Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and Characterization of a Periplasmic Nuclease of Vibrio vulnificus and Its Role in Preventing Uptake of Foreign DNA

ABSTRACT We have cloned a nuclease gene, vvn, from Vibrio vulnificus, an estuarine bacterium that causes wound infections and septicemia in humans and eels. The gene contained a 696-bp open reading frame encoding 232 amino acids (aa), including a signal sequence of 18 aa. The deduced amino acid sequence of the mature nuclease predicted a molecular mass of 25 kDa, which was confirmed by vital stain, and a pI of 8.6. Vvn was produced in the periplasm of either V. vulnificus or recombinant Escherichia coli strains and was active in the oxidized (but not the reduced) form. This nuclease was able to digest DNA and RNA, with differential thermostability in DNase and RNase activities. Expression of Vvn inE. coli DH5α reduced the frequencies of transformation with the divalent ion-treated cells and electroporation by about 6 and 2 logs, respectively. In addition, the transformation frequency of a Vvn-deficient V. vulnificus mutant (ND) was 10-fold higher than that of the parent strain. These data suggested that Vvn may be involved in preventing uptake of foreign DNA by transformation. However, Vvn expressed in the recipients had little effect on the conjugation frequency in either E. coli or V. vulnificus. Some other DNase(s) may be present in the periplasm and responsible for a residual DNase activity, which was about one-fourth of that of the parent strain, detected in the ND mutant. We also demonstrated that Vvn was not required for the virulence ofV. vulnificus mice.
What Factors Affect the Identification and Reporting of Child Abuse-related Fractures?

Child abuse is a serious problem in the United States. Because orthopaedic surgeons are responsible for identifying and reporting suspicious fractures to child protective services, we asked two primary questions: (1) How skilled are orthopaedists in distinguishing abuse-related from noninflicted fractures and making appropriate child protective services reports? ; and (2) Are decisions influenced by orthopaedist training or by the race or socioeconomic status of injured children? We developed and mailed a questionnaire containing 10 case vignettes to 974 US orthopaedists. Respondents assessed the likelihood of abuse and need to report to child protective services. Two versions of the questionnaire differed by the race and socioeconomic status of vignette families. Average respondent scores were 79% for correct diagnoses and 73% for correct reporting decisions. Pediatric orthopaedists had higher adjusted scores for identifying abuse-related versus noninflicted injuries (82% versus 73%) and for appropriately reporting to child protective services (76% versus 66%) compared with general orthopaedists. Both groups had difficulty distinguishing abuse-related from noninflicted long-bone fractures in infants and toddlers. We found no differences in appropriate identification or reporting of fractures by race but did find differences by social class. Additional training in identifying abuse-related long-bone fractures appears necessary. Orthopaedists should consider the potential for bias when assessing children with fractures for possible abuse.
The Hubbard dimer: a density functional case study of a many-body problem

This review explains the relationship between density functional theory and strongly correlated models using the simplest possible example, the two-site Hubbard model. The relationship to traditional quantum chemistry is included. Even in this elementary example, where the exact ground-state energy and site occupations can be found analytically, there is much to be explained in terms of the underlying logic and aims of density functional theory. Although the usual solution is analytic, the density functional is given only implicitly. We overcome this difficulty using the Levy–Lieb construction to create a parametrization of the exact function with negligible errors. The symmetric case is most commonly studied, but we find a rich variation in behavior by including asymmetry, as strong correlation physics vies with charge-transfer effects. We explore the behavior of the gap and the many-body Green’s function, demonstrating the ‘failure’ of the Kohn–Sham (KS) method to reproduce the fundamental gap. We perform benchmark calculations of the occupation and components of the KS potentials, the correlation kinetic energies, and the adiabatic connection. We test several approximate functionals (restricted and unrestricted Hartree–Fock and Bethe ansatz local density approximation) to show their successes and limitations. We also discuss and illustrate the concept of the derivative discontinuity. Useful appendices include analytic expressions for density functional energy components, several limits of the exact functional (weak- and strong-coupling, symmetric and asymmetric), various adiabatic connection results, proofs of exact conditions for this model, and the origin of the Hubbard model from a minimal basis model for stretched H2.
Human aldose reductase: rate constants for a mechanism including interconversion of ternary complexes by recombinant wild-type enzyme.

