Miracle-dz/UniFAR-FTUs huggingface dataset:
UV- and MMS-induced mutagenesis of lambdaO(am)8 phage under nonpermissive conditions for phage DNA replication.

Mutagenesis in Escherichia coli, a subject of many years of study is considered to be related to DNA replication. DNA lesions nonrepaired by the error-free nucleotide excision repair (NER), base excision repair (BER) and recombination repair (RR), stop replication at the fork. Reinitiation needs translesion synthesis (TLS) by DNA polymerase V (UmuC), which in the presence of accessory proteins, UmuD', RecA and ssDNA-binding protein (SSB), has an ability to bypass the lesion with high mutagenicity. This enables reinitiation and extension of DNA replication by DNA polymerase III (Pol III). We studied UV- and MMS-induced mutagenesis of lambdaO(am)8 phage in E. coli 594 sup+ host, unable to replicate the phage DNA, as a possible model for mutagenesis induced in nondividing cells (e.g. somatic cells). We show that in E. coli 594 sup+ cells UV- and MMS-induced mutagenesis of lambdaO(am)8 phage may occur. This mutagenic process requires both the UmuD' and C proteins, albeit a high level of UmuD' and low level of UmuC seem to be necessary and sufficient. We compared UV-induced mutagenesis of lambdaO(am)8 in nonpermissive (594 sup+) and permissive (C600 supE) conditions for phage DNA replication. It appeared that while the mutagenesis of lambdaO(am)8 in 594 sup+ requires the UmuD' and C proteins, which can not be replaced by other SOS-inducible protein(s), in C600 supE their functions may be replaced by other inducible protein(s), possibly DNA polymerase IV (DinB). Mutations induced under nonpermissive conditions for phage DNA replication are resistant to mismatch repair (MMR), while among those induced under permissive conditions, only about 40% are resistant.
Comorbidity and health-related quality of life in Somali women living in Sweden

Abstract Objective: To explore the relationship between low serum vitamin D levels and comorbidity in Somali women, immigrants to Sweden. Design and setting: Cohort study in a Primary Health Care Center and a University Hospital. Subjects: Somali women skin type V, n = 114, aged 18–56 years, from latitude 0–10○ N, living in Sweden, latitude 57○ N > 2 years were compared with women from a population sample, skin type II-III, n = 69, aged 38–56 years, the WHO MONICA study, Gothenburg, Sweden. Main outcome measures: Serum (S)-25(OH)D, S-parathyroid hormone (PTH), comorbidity and Health-Related Quality of Life (HRQoL) using the Short Form-36 (SF-36) and part of the EQ-5D questionnaires. All calculations were corrected for age. Results: Vitamin D deficiency (S-25(OH)D < 25 nmol/l) was found in 73% of the Somali women and in 1% of the controls (p < .0001). S-PTH was elevated (>6.9 pmol/l) in 26% and 9%, respectively (p < .004). Somali women used less medication, 16% vs. 55%, p < . 0001) but more allergy medication, 11% vs. 7% (p = .006), had fewer fractures, 2% vs. 28% (p < .0001) and lower HRQoL in 7 out of 9 scales (p < .05–.001), than native controls. There were no differences in the prevalence of diabetes mellitus, hypothyroidism, positive thyroid peroxidase antibodies, vitamin B12 deficiency, celiac disease or hypertension. Conclusions: Vitamin D deficiency was common in Somali women living in Sweden, 73%, but comorbidity was low. Both mental, and especially physical HRQoL scores were lower in the Somali women. The effects of long-lasting deficiency are unknown. Key points The aim was to explore the relationship between vitamin D deficiency (S-25(OH)D < 25 nmol/l) and comorbidity in immigrants. Vitamin D deficiency was common in Somali women living in Sweden, 73%, but comorbidity of hypothyroidism, diabetes mellitus, hypertension, fractures and use of medications was low. Both mental, and especially physical, Health-Related Quality of Life were lower in the Somali women than in native Swedish women. The effects of long-lasting deficiency are unknown.
Transcriptome analysis identifies metallothionein as biomarkers to predict recurrence in hepatocellular cacinoma

