Miracle-dz/UniFAR-FTUs huggingface dataset:
Role of Pili in Bacterial Conjugation

We describe techniques for isolating individual pairs of mating Escherichia coli and observing them under the light microscope. Some pairs achieved close cell-to-cell contact, whereas others remained loosely connected by invisible connections which may be F pili. After 30 min of mating, the pairs were separated and allowed to grow into clones. That many exconjugants derived from “loose”-mating pairs produced recombinants suggests that F pili are involved in the transfer of genetic material. The frequency of formation of recombinants from “close”-mating pairs, however, was significantly higher than that from loose-mating pairs, indicating that a close cell-to-cell contact facilitates chromosome transfer. Death rates of exconjugants from close pairs were also higher than those from loose pairs. Hfr × F− matings produced higher death rates than F+ × F− matings. Male cells were found capable of transferring genetic markers to two F− cells simultaneously. We conclude that F pili play at least three roles in mating: (i) they initiate contacts between mating pairs; (ii) they facilitate the transfer of genetic material; and (iii) they draw mating cells into a close contact which increases the fertility of the union.
Eight-month follow-up of physical activity and central adiposity: results from an Internet-delivered randomized control trial intervention.

BACKGROUND Less than half of U.S. adults engage in the recommended amount of physical activity (PA). Internet-delivered PA programs increase short-term PA but long-term adherence is largely equivocal. PURPOSE To determine whether increased PA following the 16-week Internet-delivered Active Living Every Day (ALED-I) program is maintained 8 months later in sedentary and overweight rural adults. METHODS In our previous randomized controlled trial (N = 32; 18 intent-to-treat controls, 14 ALED-I interventions), the ALED-I group increased PA (+1384 steps/day; E.S. = 0.95) and reduced central adiposity. Nine original intervention participants and ten delayed intent-to-treat control participants completed ALED-I and an 8-month followup. Pedometer-measured PA, anthropometric variables, and cardiometabolic disease risk factors were assessed at baseline, postintervention, and at 8 months. RESULTS Control crossover participants increased PA (+1337 steps/ day; P = .04). Eight months following completion of ALED-I (N = 19), PA levels relapsed (-1340 steps/day) and were similar to levels before the intervention (6850 +/- 471 steps/day vs. 6755 +/- 543 steps/day; P = .89). Total cholesterol and triglycerides improved, -9.9% and -18.2%, respectively, and reductions in central adiposity were maintained (97.1 +/- 2.2 cm vs. 97.2 +/- 2.2 cm; P = .66). CONCLUSIONS The ALED-I intervention was efficacious in the short-term but did not produce longer-term adherence to PA. Future theory-based internet-delivered interventions that produce habituation of increased PA are warranted.
Which Factors Affect Software Projects Maintenance Cost More?

Introduction The software industry has had significant progress in recent years. The entire life of software includes two phases: production and maintenance. Software maintenance cost is increasingly growing and estimates showed that about 90% of software life cost is related to its maintenance phase. Extraction and considering the factors affecting the software maintenance cost help to estimate the cost and reduce it by controlling the factors. Methods In this study, the factors affecting software maintenance cost were determined then were ranked based on their priority and after that effective ways to reduce the maintenance costs were presented. This paper is a research study. 15 software related to health care centers information systems in Isfahan University of Medical Sciences and hospitals function were studied in the years 2010 to 2011. Results and discussion Among Medical software maintenance team members, 40 were selected as sample. After interviews with experts in this field, factors affecting maintenance cost were determined. In order to prioritize the factors derived by AHP, at first, measurement criteria (factors found) were appointed by members of the maintenance team and eventually were prioritized with the help of EC software. Based on the results of this study, 32 factors were obtained which were classified in six groups. “Project” was ranked the most effective feature in maintenance cost with the highest priority. By taking into account some major elements like careful feasibility of IT projects, full documentation and accompany the designers in the maintenance phase good results can be achieved to reduce maintenance costs and increase longevity of the software.
Complementary Iterated Floor Words and the Flora Game

