ≤0.05) were detected between forelimb and hindlimb tissues including 38 new transcripts such as Rdh10, Frzb, Tbx18, and Hip that exhibit differential limb expression. A comparison of gene expression profiles in the forelimb, hindlimb, and brain revealed 24 limb‐signature genes whose expression was significantly enriched in limb autopod versus brain tissue (fold change >2, P ≤ 0.05). Interestingly, the genes exhibiting enrichment in the developing autopod also segregated into significant fore‐ and hindlimb‐specific clusters (P ≤ 0.05) suggesting that by E 12.5, unique gene combinations are being used during the differentiation of each autopod type. Developmental Dynamics 234:74–89, 2005. © 2005 Wiley‐Liss, Inc.
Image Retrieval based on LBP Transitions

One of the current theoretically significant, simple and very effective texture descriptor that describe local structure efficiently and precisely is the ‘Local Binary Pattern’ (LBP). Today LBP and its variants are applied in many areas. One of the disadvantage with LBP is it derives a total of 256 patterns out of which 58 are the Uniform LBP (ULBP) and remaining are Non Uniform LBP (NULBP). The ULBP holds the fundamental characteristic and most of the textures predominantly contain ULBP . The disadvantage with ULBP is one should consider 58 pattern features for any classification or retrieval etc. The ULBP approaches completely ignored the NULBP and grouped them into mislenious class. This leads to lot of complexity. To overcome this, present paper designed a new method for retrieval based on histogram of transitions from 0 to 1 or 1 to 0 on LBP. LBP contains only 5 such transitions (0 or 2 or 4 or 6 or 8). The proposed method is experimented on various images collected from Google data base. The experimental result indicates the efficiency of the proposed method over the various methods.
Characterization of the Roles of Hemolysin and Other Toxins in Enteropathy Caused by Alpha-Hemolytic Escherichia coli Linked to Human Diarrhea

ABSTRACT Escherichia coli strains producing alpha-hemolysin have been associated with diarrhea in several studies, but it has not been clearly demonstrated that these strains are enteropathogens or that alpha-hemolysin is an enteric virulence factor. Such strains are generally regarded as avirulent commensals. We examined a collection of diarrhea-associated hemolytic E. coli (DHEC) strains for virulence factors. No strain produced classic enterotoxins, but they all produced an alpha-hemolysin that was indistinguishable from that of uropathogenic E. coli strains. DHEC strains also produced other toxins including cytotoxic necrotizing factor 1 (CNF1) and novel toxins, including a cell-detaching cytotoxin and a toxin that causes HeLa cell elongation. DHEC strains were enteropathogenic in the RITARD (reversible intestinal tie adult rabbit diarrhea) model of diarrhea, causing characteristic enteropathies, including inflammation, necrosis, and colonic cell hyperplasia in both small and large intestines. Alpha-hemolysin appeared to be a major virulence factor in this model since it conferred virulence to nonpathogenic E. colistrains. Other virulence factors also appear to be contributing to virulence. These findings support the epidemiologic link to diarrhea and suggest that further research into the role of DHEC and alpha-hemolysin in enteric disease is warranted.
Intensive Growth Strategies and Outreach Performance of Tanzania-Based Savings and Credit Cooperative Societies

Research on performance of Microfinance Institutions (MFIs) has attracted a great attention as the demand for microfinance services increases. One of the popular microfinance models is reaching the poor through Savings and Credit Cooperative Societies (SACCOs). A critical area is to assess what drives the SACCOs performance. Most research on SACCOs concentrate on assessing their performance without looking at the contribution of key performance drivers such as growth strategies. Little research has been done on the influence of intensive growth strategies (product development and market development) particularly on the SACCOs outreach performance in Tanzania. This study investigates the contribution of both product development and market development on outreach performance (increased number of SACCOs’ members). Through a multiple regression analysis, the study tests seven hypotheses which are geared towards finding the contribution of both product development and market development on outreach performance. A cross-sectional survey design and multistage probability sampling technique enabled the participation of 167 key SACCOs’ managers (loan officers) from three zones of Tanzania whose views were collected through questionnaires. The study has revealed the significant contribution of both product development and market development on outreach performance. SACCOs need to design growth strategies which suit the needs of their clients and their characteristics. Although an outreach performance can be driven by intensive growth strategies, we suggest that, the SACCOs’ growth should also be harmonized with their financial performance.
Determining Risk for Severe Leptospirosis by Molecular Analysis of Environmental Surface Waters for Pathogenic Leptospira

Background Although previous data indicate that the overall incidence of human leptospirosis in the Peruvian Amazon is similar in urban and rural sites, severe leptospirosis has been observed only in the urban context. As a potential explanation for this epidemiological observation, we tested the hypothesis that concentrations of more virulent Leptospira would be higher in urban than in rural environmental surface waters. Methods and Findings A quantitative real-time PCR assay was used to compare levels of Leptospira in urban and rural environmental surface waters in sites in the Peruvian Amazon region of Iquitos. Molecular taxonomic analysis of a 1,200-bp segment of the leptospiral 16S ribosomal RNA gene was used to identify Leptospira to the species level. Pathogenic Leptospira species were found only in urban slum water sources (Fisher's exact test; p = 0.013). The concentration of pathogen-related Leptospira was higher in urban than rural water sources (~103 leptospires/ml versus 0.5 × 102 leptospires/ml; F = 8.406, p < 0.05). Identical 16S rRNA gene sequences from Leptospira interrogans serovar Icterohaemorrhagiae were found in urban slum market area gutter water and in human isolates, suggesting a specific mode of transmission from rats to humans. In a prospective, population-based study of patients presenting with acute febrile illness, isolation of L. interrogans-related leptospires from humans was significantly associated with urban acquisition (75% of urban isolates); human isolates of other leptospiral species were associated with rural acquisition (78% of rural isolates) (chi-square analysis; p < 0.01). This distribution of human leptospiral isolates mirrored the distribution of leptospiral 16S ribosomal gene sequences in urban and rural water sources. Conclusions Our findings data support the hypothesis that urban severe leptospirosis in the Peruvian Amazon is associated with higher concentrations of more pathogenic leptospires at sites of exposure and transmission. This combined quantitative and molecular taxonomical risk assessment of environmental surface waters is globally applicable for assessing risk for leptospiral infection and severe disease in leptospirosis-endemic regions.
Application of In-situ CaCO 3 Formation Method for Better Utilization of Recycled Fibers (1) - Enhancing Attachment of CaCO 3 to Fibers by Polymer Pre-Treatment -

ABSTRACT In-situ CaCO 3 formation on recycled wood pulp was studied to improve optical property and filler attach-ment to the fiber furnish in papermaking. We tried to attach calcium oxide (CaO) to the recycled fibers, old newspaper (ONP) in this case, by using selected polymers before in-situ CaCO 3 formation reaction on fibers, and then, CO 2 was injected to the furnish until all the CaO on fiber surfaces was consumed. It was found that the attachment of newly formed CaCO 3 to recycled fibers became stronger by attaching CaO to the fibers before in-situ CaCO 3 formation reaction. It was expected that the polymers used for the attachment of calcium source to the fiber furnishes helped to keep the newly formed CaCO 3 strongly attached to the fiber surface as well as to retain the impurities associated with calcium source and recycled fibers, if any. In-situ CaCO 3 formation gave higher brightness and much less ERIC value in ONP sheet than the case when the equivalent amount of GCC was added to the furnish.