Miracle-dz/UniFAR-FTUs huggingface dataset:
Strand Specificity of Nicking of DNA at Chi Sites by RecBCD Enzyme

RecBCD enzyme is essential for the major pathway of homologous recombination of linear DNA in Escherichia coli. It is a potent nuclease and helicase and, during its unwinding of double-stranded DNA, makes single-strand scissions in the vicinity of Chi recombination hot spots. We report here that both the strand that is cut and the position of the cuts relative to Chi depended on the ATP to Mg2+ ratio. With ATP in excess, Chi-dependent nicks occurred, as we have previously reported, four to six nucleotides to the 3′-side of the Chi octamer (5′-GCTGGTGG-3′) and were detected only on the strand bearing that sequence. Three differences were seen with Mg2+ in excess. 1) Chi-dependent 3′-ends were produced on the GCTGGTGG-containing strand closer to and within the Chi octamer. 2) Chi-dependent cuts occurred on the complementary DNA strand. 3) RecBCD enzyme destroyed the 3′-terminated strand of DNA from its entry point up to the vicinity of the Chi site, as others have previously reported. We show here that, with Mg2+ in excess, the enzyme continued to travel along DNA, after encountering a Chi site, releasing both strands of the DNA distal to Chi as single strands. We discuss potential biological consequences of these two modes of RecBCD enzyme-Chi interaction.
Blind Adaptive Channel Shortening by Unconstrained Optimization for Simplified UWB Receiver Design

Ultra wide band (UWB) systems are baseband communication systems which use extremely narrow pulses for information transfer and occupy a huge bandwidth with very low power spectral density. Due to the large bandwidth, UWB propagation channels are highly dense in multipaths, ranging from 100 to 300 in different scenarios. These multipaths are resolvable and can be captured through a RAKE receiver. Thus UWB systems are inherently safe from inter symbol interference (ISI). On the other hand, this phenomenon makes the UWB receiver structure very complex from analysis and design point of view and involves high manufacturing costs as the RAKE must implemented with a large number of fingers. Channel shortening can help in designing a simplified and cost effective UWB receiver by reducing the number of fingers in RAKE receiver. In this paper, we present a new blind adaptive channel shortening algorithm based on unconstrained optimization to enable simple and cost effective UWB receiver design.
Personality disorders and depression

Background. Personality disorders (PDs) were assessed among depressed out-patients by clinical interview before and after antidepressant treatment with fluoxetine to assess the degree of stability of PD diagnoses and determine whether changes in PD diagnoses across treatment are related to the degree of improvement in depressive symptoms. Method. Three hundred and eighty-four out-patients (55% women; mean age = 39.9±10.5) with major depressive disorder (MDD) diagnosed with the SCID-P were enrolled into an 8 week trial of open treatment with fluoxetine 20 mg/day. The SCID-II was administered to diagnose PDs at baseline and endpoint. Results. A significant proportion (64%) of our depressed out-patients met criteria for at least one co-morbid personality disorder. Following 8 weeks of fluoxetine treatment, there was a significant reduction in the proportion of patients meeting criteria for avoidant, dependent, passive-aggressive, paranoid and narcissistic PDs. From baseline to endpoint, there was also a significant reduction in the mean number of criteria met for paranoid, schizotypal, narcissistic, borderline, avoidant, dependent, obsessive–compulsive, passive aggressive and self-defeating personality disorders. While changes in cluster diagnoses were not significantly related to improvement in depressive symptoms, there were significant relationships between degree of reduction in depressive symptoms (percentage change in HAM-D-17 scores) and degree of change in the number of criteria met for paranoid, narcissistic, borderline and dependent personality disorders. Conclusions. Personality disorder diagnoses were found to be common among untreated out-patients with major depressive disorder. A significant proportion of these patients no longer met criteria for personality disorders following antidepressant treatment, and changes in personality disorder traits were significantly related to degree of improvement in depressive symptoms in some but not all personality disorders. These findings suggest that the lack of stability of PD diagnoses among patients with current MDD may be attributable in part to a direct effect of antidepressant treatment on behaviours and attitudes that comprise PDs.
Stapes Surgery: How Precisely Do Different Prostheses Attach to the Long Process of the Incus with Different Instruments and Different Surgeons?