We have used transient kinetic data for partial reactions of recombinant human aldose reductase and simulations of progress curves for D-xylose reduction with NADPH and for xylitol oxidation with NADP+ to estimate rate constants for the following mechanism at pH 8.0: E<-->E.NADPH<-->*E.NADPH<-->*E.NADPH. RCHO<-->*E.NADP+. RCH2OH <-->*E.NADP+<--> E.NADP+<-->E. The mechanism includes kinetically significant conformational changes of the two binary E.nucleotide complexes which correspond to the movement of a crystallographically identified nucleotide-clamping loop involved in nucleotide exchange. The magnitude of this conformational clamping is substantial and results in a 100- and 650-fold lowering of the nucleotide dissociation constant in the productive *E.NADPH and *E.NADP+ complexes, respectively. The transient reduction of D-xylose displays burst kinetics consistent with the conformational change preceding NADP+ release (*E.NADP+-->E.NADP+) as the rate-limiting step in the forward direction. The maximum burst rate also displays a large deuterium isotope effect (Dkburst = 3.6-4.1), indicating that hydride transfer contributes significantly to rate limitation of the sequence of steps up to and including release of xylitol. In the reverse reaction, no burst of NADPH production is observed because the hydride transfer step is overall 85% rate-limiting. Even so, the conformational change preceding NADPH release (*E.NADPH-->E.NADPH) still contributes 15% to the rate limitation for reaction in this direction. The estimated rate constant for hydride transfer from NADPH to the aldehyde of D-xylose (130 s-1) is only 5- to 10-fold lower than the corresponding rate constant determined for NADH-dependent carbonyl reduction catalyzed by lactate or liver alcohol dehydrogenase. Hydride transfer from alcohol to NADP+ (0.6 s-1), however, is at least 100- to 1000-fold slower than NAD(+)-dependent alcohol oxidation mediated by these two enzymes, resulting in a bound-state equilibrium constant for aldose reductase which greatly favors the forward reaction. The proposed kinetic model provides a basic set of rate constants for interpretation of kinetic results obtained with aldose reductase mutants generated for the purpose of examining structure-function relationships of different components of the native enzyme.
Improving performance of SIP signaling during overload using capabilities of connection-oriented transport protocol

Over the past decade, voice communications have moved from the public switched telephone networks to the Internet. The IETF has enabled this transition by developing stable standards for call setup and media transport. Session Initiation Protocol (SIP) is an application-layer protocol for creating, modifying, and terminating media sessions in the internet. SIP is becoming the core signaling protocol for Next Generation Networks. Since the built-in rejection mechanism of SIP is incapable of handling SIP overload in servers, SIP server overload management has attracted interest recently. Despite the fact that TCP is increasingly seen as the more suitable choice for SIP transport, most of the existing SIP overload control works have focused on SIP-over-UDP. Furthermore, most of researchers have focused on solving the overload problem in core servers, and therefore overload in edge servers still exists. We propose and implement novel but simple overload control mechanism which rejects a TCP connection at transport protocol level. Our work demonstrates that TCP in handshaking phase alone, is capable of managing the overload of time-critical session-based applications, which reject call requests in transport layer, with virtually no overhead. Experimental evaluation shows that with our mechanism, server capacity during overload improves from its original zero throughput in edge servers to nearly full capacity.
A monoclonal antibody that blocks the complement regulatory activity of guinea pig erythrocytes and characterization of the antigen involved as guinea pig decay-accelerating factor.

