Miracle-dz/UniFAR-FTUs huggingface dataset:
Replicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti

Many bacterial species, such as the alphaproteobacterium Sinorhizobium meliloti, are characterized by open pangenomes and contain multipartite genomes consisting of a chromosome and other large-sized replicons, such as chromids, megaplasmids, and plasmids. The evolutionary forces in both functional and structural aspects that shape the pangenome of species with multipartite genomes are still poorly understood. Therefore, we sequenced the genomes of 10 new S. meliloti strains, analyzed with four publicly available additional genomic sequences. Results indicated that the three main replicons present in these strains (a chromosome, a chromid, and a megaplasmid) partly show replicon-specific behaviors related to strain differentiation. In particular, the pSymB chromid was shown to be a hot spot for positively selected genes, and, unexpectedly, genes resident in the pSymB chromid were also found to be more widespread in distant taxa than those located in the other replicons. Moreover, through the exploitation of a DNA proximity network, a series of conserved “DNA backbones” were found to shape the evolution of the genome structure, with the rest of the genome experiencing rearrangements. The presented data allow depicting a scenario where the pSymB chromid has a distinctive role in intraspecies differentiation and in evolution through positive selection, whereas the pSymA megaplasmid mostly contributes to structural fluidity and to the emergence of new functions, indicating a specific evolutionary role for each replicon in the pangenome evolution.
The Reinforcement Learning Competitions

This article reports on the reinforcement learning competitions, which have been held annually since 2006. In these events, researchers from around the world developed reinforcement learning agents to compete in domains of various complexity and difficulty. We focus on the 2008 competition, which employed fundamentally redesigned evaluation frameworks that aimed systematically to encourage the submission of robust learning methods. We describe the unique challenges of empirical evaluation in reinforcement learning and briefly review the history of the previous competitions and the evaluation frameworks they employed. We describe the novel frameworks developed for the 2008 competition as well as the software infrastructure on which they rely. Furthermore, we describe the six competition domains, present selected competition results, and discuss the implications of these results. Finally, we summarize the 2009 competition, which used the same evaluation framework but different events, and outline ideas for the future of the competition.
ARTDroid: A Virtual-Method Hooking Framework on Android ART Runtime

Various static and dynamic analysis techniques are developed to detect and analyze Android malware. Some advanced Android malware can use Java reflection and JNI mechanisms to conceal their malicious behaviors for static analysis. Furthermore, for dynamic analysis, emulator detection and integrity selfchecking are used by Android malware to bypass all recent Android sandboxes. In this paper, we propose ARTDroid, a framework for hooking virtual-methods calls supporting the latest Android runtime (ART). A virtualmethod is called by the ART runtime using a dispatch table (vtable). ARTDroid can tamper the vtable without any modifications to both Android framework and app’s code. The ARTDroid hooking framework can be used to build an efficient sandbox on real devices and monitor sensitive methods called in both Java reflection and JNI ways.
On the Issue of Causality in the Economic Model of Crime and Law Enforcement: Some Theoretical Considerations and Experimental Evidence

The identification of the true causal relationship underlying an apparent empirical association between specific variables of interest is a central issue of concern in all statistical analyses, but especially in social science research where the opportunity to conduct controlled experiments is not available as a rule. In econometric investigations of the incidence of criminal activities the problem concerns, in part, the identification of "supply-of-offenses" and "demand-forenforcement or protection" functions from scatters of observations concerning crime rates and deterrence variables. While an increase in severity and certainty of punishment is expected to cause a reduction in offenses, an autonomous rise in the risk of victimization is expected to increase public and private enforcement and protection activities, and thus the magnitude of deterrence variables, and generally lower the prospects of illegitimate payoffs. '
Effects of imposed resistance on tidal volume with 5 neonatal nasal continuous positive airway pressure systems.

