Miracle-dz/UniFAR-FTUs huggingface dataset:
AdpA, key regulator for morphological differentiation regulates bacterial chromosome replication

AdpA, one of the most pleiotropic transcription regulators in bacteria, controls expression of several dozen genes during Streptomyces differentiation. Here, we report a novel function for the AdpA protein: inhibitor of chromosome replication at the initiation stage. AdpA specifically recognizes the 5′ region of the Streptomyces coelicolor replication origin (oriC). Our in vitro results show that binding of AdpA protein decreased access of initiator protein (DnaA) to the oriC region. We also found that mutation of AdpA-binding sequences increased the accessibility of oriC to DnaA, which led to more frequent replication and acceleration of Streptomyces differentiation (at the stage of aerial hyphae formation). Moreover, we also provide evidence that AdpA and DnaA proteins compete for oriC binding in an ATP-dependent manner, with low ATP levels causing preferential binding of AdpA, and high ATP levels causing dissociation of AdpA and association of DnaA. This would be consistent with a role for ATP levels in determining when aerial hyphae emerge.
Name Nationality Classification with Recurrent Neural Networks

Personal names tend to have many variations differing from country to country. Though there exists a large amount of personal names on the Web, nationality prediction solely based on names has not been fully studied due to its difficulties in extracting subtle character level features. We propose a recurrent neural network based model which predicts nationalities of each name using automatic feature extraction. Evaluation of Olympic record data shows that our model achieves greater accuracy than previous feature based approaches in nationality prediction tasks. We also evaluate our proposed model and baseline models on name ethnicity classification task, again achieving better or comparable performances. We further investigate the effectiveness of character embeddings used in our proposed model.
Self-organized trail systems in groups of humans

We have developed an experimental platform for studying the trail systems that spontaneously emerge when people are motivated to take advantage of the trails left by others. In this virtual environment, the participants' task is to reach randomly selected destinations while minimizing travel costs. The travel cost of every patch in the environment is inversely related to the number of times the patch was visited by others. The resulting trail systems are a compromise between people going to their destinations and going where many people have previously traveled. We compare the results from our group experiments to the Active Walker model of pedestrian motion from biophysics. The Active Walker model accounted for deviations of trails from the beeline paths, the gradual merging of trails over time, and the influences of scale and configuration of destinations on trail systems, as well as correctly predicting the approximate spatial distribution of people's steps. Two deviations of the model from empirically obtained results were corrected by (1) incorporating a distance metric sensitive to canonical horizontal and vertical axes, and (2) increasing the influence of a trail's travel cost on an agent's route as the agent approaches its destination. © 2006 Wiley Periodicals, Inc. Complexity 11: 43–50, 2006
Measuring the Relationship between Attributions for "The Gap" and Educational Policy Attitudes: Introducing the Attributions for Scholastic Outcomes Scale-Black

Abstract:This study provides empirical support for the Attributions for Scholastic Outcomes Scale—Black (ASO-B) as an instrument for measuring two latent traits that influence causal reasoning about the Black-White achievement gap: culture-blaming and structure-blaming. Within this conceptual framework, culture-blaming refers to the belief that Black parents cultivate an anti-academic mindset in their children and structure-blaming refers to the belief that racially biased opportunity and reward structures within the U.S. schooling system create racial differences in achievement. Results indicate that culture-blaming and structure-blaming are distinct perspectives that are statistically related to attitudes toward parent education, teaching and enforcing "proper" English, standardized testing, and resource redistribution as methods of closing the gap.
The Relationship Between Alienation and Other Demographic Variables Among High School Students.

problem of growing concern to educators is the increasing proportion of youth who have lost faith in their society and are becoming alienated from it. "While often thought of as a problem that occurs only in minority groups, feelings of alienation are present in suburbia as well as the inner city; in affuence as well as poverty; in majority groups as well as minority groups; in the conformist as well as the hippie. "1 Writers such as Friedenberg,2 Jackson,3 Keniston,4 and Goodman5 believe the major cause of this growing problem is the increasing tendency of our society to treat individuals as commodities or pawns to be dealt with as the society sees fit.
A Two-by-Two Factorial Trial Comparing Oral with Transdermal Estrogen Therapy and Fenretinide with Placebo on Breast Cancer Biomarkers