Liver cancer is the fifth most common cancer, and hepatocellular carcinoma (HCC) is the major liver tumor type seen in adults. HCC is usually caused by chronic liver disease such as hepatitis B virus or hepatitis C virus infection. One of the promising treatments for HCC is liver transplantation, in which a diseased liver is replaced with a healthy liver from another person. However, recurrence of HCC after surgery is a significant problem. Therefore, it is important to discover reliable cellular biomarkers that can predict recurrence in HCC.
Assessing reading performance in the periphery with a Bayesian adaptive approach: The qReading method

Reading is a crucial visual activity and a fundamental skill in daily life. Rapid Serial Visual Presentation (RSVP) is a text-presentation paradigm that has been extensively used in the laboratory to study basic characteristics of reading performance. However, measuring reading function (reading speed vs. print size) is time-consuming for RSVP reading using conventional testing procedures. In this study, we develop a novel method, qReading, utilizing the Bayesian adaptive testing framework to measure reading function in the periphery. We perform both a psychophysical experiment and computer simulations to validate the qReading method. In the experiment, words are presented using an RSVP paradigm at 10° in the lower visual field. The reading function obtained from the qReading method with 50 trials exhibits good agreement (i.e., high accuracy) with the reading function obtained from a conventional method (method of constant stimuli [MCS]) with 186 trials (mean root mean square error: 0.12 log10 units). Simulations further confirm that the qReading method provides an unbiased measure. The qReading procedure also demonstrates excellent precision (half width of 68.2% credible interval: 0.02 log10 units with 50 trials) compared to the MCS method (0.03 log10 units with 186 trials). This investigation establishes that the qReading method can adequately measure the reading function in the normal periphery with high accuracy, precision, and efficiency, and is a potentially valuable tool for both research and clinical assessments.
Maternal mortality and Millennium Development Goal 5.

INTRODUCTION The maternal mortality ratio (MMR) is a key indicator for measurement of progress against Millennium Development Goal 5 (MDG 5). For many countries, especially those with a presumed high number of maternal deaths, only estimates are available. SOURCES OF DATA Recent global estimates and the reasons for high maternal mortality are reviewed. AREAS OF AGREEMENT There is international consensus that efforts to reduce maternal mortality globally need to be intensified. AREAS OF CONTROVERSY Many countries lack accurate data on number of deaths in women of reproductive age and number of births. Therefore, statistical modelling has been used to calculate estimates, which generally have wide confidence intervals and may be disputed by individual countries. GROWING POINTS There is renewed focus on MMR as 2015 approaches. AREAS TIMELY FOR DEVELOPING RESEARCH There is a need to adapt and implement methods for measuring maternal mortality to generate more accurate estimates. More data on cause of death are needed.
Food Insecurity and Associated Factors Among University Students

Background: Food insecurity is a growing public health issue and a barrier to students achieving adequate nutrition. Data regarding food insecurity among university students in Nigeria are scarce. Objective: The study assessed the prevalence of food insecurity and associated factors among university students, southeast Nigeria. Methods: A cross-sectional survey of 398 randomly selected students recruited from 2 universities in southeast Nigeria was conducted. Food security status was assessed using the 10-item US Household Food Security Scale Module. Anthropometric measurements and sociodemographic data were collected. Multivariate logistic regression was used to identify factors associated with food insecurity. Results: A majority of the students were categorized as food insecure. Of this, about 35.7% and 45.0% were considered to have low and very low food insecurity, respectively. Food insecurity was significantly associated with monthly allowance, daily amount spent on food, and source of income. The odds of food insecurity was significantly higher for students whose fathers were farmers (4.6, 95% confidence interval [CI]: 1.453-14.737), but lower for those whose mothers were farmers (0.18, 95% CI: 0.059-0.564). Conclusion: The result provides an insight into the food security status of university students in Nigeria. The prevalence of food insecurity was high among the students. Therefore, further studies involving different urban and rural (and/or public and private) universities in Nigeria are suggested in order to have a deeper understanding of the magnitude and contributing factors among this population group.
CEP–CEPR1 signalling inhibits the sucrose-dependent enhancement of lateral root growth