BACKGROUND Neonates with respiratory distress syndrome are often treated with nasal continuous positive airway pressure (CPAP). Nasal CPAP methods include electronic feedback control, underwater seal, flow opposition, and flow opposition with fluidic flow reversal on expiration. Few studies have compared those modes, and the results have been contradictory. METHODS We compared the effect of resistive load on simulated tidal volume (V(T)) with 5 neonatal nasal CPAP systems: Fisher and Paykel nasal CPAP tubing with Maquet Servo-i ventilator in NIV CPAP mode; Cardinal Health AirLife nasal CPAP system; Fisher and Paykel nasal CPAP tubing with water-seal pressure generator; AirLife infant nasal CPAP generator kit; and Hamilton Medical Arabella fluidic nasal CPAP generator. The lung simulator settings were: compliance 0.5 mL/cm H2O, resistance 125 H2O/L/s, sinusoidal patient-effort range 6.5-26 cm H2O, rise 25%, hold 0%, release 25%, respiratory rate 65 breaths/min. We compared the mean values from 10 breaths. RESULTS The mean inspiratory pressure drop and V(T) difference (compared to the simulator alone, unloaded) increased with V(T), respectively, from 0.32 cm H2O to 1.73 cm H2O, and from -0.04 mL to -0.40 mL. Flow opposition had the smallest pressure drop (from 0.10 cm H2O to 0.64 cm H2O, P < .001). At V(T) of < or = 6 mL, the bubble nasal CPAP's pressure drop was largest (P < .001), whereas at V(T) of > or = 9 mL the electronic nasal CPAP's pressure drop was largest (P < .001). All systems except the ventilator did not have an average end-expiratory pressure of the targeted 5 cm H2O. CONCLUSIONS The differences in these nasal CPAP systems correlate with the differences in unassisted V(T) due to loading effects. The ventilator imposed the least load, and the AirLife nasal CPAP system imposed the most.
NYPD Battles Crime: Innovative Strategies in Policing

In the last five years, New York City has experienced the nation's most dramatic reduction in crime. While the New York Police Department is receiving extensive publicity and praise as the key agent for the sharp decline, many experts downplay the NYPD's role, arguing instead that prevailing social, economic, and demographic conditions are the primary reasons for the unprecedented drop in crime rates. This timely book informs the debate by detailing how innovative strategies adopted in 1994 by then-police commissioner William Bratton had the immediate and sustained effect of lowering incidents of crime in every city precinct. Eli B. Silverman begins his study with a historical review of the evolution of police reform movements in New York City, showing that the achievements and failures of earlier external and internal initiatives formed the foundation for today's re-engineered NYPD. Drawing on privileged access to police documents and meetings, he then examines how the dynamic interaction of specific strategic, organizational, and managerial changes redefined the approach to policing, transforming the department from a reactive to a proactive force. In particular, Silverman focuses on Compstat, a sophisticated computer program that compiles crime statistics, as the crucial mechanism for linking the development of new policies with effective tactics to control crime. The up-to-date and accurate information provided by Compstat drives twice-weekly crime strategy meetings that ensure essential planning, coordination, evaluation, and accountability. NYPD Battles Crime is a fascinating story of organizational change, innovation, and continuity.
How Social Are Task Representations?

The classical Simon effect shows that actions are carried out faster if they spatially correspond to the stimulus signaling them. Recent studies revealed that this is the case even when the two actions are carried out by different people; this finding has been taken to imply that task representations are socially shared. In work described here, we found that the “interactive” Simon effect occurs only if actor and coactor are involved in a positive relationship (induced by a friendly-acting, cooperative confederate), but not if they are involved in a negative relationship (induced by an intimidating, competitive confederate). This result suggests that agents can represent self-generated and other-generated actions separately, but tend to relate or integrate these representations if the personal relationship between self and other has a positive valence.
Distinct epithelial gene expression phenotypes in childhood respiratory allergy