Purpose: Oral conjugated equine estrogen (CEE) and medroxyprogesterone acetate (MPA) increase breast cancer risk, whereas the effect of transdermal estradiol (E2) and MPA is less known. Fenretinide may decrease second breast malignancies in premenopausal women but not in postmenopausal women, suggesting a hormone-sensitizing effect. We compared the 6 and 12-month changes in insulin-like growth factor-I (IGF-I), IGF-binding protein-3 (IGFBP-3), IGF-I:IGFBP-3 ratio, sex-hormone binding-globulin, and computerized mammographic percent density during oral CEE or transdermal E2 with sequential MPA and fenretinide or placebo. Experimental Design: A total of 226 recent postmenopausal healthy women were randomly assigned in a two-by-two factorial design to either oral CEE 0.625 mg/day (n = 111) or transdermal E2, 50 μg/day (n = 115) and to fenretinide 100 mg/twice a day (n = 112) or placebo (n = 114) for 12 months. Treatment effects were investigated by the Kruskall-Wallis test and analysis of covariance. P values were two-sided. Results: After 12 months, oral CEE decreased IGF-I by 26% [95% confidence interval (CI), 22–30%] and increased sex-hormone binding-globulin by 96% (95% CI, 79–112%) relative to baseline, whereas no change occurred with transdermal E2 (P < 0.001 between groups). Fenretinide decreased IGFBP-3 relative to placebo (P = 0.04). Percentage of breast density showed an absolute increase of 3.5% (95% CI, 2.5–4.6%) during hormone therapy without differences between groups (P = 0.39). Conclusions: Oral CEE has more favorable changes than transdermal E2 on circulating breast cancer risk biomarkers but gives similar effects on mammographic density. Fenretinide exerted little modulation on most biomarkers. The clinical implications of these findings require additional studies.
Conflict in Families and Nursing Home Placement: A Phenomenological Study

p. vii Chapter 1– Introduction p. 1 Chapter 2 – Literature Review p. 20 Chapter 3– Methodology p. 56 Chapter 4–Data Analysis and Findings, Part I Family History p. 82 Chapter 5 – Data Analysis and Findings, Part II Siblings and Gendered Caregiving.p. 90 Chapter 6 – Data Analysis and Findings, Part III – Communication p. 107 Chapter 7 – Data Analysis and Findings, Part IV – Reflections p. 114 Chapter 8 – Discussion p. 118 References p. 132 Appendix A – Recruitment Poster p. 182 Appendix B – Interview Guide p. 183 Appendix C – STU Third Age Center Electronic Advertising p. 184 Appendix D – First Cycle Codes p. 185 Appendix E – Province of New/Nouveau Brunswick, Canada p. 186
Journal of Insect Science: Vol. 2006 | Article 25

The roles of consumers (top-down forces) versus resources (bottom-up forces) as determinants of alpha diversity in a community are not well studied. Numerous community ecology models and empirical studies have provided a framework for understanding how density at various trophic levels responds to variation in the relative strength of top-down and bottom-up forces. The resulting trophic theory can be applied to understanding variation in insect diversity at different trophic levels. The objective of this research was to elucidate the strengths of direct and indirect interactions between plants and entire arthropod communities to determine the effects of trophic interactions on arthropod diversity. Grassland plant and insect diversity was measured in July 2001 to document patterns of diversity at multiple trophic levels. The study site includes riparian grasslands in North-Central Colorado on the Carpenter Ranch, owned and managed by The Nature Conservancy. This pastureland consists of sites with different management regimes: unmanaged pasture intermixed along riparian forest, and cattle grazed pasture with flood irrigation. Plant abundance and richness were higher on the grazed-irrigated pasture versus the unmanaged field. Path analysis revealed strong effects of herbivore diversity on diversity of other trophic levels. For the managed fields, top-down forces were important, with increases in enemy diversity depressing herbivore diversity, which in turn depressed plant abundance. For the unmanaged fields, bottom-up forces dominated, with increases in plant diversity causing increased herbivore diversity, which in turn increased enemy diversity. These results support hypotheses from other empirical studies, demonstrating that changes in diversity of a single trophic level can cascade to effect diversity at other, nonadjacent trophic levels.
Psychological assessment of candidates for bariatric surgery

