Miracle-dz/UniFAR-FTUs huggingface dataset:
Microbial DNA Typing by Automated Repetitive-Sequence-Based PCR

ABSTRACT Repetitive sequence-based PCR (rep-PCR) has been recognized as an effective method for bacterial strain typing. Recently, rep-PCR has been commercially adapted to an automated format known as the DiversiLab system to provide a reliable PCR-based typing system for clinical laboratories. We describe the adaptations made to automate rep-PCR and explore the performance and reproducibility of the system as a molecular genotyping tool for bacterial strain typing. The modifications for automation included changes in rep-PCR chemistry and thermal cycling parameters, incorporation of microfluidics-based DNA amplicon fractionation and detection, and Internet-based computer-assisted analysis, reporting, and data storage. The performance and reproducibility of the automated rep-PCR were examined by performing DNA typing and replicate testing with multiple laboratories, personnel, instruments, DNA template concentrations, and culture conditions prior to DNA isolation. Finally, we demonstrated the use of automated rep-PCR for clinical laboratory applications by using isolates from an outbreak of Neisseria meningitidis infections. N. meningitidis outbreak-related strains were distinguished from other isolates. The DiversiLab system is a highly integrated, convenient, and rapid testing platform that may allow clinical laboratories to realize the potential of microbial DNA typing.
Association of KIBRA with episodic and working memory: A meta‐analysis

WWC1 was first implicated in human cognition through a genome wide association study in 2006 that reported an association of the intronic single nucleotide polymorphism (SNP) rs17070145 with episodic memory performance. WWC1 encodes the protein KIBRA, which is almost ubiquitously expressed. Together with its binding partners, KIBRA is assumed to play a role in synaptic plasticity. T‐allele carriers of SNP rs17070145 have been reported to outperform individuals that are homozygous for the C‐allele in episodic memory tasks. Here we report two random effects meta‐analyses testing the association of rs17070145 with episodic and working memory. All currently available population‐based association studies that investigated effects of rs17070145 on episodic or working memory were included in the analyses. Where performance measures for multiple domain‐specific tasks were available for a given study population, averaged effect size estimates were calculated. The performed meta‐analyses relied on 17 samples that were tested for episodic memory performance (N = 8,909) and 9 samples that had performed working memory tasks (N = 4,696). We report a significant association of rs17070145 with both episodic (r = 0.068, P = 0.001) and working memory (r = 0.035, P = 0.018). In summary, our findings indicate that SNP rs17070145 located within KIBRA explains 0.5% of the variance for episodic memory tasks and 0.1% of the variance for working memory tasks in samples of primarily Caucasian background. © 2012 Wiley Periodicals, Inc.
Infectious dna recovered from avian tumor‐virus‐producing cells

A single treatment of chick embryo fibroblasts with DNA recovered from chick embryo fibroblasts productively infected and transformed with four different strains of RSV, or productively infected with two different strains of RAV, resulted in virus production and cell transformation (in the case of RSV) two or three passages after treatment (8–25 days). The virus recovered from cultures was phenotypically identical to that produced by the donor cells. No virus production nor cell transformation resulted from treatment of control cultures with DNA digested with DNAse. Infectious RSV‐DNA was recovered from purified donor cell nuclei and was associated with the precipitable fraction of DNA prepared according to the method of Hirt (1967). It also sedimented with cellular DNA in density gradients, and with high molecular weight DNA (2–4 × 107 daltons) in sucrose gradients, which suggests that it is associated and may be integrated with chromosomal DNA. In some experiments, DNA fractions of lower molecular weight (down to 6 × 106 daltons) were also infectious. DNA from virus‐producing RSV‐transformed cells also gave rise to virus and Rous cells in cultures of fibroblasts from gs‐ embryos. However, the amount of DNA required for successful infection varied widely between experiments, and no reproducible dose‐effect relationship was observed. The frequency of DNA‐treated cells which produced virus remained low, even when the assay cultures were pretreated with 5‐bromodeoxyuridine.
Predictors of malignancy in EUS-guided FNA for mediastinal lymphadenopathy in patients without history of lung cancer