Let $\varphi=(1+\sqrt{5})/2$ denote the golden section. We investigate relationships between unbounded iterations of the floor function applied to various combinations of $\varphi$ and $\varphi^2$. We use them to formulate an algebraic polynomial-time winning strategy for a new four-pile take-away game Flora, which is motivated by partitioning the set of games into subsets CompGames and PrimGames. We further formulate recursive, arithmetic, and word-mapping winning strategies for it. The arithmetic one is based on the Fibonacci numeration system. We further show how to generate the floor words induced by the iterations using word-mappings and characterize them using the Fibonacci numeration system. We also exhibit an infinite array of such sequences.
A discrete algorithm for fixed-path trajectory generation at kinematic singularities

An algorithm is presented for computing the necessary time-scaling to allow a non-redundant manipulator to follow a fixed Cartesian path containing kinematic singularities. The resulting trajectory is close to minimum-time, subject to bounds on joint velocities and accelerations. The algorithm assigns a series of knot points along the path, increasing the knot density in the vicinity of singularities. Appropriate path velocities are then computed for each knot point. Two experiments involving the PUMA manipulator are shown.
Al–Cu Pattern Wafer Study on Metal Corrosion Due to Chloride Ion Contaminants

Chloride ions in the cleanroom environment induce metal corrosion of integrated circuits, and cause wafer scrap events. In this paper, pattern wafers were designed to monitor critical concentration which leads to metal corrosion effects in a simulated airborne molecular contamination (AMC) environment. The simulated contamination environment was established by placing different numbers of preventive maintenance (PM) wipers in wafer pods and monitored simultaneously by ion mobility spectrometer (IMS) and chromatography (IC) instruments. The exposed Al-Cu pattern wafers were analyzed by the KLA surface scanner and the scanning electron microscope/energy dispersive X-ray spectroscopy analyzer. The results indicate that the IMS and the instruments provide consistent HCl monitoring data. Furthermore, they suggest that pattern wafer exposure tests can be an effective method to monitor metal corrosion. The PM wipers are a simple and effective method to establish simulated source of HCl for studying the AMC effect in ppbv levels. The critical HCl concentration where particles could be found on the wafer surface is around 2.0-3.5 ppbv, and the critical HCl concentration that results in metal corrosion defects is around 4.1-6.4 ppbv.
Relationship Lending and Credit Quality

We analyse whether relationship lending reduces borrowers’ probability of default and, if so, whether this beneficial effect also applies to borrowers who are more exposed to the economic downturn. By using unique, matched data of 43,000 firms and their lending institutions between 2008 and 2010, we document that the probability that a firm becomes distressed decreases if the creditor concentration is high and if the duration of bank-firm relationships is long. While these results appear to support the beneficial effect of relationship lending practices, we note that the organisational distance of banks also matters both as a determinant of loan distress and loan downgrading. The results are stronger for smaller firms.
Upward Mobility: Experiences with Families of Origin Among College-Educated African American Women

Research indicates that a significant number of African American women from lower-class statuses work hard to become upwardly mobile. The purpose of this qualitative study was to explore the interpersonal experiences of upwardly mobile African American women, particularly their interactions with their family and community of origin. The purposefully selected sample was composed of 13 African American women holding various positions at a Midwestern university. To maximize variation of experiences, respondents were graduate students, faculty members, and staff. The primary data collection method was in-depth interviews along with examination of supplemental materials which included respondents’ journal entries, e-mail exchanges, field notes, and researcher memos. I analyzed the collected data following the procedures of open, axial, and selective coding. A theory emerged from my interpretation of data gathered to answer the research question “What is the process by which African American women from working-class families manage relationships with members of their family of origin during and/or following the attainment of a graduate degree? ” Evidence from this exploratory study suggests that the women develop a bicultural identity out of necessity after being confronted with conflicting experiences and worldviews. The emergent theory highlights the changes that occur in the women’s lives and some of the conflicting life experiences they have with their family of origin as they progress through academia. The theory also describes strategies used by the respondents to manage their emerging bicultural identity. The attainment of a bicultural identity allows African American women to function in their life as well-educated women and to retain string ties to their family and community of origin.
GRB 130606A AS A PROBE OF THE INTERGALACTIC MEDIUM AND THE INTERSTELLAR MEDIUM IN A STAR-FORMING GALAXY IN THE FIRST Gyr AFTER THE BIG BANG