Hypothesis The goal of this study was to compare the attachment of stapes prostheses with differently shaped loops to the long process of the incus. Background In stapes surgery, the attachment of the prosthesis to the long process of the incus plays an important role concerning the gain in hearing and the development of late complications such as incus erosion and necrosis. Band-shaped and spiral loops have been developed to achieve a broad, firm attachment to the long process of the incus. During stapes surgery, the view at the prosthesis is restricted, making it impossible to evaluate the effects of the differently shaped loops. Methods Gold, steel/Teflon, platinum/Teflon, and two different titanium stapes prostheses were inserted in 30 specially prepared temporal bones by three experienced surgeons using the Fisch technique with the McGee and straight alligator forceps for the crimping of the loops. Photographs were taken with 0- and 70-degree rod lens telescopes at defined views. Results In all prostheses, a sufficiently firm attachment to the long process of the incus was achieved. The attachment of band-shaped loops proved to be better with the straight alligator forceps. The band-shaped loops showed a better contact with the incus than did the wire loops. However, the broad spiral-shaped loops led to a loss of the perpendicular axis of the piston to the long incus process. Conclusion The geometry of the loop affects the final length of the piston in the vestibule and its angle to the long process of the incus.
Chloroquine for the treatment of uncomplicated malaria in Guyana

Abstract At a public hospital in Georgetown, Guyana, 44 patients seeking treatment for symptomatic, slide-confirmed malaria were given standard chloroquine (CQ) therapy and followed for 28 days. The patients apparently had pure infections with Plasmodium falciparum (14), P. vivax (13) or P. malariae (one), or mixed infections either of P. falciparum and P. vivax (17) or of P. falciparum, P. malariae and P. vivax (two). Each received supervised treatment with 10 mg CQ base/kg on each of days 0 and 1, and 5 mg/kg on day 2. On the day of enrollment (day 0), the patients complained of fever (100%), headache (100%), malaise (94%), myalgia (79%), nausea (67%), vertigo (49%) and vomiting (33%). Many (39%) were ill enough to confine themselves to bed. On day 4, fewer of the subjects complained of fever (15%), headache (15%), malaise (6%), myalgia (21%), nausea (6%), vertigo (24%) or vomiting (0%) despite the relatively high (>48%) risk of therapeutic failure. The cumulative incidence of parasitological failure against P. falciparum was 15% at day 4, 33% at day 7 and 48% at day 14. All of the P. vivax and P. malariae infections cleared before day 4 and none recurred by day 7. Two infections with P. vivax recurred later (on day 14 or 28) but in the presence of less than adequate, whole-blood concentrations of CQ plus desethyl-chloroquine (i.e. <100 ng/ml). Taken together, the results indicate a high risk of therapeutic failure of CQ against P. falciparum but also indicate that resistance to CQ in P. vivax occurs infrequently in Guyana.
Identification of two core types in lipopolysaccharides of Actinobacillus pleuropneumoniae representing serotypes 1 to 12.

Lipopolysaccharides (LPS) of Actinobacillus pleuropneumoniae were separated by Tricine-SDS-polyacrylamide gel electrophoresis, which has been shown to improve resolution of low-molecular-mass fast migrating bands. Strains representing the 12 serotypes of A. pleuropneumoniae can be divided in two groups according to the gel mobility of the core - lipid A region of their LPS. The first electromorphic core type (core type I), found in serotypes 1, 6, 9, and 11, had a migration slower than Salmonella typhimurium Ra LPS. The second electromorphic core type (core type II), found in the remaining serotypes (i.e., 2, 3, 4, 5, 7, 8, 10, and 12) had a migration similar to S. typhimurium Ra LPS. Furthermore, we observed that these two core types were antigenically different. Western blot analyses indicated that core - lipid A region of LPS from electromorphic core type I strains reacted when probed with serum from a pig experimentally infected with a core type I strain but not when probed with serum from a pig experimentally infected with a core type II strain. Conversely, core - lipid A region of LPS from electromorphic core type II strains reacted only when probed with serum from a pig experimentally infected with a core type II strain. Our results, based on both electrophoretic mobility and antigenicity, suggest the presence of two LPS core types in A. pleuropneumoniae.
The Real Estate Investment Trust Industry and the Financial Crisis: Modeling Volatility (1985-2016)

