Miracle-dz/UniFAR-FTUs huggingface dataset:
Critical Coagulation Concentration–Based Salt Titration for Visual Quantification in Gold Nanoparticle–Based Colorimetric Biosensors

In gold nanoparticle (GNP)–based colorimetric biosensors, the gradual color shift is often used to correlate with the concentration of target molecules, and therefore a UV-vis spectrometer is usually required for accurate quantification. Here, we present a critical coagulation concentration (CCC)–based salt titration as a generic and simple way to enable accurate quantification in GNP-based colorimetric biosensors without any analytical equipment. The titration is carried out by stepwise addition of a salt titrant to the premixture of sample and GNPs until the color changes rapidly from red to blue, determined solely by visual inspection. The number of titration steps or the final salt concentration required for a rapid color shift (i.e., CCC) is then used to quantitatively correlate with the concentration of target molecules in the sample. The salt titration–based quantification has been demonstrated with two previously reported GNP-based colorimetric biosensors. Compared with quantification based on the gradual color shift with a spectrometer, the visual quantification based on the rapid color shift in the salt titration eliminates the need for any analytical equipment without sacrificing the performance (i.e., sensitivity and accuracy) and therefore is highly suitable for applications in low-resource settings.
Chart analysis and recognition in document images

Hidden Markov models are a probabilistic modeling tool for time series data. It has been successfully applied to many areas, such as speech recognition, hand-written character recognition, etc. In this paper, we present a novel statistical approach using ergodic hidden Markov models to recognize scientific charts. We also present a newly developed feature extraction method for chart images. Unlike traditional primitive-based diagram recognition method, our approach need not recognize the graphic primitives in charts thus bypassing the recognition error problem caused by the inaccurate primitive extraction that is also a major obstacle to the construction of a general chart recognition system.
Transcriptional regulation in endoderm development: characterization of an enhancer controlling Hnf3g expression by transgenesis and targeted mutagenesis

The hepatic nuclear factor 3γ (Hnf3g) is a member of the winged helix gene family of transcription factors and is thought to be involved in anterior–posterior regionalization of the primitive gut. In this study, cis‐regulatory elements essential for the expression of Hnf3g in vivo have been characterized. To this end, a 170 kb yeast artificial chromosome (YAC) carrying the entire Hnf3g locus was isolated and modified with a lacZ reporter gene. The two mouse lines carrying the unfragmented Hnf3g–lacZ YAC showed tissue‐specific, copy number‐dependent and position‐independent expression, proving that 170 kb of the Hnf3g locus contain all elements important in the regulation of Hnf3g. Cis‐regulatory elements necessary for expression of Hnf3g were identified in a three‐step procedure. First, DNase I hypersensitive site mapping was used to delineate important chromatin regions around the gene required for tissue‐specific activation of Hnf3g. Second, plasmid‐derived transgenes and gene targeting of the endogenous Hnf3g gene locus were used to demonstrate that the 3′‐flanking region of the gene is necessary and sufficient to direct reporter gene expression in liver, pancreas, stomach and small intestine. Third, a binding site for HNF‐1α and β, factors expressed in organs derived from the endoderm such as liver, gut and pancreas, was identified in this 3′‐enhancer and shown to be crucial for enhancer function in vitro. Based on its expression pattern we inferred that HNF‐1β is a likely candidate for directly activating Hnf3g gene expression during development.
Changes to prothrombin international normalized ratio in patients receiving hemodialysis.