MCA44 is a mAb with the capacity to sensitize neuraminidase-treated guinea pig E for hemolysis by homologous guinea pig C, and the Fab fragments of this mAb could also sensitize guinea pig E interfering with the function of a membrane inhibitor of C on guinea pig E. Using an immunosorbent column to which MCA44 was coupled, the antigenic molecule termed 44Ag was purified from the glycoprotein fraction extracted from E membranes. C intermediate sheep E treated with guinea pig C1 and C4 after sensitization with Ab (EAC14b cells) lost the ability to generate C3 convertase with C2 after incubation with 44Ag. Treatment of guinea pig E and PBL with phosphatidyl-inositol specific phospholipase C (PIPLC) partially removed 44Ag, as determined by flow cytometric analysis after immunofluorescence staining with MCA44. However, 125I-labeled 44Ag adsorbed to human E was efficiently removed by PIPLC treatment with a slight reduction in M(r). The 44Ag purified on an immunosorbent column showed three bands on SDS-PAGE. However, partial N-terminal amino acid sequences of the 55-kDa, 70-kDa, and 88-kDa bands under nonreducing conditions were identical and the sequence was 55% homologous to the N-terminal sequence of human decay accelerating factor (CD55). Intracutaneous administration of MCA44 or its F(ab')2 fragment resulted in increased capillary permeability, even after 3 days, as determined by the appearance of Evans blue spots after i.v. administration of the dye. Because control Abs including anti-class I-MHC did not cause such increased capillary permeability, the increase in permeability caused by MCA44 was likely induced by blocking the function of 44Ag in vivo, indicating a crucial role for these molecules in preventing over-activation of C at the site.
Preventing the Tyranny of the Majority - Experimental Evidence on the Choice of Voting Thresholds in Bayesian Games

In democracies, an absolute majority of the population may choose policies that are harmful to the rest of the population. A purpose of super-majority rules is to prevent this from happening. We study whether individuals optimally choose sub- or super-majority rules when the rights of minorities should be protected. Subjects propose more extreme voting rules for more skewed distributions, but we also find that rule choices are biased towards balanced rules, leading substantial welfare losses.
Research on the Trans-Boundary Ecological Strategic Transformation Model of Enterprises: XR & DR Double Case

With the continuous development of new technologies represented by the Internet, the traditional business rules are constantly being overturned. How to promote the development of new industries through enterprise strategy has become an important topic widely discussed. As the world's second largest economy, the government has issued multiple documents to promote the development of new energy industry. The enterprises represented by new energy and new information technology are leading a new upsurge of new industry development. Therefore, taking the new energy industry enterprises in China as the object of study, this paper explores the transformation mechanism of enterprise ecological strategy from the perspective of cross border with exploratory case study. Through the realization and transformation of the ecological strategy of the enterprise, the dependence of the customers is cultivated and the commercial ecology is realized.
Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities

Sequencing environmental DNA (eDNA) is increasingly being used as an alternative to traditional morphological-based identification to characterize biological assemblages and monitor anthropogenic impacts in marine environments. Most studies only assess eDNA which, compared to eRNA, can persist longer in the environment after cell death. Therefore, eRNA may provide a more immediate census of the environment due to its relatively weaker stability, leading some researchers to advocate for the use of eRNA as an additional, or perhaps superior proxy for portraying ecological changes. A variety of pre-treatment techniques for screening eDNA and eRNA derived operational taxonomic units (OTUs) have been employed prior to statistical analyses, including removing singleton taxa (i.e., OTUs found only once) and discarding those not present in both eDNA and eRNA datasets. In this study, we used bacterial (16S ribosomal RNA gene) and eukaryotic (18S ribosomal RNA gene) eDNA- and eRNA-derived data from benthic communities collected at increasing distances along a transect from an oil production platform (Taranaki, New Zealand). Macro-infauna (visual classification of benthic invertebrates) and physico-chemical data were analyzed in parallel. We tested the effect of removing singleton taxa, and removing taxa not present in the eDNA and eRNA libraries from the same environmental sample (trimmed by shared OTUs), by comparing the impact of the oil production platform on alpha- and beta-diversity of the eDNA/eRNA-based biological assemblages, and by correlating these to the morphologically identified macro-faunal communities and the physico-chemical data. When trimmed by singletons, presence/absence information from eRNA data represented the best proxy to detect changes on species diversity for both bacteria and eukaryotes. However, assessment of quantitative beta-diversity from read abundance information of bacteria eRNA did not, contrary to eDNA, reveal any impact from the oil production activity. Overall, the data appeared more robust when trimmed by shared OTUs, showing a greater effect of the platform on alpha- and beta-diversity. Trimming by shared OTUs likely removes taxa derived from legacy DNA and technical artefacts introduced through reverse transcriptase, polymerase-chain-reaction and sequencing. Findings from our scoping study suggest that metabarcoding-based biomonitoring surveys should, if funds, time and expertise allow, be assessed using both eDNA and eRNA products.
Genome‐wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.

Summary Genetic improvement of fibre quality is one of the main breeding goals for the upland cotton, Gossypium hirsutum, but there are difficulties with precise selection of traits. Therefore, it is important to improve the understanding of the genetic basis of phenotypic variation. In this study, we conducted phenotyping and genetic variation analyses of 719 diverse accessions of upland cotton based on multiple environment tests and a recently developed Cotton 63K Illumina Infinium SNP array and performed a genome‐wide association study (GWAS) of fibre quality traits. A total of 10 511 polymorphic SNPs distributed in 26 chromosomes were screened across the cotton germplasms, and forty‐six significant SNPs associated with five fibre quality traits were detected. These significant SNPs were scattered over 15 chromosomes and were involved in 612 unique candidate genes, many related to polysaccharide biosynthesis, signal transduction and protein translocation. Two major haplotypes for fibre length and strength were identified on chromosomes Dt11 and At07. Furthermore, by combining GWAS and transcriptome analysis, we identified 163 and 120 fibre developmental genes related to length and strength, respectively, of which a number of novel genes and 19 promising genes were screened. These results provide new insight into the genetic basis of fibre quality in G. hirsutum and provide candidate SNPs and genes to accelerate the improvement of upland cotton.
Sperm competition enhances functional capacity of mammalian spermatozoa

When females mate promiscuously, sperm from rival males compete within the female reproductive tract to fertilize ova. Sperm competition is a powerful selective force that has shaped sexual behavior, sperm production, and sperm morphology. However, nothing is known about the influence of sperm competition on fertilization-related processes, because it has been assumed that sperm competition only involves a race to reach the site of fertilization. We compared four closely related rodent species with different levels of sperm competition to examine whether there are differences in the proportion of spermatozoa that become ready to interact with the ovum (“capacitated”) and in the proportion of spermatozoa that experience the acrosome reaction in response to a natural stimulant. Our results show that differences between species in levels of sperm competition were associated with the proportion of spermatozoa that undergo capacitation and with the proportion of spermatozoa that respond to progesterone, an ovum-associated signal. Sperm competition thus favors a larger population of spermatozoa that are competent to fertilize, and spermatozoa that are more sensitive to the signals emitted by the ovum and that may penetrate the ova vestments more rapidly. These results suggest that, contrary to previous assumptions, competition between spermatozoa from rival males continues at the site of fertilization. These findings may have further evolutionary implications because the enhanced competitiveness of spermatozoa during fertilization may increase the risk of polyspermy to females. This could lead to antagonistic coevolution between the sexes and may contribute to the explanation of the rapid divergence observed in fertilization-related traits.
Asset price bubbles and the quantification of credit risk capital with sensitivity analysis, empirical implementation and an application to stress testing