We present high signal-to-noise ratio Gemini and MMT spectroscopy of the optical afterglow of the gamma-ray burst (GRB) 130606A at redshift z = 5.913, discovered by Swift. This is the first high-redshift GRB afterglow to have spectra of comparable quality to those of z ≈ 6 quasars. The data exhibit a smooth continuum at near-infrared wavelengths that is sharply cut off blueward of 8410 Å due to absorption from Lyα at redshift z ≈ 5.91, with some flux transmitted through the Lyα forest between 7000 and 7800 Å. We use column densities inferred from metal absorption lines to constrain the metallicity of the host galaxy between a lower limit of [Si/H] ≳ −1.7 and an upper limit of [S/H] ≲ −0.5 set by the non-detection of S ii absorption. We demonstrate consistency between the dramatic evolution in the transmission fraction of Lyα seen in this spectrum over the redshift range z = 4.9–5.85 with that previously measured from observations of high-redshift quasars. There is an extended redshift interval of Δz = 0.12 in the Lyα forest at z = 5.77 with no detected transmission, leading to a 3σ upper limit on the mean Lyα transmission fraction of ≲0.2% (or (Lyα) > 6.4). This is comparable to the lowest-redshift Gunn–Peterson troughs found in quasar spectra. Some Lyβ and Lyγ transmission is detected in this redshift window, indicating that it is not completely opaque, and hence that the intergalactic medium (IGM) is nonetheless mostly ionized at these redshifts. We set a 2σ upper limit of 0.11 on the neutral fraction of the IGM at the redshift of the GRB from the lack of a Lyα red damping wing, assuming a model with a constant neutral density. GRB 130606A thus for the first time realizes the promise of GRBs as probes of the first galaxies and cosmic reionization.
Strengths and Satisfaction Across the Adult Lifespan

Positive psychology has recently developed a classification of human strengths (Peterson & Seligman, in press). We aimed to evaluate these strengths by investigating the strengths and life satisfaction in three adult samples recruited from the community (young adult, middle-aged, and older adult), as well as in the surviving men of the Grant study of Harvard graduates. In general, older adults had higher levels of interpersonal and self-regulatory strengths, whereas younger adults reported higher levels of strengths related to exploring the world. Grant study men tended to report lower strength levels than older adults from the community. Among the young adults, only hope significantly predicted life satisfaction, whereas among the middle-aged individuals, the capacity for loving relationships was the only predictor. Among community-dwelling older adults, hope, citizenship, and loving relationships all positively and uniquely predicted life satisfaction, compared with loving relationships and appreciation of beauty in the Grant sample.
Licensing in the Eating Domain: Implications for Effective Self-Control Maintenance

Licensing in the Eating Domain: Implications for Effective Self-Control Maintenance by Jennifer Camille Isherwood Department of Psychology & Neuroscience Duke University Date:_______________________ Approved: _______________________ Rick H. Hoyle, Supervisor _______________________ Mark R. Leary _______________________ Gary G. Bennett _______________________ Gavan J. Fitzsimons An abstract of a dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the Department of Psychology & Neuroscience in the Graduate School of Duke University 2015 Copyright by Jennifer Isherwood 2015
Development of in vitro systems for nanotoxicology: methodological considerations

Due to the rapid development of a diverse array of nanoparticles, used in a wide variety of products, there are now many international activities to assess the potential toxicity of these materials. These particles are developed due to properties such as catalytic reactivity, high surface area, light emission properties, and others. Such properties have the potential to interfere in many well-established toxicity testing protocols. This article outlines some of the most frequently used assays to assess the cytotoxity and biological reactivity of nanoparticles in vitro. The article identifies key issues that need to be addressed in relation to inclusion of relevant controls, assessing particles for their ability to interfere in the assays, and using systematic approaches to prevent misinterpretation of data. The protocols discussed range from simple cytotoxicity assays, to measurement of reactive oxygen species and oxidative stress, activation of proinflammatory signaling, and finally genotoxicity. The aim of this review is to share knowledge relating to nanoparticle toxicity testing in order to provide advice and support for guidelines, regulatory bodies, and for scientists in general.
Extreme Killing: Understanding Serial and Mass Murder