This work measures the sensitivity of the residual volatility of the risk premiums of various Real Estate Investment Trusts (REITs) sectors to systemically important economic events between January 2, 1985, and December 30, 2016. To this end, the residual yields of the REITs are calculated and, with them, a GARCH (1,1) model is estimated, with dummy variables that identify eleven sub-periods delimited by systemic events that occurred in the American economy. The volatility of residual yields is found to decrease with the S&P500 risk premium, and increases only for some sectors with increases in Treasury Bond yields (T-Bills). Similarly, residual yield volatility increased in some periods (e.g., after the Black Monday crash, the low-quality mortgage crisis, and the Great Recession), but did not during the period of stock market collapse caused by companies in the “new economy” (known as the dot-com bubble). Knowledge of these stylized facts opens up new risk management possibilities for those investors considering in including these alternative investments in their portfolios.
Use of Autologous Epithelium Transplantation on Various Scaffolds to Cover Tissue Loss in Oral Cavity: Long-Term Observation

Background The aim of this study was to investigate the application of mucous membrane keratinocyte cultures on amniotic membrane and on poly(L-lactic acid) (PLLA) Purasorb PL38 to cover tissue loss in the oral cavity. Developments in molecular biology techniques and tissue engineering allow the culturing and identification of cells that can be anchored in the wound to achieve integrity of the tissue. Transplantation of tissues obtained from the patient's own cells is superior to allogenous transplantation where there is a possibility of transfection, rejection and the need for long-term immunosuppression. Methods In 9 patients (15 procedures) keratinocytes cultured on amniotic membrane and PLLA were transplanted to cover antro-oral fistulas and bone loss after osteoradionecrosis. Results In all 6 patients with outlasting antro-oral fistulas, the defects were healed. In 3 patients with 5 cases of tissue loss after osteoradionecrosis, we obtained healing of the wound in only 1 case. Histological examination of the cultures indicated that cultured cells formed well-differentiated layers, very similar to the keratinocytes of mucous membranes, although those seeded on amniotic membrane formed a single layer of cells, while those seeded on the PLLA scaffold were arranged on 2 or more layers: these differences were shown to be statistically significant with a morphometric analysis. Conclusions Autologous transplants of epithelium cultured on amniotic membrane and PLLA constitute a new and effective way of covering nonhealing tissue loss in the oral cavity in chosen cases, using modern methods of tissue engineering.
Public attitudes about genetic testing in the newborn period.

OBJECTIVE To measure attitudes toward newborn genetic testing in our jurisdiction. DESIGN A cross-sectional, pen-and-paper survey. SETTING The survey was administered to the general public and prospective parents in Eastern Canada between April 2010 and December 2010. PARTICIPANTS A total of 648 individuals completed surveys. RESULTS Positive attitudes were found toward newborn genetic testing, regardless of whether an effective treatment existed for the disorder in question or whether the disorder developed in adulthood. A majority agreed (69%) that testing should be available for any condition to assist with future reproductive decisions. Most respondents (93%) agreed parents should provide informed consent before newborn screening (NBS) was undertaken and that parents had a fundamental right to access NBS if they so choose. CONCLUSION Interest in NBS for genetic disorders is generally high, regardless of whether an effective treatment exists. Findings lend support to the expansion of NBS panels to include those disorders currently lacking treatment but highlight consumers' desire for informed consent before testing is undertaken.
An LMI-based global non-quadratic observer design via Takagi-Sugeno models and Levant's robust differentiators