BACKGROUND The clinical utility of factor Xa inhibitors (xabans) has been demonstrated, but these inhibitors are contraindicated in patients undergoing dialysis therapy. Therefore, warfarin remains the mainstay for oral anticoagulation treatment of patients receiving hemodialysis (HD). OBJECTIVE This study investigated the changes in international normalized ratio (INR) during HD treatment of patients receiving warfarin. METHODS Changes in INR and serum albumin levels were determined before (pre-) and after (post-) HD in six consecutive HD sessions. 30 patients (23 males, 7 females; mean age, 72 ± 8 years) were enrolled, and a total of 180 measurements were performed. RESULTS Post-HD INR levels were significantly decreased compared with pre-HD levels (2.07 ± 0.52 to 1.99 ± 0.50, p < 0.0001), while serum albumin levels were significantly increased post-HD compared with pre-HD (p < 0.0001). There was a significant negative correlation between changes in INR and serum albumin during HD (r = -0.383, p = 0.0002). CONCLUSION INR is significantly decreased post-HD compared with pre-HD. Although the therapeutic range of INR differs according to the disease, close monitoring of the degree of anticoagulation in patients receiving warfarin is recommended to minimize the risk of thrombosis and hemorrhagic complications.
Comparative genomics of clinical and environmental Vibrio mimicus

Whether Vibrio mimicus is a variant of Vibrio cholerae or a separate species has been the subject of taxonomic controversy. A genomic analysis was undertaken to resolve the issue. The genomes of V. mimicus MB451, a clinical isolate, and VM223, an environmental isolate, comprise ca. 4,347,971 and 4,313,453 bp and encode 3,802 and 3,290 ORFs, respectively. As in other vibrios, chromosome I (C-I) predominantly contains genes necessary for growth and viability, whereas chromosome II (C-II) bears genes for adaptation to environmental change. C-I harbors many virulence genes, including some not previously reported in V. mimicus, such as mannose-sensitive hemagglutinin (MSHA), and enterotoxigenic hemolysin (HlyA); C-II encodes a variant of Vibrio pathogenicity island 2 (VPI-2), and Vibrio seventh pandemic island II (VSP-II) cluster of genes. Extensive genomic rearrangement in C-II indicates it is a hot spot for evolution and genesis of speciation for the genus Vibrio. The number of virulence regions discovered in this study (VSP-II, MSHA, HlyA, type IV pilin, PilE, and integron integrase, IntI4) with no notable difference in potential virulence genes between clinical and environmental strains suggests these genes also may play a role in the environment and that pathogenic strains may arise in the environment. Significant genome synteny with prototypic pre-seventh pandemic strains of V. cholerae was observed, and the results of phylogenetic analysis support the hypothesis that, in the course of evolution, V. mimicus and V. cholerae diverged from a common ancestor with a prototypic sixth pandemic genomic backbone.
An Overview of Corroded Pipe Repair Techniques Using Composite Materials

— Polymeric composites are being increasingly used as repair material for repairing critical infrastructures such as building, bridge, pressure vessel, piping and pipeline. Technique in repairing damaged pipes is one of the major concerns of pipeline owners. Considerable researches have been carried out on the repair of corroded pipes using composite materials. This article attempts a short review of the subject matter to provide insight into various techniques used in repairing corroded pipes, focusing on a wide range of composite repair systems. These systems including pre-cured layered, flexible wet lay-up, pre-impregnated, split composite sleeve and flexible tape systems. Both advantages and limitations of these repair systems were highlighted. Critical technical aspects have been discussed through the current standards and practices. Research gaps and future study scopes in achieving more effective design philosophy are also presented.
Negative life events and symptoms of depression and anxiety: stress causation and/or stress generation

Background and Objectives: Stressful life events are known to contribute to development of depression; however, it is possible this link is bidirectional. The present study examined whether such stress generation effects are greater than the effects of stressful life events on depression, and whether stress generation is also evident with anxiety. Design: Participants were two large age cohorts (N = 732 aged 44 years; N = 705 aged 63 years) from the West of Scotland Twenty-07 study. Methods: Stressful life events, depression, and anxiety symptoms were measured twice five years apart. Cross-lagged panel analysis examined the mutual influences of stressful life events on depression and on anxiety over time. Results: Life events predicted later depressive symptomatology (p = .01), but the depression predicting life events relationship was less strong (p = .06), whereas earlier anxiety predicted life events five years later (p = .001). There was evidence of sex differences in the extent to which life events predicted later anxiety. Conclusions: This study provides evidence of stress causation for depression and weaker evidence for stress generation. In contrast, there was strong evidence of stress generation for anxiety but weaker evidence for stress causation, and that differed for men and women.
A1 Adenosine Receptor‐G Protein Coupling in Bovine Brain Membranes: Effects of Guanine Nucleotides, Salt, and Solubilization