Abstract Objectives: National Institute of Clinical Excellence guidelines indicate that pre-surgical assessment of patients wishing to undergo bariatric surgery should include consideration of psychological factors. This paper describes the psychological characteristics of a cohort of 59 patients. Method: Patients were interviewed and completed the following psychometric assessments: the Hospital Anxiety and Depression Scale, the Dieting Belief Scale, the Binge Eating Scale, the Emotional Eating Scale, the Generalised Self Efficacy Scale, and the Social Support Questionnaire. Results: High levels of psychological distress and binge eating were reported. Men more commonly reported a history of alcohol misuse. There was evidence to suggest that psychological distress predated obesity in the majority of cases. Conclusion: Compulsive eating leading to obesity appears to be both a consequence and a cause of psychological distress. Replacing compulsive eating represents a major post-surgical challenge in the majority of cases. Psychological assessment and follow-up should be offered to each patient.
Stability over Time and the Role of Attachment in Emerging Personality Disorder in Adolescence: A Two Year Longitudinal Study

The overall focus of the thesis is on Personality Disorders (PD) and the factors that influence the development and maintenance of these. This thesis consists of three parts. Part one presents a systematic literature review on the relationship between childhood emotional abuse and emotional neglect and Borderline Personality Disorder (BPD). Although existing research evidences the link between childhood trauma and BPD, no systematic review has considered the specific impact of emotional abuse and emotional neglect as opposed to sexual or physical abuse. Evidence of variables that may account for or contribute to the relationship is considered. Part two is an empirical paper on the stability of PDs in adolescence over a two year period and the role that attachment plays in the maintenance of PD traits during this time. The results showed that PD traits in adolescence decline over time to an extent. Higher levels of overall quality of attachment and lower levels of alienation from peers, as measured at baseline, were predictive of improvement in the number of PD traits over time. The validity of the results is discussed in relation to problems of sample size and statistical power. The data collection for this study was conducted jointly with another trainee and in conjunction with a trial into Mentalization-Based Therapy (MBT) for adolescents with emerging PD. Part three is a critical appraisal discussing reflections on issues that arose during the process of the research and commenting more generally on current debates within the field of PD research.
MAPK7 Regulates EMT Features and Modulates the Generation of CTCs

Epithelial-to-mesenchymal transition (EMT) has been implicated in models of tumor cell migration, invasion, and metastasis. In a search for candidate therapeutic targets to reverse this process, nontumorigenic MCF10A breast epithelial cells were infected with an arrayed lentiviral kinome shRNA library and screened for either suppression or enhancement of a 26-gene EMT RNA signature. No individual kinase gene knockdown was sufficient to induce EMT. In contrast, grouped epithelial markers were induced by knockdown of multiple kinases, including mitogen activated protein kinase 7 (MAPK7). In breast cancer cells, suppression of MAPK7 increased E-cadherin (CDH1) expression and inhibited cell migration. In an orthotopic mouse model, MAPK7 suppression reduced the generation of circulating tumor cells and the appearance of lung metastases. Together, these observations raise the possibility that targeting kinases that maintain mesenchymal cell properties in cancer cells, such as MAPK7, may lessen tumor invasiveness. Implications: Suppression of MAPK7 induces epithelial markers, reduces generation of circulating tumor cells and appearance of lung metastases. Mol Cancer Res; 13(5); 934–43. ©2015 AACR.
Within and Across Class Envy: Anti-Social Behaviour in Hierarchical Groups

Models of social preferences (i.e. inequality aversion), assuming society is defined by a hierarchy based on income or wealth, predict that the poor envy the rich. Reference Group Theory predicts that the poor (rich) envy others from the same social group or class. We report results from a game designed to stimulate feelings of envy. Players are defined both by their place within an overarching hierarchy as well as by their place within the hierarchy of their specific class (i.e. their reference groups). We find that, while across class envy is common; within class envy motivates the most anti-social behaviour.
Temporal Coherency based Criteria for Predicting Video Frames using Deep Multi-stage Generative Adversarial Networks