Epithelial cell contribution to the natural history of childhood allergic respiratory disease remains poorly understood. Our aims were to identify epithelial pathways that are dysregulated in different phenotypes of respiratory allergy. We established gene expression signatures of nasal brushings from children with dust mite-allergic rhinitis, associated or not associated with controlled or uncontrolled asthma. Supervised learning and unsupervised clustering were used to predict the different subgroups of patients and define altered signalling pathways. These profiles were compared with those of primary cultures of human nasal epithelial cells stimulated with either interleukin (IL)-4, IL-13, interferon (IFN)-&agr;, IFN-&bgr; or IFN-&ggr;, or during in vitro differentiation. A supervised method discriminated children with allergic rhinitis from healthy controls (prediction accuracy 91%), based on 61 transcripts, including 21 T-helper cell (Th) type 2-responsive genes. This method was then applied to predict children with controlled or uncontrolled asthma (prediction accuracy 75%), based on 41 transcripts: nine of them, which were down-regulated in uncontrolled asthma, are directly linked to IFN. This group also included GSDML, which is genetically associated with asthma. Our data revealed a Th2-driven epithelial phenotype common to all children with dust mite allergic rhinitis. It highlights the influence of epithelially expressed molecules on the control of asthma, in association with atopy and impaired viral response.
ASSESSMENT OF ACADEMIC SKIUS OF LEARNING DISABLED STUDENTS WITH CLASSROOM MICROCOMPUTERS

Computer assisted tests have been recommended a. , a method to make individualized learning systems more manageable, accurate, and efficient. However, until recently the use of computer-assisted testing has been restricted to settings where sophisticated computing technology and assistance were available. Recent advances in computer technology have made computer-assisted testing possible on microcomputers within typical classroom settings. In the present uwestigation ,a criterion -referenced capitalization test was administered to learning disabled elementary school students in microcomputer and paper-and-pencil versions. Results indicated that similar instru ctional interventions were generated by both versions of the test, but effiCiency and student attitudes favored the computerized test. In addition, students completed the computerized version of the test much quicker than the conventional version, and answers were automatically scored by the computer, subsequently reducing test-scoring time and eliminating the possibility of hand-scoring errors. It was concluded that microcomputer-assisted testing. utilizing a tailored testing or adaptive testing model, holds considerable promise in the as. "'iessment of educational s ki.1Is and the design of instructional programs.
Randomized Phase II Study of Docetaxel plus Personalized Peptide Vaccination versus Docetaxel plus Placebo for Patients with Previously Treated Advanced Wild Type EGFR Non-Small-Cell Lung Cancer

Objectives. To evaluate the efficacy and safety of personalized peptide vaccination (PPV) combined with chemotherapy for patients with previously treated advanced non-small-cell lung cancer (NSCLC). Patients and Methods. Previously treated PS0-1 patients with IIIB/IV EGFR (epidermal growth factor receptor) wild genotype NSCLC were randomly assigned to docetaxel (60 mg/m2 on Day 1) plus PPV based on preexisting host immunity or docetaxel plus placebo. Docetaxel administration was repeated every 3 weeks until disease progression. Personalized peptides or placebo was injected subcutaneously weekly in the first 8 weeks and biweekly in subsequent 16 weeks. The primary efficacy endpoint was progression-free survival (PFS). Results. PPV related toxicity was grade 2 or less skin reaction. The median PFS for placebo arm and PPV arm was 52 days and 59 days, respectively. There was no significant difference between two arms by log-rank test (p = 0.42). Interestingly, PFS and overall survival (OS) in humoral immunological responder were significantly longer than those in nonresponder. Conclusion. PPV did not improve the survival in combination with docetaxel for previously treated advanced NSCLC. However, PPV may be efficacious for the humoral immunological responders and a further clinical investigation is needed.
Preliminary morphological and anatomical study of orthosiphon stamineus

