Miracle-dz/UniFAR-FTUs huggingface dataset:
Dps Protects Cells against Multiple Stresses during Stationary Phase

ABSTRACT Dps, the nonspecific DNA-binding protein from starved cells, is the most abundant protein in stationary-phase Escherichia coli. Dps homologs are found throughout the bacteria and in at least one archaeal species. Dps has been shown to protect cells from oxidative stress during exponential-phase growth. During stationary phase, Dps organizes the chromosome into a highly ordered, stable nucleoprotein complex called the biocrystal. We show here that Dps is required for long-term stationary-phase viability under competitive conditions and that dps mutants have altered lag phases compared to wild-type cells. We also show that during stationary phase Dps protects the cell not only from oxidative stress but also from UV and gamma irradiation, iron and copper toxicity, thermal stress, and acid and base shock. The protective roles of Dps are most likely achieved through a combination of functions associated with the protein-DNA binding and chromosome compaction, metal chelation, ferroxidase activity, and regulation of gene expression.
Sign Detection based on Convolutional Neural Networks

We propose an approach for traffic sign detection based on Convolutional Neural Networks (CNN). We first transform the original image into the gray scale image by using support vector machines, then use convolutional neural networks with fixed and learnable layers for detection and recognition. The fixed layer can reduce the amount of interest areas to detect, and crop the boundaries very close to the borders of traffic signs. The learnable layers can increase the accuracy of detection significantly. Besides, we use bootstrap methods to improve the accuracy and avoid overfitting problem. In the German Traffic Sign Detection Benchmark, we obtained competitive results, with an area under the precision-recall curve(AUC) of 99.73% in the category “Danger”, and an AUC of 97.62% in the category “Mandatory”.
Evaluation of the LightCycler Methicillin-Resistant Staphylococcus aureus (MRSA) Advanced Test for Detection of MRSA Nasal Colonization

ABSTRACT Rapid detection of methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization is crucial for the prevention and control of MRSA infections in health care settings. The LightCycler MRSA Advanced Test (Roche Diagnostics) is a commercially available real-time PCR assay for direct detection of MRSA nasal colonization by targeting of the staphylococcal cassette chromosome mec (SCCmec)-orfX junction. The diagnostic performance of the assay was compared with that of ChromID MRSA agar (bioMérieux) culture and an in-house duplex real-time PCR assay. Among 1,246 nasal swab specimens collected from 2 general hospitals in Hong Kong, 174 (14%) were considered true positive for MRSA. Chromogenic culture and the in-house real-time PCR assay identified 147 (84.5%) and 133 (76.4%) true-positive cases with specificities of 100% and 98.6%, respectively. Based on the target melting temperature (Tm ) values (57.0 to 62.0°C) defined by the manufacturer, the LightCycler MRSA Advanced Test identified only 85 (48.9%) true-positive specimens. Interestingly, an additional 60 (34.5%) true-positive specimens were detected despite atypical Tm values of 55°C, providing overall sensitivity and specificity values of 83.3% and 99%, respectively. Among isolates with Tm values of 55°C, most were typed as clonal complex 45 (CC45). By sequence analysis of the SCCmec-orfX junction, characteristic single-nucleotide polymorphisms (SNPs) were identified only in isolates with Tm values of 55°C and not in those with typical Tm values. It is conceivable that those SNPs were located inside the target region of the proprietary hybridization probes, which resulted in a Tm shift in the melting curve analysis. Our study highlights the importance of a global evaluation of commercial kits so that the interpretation algorithm covers different lineages of MRSA clones prevalent in various geographical regions.
A quantitative assessment of bone area increase due to ornamentation in the Crocodylia