BACKGROUND: Mediastinal lymphadenopathy (ML) poses a great diagnostic challenge. OBJECTIVE: To investigate the predictors of malignancy in endoscopic ultrasound (EUS)-guided fine-needle aspiration (FNA) of ML in patients without known lung cancer. DESIGN: Retrospective study. SETTING: Tertiary referral center. METHODS: One hundred eight patients without known lung cancer who underwent EUS guided-FNA for ML between 2000 and 2007. All subjects underwent EUS-guided FNA. Data was collected on patients′ demographics, and lymph node (LN) characteristics. Diagnosis of LN malignancy was based on FNA findings and clinical follow-up. RESULTS: One hundred eight patients were analyzed; 58 (54%) were men and 87 (79%) were Caucasian. Mean age was 55 years. Prior malignancy was present in 48 (43%) patients. A total of 126 FNA samples from 126 distinct LNs were performed. Twenty-five (20%) LNs were positive for malignancy. Mean short and long-axis for LNs were 13 and 29 mms respectively. Round shape and sharp borders were found in 29 (15%) and 25 (22%) LNs, correspondingly. Independent predictors of a malignant FNA were: Prior cancer (OR 13.10; 95% CI 2.7-63.32; P = 0.001), short axis (OR 1.10; 95% CI 1.00-1.22; P = 0.041) and sharp LN borders (OR 5.47; 95% CI 1.01-29.51; P = 0.048). Age, race, gender, long axis, round shape were not associated with cancer in our cohort. LIMITATIONS: Retrospective design and lack of surgical gold standard. CONCLUSIONS: Increased risk of malignancy was associated with prior history of cancer, larger LN short axis and presence of LN sharp borders. These predictors may help guide endoscopists perform FNA in malignant LNs, increasing the overall efficiency of EUS-FNA for ML.
Development of a DIVA (Differentiating Infected from Vaccinated Animals) strategy using a vaccine containing a heterologous neuraminidase for the control of avian influenza

The present paper reports of the development and validation of a control strategy for avian influenza infections in poultry. The "DIVA" (Differentiating Infected from Vaccinated Animals) strategy is based on the use of an inactivated oil emulsion vaccine containing the same haemagglutinin (H) subtype as the challenge virus, but a different neuraminidase (N). The possibility of using the heterologous N subtype, to differentiate between vaccinated and naturally infected birds, was investigated through the development of an "ad hoc" serological test based on the detection of specific anti-N1 antibodies. This was achieved using a baculovirus expressing a recombinant N1 protein. The A/ck/Pakistan/H7N3 virus was used as a vaccine and birds were challenged with the HPAI A/ty/Italy/4580/V99/H7N1 strain. The homologous H group ensured a clinical protection of 93% regardless of the vaccination scheme used, and was able to prevent viraemia and muscle colonization in the clinically healthy challenged birds. However, it was not able to prevent viral shedding. The "ad hoc" serological assay was developed as an indirect immunofluorescence test, and was validated using 608 field sera, and showed an "almost perfect agreement" (Kappa value) with the HI test, with relative sensitivity and specificity values of 98.1 and 95.7, respectively. The results of the present investigation suggest that the "DIVA" control strategy may represent a tool for the control of avian influenza infections in poultry.
A role for activin A and betacellulin in human fetal pancreatic cell differentiation and growth.