This study focuses on the characterization of morphological and anatomical traits of Orthosiphon stamineus which belongs to the Lamiaceae family. Orthosiphon stamineus, better known as “Misai Kucing” or “cats whiskers” by the locals, contained active phenolics compounds such as flavanoids. Despite its wide usage as a medicinal plant, information regarding Orthosiphon stamineus specific developmental stages is relatively scarce. Furthermore, to date, no anatomical data of this plant is available. Therefore, this study aims to systematically identify the developmental stages and its anatomy which may provide more insight to its medical application. The result showed some distinct morphological and anatomical characteristics. In the morphological study, it was observed that Orthosiphon stamineus is a herbal shrub with well-developed creeping rootstock. The leaves are simple, green, and arranged in opposite pairs. The stem is approximately 28 cm in height at the stage (12 days). The flowers have long wispy stamens shaped with pale purple color. In anatomical study, the cross sections of the stem for tow stage (32) and (62) days of this plant were examined. All the detailed systematic study of this plant has not worked earlier.
Requirements and Approaches for Modeling Individuals Within Organizational Simulations

The past decade has witnessed a growth of interest in modeling and simulation of individuals and organizations. From a research perspective, these simulations are important because they enable explorations of both individual and organizational decision-making mechanisms. From an applied perspective, these simulations aid organizational design, improve the realism and effectiveness of training and assessment systems, help in the assessment of enterprise workflow, and aid in behavior prediction. The human behavior modeling community has traditionally been divided into those addressing individual behavior models, and those addressing organizational and team models. And yet it is clear that these extremes do not reflect the complex reality of the mutually-constraining interactions between an individual and his/her organizational environment. In this chapter we argue that realistic models of organizations may require not only models of individual decision-makers, but also explicit models of a variety of individual differences influencing their decision-making and behavior, such as cognitive styles, personality traits, and affective states. Following a brief overview of relevant research in individual differences, and cognitive architectures, we outline the knowledge, representational, and inferencing requirements for two alternative approaches to modeling the individual within an organizational simulation: one focusing on cognitive architectures and the other centered on profile-based social network models. We illustrate each approach with concrete examples from existing prototypes, and discuss how these two approaches could be integrated within organizational simulations. We conclude with a discussion of some of the critical challenges in modeling individuals within organizational simulations.
Numb Protects Renal Proximal Tubular Cells from Puromycin Aminonucleoside-Induced Apoptosis through Inhibiting Notch Signaling Pathway

Numb was originally discovered as an intrinsic cell fate determinant in Drosophila by antagonizing Notch signaling. The present study is to characterize the role of Numb in oxidative stress-induced apoptosis of renal proximal tubular cells. Exposure of NRK52E cells to puromycin aminonucleoside (PA) resulted in caspase 3-dependent apoptosis. Numb expression was downregulated by PA in a time- and dose-dependent manner. Knocking down endogenous Numb by siRNA sensitized NRK52E cells to PA-induced apoptosis, whereas overexpressing Numb protected NRK52E cells from PA-induced apoptosis. Moreover, PA activated Notch signaling in a time- and dose-dependent manner as indicated by increased expression of the intracellular domain of Notch and Hes-1. Notch signaling inhibitor DAPT significantly attenuated Numb siRNA-augmented apoptosis. On the other hand, overexpression of intracellular domain of Notch1 could reverse the protective effect of Numb on PA-induced apoptosis. Taken together, our data demonstrated that, in renal proximal tubular cells, Numb functions as a protective molecule on PA-induced apoptosis through antagonizing Notch signaling activity.
Effects of Remifemin Treatment on Bone Integrity and Remodeling in Rats with Ovariectomy-Induced Osteoporosis

This study aims to evaluate the effects of Remifemin (isopropanolic extract of Cimicifuga Racemosa) on postmenopausal osteoporosis. 120 female Sprague-Dawley rats were randomly assigned to four groups: sham surgery with vehicle, ovariectomy with vehicle, ovariectomy with estradiol valerate, or ovariectomy with Remifemin. Daily oral administrations of the vehicle, estradiol valerate, or Remifemin began 2 weeks after surgery and lasted to 4, 8, or 12 weeks. Ten rats in each group were sacrificed at each timestep with assessment of bone mineral density, trabecular bone structure, and biomechanical parameters of the femur and lumbar vertebra. Bone turnover markers were evaluated 12 weeks after surgery. Both drugs prevented bone density loss in the distal end of the femur and preserved the trabecular bone structure in both the lumbar vertebra and distal end of the femur following ovariectomy. Both drugs protected bone stiffness at the tested regions and reduced bone reabsorption in ovariectomized rats. The preventive effects of Remifemin against bone-loss can rival those of estradiol valerate if treatment duration is adequately extended. In conclusion, Remifemin may demonstrate equivalent effects to estradiol valerate in terms of preventing postmenopausal osteoporosis.
Ambient Temperature and Stroke Occurrence: A Systematic Review and Meta-Analysis