Bone ornamentation, in the form of highly repetitive motives created by pits and ridges, is a frequent feature on vertebrate skull roofs and osteoderms. The functional significance of this character remains a matter of controversy and speculation. The many diverging hypotheses proposed to explain it all share a common logical prerequisite: bone ornamentation should increase significantly the surface area of the bones that bear it. In order to test this assumption in the Crocodylia, we developed a method for quantifying the gain in area due to ornamentation using a three‐dimensional‐surface scanner. On crocodylian osteoderms, the gain in area can be up to 40%, and on the cranial table, it ranges between 10 and 32% in adult specimens (in both cases, it shows substantial differences between the adults of the various species included in the sample). Area gain on the snout is lesser (0–20% in adults), and more variable between species. In general, bone ornamentation is less pronounced, and results in fewer area gains in juvenile specimens. The main morphometric results yielded by this study are discussed in reference to the few comparative data available hitherto, and to the functional interpretations proposed by previous authors. J. Morphol. 276:1183–1192, 2015. © 2015 Wiley Periodicals, Inc.
Comparative study of IEC 60270 compliant instruments for partial discharge pattern acquisition

The petrochemical industry considers offline partial discharge (PD) measurement an important quality assessment for new medium voltage motor and generator stator windings. A recent edition of API 541 requires an instrument compliant with IEC 60270 for the measurement of PD on sacrificial stator coils, and proposes 100 pC (pico-Coulombs) for guidance on acceptance criteria until more data becomes available. Given the industry's faith in PD as an acceptance test based on a representative sample, it warrants closer scrutiny. The characteristic PD distribution pattern produced by each test instrument provides information on the origin of the discharges and therefore can be used to determine what type of defect has produced them. This paper shows how external factors such as instrument selection, testing environment, and time interval between tests can influence PD test results. Three different IEC-compliant instruments were used to measure PD from sample coils of the same design, under identical conditions. Each sample coil was modified to create the same imposed defect, with the same technique used to interpret the PD magnitude and distribution pattern produced in each case. Each instrument recorded a different charge magnitude and characteristic PD pattern. The variation in charge magnitude measured by each instrument exceeds the proposed API 541 acceptance limit, and the observed PD patterns did not accurately reflect the imposed coil defect. Offline PD measurement therefore lacks sufficient repeatability, reproducibility and accuracy to support a standard acceptance limit.
Specificity in lipases: A computational study of transesterification of sucrose

Computational conformational searches of putative transition states of the reaction of sucrose with vinyl laurate catalyzed by lipases from Candida antarctica B and Thermomyces lanuginosus have been carried out. The dielectric of the media have been varied to understand the role of protein plasticity in modulating the observed regioselective transesterification. The binding pocket of lipase from Candida adapts to the conformational variability of the various substates of the substrates by small, local adjustments within the binding pocket. In contrast, the more constrained pocket of the lipase from Thermomyces adapts by adjusting through concerted global motions between subdomains. This leads to the identification of one large pocket in Candida that accommodates both the sucrose and the lauroyl moieties of the transition state, whereas in Thermomyces the binding pocket is smaller, leading to the localization of the two moieties in two distinct pockets; this partly rationalizes the broader specificity of the former relative to the latter. Mutations have been suggested to exploit the differences towards changing the observed selectivities.
Derivative Security Markets, Market Manipulation, and Option Pricing Theory

Abstract This paper studies a new theory for pricing options in a large trader economy. This theory necessitates studying the impact that derivative security markets have on market manipulation. In an economy with a stock, money market account, and a derivative security, it is shown, by example, that the introduction of the derivative security generates market manipulation trading strategies that would otherwise not exist. A sufficient condition is provided on the price process such that no additional market manipulation trading strategies are introduced by a derivative security. Options are priced under this condition, where it is shown that the standard binomial option model still applies but with random volatilities.
Synthetic biology of minimal systems