Abstract Lateral root (LR) proliferation is a major determinant of soil nutrient uptake. How resource allocation controls the extent of LR growth remains unresolved. We used genetic, physiological, transcriptomic, and grafting approaches to define a role for C-TERMINALLY ENCODED PEPTIDE RECEPTOR 1 (CEPR1) in controlling sucrose-dependent LR growth. CEPR1 inhibited LR growth in response to applied sucrose, other metabolizable sugars, and elevated light intensity. Pathways through CEPR1 restricted LR growth by reducing LR meristem size and the length of mature LR cells. RNA-sequencing of wild-type (WT) and cepr1-1 roots with or without sucrose treatment revealed an intersection of CEP–CEPR1 signalling with the sucrose transcriptional response. Sucrose up-regulated several CEP genes, supporting a specific role for CEP–CEPR1 in the response to sucrose. Moreover, genes with basally perturbed expression in cepr1-1 overlap with WT sucrose-responsive genes significantly. We found that exogenous CEP inhibited LR growth via CEPR1 by reducing LR meristem size and mature cell length. This result is consistent with CEP–CEPR1 acting to curtail the extent of sucrose-dependent LR growth. Reciprocal grafting indicates that LR growth inhibition requires CEPR1 in both the roots and shoots. Our results reveal a new role for CEP–CEPR1 signalling in controlling LR growth in response to sucrose.
Improving the performance of arrival on time in stochastic shortest path problem

Facing various uncertainties in real world traffic, navigation services are typically formulated as a certain stochastic shortest path problem (SSPP). In the past several years, many stochastic objectives in SSPP has been proposed, among which maximizing the probability of arrival on time draws certain attentions from researchers as it takes, besides absolute travel time, an extra dimension of information (user-specified deadlines) into consideration. This paper extends a recently proposed data-driven approach for SSPP in the following two aspects: (1) when deadline is loose enough, the original method may return more than one paths since all of them meet deadline with 100% probability. We propose to return a unique path with the least number of intersections by reformulating the objective function. (2) we extend the arrive-on-time problem to the case of visiting several fixed locations, which is a common scenario in real world application. Experimental results show the accuracy and effectiveness of the improved data-driven method.
Feature analysis and extraction for audio automatic classification

Feature analysis and extraction are the foundation of audio automatic classification. This paper divides audio streams into five classes: silence, noise, pure speech, speech over background sound and music. We present our work on audio feature analysis and extraction on the frame level and clip level. Four new features are proposed, including silence ratio, pitch frequency standard deviation, harmonicity ratio and smooth pitch ratio. We have presented an SVM based approach to classification. The effectiveness of the features is evaluated in experiments. Experiment results show that the features we selected and proposed are rational and effective.
Mission-Level Path Planning for Rover Exploration

We present TEMPEST, an autonomous, energy-cognizant planner for long-range rover navigation. Its purpose is to plan sequences of actions that avoid large-scale obstacles, balance energy expenses against available resources, and satisfy operational constraints while attaining a distant goal. An algorithm called Incremental Search Engine (ISE) enables TEMPEST to search over high-dimensional spaces, and provides highly efficient re-planning in response to changes in state transition costs. Models of the world and rover adapt ISE to the rover navigation domain. We propose the concept of Mission-Level Path Planning, then describe how TEMPEST uses ISE to solve for mission-level plans in a spatial, temporal and energy space. A simple application problem aims to illustrate TEMPEST behavior under various time and rover locomotion power conditions.
Web page classification without the web page