Abstract: The effects of guanine nucleotides, NaCl, and solubilization on the interaction of antagonists and agonists with the A1 adenosine receptor of bovine brain membranes were studied using the high‐affinity antagonist radioligand [3H]xanthine amine congener ([3H]XAC). In membranes, guanine nucleotides and NaCl had no effect on [3H]XAC saturation curves. Using agonist (R)‐phenylisopropyladenosine (R‐PIA) competition curves versus [3H]XAC, it was demonstrated that agonists could differentiate two affinity states having high and low affinity for agonist and that guanine nucleotides shifted the equilibrium to an all‐low‐affinity state that was indistinguishable from the low‐affinity state in the absence of guanine nucleotides. In contrast, NaCl decreased agonist affinity by a distinctly different mechanism characterized by a parallel rightward shifted agonist curve such that R‐PIA still recognized two affinity states albeit of lower affinity than in the absence of salt. R‐PIA competition curves in the presence of both guanine nucleotides and salt were still shallow but were shifted far to the right, and two very low affinity states were discerned. On solubilization, guanine nucleotides in a reversible, concentration‐dependent manner increased antagonist ([3H]XAQ but not agonist (R‐N6‐−[3H]phenyl‐isopropyladenosine) binding. This was consequent to a change in maximal binding capacity. R‐PIA competition curves (versus [3H]XAC) in solubilized preparations demonstrated that agonist could still differentiate two agonist specific affinity states which were modulated by guanine nucleotides. In the presence of guanine nucleotides all the receptors were shifted to a uniform low‐affinity state. In contrast, NaCl had no effect on agonist affinity as determined by agonist competition curves in a solubilized receptor preparation. This is firm evidence that guanine nucleotides and NaCl must decrease agonist affinity by distinct mechanisms.
Nucleic Acids Research Induction of B 2 RNA polymerase III transcription by heat shock : enrichment for heat shock induced sequences in rodent cells by hybridization subtraction

When hybridization subtraction was used to enrich for sequences induced by heat shock in Chinese hamster cells, B2 sequences were found to be one of the major sequences enriched With cloned B2 probes, we found that the level of the short, 0.1 to 0.6 kb, polyadenylated RNA polymerase JH transcripts of this repetitive genetic element increased approximately 10 to 20 fold after heat shock. Transcription of B2 RNA by RNA polymerase JH was rapidly induced after heat shock based on time course studies and nuclear runoff experiments. The induction of B2 RNA was not a nonspecific response to lethality or cellular injury because maximum B2 RNA induction was observed with even nontoxic heating while no induction occurred with other agents such as UV or X-radiation. Since B2 RNA increased after heat shock in several different Chinese hamster and mouse cell lines, induction of B2 RNA by heat shock is probably common in rodent cells. B2 RNA may also be the most abundant transcript induced by heat shock because the level of B2 RNA was substantially higher than several other abundant transcripts induced by heat shock including a rodent HSP70. Our finding of the induction of high levels of RNA polymerase HI B2 transcripts in different rodent cells raise the possibility of a role in the heat shock response.
Temperature-sensitive catabolite activator protein in Escherichia coli BUG6