Predicting the future from a sequence of video frames has been recently a sought after yet challenging task in the field of computer vision and machine learning. Although there have been efforts for tracking using motion trajectories and flow features, the complex problem of generating unseen frames has not been studied extensively. In this paper, we deal with this problem using convolutional models within a multi-stage Generative Adversarial Networks (GAN) framework. The proposed method uses two stages of GANs to generate a crisp and clear set of future frames. Although GANs have been used in the past for predicting the future, none of the works consider the relation between subsequent frames in the temporal dimension. Our main contribution lies in formulating two objective functions based on the Normalized Cross Correlation (NCC) and the Pairwise Contrastive Divergence (PCD) for solving this problem. This method, coupled with the traditional L1 loss, has been experimented with three real-world video datasets, viz. Sports-1M, UCF-101 and the KITTI. Performance analysis reveals superior results over the recent state-of-the-art methods.
Growth failure as a prognostic indicator of mortality in pediatric HIV infection.

OBJECTIVE To study the effect of perinatally acquired human immunodeficiency virus (HIV) on somatic growth and examine the relationship of nutritional status to mortality in HIV-infected infants. METHOD Pregnant women attending the antenatal clinic at Mulago hospital in Kampala, Uganda, were enrolled. All live-born babies born to HIV-1 seropositive (HIV+) women, and to every fourth age-matched HIV-1 seronegative (HIV-) woman, were followed for 25 months. RESULTS The mean weight-for-age and length-for-age curves of HIV+ children were significantly lower than those of HIV- controls and seroeverters. Forty-five (54%) of the 84 HIV+ infants died before their second birthday, as compared with a 1.6% and 5.6% mortality in HIV- and seroeverters. HIV+ infants with an average weight-for-age Z-score below -1.5 in the first year of life have a nearly fivefold risk of dying before 25 months of age compared with noninfected controls. CONCLUSION Perinatally acquired HIV infection is associated with early and progressive growth failure. The severity of growth failure is associated with an increased risk of mortality. The effect of early, aggressive nutritional intervention in delaying HIV progression and mortality should be evaluated by controlled intervention studies.
Incomplete Parenthesis: an Overview 1 Introduction

What we find in each case is that more is understood than what is explicitly uttered: the elliptical parts of the expressions are ‘heard’ by themind, but not by the ear. Theamount of omittedmaterial can range fromasingle verb (as in (1a), known as Gapping) to missing NPs (1b) and VPs (1c), to an entire clause (as in Sluicing and fragment answers (1d,e)). Conditions on ellipsis in syntactic and discursive environments such as those in (1) have been studied extensively in the literature. The contributions to the present volume focus on instances of ellipsis in lesserstudied configurations. Natural languages provide various means of explicitly relating internally coherent expressions to one another, both grammatically (e.g., hypotaxis, coordination, etc.) and discursively (e.g., anaphoric pronouns, discourse topics, etc.). Another form of relating expressions is parenthesis, manifest in appositive NPs and relative clauses, comment clauses, interruptions, dislocated elements, etc.
Population‐based type‐specific prevalence of high‐risk human papillomavirus infection in middle‐aged Swedish Women

Human papillomavirus (HPV) DNA testing can be used to identify women at risk of the development of cervical cancer. The cost‐effectiveness of HPV screening is dependent on the type‐specific HPV prevalence in the general population. The present study describes the prevalence and spectrum of high‐risk HPV types found in a large real‐life population‐based HPV screening trial undertaken entirely within the cervical screening program offered to middle‐aged Swedish women. Cervical brush samples from 6,123 women aged 32–38 years were analyzed using a general HPV primer (GP5+/6+) polymerase chain reaction‐enzyme immunoassay (PCR‐EIA) combined with reverse dot‐blot hybridization for confirmation and HPV typing by a single assay. In this study, 6.8% (95% CI 6.2–7.5) (417/6,123) were confirmed as high‐risk HPV positive. Infections with 13 different high‐risk HPV types were detected, of which HPV 16 was the most prevalent type (2.1%; 128/6,123), followed by HPV 31 (1.1%; 67/6,123). Any one of the HPV types 18, 33, 35, 39, 45, 51, 52, 56, 58, 59, or 66 was detected in 3.6% (223/6,123) of the women. Infection with two, three, and five types simultaneously was identified in 32, 5, and 1 women, respectively. The combination of PCR‐EIA as a screening test and reverse dot‐blot hybridization as a confirmatory test, was found to be readily applicable to a real‐life population‐based cervical screening. The type‐specific HPV prevalence found support in previous modeling studies suggesting that HPV screening may be a favorable cervical screening strategy. J. Med. Virol. 66:535–541, 2002. © 2002 Wiley‐Liss, Inc.
The Manchester Acute Coronary Syndromes (MACS) decision rule for suspected cardiac chest pain: derivation and external validation