Preface Acknowledgments PART I. Multiple Murder 1. America's Fascination With Multiple Homicide The Gein Legacy Multiple Murder in Popular Culture The Selling of Multiple Murder Craving Attention Killer Communication Killer Groupies The Impact of Celebrating Murderers Sensitize, Not Sanitize 2. Defining Multiple Murder Mass, Serial, and Spree A Typology of Multiple Murder PART II. Serial Murder 3. An Anatomy of Serial Murder Prevalence of Serial Murder Extraordinarily Ordinary A Profile of the Typical Serial Killer 4. With Deliberation and Purpose When Killing Is Thrilling On a Deadly Mission of Terror or Revenge Killing for Expediency For Love and Loyalty 5. Murder Without Guilt Self-Control and Social Control The Sociopathic Personality The Culture of Sociopathy Empathy and Serial Killers Borderline Personality Disorder Normalcy in Serial Murder Rehumanizing the Victims 6. Partners in Murder Insanity in the Relationship Partners for Profit Partnerships of Men and Women 7. Killing for Company Placing the Blame Killing for Companionship The Functions of Cannibalism Desire for Total Control and Ownership 8. Fantasyland Keeping Souvenirs Normal and Abnormal Fantasies The Impact of Pornography 9. The Making of a Serial Killer Childhood Suffering Testimony Under Hypnosis Child Abuse and Murder Inordinate Need for Power Animal Cruelty and Violence Against Humans Challenges of Predicting Serial Murder Biological Predisposition Blaming the Family 10. Nonsexual Control Power Over Patients Female Serial Killers Munchausen Syndrome by Proxy 11. Killing Cults Killing for a Cause The Appeal of Dangerous Cults Suicide or Homicide? Satanism and Serial Murder 12. So Many Victims Vulnerable Victims Preferred Catching the Serial Killer Behavioral Profiling Reducing Linkage Blindness Lucky Breaks PART III. Massacres 13. For Love, Money or Revenge Relative Obscurity A Profile of Mass Killers Selective and Methodical When Love Kills Sweet Revenge Profiting From Mass Murder Explaining Mass Murder The Great Equalizer Contributing Factors 14. Family Annihilation A Profile of the Family Annihilator Impact of Unemployment Murdering Moms The Defiant Son 15. Firing Back Profile of the Workplace Avenger The Impact of Frustration Mixed Motives Workplace Murder by Proxy Romantic Obsession Externalizing Responsibility Social Isolation Screening Out Problem Workers Going Postal 16. Schooled in Mass Murder Student Massacres On to College Shooting for Infamy Overstating the Copycat Effect 17. Fighting City Hall Attacking the System Legal Battles Filing a Grievance Increasing Alienation 18. Hate-Motivated Mass Murder Choice of Victims A Life of Frustration Blaming Women The Killer as Victim Settling a Grudge With a Gun Minority Against Majority 19. Going Berserk Paranoid Thinking Confused State of Mind Long-Standing Mental Illness Civilian Battlefields Brain Abnormalities Deadly Weapons PART IV. Epilogue 20. Remembering the Victims References Credits and Sources Index About the Authors
Beyond Corroboration: Strengthening Model Validation by Looking for Unexpected Patterns

Models of emergent phenomena are designed to provide an explanation to global-scale phenomena from local-scale processes. Model validation is commonly done by verifying that the model is able to reproduce the patterns to be explained. We argue that robust validation must not only be based on corroboration, but also on attempting to falsify the model, i.e. making sure that the model behaves soundly for any reasonable input and parameter values. We propose an open-ended evolutionary method based on Novelty Search to look for the diverse patterns a model can produce. The Pattern Space Exploration method was tested on a model of collective motion and compared to three common a priori sampling experiment designs. The method successfully discovered all known qualitatively different kinds of collective motion, and performed much better than the a priori sampling methods. The method was then applied to a case study of city system dynamics to explore the model’s predicted values of city hierarchisation and population growth. This case study showed that the method can provide insights on potential predictive scenarios as well as falsifiers of the model when the simulated dynamics are highly unrealistic.
Effects of Fixation and Storage of Human Tissue Samples on Nucleic Acid Preservation