“Synthetic biology” is a concept that has developed together with, or slightly after, “systems biology”. But while systems biology aims at the full understanding of large systems by integrating more and more details into their models, synthetic biology phrases different questions, namely: what particular biological function could be obtained with a certain known subsystem of reduced complexity; can this function be manipulated or engineered in artificial environments or genetically modified organisms; and if so, how? The most prominent representation of synthetic biology has so far been microbial engineering by recombinant DNA technology, employing modular concepts known from information technology. However, there are an increasing number of biophysical groups who follow similar strategies of dissecting cellular processes and networks, trying to identify functional minimal modules that could then be combined in a bottom-up approach towards biology. These modules are so far not as particularly defined by their impact on DNA processing, but rather influenced by core fields of biophysics, such as cell mechanics and membrane dynamics. This review will give an overview of some classical and some quite new biophysical strategies for constructing minimal systems of certain cellular modules. We will show that with recent advances in understanding of cytoskeletal and membrane elements, the time might have come to experimentally challenge the concept of a minimal cell.
Aspergillus-induced Malignant Glaucoma

Purpose: To report a case of Aspergillus flavus-induced keratomycotic malignant glaucoma. Methods: A 48-year-old woman presented with a severe corneal ulcer. She had received topical steroids for 10 days before presentation. Results: Microbiological studies revealed A. flavus as the offending pathogen. Nonresponsive high intraocular pressure with associated shallow anterior chamber was present. With a diagnosis of keratomycotic malignant glaucoma, the patient underwent therapeutic keratoplasty with cataract extraction with posterior chamber wash. However, there was a recurrence of malignant glaucoma in the postoperative period. Patient underwent limited pars plana vitrectomy. Conclusions: Keratomycotic malignant glaucoma is a rare complication of severe fungal ulcer. We believe that the use of topical steroids in this case probably led to increased fungal penetration, with the formation of a lens-iris fungal mass and subsequent malignant glaucoma. Nonresponse to medical therapy warrants urgent surgical intervention. To the best of our knowledge, Aspergillus-induced keratomycotic glaucoma has never been reported previously. This report also highlights that therapeutic keratoplasty with cataract extraction alone may not be sufficient for management of such cases, and a limited pars plana vitrectomy may be needed.
Coadaptation of Prenatal and Postnatal Maternal Effects*

In a wide variety of species, a female’s age of first reproduction influences offspring size and survival, suggesting that there exists an optimal timing of reproduction. Mothers in many species also influence offspring size and survival after birth through variation in parental care. We experimentally separated these effects in the burying beetle Nicrophorus vespilloides to test for coadaptation between prenatal and postnatal maternal effects associated with age at first reproduction. Females that reproduced early produced offspring with lower birth weight. The amount of parental care depended on the age of first reproduction of the caretaker, as did the extent of offspring begging. As predicted for a coadaptation of maternal effects, prenatal and postnatal effects were opposite for different‐aged mothers, and larval weight gain and survival was greatest when the age of the caretaker and birth mother matched. Thus, prenatal effects intrinsically associated with age of first reproduction can be ameliorated by innate plasticity in postnatal care. A coadaptation of prenatal and postnatal maternal effects may evolve to allow variable timing of the first reproductive attempt. Such a coadaptation might be particularly valuable when females are constrained from reproducing at an optimal age, as, for example, in species that breed on scarce and unpredictable resources.
Persistence of coronary vasodilator reserve despite functionally significant flow reduction.

This study was done to determine whether coronary vasodilator reserve is exhausted when coronary flow falls and regional function becomes abnormal during low-pressure perfusion. In 10 open-chest, anesthetized dogs the left circumflex coronary artery (LC) was cannulated and perfused via a blood-filled reservoir. At LC pressures of 35 and 50 mmHg, regional segment lengths were measured with sonomicrometer crystals and regional flow with radiolabeled microspheres before and after adenosine vasodilation. Control measurements were made at 80 mmHg perfusion pressure. Prior to adenosine, flow fell transmurally when LC pressure was reduced to 50 and 35 mmHg and rose significantly following adenosine. No change in function occurred at an LC pressure of 50 mmHg, but at 35 mmHg LC segmental shortening fell to 30 +/- 14% of control, and LC flow fell to 42 +/- 5% of control, with endocardial and epicardial flows of 0.40 +/- 0.04 and 0.70 +/- 0.09 ml . min-1 . g-1, respectively. After adenosine, endocardial and epicardial LC flow rose to 0.69 +/- 0.08 and 1.81 +/- 0.47 ml . min-1 . g-1, respectively (P less than 0.05). LC segment shortening improved modestly to 50 +/- 15% of control (P less than 0.02). We conclude that transmural vasodilator reserve is maintained in the face of functionally significant reductions of coronary flow at low perfusion pressure. Adenosine-induced flow increases are associated with a modest improvement in segmental function.
An Assessment of Grading Scales for Meibography Images