Biologically plausible associations exist between climatic conditions and stroke risk, but study results are inconsistent. We aimed to summarize current evidence on ambient temperature and overall stroke occurrence, and by age, sex, and variation of temperature. We performed a systematic literature search across MEDLINE, Embase, PsycINFO, CINAHL, Web of Science, and GEOBASE, from inception to 16 October 2015 to identify all population-based observational studies. Where possible, data were pooled for meta-analysis with Odds ratios (OR) and corresponding 95% confidence intervals (CI) by means of the random effects meta-analysis. We included 21 studies with a total of 476,511 patients. The data were varied as indicated by significant heterogeneity across studies for both ischemic stroke (IS) and intracerebral hemorrhage (ICH). Pooled OR (95% CI) in every 1 degree Celsius increase in ambient temperature was significant for ICH 0.97 (0.94–1.00), but not for IS 1.00 (0.99–1.01) and subarachnoid hemorrhage (SAH) 1.00 (0.98–1.01). Meta-analysis was not possible for the pre-specified subgroup analyses by age, sex, and variation of temperature. Change in temperature over the previous 24 h appeared to be more important than absolute temperature in relation to the risk of stroke, especially in relation to the risk of ICH. Older age appeared to increase vulnerability to low temperature for both IS and ICH. To conclude, this review shows that lower mean ambient temperature is significantly associated with the risk of ICH, but not with IS and SAH. Larger temperature changes were associated with higher stroke rates in the elderly.
Correction of Sickle Cell Disease in Adult Mice by Interference with Fetal Hemoglobin Silencing

Manipulation of a transcriptional repressor promotes expression of protective fetal globin genes. Persistence of human fetal hemoglobin (HbF, α2γ2) in adults lessens the severity of sickle cell disease (SCD) and the β-thalassemias. Here, we show that the repressor BCL11A is required in vivo for silencing of γ-globin expression in adult animals, yet dispensable for red cell production. BCL11A serves as a barrier to HbF reactivation by known HbF inducing agents. In a proof-of-principle test of BCL11A as a potential therapeutic target, we demonstrate that inactivation of BCL11A in SCD transgenic mice corrects the hematologic and pathologic defects associated with SCD through high-level pancellular HbF induction. Thus, interference with HbF silencing by manipulation of a single target protein is sufficient to reverse SCD.
How America Graduated from High School: 1910 to 1960

Human capital accumulation and technological change were to the twentieth century what physical capital accumulation was to the nineteenth century -- the engine of growth. The accumulation of human capital accounts for almost 60% of all capital formation and 28% of the per capita growth residual from 1929 to 1982. Advances in secondary schooling account for about 70% of the increase in total educational attainment from 1930 to 1970 for men 40 to 44 years old. High school, not college, was responsible for the enormous increase in the human capital stock during much of this century. In this paper I answer when and where high schools advanced in the 1910 to 1960 period. The most rapid expansion in the non-South regions occurred in the brief period from 1920 to 1935. The 1920s provided the initial burst in high school attendance, but the Great Depression added significantly to high school enrollment and graduation rates. Attendance rates were highest in states, regions, and cities with the least reliance on manufacturing and in areas where agricultural income per worker was high. Schooling was particularly low where certain industries that hired youths were dominant and where the foreign born had entered in large numbers before the immigration restriction of the 1920s. More education enabled states to converge to a higher level of per capita income between 1929 and 1947, and states rich in agricultural resources, yet poor in manufacturing, exported educated workers in later decades.