Activin A (Act.A), a member of the transforming growth factor beta family of secreted proteins, has been implicated in the regulation of growth and differentiation of various cell types. Betacellulin (BTC), a member of the epidermal growth factor family, converts exocrine AR42J cells to insulin-expressing cells when combined with Act.A. We have used primary cultures of human fetal pancreatic tissue to identify the effects of Act.A and/or BTC on islet development and growth. Exposure to Act.A resulted in a 1.5-fold increase in insulin content (P < 0.005) and a 2-fold increase in the number of cells immunopositive for insulin (P < 0.005). The formation of islet-like cell clusters, containing mainly epithelial cells, during a 5-day culture, was stimulated 1.4-fold by BTC (P < 0.05). BTC alone caused a 2.6-fold increase in DNA synthesis (P < 0.005). These data suggest that Act.A induces endocrine differentiation, whereas BTC has a mitogenic effect on human undifferentiated pancreatic epithelial cells.
Perceived Sources of Team Confidence in Soccer and Basketball.

PURPOSE Although it is generally accepted that team confidence is beneficial for optimal team functioning and performance, little is known about the predictors of team confidence. The present study was aimed to shed light on the precursors of both high and low team confidence in two different sports. A distinction is made between sources of process-oriented team confidence (i.e., collective efficacy) and sources of outcome-oriented team confidence (i.e., team outcome confidence), which have often been confounded in previous research. METHODS In a first step, two qualitative studies were conducted to identify all possible sources of team confidence in basketball and in soccer. In a second step, three quantitative studies were conducted to further investigate the sources of team outcome confidence in soccer (N = 1028) and in basketball (N = 867), and the sources of collective efficacy in basketball (N = 825). RESULTS Players perceived high-quality performance as the most important factor for their team outcome confidence. With regard to collective efficacy, team enthusiasm was perceived as most predictive determinant. Positive coaching emerged as second most decisive factor for both types of team confidence. In contrast, negative communication and expression by the players or the coach was perceived as the most decisive predictor of low levels of team confidence. At item level, all studies pointed to the importance of team confidence expression by the athlete leaders (i.e., leader figures within the team) and the coach. CONCLUSION The present manuscript sheds light on the precursors of high and low levels of team confidence. Athlete leaders and the coach emerged as key triggers of both upward and downward spirals of team confidence, thereby contaminating all team members.
Analysis of functional domains of the v-fms-encoded protein of Susan McDonough strain feline sarcoma virus by linker insertion mutagenesis

The Susan McDonough strain of feline sarcoma virus contains an oncogene, v-fms, which is capable of transforming fibroblasts in vitro. The mature protein product of the v-fms gene (gp140fms) is found on the surface of transformed cells; this glycoprotein has external, transmembrane, and cytoplasmic domains. To assess the functional role of these domains in transformation, we constructed a series of nine linker insertion mutations throughout the v-fms gene by using a dodecameric BamHI linker. The biological effects of these mutations on the function and intracellular localization of v-fms-encoded proteins were determined by transfecting the mutated DNA into Rat-2 cells. Most of the mutations within the external domain of the v-fms-encoded protein eliminated focus formation on Rat-2 cells; three of these mutations interfered with the glycosylation of the v-fms protein and interfered with formation of the mature gp140fms. One mutation in the external domain led to cell surface expression of v-fms protein even in the absence of complete glycosylational processing. Cell surface expression of mutated v-fms protein is probably necessary, but is not sufficient, for cell transformation since mutant v-fms protein was found on the surface of several nontransformed cell lines. Mutations that were introduced within the external domain had little effect on in vitro kinase activity, whereas mutations within the cytoplasmic domain all had strong inhibitory effects on this activity.
How collaboration networks affect innovation in Korea’s information and communication technology industry in the era of Internet of Things

Innovation is the outcome of interactions among multiple actors and institutions. In actor-based innovation system studies, researchers have investigated with whom actors should collaborate to create innovation. In reality, however, actors do not choose their collaboration network only based on information at the actor level; they also consider ‘something’ specific that their partner may possess. In the era of Internet Things, collaboration network is more important than ever because it is getting more difficult for a firm to innovate alone, as information and communication technology (ICT) converges with other industries. This paper introduces a factor-based innovation system and then derives via an empirical analysis the effect of factor networks in the innovation system on innovation with adaption to the Korean ICT industry.
Unintended Consequences: The Regressive Effects of Increased Access to Courts