Purpose: To evaluate the within- and between-reader reliability and the interrelation between 2 methods of grading meibography images. Methods: A video meibography sequence (1200 frames) was captured from 290 patients using near-infrared light (650-700 nm) and a near-infrared CCD camera. One frame was selected for grading by 2 masked readers using 2 scales, where the first reader graded the image on 2 occasions and the second reader graded the image on 1 occasion. The first grading scale was a gestalt assessment (categorically graded), which is an assessment of partial meibomian glands within the image. The second was a count of individual whole glands. Within- and between-reader reliability and concurrent validity between the scales were examined. Results: Within-reader reliability of the gestalt scale was moderate to high (simple κ = 0.78, 95% confidence interval [CI] = 0.71-0.85 and weighted κ = 0.91, 95% CI = 0.88-0.95). Within-reader reliability of individual gland counting was moderate via a 95% limits of agreement analysis (−2.84-2.76 glands). Between-reader reliability of the gestalt scale was fair (simple κ = 0.38, 95% CI = 0.30-0.46 and weighted κ = 0.57, 95% CI = 0.47-0.68). Between-reader reliability of gland counting was fair via a 95% limits of agreement analysis (−4.46-5.08 glands). There was a strong relation between the gestalt scale and gland counting indicating good concurrent validity (Z = −15.15, P < 0.0001). Conclusions: These methods of grading meibography images demonstrate good within-reader reliability and fair between-reader reliability. Responsiveness to change will need to be addressed in future studies.
Stock Market and No-Dividend Stocks

We develop a model of the aggregate stock market featuring both dividend-paying and no-dividend stocks within a familiar, parsimonious consumption-based equilibrium framework. We find that such a simple feature leads to profound qualitative implications that support several empirical regularities on the stock market which leading consumption-based asset pricing models have difficulty in reconciling. We show that the presence of no-dividend stocks in the stock market leads to a lower correlation between the stock market return and aggregate consumption growth rate, a non-monotonic and even a negative relation between the stock market risk premium and its volatility, and a downward sloping term structure of equity risk premia. We also find that no-dividend stocks command lower mean returns, but have higher return volatilities and higher market betas than comparable dividend-paying stocks, consistently with empirical evidence. We provide straightforward intuition for all these results and the underlying economic mechanisms at play.
Factor H-Related (FHR)-1 and FHR-2 Form Homo- and Heterodimers, while FHR-5 Circulates Only As Homodimer in Human Plasma

The complement factor H-related (FHR) proteins are hypothesized to fine-tune the regulatory role of complement factor H (FH) in the alternative pathway of the complement system. Moreover, FHR-1, FHR-2, and FHR-5 have been proposed to be dimers, which further complicates accurate analysis. As FHRs are highly similar among themselves and toward FH, obtaining specific reagents for quantification of serum levels and functional analysis is challenging. In this study, we generated antibodies and developed ELISAs to measure FHR-1, FHR-2, and FHR-5 in serum. We used both recombinant and serum-derived proteins to show that four dimers occur in human circulation: homodimers of FHR-1, FHR-2, and FHR-5, as well as FHR-1/FHR-2 heterodimers. Heterodimers containing FHR-5 were not found. In individuals with homozygous CFHR1 deletions or compound heterozygous CFHR2 missense/nonsense mutations identified in this study, the respective FHR-1 and FHR-2 homo- and heterodimers were absent. Using FRET, we found that recombinant FHR dimers exchange monomers rapidly. This was confirmed ex vivo, using FHR-1- and FHR-2-deficient sera. Of all FHR dimers, FHR-5/5 homodimers demonstrated strong binding affinity toward heparin. Specific ELISAs demonstrated that serum levels of FHR-1/1, FHR-1/2, FHR-2/2, and FHR-5/5 dimers were low compared to FH, which circulates at a 10- to 200-fold molar excess. In summary, FHR-1, FHR-2, and FHR-5 homodimerize, with FHR-1 and FHR-2 forming heterodimers as well, and equilibrate quickly in plasma.
Influence of Innovativeness, Environmental Competitiveness and Government, Industry and Professional Networks on SME Export Likelihood