An innovative solution for global non-quadratic observer design of nonlinear systems is presented in this report. Via an exact convex representation of the model in the Takagi-Sugeno form, an observer which employs the nonlinearities of the system as well as a discontinuous function of their time derivatives, is proposed. It is shown that such a structure, when combined with a non-quadratic Lyapunov function, enhances former results by reaching global conditions up to the modeling region, while being able to deal with the time derivatives of the nonlinearities in the Lyapunov function. The required derivatives are obtained in finite-time from an s-th order Levant's robust differentiator, which better fits with the discontinuous nature of the observer. Design conditions are expressed as linear matrix inequalities. Examples are provided that show the advantages as well as the limitations of the novel approach.
SOCIOECONOMIC FACTORS INFLUENCING MARKET PARTICIPATION OF HORTICULTURAL SMALLHOLDER FARMERS IN THE ALFRED NZO DISTRICT, EASTERN CAPE, SOUTH AFRICA

The purpose of this paper is to identify the socioeco- nomic factors influencing market participation of horticultural smallholder farmers in the Alfred Nzo district. Cross-sectional data was collected by the Agricultural Research Council and the Department of Rural Development and Land Reform in Janu- ary 2014 from 48 horticultural smallholder farmers in Alfred Nzo district using a structured questionnaire. Binomial logistic regression analysis was used to analyze the data. The results showed that market participation was influenced by access to market information, type of road and availability of transport to market. The empirical results will be useful for horticulture farmers, marketers and policy makers in developing efficient production and marketing strategies. The government and pri- vate sector should establish a model specific to the actual needs of smallholder farmers of the Alfred Nzo district, which should include improvement of roads to farming sites and a well- coordinated and efficient transporting system which must be designed specifically for smallholder farmers in the district.
TLR4 Influences Hepatitis B Virus Related Hepatocellular Carcinoma by Regulating the Wnt/β-Catenin Pathway

Background/Aims: We investigated the correlation between toll-like receptor 4 (TLR4) and β-catenin for disclosing the potential pathogenesis of hepatocellular carcinoma (HCC). Methods: Immunohistochemical toolkit was implemented to measure the expression of TLR4 and β-catenin in 98 cases of HCC tissues and adjacent tissues. After setting up the HepG2.2. 15 hepatitis B virus (HBV) related HCC cell line, we divided the cells into the control group, TLR4 siRNA group, β-catenin siRNA group, and pcDNA.3. 1 TLR4 + β-catenin siRNA group. Western blot, CCK-8 method, Transwell and flow cytometry were used to detect protein expression, cell proliferation, cell migration and invasion as well as cell apoptosis, respectively. Nude mice tumor model was established to observe the effects of TLR4 and β-catenin on the progression of HBV-related HCC in vivo. Results:The positive rates of TLR4 and β-catenin were higher in HCC tissues compared with normal tissues. Both the TLR4 siRNA group and β-catenin siRNA group exhibited a decreased expression of β-catenin. The proliferation, migration and invasion of tumor cells in the above two groups were suppressed, while the cell apoptosis appeared to be stimulated. As suggested by the results from in vivo and in vitro experiments, the up-regulation of TLR4 could antagonize the corresponding effect of β-catenin siRNA. Conclusions: TLR4 can affect the expression of β-catenin and hence influence the progression of HBV-related HCC.
Time-Varying Coefficient Estimation in SURE Models. Application to Portfolio Management*

This paper provides a detailed analysis of the asymptotic properties of a kernel estimator for a seemingly unrelated regression equations model with time-varying coefficients (tv-SURE) under general conditions. Theoretical results together with a simulation study differentiate the cases for which the estimation of a tv-SURE outperforms the estimation of a single regression equations model with time-varying coefficients. The study shows that Zellner’s results cannot be straightforwardly extended to the time-varying case. The tv-SURE is applied to the Fama and French five-factor model using data from four different international markets. Finally, we provide the estimation under cross-restriction and discuss a testing procedure.
The validation process of incorporating simulation-based accreditation into the anesthesiology Israeli national board exams.