BUG6 is a temperature-sensitive cell division mutant which forms filaments at the nonpermissive temperature. Synthesis of the maltose- and galactose-binding protein-dependent transport systems is also temperature sensitive in BUG6. Using operon and protein fusions of the maltose transport genes to lacZ, we observed that the temperature-sensitive control of the maltose transport system in BUG6 occurs at the transcriptional level. By P1-mediated transductions, we found that BUG6 contains two independent temperature-sensitive mutations. One maps between 2 and 3 min on the Escherichia coli linkage map, in close proximity to the fts-envA region. This mutation is responsible for temperature-sensitive cell division. The other mutation maps at 73 min in crp, the structural gene of the catabolite activator protein. The latter could be complemented by a hybrid plasmid carrying the wild-type crp as the only gene on a 0.9-kilobase HindIII-AluI restriction fragment. The mutation in crp alone was found to be responsible for the temperature-sensitive synthesis of the maltose transport system. Although it causes a complete block of transcription of the maltose transport genes at 41 degrees C, this mutation had only a marginal effect on the transcription of the lac operon.
Bicyclic guanidinium tetraphenylborate: a photobase generator and a photocatalyst for living anionic ring-opening polymerization and cross-linking of polymeric materials containing ester and hydroxy groups.

1,5,7-Triazabicyclo[4.4. 0]dec-5-ene (TBD) with pKa of 26.03 in acetonitrile can be effectively released by photolysis of TBD.HBPh4 salt, which represents a new family of short-wave UV photobase generators. This photobase generator enables the photoinduced living ring-opening polymerization of cyclic esters and the photoinduced cross-linking of various polymeric materials containing the hydroxyl-ester groups.
Global CLF stabilization of systems allowing the null-control input in the boundary of compact control value sets: An approximation approach

Our aim in this paper is the study of the global asymptotic stabilization (GAS) of an affine control system, when the control value set (CVS) is a compact (convex) set U ⊆ ℝm with 0 ∈ U. Hence, we allow the null-control input to be in its boundary, 0 ∈ ∂U, i.e. a mix of signed/positive bounded control input components. First, we study the geometry of the control Lyapunov function (CLF) theory (due to Artstein and Sontag) in order to address the GAS of a system using signed/positive feedback controls valued in a CVS U. Then, we propose a control formula for admissible (bounded and regular) controls. Finally, we design an explicit admissible control formula that renders a system GAS, but having at most one positive input component, and small overflows in the signed input component values.
Stabilization of botulinum toxin type A during lyophilization

Botulinum toxin for medical use is diluted to very low concentrations (nanograms per milliliter); when it is preserved by lyophilization, considerable loss of activity can occur. In the present study, conditions that gave > 90% recovery of the toxicity after lyophilization of solutions containing 20 to 1,000 mouse 50% lethal doses per ml were found. Toxicity was recovered upon drying 0.1 ml of toxin solution when the pH was maintained below 7 and bovine or human serum albumins were used as stabilizers. Various other substances tested with albumin, including glucose, sucrose, trehalose, mannitol, glycine, and cellibiose, did not increase recovery on drying.
A long–term follow–up of lung function in survivors of paraquat poisoning

1 Respiratory failure is a frequent cause of death in moderate to severe paraquat poisoning, and a tran- sient fall in the gas transfer factor may be seen in mild poisoning. 2 The objectives of this study were to detect long-term changes in lung function in survivors of paraquat poisoning. 3 We analyzed 12 survivors retrospectively for age, sex, signs and symptoms, laboratory findings, chest X-ray findings, serum paraquat level, and lung function test. The first and the follow-up lung tests were performed at 3.7 + 1.4 weeks and 3.4 + 1.4 years, respectively. 4 Serum paraquat levels were assayed in all patients and 3/12 were above the Proudfoot's predictive line. Liver dysfunction (GOT > 50) and renal dysfunction (BUN > 30) were noted in 5/12 and 8/12, respectively. DL/VA was lower than the normal limit in the first study (3.9 + 0.6 L), but increased significantly and returned to the normal range in the follow-up study (4.5 + 0.6 L). %VC was within the normal range in either examina- tion, but significantly decreased in the follow-up. %TLC was within the normal range in the first study (87 + 13%), but significantly decreased below the normal limit in the follow-up (81 + 13%). 5 These results indicate that survivors of paraquat poisoning may be left with a restrictive type of pulmonary dysfunction and suggest that a long-term follow-up of lung function may be necessary for survivors of paraquat poisoning.
Attempted elimination of porcine reproductive and respiratory syndrome virus from a seedstock farm by vaccination of the breeding herd and nursery depopulation