Background Because of recent advances in the molecular diagnosis of cancer patients, tissue quality has become more important in daily practice. Methods To evaluate the effects of fixative, duration of fixation, decalcification, and storage periods on nucleic acid integrity, DNA and RNA were extracted from gastrointestinal cancer tissue. The yield and purity were analyzed, and polymerase chain reaction (PCR) for glyceraldehyde 3-phosphate dehydrogenase (GAPDH; 60 bp), β-actin (148 bp), and human growth hormone (hGH; 434 bp) and real-time reverse transcription-PCR for β-actin (97 bp) were performed. Results All formalin-fixed paraffin-embedded (FFPE) and methacarn-fixed paraffin-embedded (MFPE) samples tested positive for GAPDH and β-actin by PCR. hGH was successfully detected in all MFPE samples, but in only 46.7% of the FFPE samples. Prolonged formalin fixation resulted in fewer GAPDH and β-actin PCR products, and amplification of hGH was not successful. The PCR and reverse transcription-PCR results were significantly affected by the duration of decalcification. The yield, purity, and integrity of mRNA progressively decreased with increased storage periods of paraffin blocks. Conclusions Fixation and storage should therefore be standardized in order to improve the quality of molecular pathologic diagnosis.
Effect of ethylenediaminetetraacetic acid gel on the incidence of dentinal cracks caused by three novel nickel-titanium systems.

The aim of this study is to evaluate the incidence of crack formation while using Reciproc, WaveOne and Twisted File Adaptive with and without ethylenediaminetetraacetic acid (EDTA) gel. Seventy extracted mandibular premolars were included. The teeth were decoronated until roots of 16 mm were obtained. Samples were distributed into seven groups: group 1, no canal preparation (control); other groups were instrumented so; group 2, Reciproc; group 3, Reciproc + EDTA; group 4, WaveOne; group 5, WaveOne + EDTA; group 6, Twisted File Adaptive; group 7, Twisted File Adaptive + EDTA. Roots were horizontally sectioned from 3, 6 and 9 mm from apex and observed under stereomicroscope. The number and the incidence of cracks were recorded and statistically analysed with chi-squared and Kruskal-Wallis tests. Control group did not reveal any cracks. Crack formation with three novel Ni-Ti instruments was similar. Using EDTA gel did not reduce crack occurrence.
The Structure of the First Coordination Shell in Liquid Water

X-ray absorption spectroscopy and x-ray Raman scattering were used to probe the molecular arrangement in the first coordination shell of liquid water. The local structure is characterized by comparison with bulk and surface of ordinary hexagonal ice Ih and with calculated spectra. Most molecules in liquid water are in two hydrogen–bonded configurations with one strong donor and one strong acceptor hydrogen bond in contrast to the four hydrogen–bonded tetrahedral structure in ice. Upon heating from 25°C to 90°C, 5 to 10% of the molecules change from tetrahedral environments to two hydrogen–bonded configurations. Our findings are consistent with neutron and x-ray diffraction data, and combining the results sets a strong limit for possible local structure distributions in liquid water. Serious discrepancies with structures based on current molecular dynamics simulations are observed.
An Active Galactic Nucleus Sample with High X-Ray-to-Optical Flux Ratio from RASS. II. Optical Emission Line Properties of Seyfert 1-Type Active Galactic Nuclei

This work studies the optical emission line properties of a sample of 155 low-redshift bright X-ray-selected ROSAT Seyfert 1-type active galactic nuclei for which adequate signal-to-noise ratio spectroscopic observations are available. We measured emission-line properties by performing multicomponent fits to the emission-line profiles, covering the effect of blended iron emission. We also obtained continuum parameters, including 250 eV X-ray luminosities derived from the ROSAT database. In addition, the measured properties are gathered for a correlation analysis, which confirms the well-known relations between the strengths of Fe II, [O III] emission and the X-ray slope. We also detect striking correlations between Hβ redshift (or blueshift) and flux ratios of Fe II to Hβ broad component and [O III] to Hβ narrow component. These trends are most likely driven by the Eddington ratio.