Uniform resource locators (URLs), which mark the address of a resource on the World Wide Web, are often human-readable and can hint at the category of the resource. This paper explores the use of URLs for webpage categorization via a two-phase pipeline of word segmentation/expansion and classification. We quantify its performance against document-based methods, which require the retrieval of the source document.
II Spectrum Disorders Randomized , Controlled Trial of the LEAP Model of Early Intervention for Young Children With Autism

A clustered randomized design was used in which 28 inclusive preschool classrooms were randomly assigned to receive 2 years of training and coaching to fidelity in the LEAP (Learning Experiences and Alternative Program for Preschoolers and Their Parents) preschool model, and 28 inclusive classes were assigned to receive intervention manuals only. In total, 177 intervention classroom children and 117 comparison classroom children participated. Children were similar on all measures at start. After 2 years, experimental class children were found to have made significantly greater improvement than their comparison cohorts on measures of cognitive, language, social, and problem behavior, and autism symptoms. Behavior at entry did not predict outcome nor did family socioeconomic status. The fidelity with which teachers implemented LEAP strategies did predict outcomes. Finally, social validity measurement showed that procedures and outcomes were favorably viewed by intervention class teachers.
A tale of two tracts: history, current advances, and future directions of research on sexual differentiation of reproductive tracts†

Abstract Alfred Jost's work in the 1940s laid the foundation of the current paradigm of sexual differentiation of reproductive tracts, which contends that testicular hormones drive the male patterning of reproductive tract system whereas the female phenotype arises by default. Once established, the sex-specific reproductive tracts undergo morphogenesis, giving rise to anatomically and functionally distinct tubular organs along the rostral–caudal axis. Impairment of sexual differentiation of reproductive tracts by genetic alteration and environmental exposure are the main causes of disorders of sex development, and infertility at adulthood. This review covers past and present work on sexual differentiation and morphogenesis of reproductive tracts, associated human disorders, and emerging technologies that have made impacts or could radically expand our knowledge in this field. Summary Sentence This review covers past and present work on sexual differentiation and morphogenesis of reproductive tracts, associated human disorders, and emerging technologies that have made impacts or could radically expand our knowledge in this field.
The One-Hidden Layer Non-parametric Bayesian Kernel Machine

In this paper, we present a nonparametric Bayesian approach towards one-hidden-layer feed forward neural networks. Our approach is based on a random selection of the weights of the synapses between the input and the hidden layer neurons, and a Bayesian marginalization over the weights of the connections between the hidden layer neurons and the output neurons, giving rise to a kernel-based nonparametric Bayesian inference procedure for feed forward neural networks. Compared to existing approaches, our method presents a number of advantages, with the most significant being: (i) it offers a significant improvement in terms of the obtained generalization capabilities, (ii) being a nonparametric Bayesian learning approach, it entails inference instead of fitting to data, thus resolving the over fitting issues of non-Bayesian approaches, and (iii) it yields a full predictive posterior distribution, thus naturally providing a measure of uncertainty on the generated predictions (expressed by means of the variance of the predictive distribution), without the need of applying computationally intensive methods, e.g., bootstrap. We exhibit the merits of our approach by investigating its application to two difficult multimedia content classification applications: semantic characterization of audio scenes based on content, and yearly song classification, as well as a set of benchmark classification and regression tasks.
Development of Fatty Acid-Producing Corynebacterium glutamicum Strains