An attempt was made to eliminate the virus of porcine reproductive and respiratory syndrome from a seedstock farm by using the combined strategies of vaccination and nursery depopulation. The breeding herd was vaccinated with a modified- live virus vaccine; all breeding and lactating adult animals were vaccinated twice, with a 30-day interval between vaccinations. All the sows were vaccinated in this way except for those in the third trimester of gestation (66 to 114 days) which were vaccinated on day 7 of lactation and 30 days later. A serological profiling system was developed to assess when the piglets became infected. Pigs from vaccinated sows were profiled at weekly intervals after weaning, using immunofluorescence tests for the detection of IgM and IgG, a serum neutralising antibody test, and virus isolation. After completion of the protocol, the nursery and finishing sites were monitored for 15 months. Evidence of reinfection in the finishing stage was detected 16 months after depopulation, but not in the nursery or the breeding herd. The source of the virus was not determined, but suspected origins included a lack of biosecurity, aerosol transmission from another infected farm or a persistently infected pig.
A Robust Bayesian Random Effects Model for Nonlinear Calibration Problems

Summary In the context of a bioassay or an immunoassay, calibration means fitting a curve, usually nonlinear, through the observations collected on a set of samples containing known concentrations of a target substance, and then using the fitted curve and observations collected on samples of interest to predict the concentrations of the target substance in these samples. Recent technological advances have greatly improved our ability to quantify minute amounts of substance from a tiny volume of biological sample. This has in turn led to a need to improve statistical methods for calibration. In this article, we focus on developing calibration methods robust to dependent outliers. We introduce a novel normal mixture model with dependent error terms to model the experimental noise. In addition, we propose a reparameterization of the five parameter logistic nonlinear regression model that allows us to better incorporate prior information. We examine the performance of our methods with simulation studies and show that they lead to a substantial increase in performance measured in terms of mean squared error of estimation and a measure of the average prediction accuracy. A real data example from the HIV Vaccine Trials Network Laboratory is used to illustrate the methods.
Monaural sound localization revisited.

Research reported during the past few decades has revealed the importance for human sound localization of the so-called "monaural spectral cues. " These cues are the result of the direction-dependent filtering of incoming sound waves accomplished by the pinnae. One point of view about how these cues are extracted places great emphasis on the spectrum of the received sound at each ear individually. This leads to the suggestion that an effective way of studying the influence of these cues is to measure the ability of listeners to localize sounds when one of their ears is plugged. Numerous studies have appeared using this monaural localization paradigm. Three experiments are described here which are intended to clarify the results of the previous monaural localization studies and provide new data on how monaural spectral cues might be processed. Virtual sound sources are used in the experiments in order to manipulate and control the stimuli independently at the two ears. Two of the experiments deal with the consequences of the incomplete monauralization that may have contaminated previous work. The results suggest that even very low sound levels in the occluded ear provide access to interaural localization cues. The presence of these cues complicates the interpretation of the results of nominally monaural localization studies. The third experiment concerns the role of prior knowledge of the source spectrum, which is required if monaural cues are to be useful. The results of this last experiment demonstrate that extraction of monaural spectral cues can be severely disrupted by trial-to-trial fluctuations in the source spectrum. The general conclusion of the experiments is that, while monaural spectral cues are important, the monaural localization paradigm may not be the most appropriate way to study their role.