This study presents an analysis of the impact of asset price bubbles on standard credit risk measures, including Expected Loss (“EL”) and Credit Value-at-Risk (“CVaR”). We present a styled model of asset price bubbles in continuous time, and perform a simulation experiment of a 2 dimensional Stochastic Differential Equation (“SDE”) system for asset value determining Probability of Default (“PD”) through a Constant Elasticity of Variance (“CEV”) process, as well as a correlated a Loss-Given-Default (“LGD”) through a mean reverting Cox-Ingersoll-Ross (“CIR”) process having a long-run mean dependent upon the asset value. Comparing bubble to non-bubble economies, it is shown that asset price bubbles may cause an obligor’s traditional credit risk measures, such as EL and CVaR to decline, due to a reduction in the right skewness of the credit loss distribution. We propose a new risk measure in the credit risk literature to account for losses associated with a bubble bursting, the Expected Holding Period Credit Loss (“EHPCL”). We present evidence that asset price bubbles are a phenomenon that must be taken into consideration in the proper determination of economic capital for both credit risk management and measurement purposes. We also perform a sensitivity analysis of the SDE parameters upon the resulting credit risk measures, as well as the changes in their relationship to the CEV parameter, illustrating an application of an important model validation procedure.
Targeting mutant p53 in cancer: a long road to precision therapy

The TP53 tumor suppressor is the most frequently mutated gene in human cancers. In recent years, a blooming of research efforts based on both cell lines and mouse models have highlighted how deeply mutant p53 proteins affect fundamental cellular pathways with cancer‐promoting outcomes. Neomorphic mutant p53 activities spread over multiple levels, impinging on chromatin structure, transcriptional regulation and microRNA maturation, shaping the proteome and the cell's metabolic pathways, and also exerting cytoplasmic functions and displaying cell‐extrinsic effects. These tumorigenic activities are inextricably linked with the blend of highly corrupted processes that characterize the tumor context. Recent studies indicate that successful strategies to extract core aspects of mutant p53 oncogenic potential and to identify unique tumor dependencies entail the superimposition of large‐scale analyses performed in multiple experimental systems, together with a mindful use of animal models. This will hopefully soon lead to the long‐awaited inclusion of mutant p53 as an actionable target of clinical antitumor therapies.
The effect of positive‐lens addition and base‐in prism on accommodation accuracy and near horizontal phoria in Chinese myopic children

The effect of positive‐lens addition (0, +0.75, +1.50, +2.25, +3.00 D each eye) and base‐in prism power (0, 1.5, 3 Δ each eye) on both near focusing errors and latent horizontal deviations was evaluated in 29 Chinese myopic children (age: 10.3 ± 1.9 years, refractive error: −2.73 ± 1.31 D). Accommodation response and phoria were measured by the Shin‐Nippon auto‐refractor (right eye) and Howell–Dwyer near phoria card at 33 cm with each of the 15 lens/prism combinations in random order. The initial accommodative error was −0.96 ± 0.67 D (lag) and near phoria was −0.8 ± 5.0 Δ (exophoria). The positive‐lens addition decreased the accommodative lag but increased the exophoria as the power increased (e.g. up to −9.1 ± 4.1 Δ with +3 D). A 6‐Δ base‐in prism totally controlled the exophoria induced by a +1.50 D addition (−0.3 ± 4.3 Δ), but the accommodative lag was still considerable (−0.69 ± 0.54 D). In the graphical analysis of the data, a lens addition of +2.25 D combined with a 6‐Δ base‐in prism minimized both the lag and lens‐induced exophoria to −0.33 D and −2.4 Δ respectively (regression analysis). This lens and prism combination decreased the lens‐induced exophoria by 4.5 Δ compared with that measured with +2.25 D alone (−2.4 Δ vs −6.9 Δ). The results suggest that incorporating near base‐in prism when prescribing bifocal lenses for young progressing myopes with exophoria could reduce the positive lens‐induced oculomotor imbalance.