ABSTRACT To date, no information has been made available on the genetic traits that lead to increased carbon flow into the fatty acid biosynthetic pathway of Corynebacterium glutamicum. To develop basic technologies for engineering, we employed an approach that begins by isolating a fatty acid-secreting mutant without depending on mutagenic treatment. This was followed by genome analysis to characterize its genetic background. The selection of spontaneous mutants resistant to the palmitic acid ester surfactant Tween 40 resulted in the isolation of a desired mutant that produced oleic acid, suggesting that a single mutation would cause increased carbon flow down the pathway and subsequent excretion of the oversupplied fatty acid into the medium. Two additional rounds of selection of spontaneous cerulenin-resistant mutants led to increased production of the fatty acid in a stepwise manner. Whole-genome sequencing of the resulting best strain identified three specific mutations (fasR20, fasA63 up, and fasA2623). Allele-specific PCR analysis showed that the mutations arose in that order. Reconstitution experiments with these mutations revealed that only fasR20 gave rise to oleic acid production in the wild-type strain. The other two mutations contributed to an increase in oleic acid production. Deletion of fasR from the wild-type strain led to oleic acid production as well. Reverse transcription-quantitative PCR analysis revealed that the fasR20 mutation brought about upregulation of the fasA and fasB genes encoding fatty acid synthases IA and IB, respectively, by 1.31-fold ± 0.11-fold and 1.29-fold ± 0.12-fold, respectively, and of the accD1 gene encoding the β-subunit of acetyl-CoA carboxylase by 3.56-fold ± 0.97-fold. On the other hand, the fasA63 up mutation upregulated the fasA gene by 2.67-fold ± 0.16-fold. In flask cultivation with 1% glucose, the fasR20 fasA63 up fasA2623 triple mutant produced approximately 280 mg of fatty acids/liter, which consisted mainly of oleic acid (208 mg/liter) and palmitic acid (47 mg/liter).
Antioxidant and Antidiabetic Effect of Aqueous Fruit Extract of Passiflora ligularis Juss. on Streptozotocin Induced Diabetic Rats

Diabetes mellitus is the most common endocrine disorder that impairs glucose homeostasis resulting in severe diabetic complications including retinopathy, angiopathy, nephropathy, and neuropathy causing neurological disorders due to perturbation in utilization of glucose. Hypoglycemic activity was detected in aqueous extract of Passiflora ligularis, a traditionally used medicinal plant, using streptozotocin (STZ, 30 mg/kg body weight) induced diabetic rat model. Oral administration of aqueous extract of Passiflora ligularis to diabetic rats for 30 days resulted in a decrease in blood glucose. The diabetic rats had decreased levels of serum total protein, albumin, globulin, and albumin/globulin ratio as compared to control rats. In addition, the activities of hepatic and renal markers were significantly elevated in diabetic rats as compared to control rats. Treatment with aqueous fruit extract of P. ligularis and glibenclamide reversed these parameters to near normal. Extract at a dose of 400 mg/kg given orally for 30 days showed significant elevation in enzymatic (SOD, catalase, and Gpx) and nonenzymatic antioxidants (vitamin C, vitamin E, and reduced glutathione). Plant extract treated groups showed significant decrease in lipid peroxidation (LPO). Aqueous extract of Passiflora ligularis fruit can decrease the blood glucose and reduce the oxidative stress by removing free radicals in diabetes.
Resective-reconstructive treatment of abnormally invasive placenta: Inter Institutional Collaboration by telemedicine (eHealth)

Abstract Introduction: Resective-reconstructive treatment of an abnormally invasive placenta, also known as conservative surgical management, allows a comprehensive treatment of the pathology in only one surgery; however, this alternative is not generally included in international consensus, as it requires specific training. Here, we report our experience of this type of treatment and its plausibility after training facilitated by interinstitutional collaboration via telemedicine. Materials and methods: A total of 48 women who were diagnosed with abnormally invasive placenta, before and after changes due to the resection-reconstruction protocol were included in the study. Results: In total, 14 conservative reconstructive procedures were performed with outcomes of a lower rate of bleeding, reduced transfusions and complications, and a shorter duration of hospitalization than women with hysterectomy. Conclusion: Conservative surgical management is a safe alternative when implemented at specialized centers by trained groups of professionals. Interinstitutional collaboration, using appropriate telemedicine is a safe and effective alternative to enable training in resective-conservative management of abnormally invasive placenta.