BACKGROUND The Israeli Board of Anesthesiology Examination Committee added a simulation-based Objective Structured Clinical Evaluation component to the board examination process. This addition was made in order to evaluate medical competence and considers certain domains that contribute to professionalism. This unique and new process needed to be validated. OBJECTIVES To validate and evaluate the reliability and realism of incorporating simulation-based OSCE into the Israeli Board Examination in Anesthesia. METHODS Validation was performed before the exam regarding Content Validity using the modified Delphi technique by members of the Task Force of the Israeli Board Examination Committee in Anesthesiology. RESULTS The examination has been administered six times in the past 3 years to a total of 145 examinees. The pass rate ranged from 62% (trauma) to 91% (regional anesthesia). The mean inter-rater correlations for the total score (all items), for the Critical checklist items score, and for the Global (General) rating were 0.89, 0.86 and 0.76, respectively. The inter-correlations between the five OSCE stations scores were significant (P< 0.01) only between Trauma & Ventilation for the Total score (r = 0.32, n=63), and between Resuscitation & Regional and OR-crisis for the Global score (r = 0.42 and 0.27, n=64 and 104, respectively). The correlation between the OSCE examination score and the success rate at each of the eight different clinical domains of the oral board examination did not reach statistical significance. Most participants (70-90%) found the difficulty level of the examination stations reasonable to very easy. All major errors, which were identified in the initial two exam periods, disappeared later in the next two exam periods. CONCLUSIONS The exam has gradually progressed from being an optional part of the oral board examination to a prerequisite component of this test. Other anesthesiology programs or medical professions can adopt the model described here.
The European Foundation for Quality Management (EFQM) excellence model in a low voltage switchgear company

The Turkish low voltage switchgear sector is made up of several local and international companies. Generally, local companies operating in this sector try to get a competitive advantage by fabricating cheap products , in order to cope with the competition that focuses more on quality. What’s more, international corporations perform quality activities under the organization and control of their top-managements from abroad. Although VIKO is a local producer, it is a company willing to invest more in quality, as well as in research and development. VIKO company is the focus of this self-assessment study, since it lies at the conjunction of companies operating in this sector, it being a local company performing various quality enhancement activities . Simultaneously, the authors consider that this study shall prove useful to create an overview over the entire Turkish low voltage switchgear sector. The evaluation of the company and its core-activities was based upon nine criteria of the European Foundation for Quality Management (EFQM) Excellence Model, in order to identify the strengths, the weaknesses and aspects that require improvements . This is the first study worldwide performed in the low voltage switchgear sector and it is aimed at motivating other Turkish companies that operate in this sector to implement The European Foundation for Quality Management (EFQM) Excellence Model in their TQM activities (Total Quality Management).
THE EFFECT OF SHORT‐TERM USE OF TESTOSTERONE ENANTHATE ON MUSCULAR STRENGTH AND POWER IN HEALTHY YOUNG MEN

Use of testosterone enanthate has been shown to significantly increase strength within 6–12 weeks of administration (2, 9), however, it is unclear if the ergogenic benefits are evident in less than 6 weeks. Testosterone enanthate is classified as a prohibited substance by the World Anti- Doping Agency (WADA) and its use may be detected by way of the urinary testosterone/epitestosterone (T/E) ratio (16). The two objectives of this study were to establish (a) if injection of 3.5 mg·kg-1 testosterone enanthate once per week could increase muscular strength and cycle sprint performance in 3–6 weeks; and (b) if the WADA-imposed urinary T/E ratio of 4:1 could identify all subjects being administered 3.5 mg·kg-1 testosterone enanthate. Sixteen healthy young men were match-paired and were assigned randomly in a double-blind manner to either a testosterone enanthate or a placebo group. All subjects performed a structured heavy resistance training program while receiving either testosterone enanthate (3.5 mg·kg-1) or saline injections once weekly for 6 weeks. One repetition maximum (1RM) strength measures and 10-second cycle sprint performance were monitored at the pre (week 0), mid (week 3), and post (week 6) time points. Body mass and the urinary T/E ratio were measured at the pre (week 0) and post (week 6) time points. When compared with baseline (pre), 1RM bench press strength and total work during the cycle sprint increased significantly at week 3 (p < 0.01) and week 6 (p < 0.01) in the testosterone enanthate group, but not in the placebo group. Body mass at week 6 was significantly greater than at baseline in the testosterone enanthate group (p < 0.01), but not in the placebo group. Despite the clear ergogenic effects of testosterone enanthate in as little as 3 weeks, 4 of the 9 subjects in the testosterone enanthate group (−44%) did not test positive to testosterone under current WADA urinary T/E ratio criteria.