Small claims courts enable parties to resolve their disputes relatively quickly and cheaply. The court’s limiting feature, by design, is that alleged damages must be small, in accordance with the jurisdictional limit at that time. Accordingly, one might expect that a large increase in the upper limit of claim size would increase the court’s accessibility to a larger and potentially more diverse pool of litigants. We examine this proposition by studying the effect of an increase in the jurisdictional limit of the Ontario Small Claims Court. Prior to January 2010, claims up to $10,000 could be litigated in the small claims court. After January 2010, this jurisdictional limit increased to include all claims up to $25,000. We study patterns in nearly 625,000 disputes over the period 2006-2013. In this paper, we investigate plaintiff behavior. Interestingly, the total number of claims filed by plaintiffs does not increase significantly with the increased jurisdictional limit. We do find, however, changes to the composition of plaintiffs. Following the jurisdictional change, we find that plaintiffs using the small claims court are, on average, from richer neighborhoods. We also find that proportion of plaintiffs from poorer neighborhoods drops. The drop-off is most pronounced in plaintiffs from the poorest 10% of neighborhoods.We explore potential explanations for this regressive effect, including crowding out, congestion, increased legal representation, and behavioral influences. Our findings suggest that legislative attempts to make the courts more accessible may have unintended regressive consequences.
Markers and Biomarkers of Endothelium: When Something Is Rotten in the State

Endothelium is a community of endothelial cells (ECs), which line the blood and lymphatic vessels, thus forming an interface between the tissues and the blood or lympha. This strategic position of endothelium infers its indispensable functional role in controlling vasoregulation, haemostasis, and inflammation. The state of endothelium is simultaneously the cause and effect of many diseases, and this is coupled with modifications of endothelial phenotype represented by markers and with biochemical profile of blood represented by biomarkers. In this paper, we briefly review data on the functional role of endothelium, give definitions of endothelial markers and biomarkers, touch on the methodological approaches for revealing biomarkers, present an implicit role of endothelium in some toxicological mechanistic studies, and survey the role of reactive oxygen species (ROS) in modulation of endothelial status.
Vitamin D status in mothers with pre-eclampsia and their infants: a case–control study from Serbia, a country without a vitamin D fortification policy

Abstract Objective The objective of the present study was to determine if vitamin D intake and status are associated with pre-eclampsia in a country without a vitamin D fortification policy. Design A case–control study of pregnancies with (case) and without (control) pre-eclampsia was conducted from January to April when UVB is minimal. Maternal and cord blood obtained at delivery were measured for plasma 25-hydroxycholecalciferol (25-OH-D3), 3-epimer of 25-OH-D3 (3-epi-25-OH-D3) and 24,25-dihydroxycholecalciferol (24,25-(OH)2D3) by LC–MS/MS and maternal 1,25-dihydroxyvitamin D (1,25-(OH)2D). Differences between groups were tested with ANOVA and Bonferroni post hoc tests (P<0·05). Setting Clinical Center of Serbia. Subjects Pregnant women with and without pre-eclampsia (n 60) and their infants. Results Exogenous vitamin D intake (0·95–16·25 µg/d (38–650 IU/d)) was not significantly different between groups. Women with pre-eclampsia delivered infants at an earlier gestational age and had significantly lower mean total plasma 25-hydroxyvitamin D (25-OH-D; case: 11·2 (sd 5·1); control: 16·1 (sd 5·7) ng/ml; P=0·0006), 25-OH-D3 (case: 10·0 (sd 4·9); control: 14·2 (sd 5·8) ng/ml; P=0·002), 3-epi-25-OH-D3 (case: 0·5 (sd 0·2); control: 0·7 (sd 0·2) ng/ml; P=0·0007) and 1,25-(OH)2D (case: 56·5 (sd 26·6); control: 81·0 (sd 25·7) pg/ml; P=0·018), while 24,25-(OH)2D3 was not different between groups. Infants did not differ in total plasma 25-OH-D, 25-OH-D3, 3-epi-25-OH-D3 and 24,25-(OH)2D3, but the mean proportion of 3-epi-25-OH-D3 was higher in the infant case group (case: 7·9 (sd 1·1); control: 7·0 (sd 1·4) % of total 25-OH-D3; P=0·005). Conclusions A high prevalence of vitamin D deficiency, as defined by plasma 25-OH-D<12 ng/ml, was observed in 47 % of all mothers and 77 % of all infants. These data underscore the need for prenatal vitamin D supplementation and a food fortification policy in Serbia.
IL-15: A Novel Prosurvival Signaling Pathway in Cardiomyocytes