Objective We aimed to derive and validate a clinical decision rule (CDR) for suspected cardiac chest pain in the emergency department (ED). Incorporating information available at the time of first presentation, this CDR would effectively risk-stratify patients and immediately identify: (A) patients for whom hospitalisation may be safely avoided; and (B) high-risk patients, facilitating judicious use of resources. Methods In two sequential prospective observational cohort studies at heterogeneous centres, we included ED patients with suspected cardiac chest pain. We recorded clinical features and drew blood on arrival. The primary outcome was major adverse cardiac events (MACE) (death, prevalent or incident acute myocardial infarction, coronary revascularisation or new coronary stenosis >50%) within 30 days. The CDR was derived by logistic regression, considering reliable (κ>0.6) univariate predictors (p<0.05) for inclusion. Results In the derivation study (n=698) we derived a CDR including eight variables (high sensitivity troponin T; heart-type fatty acid binding protein; ECG ischaemia; diaphoresis observed; vomiting; pain radiation to right arm/shoulder; worsening angina; hypotension), which had a C-statistic of 0.95 (95% CI 0.93 to 0.97) implying near perfect diagnostic performance. On external validation (n=463) the CDR identified 27.0% of patients as ‘very low risk’ and potentially suitable for discharge from the ED. 0.0% of these patients had prevalent acute myocardial infarction and 1.6% developed MACE (n=2; both coronary stenoses without revascularisation). 9.9% of patients were classified as ‘high-risk’, 95.7% of whom developed MACE. Conclusions The Manchester Acute Coronary Syndromes (MACS) rule has the potential to safely reduce unnecessary hospital admissions and facilitate judicious use of high dependency resources.
Identification of a Candidate Regulatory Element within the 5′ Flanking Region of the Mouse Igh Locus Defined by Pro-B Cell-Specific Hypersensitivity Associated with Binding of PU.1, Pax5, and E2A1

The Igh locus is controlled by cis-acting elements, including Eμ and the 3′ IgH regulatory region which flank the C region genes within the well-studied 3′ part of the locus. Although the presence of additional control elements has been postulated to regulate rearrangements of the VH gene array that extends to the 5′ end of the locus, the 5′ border of Igh and its flanking region have not been characterized. To facilitate the analysis of this unexplored region and to identify potential novel control elements, we physically mapped the most D-distal VH segments and scanned 46 kb of the immediate 5′ flanking region for DNase I hypersensitive sites. Our studies revealed a cluster of hypersensitive sites 30 kb upstream of the most 5′ VH gene. Detection of one site, HS1, is restricted to pro-B cell lines and HS1 is accessible to restriction enzyme digestion exclusively in normal pro-B cells, the stage defined by actively rearranging Igh-V loci. Sequence motifs within HS1 for PU.1, Pax5, and E2A bind these proteins in vitro and these factors are recruited to HS1 sequence only in pro-B cells. Transient transfection assays indicate that the Pax5 binding site is required for the repression of transcriptional activity of HS1-containing constructs. Thus, our characterization of the region 5′ of the VH gene cluster demonstrated the presence of a single cluster of DNase I hypersensitive sites within the 5′ flanking region, and identified a candidate Igh regulatory region defined by pro-B cell-specific hypersensitivity and interaction with factors implicated in regulating V(D)J recombination.