The purpose of this study is to examine how small to medium‐sized enterprises (SMEs) in different industry segments utilize government, industry, and professional networks and to test the influence of SME innovativeness, environmental competitiveness and network type for SME export likelihood. Previous studies on networks and exports tend to be qualitative and based on small samples. This study adds to previous scholarship by investigating a large database consisting of 2,263 Australian SMEs. Results indicate SME innovativeness contributes positively to export likelihood while contrary to extant studies, no significant relationship is observed between environmental competitiveness and export likelihood. Moreover, a significant, positive relationship exists between government networks and export likelihood, and a positive though weaker relationship between industry networks and export likelihood. On average, the likelihood of SMEs receiving export income increases by 47 percent if all three network types are accessed between one and three times a year, controlling for other factors. Further analyses of industry sub‐segments indicate a stronger relationship between industry networks and export likelihood.
A fully automated blood typing system for hospital transfusion services. ABS2000 Study Group.

BACKGROUND The results of routine blood bank testing by a fully automated blood typing system (ABS2000) were compared with those obtained by standard manual methods in six hospital transfusion services. STUDY DESIGN AND METHODS The ABS2000 system uses microtiter plates for determining ABO and D types, solid-phase red cell adherence (SPRCA) assays for antibody detection, and modified SPRCA plates for IgG crossmatches. The transfusion services used their standard manual test tube methods. RESULTS Of 3779 donors' samples tested for ABO types (red cell typings only), 3.0 percent could not be interpreted by the ABS2000 system's neural network, because of clots, hemolysis, or lipemic samples. The results for ABO types were concordant for 99.8 percent of the remaining samples. Of 3779 donors' samples tested for D types, the results were concordant for 98.7 percent. Of 7580 patients' samples tested for ABO types (red cell and plasma typings), 5.8 percent could not be interpreted by the ABS2000 system. There was 100-percent concordance of ABO typing results for the remaining 7140 samples. There was 99. 7-percent concordance of results for patients' D types. The results of 96.7 percent of antibody detection tests and 98.8 percent of crossmatches were concordant. Neither method failed to detect a serologically incompatible crossmatch that was associated with a specific, clinically significant alloantibody. The ABS2000 system performed 45 confirmatory donor ABO and D types in 115 minutes, 22 antibody detection tests in 116 minutes, 16 patients' ABO/D types in 149 minutes, and 40 crossmatches in 140 minutes. CONCLUSION The ABS2000 blood typing system automates routine blood bank tests with accuracy comparable to that of hospital transfusion services' standard manual methods.
Development of a Competitive Index Assay To Evaluate the Virulence of Listeria monocytogenes actAMutants during Primary and Secondary Infection of Mice

ABSTRACT We developed a competitive index assay for murine listeriosis that tests the virulence of Listeria monocytogenes strains in different organs and at various times postinoculation. Studies presented here demonstrate the reproducibility of this assay during primary and secondary infection of inbred and outbred mice. We verified the validity of this assay by performing competitive index analysis of a well-characterized strain of L. monocytogenes lacking the actA gene. In addition, we found that whileL. monocytogenes strains unable to recruit vasodilator-stimulated phosphoprotein (VASP) to their surface exhibit a 10-fold virulence attenuation in the livers of naive animals, they display a 50-fold survival defect in the liver during secondary listeriosis.