Abstract: Cardiovascular disease is the leading cause of death in Western countries. A major limitation of current treatments is the inability to efficiently repair or replace dead myocardium. Recently, stem cell–based therapies have been explored as an avenue to circumvent current therapeutic limitations. Overall, these therapies seem to result in small improvements in the contractile function of the heart. The exact mechanism(s) of action that underlie these improvements remain unknown, and it is believed that paracrine effects play a significant role. Previously, we had reported that an extract derived from bone marrow cells, in the absence of any live cell, contained cardioprotective soluble factors. In this study, we identify IL-15 as a putative cardioprotectant within the bone marrow cells paracrine profile. Using an in vitro culture system, we assessed the ability of IL-15 to protect cardiomyocytes under hypoxic conditions. For the first time, we have identified IL-15 receptors on the surface of cardiomyocytes and delineated the signaling system by which hypoxic cardiomyocytes may be protected from cellular death and rescued from oxidative stress with IL-15 treatment.
More vein, less plastic

SUMMARY: Use of arteriovenous fistulas, grafts and central venous catheters for haemodialysis access varies considerably, because of perceived patient variables and preferences of surgeons, nephrologists and dialysis staff. Evidence clearly indicates that the arteriovenous fistula is superior to other methods of access in terms of patient survival, flow rates, patency, infection rates, expense and ease of maintenance. Strategies to increase the use and longevity of fistulas for definitive haemodialysis access include vein preservation, early referral for fistula surgery, preoperative clinical and ultrasound assessment of the venous and arterial systems, access surveillance, good cannulation technique, and aggressive conservatism in surgical and/or radiological correction of fistula problems.
Energy Technological Change and Capacity Under Uncertainty in Learning

This paper explores the role of learning in managing the capacities of existing and emerging energy technologies. Specifically, we address how uncertainties in learning rates impact R&D investments into a range of electricity generating technologies. Understanding managerial strategic response under learning uncertainty is particularly important as decision makers face competing R&D portfolios, dwindling and unstable financial resources, and an imminent energy policy. We develop a risk-minimizing optimization model of an abridged global energy system to investigate the effects of uncertainties in technological learning on electricity capacity additions. Addressing the risks associated with uncertainties in technological learning is relevant to distill cost-effective decisions, and to develop risk-hedging strategies. We find that 1) the willingness to hedge against the inherent risks associated with uncertainty in energy technological learning is positively correlated with the risk premium; 2) near-term or early investments are required to achieve a mix of sustainable energy technological portfolios as a hedge against R&D uncertainty; and 3) the management of electricity generation capacities under learning uncertainty allows decision makers to chart a more prudent intermediate path for energy technological growth through the creation of a more diversified technological portfolio.
Enhancing patient-physician communication: a community and culturally based approach.

BACKGROUND African American women are more likely to be diagnosed at later stages of breast cancer. METHODS A total of 15 residents participated in a program to increase their self-efficacy in communication skills relevant to understanding and responding to African American cultural issues associated with mammography screening. RESULTS Physicians reported increasing confidence in their ability to elicit barriers to mammography; assess cultural beliefs and norms; assess perceived health benefits and emotional adjustment; engage in emotional talk; motivate; and negotiate and build partnerships with patients. CONCLUSIONS A brief program can increase physician communication skills to meet the needs of a diverse population.