Miracle-dz/UniFAR-FTUs huggingface dataset:
Cloning and Expression of the Lactococcus lactis purDEK Genes, Required for Growth in Milk

ABSTRACT An operon containing the genes purD andpurE and part of the purK gene was cloned from the facultative anaerobic gram-positive bacterium Lactococcus lactis by complementation of the purD mutation inEscherichia coli SØ609. The genes encode enzymes in the de novo pathway of purine nucleotides. The expression of the genes was regulated approximately 35-fold at the transcription level by the availability of purines in the growth medium. Deletion analysis of the nucleotide region upstream of purD indicated that a region of 145 bp is enough to give regulated expression of the reporterlacLM genes, which encode β-galactosidase. Deletion of a region 79 bp upstream of the transcription start point reduced the promoter activity 33-fold when incubated in a purine-free medium and to values below the detection limit when incubated in a purine-containing medium. No secondary transcription start points were mapped in or close to this region, indicating that a putative activator site and not a promoter was deleted or partly destroyed.
Genomes of murine leukemia viruses isolated from wild mice

The genomes of murine leukemia viruses (MuLV) isolated from wild mice have been studied. Detailed restriction endonuclease maps of the 8.8-kilobase (kb) unintegrated linear viral DNAs were derived for five ecotropic and five amphotropic MuLV's from California field mice, for Friend MuLV, and for one ecotropic and one xenotropic MuLV from Mus musculus castaneus. In general, the California MuLV's were similar in their leftward 6 kb (corresponding to the leftward long terminal repeat [LTR], gag, and pol) and rightward 1 kb (7.8 to 8.8 kb, corresponding to p15E and the rightward LTR). For the region spanning 6.0 to 7.7 kb (which includes the sequences that encode gp70) the amphotropic MuLV's shared few enzyme sites with the ecotropic MuLV's, although the California ecotropic MuLV's were highly related to each other in this region, as were the amphotropic MuLV's. Cross-hybridization studies between amphotropic and California ecotropic MuLV DNAs indicated that they were not homologous in the region 6.3 to 7.6 kb; the California ecotropic viral DNAs cross-hybridized in this region to AKR ecotropic MuLV. When the California viral DNAs were compared with AKR ecotropic viral DNA, many differences in enzyme sites were noted throughout the genome. The U3 regions of the wild mouse LTRs showed partial homology to this region in AKR MuLV. The LTR of Moloney MuLV was highly related to that of the California MuLV's, whereas the LTR of Friend MuLV appeared to be a recombinant between the two types of LTRs. The M. musculus castaneus isolates were most closely related to ecotropic and xenotropic MuLV's isolated from inbred mice. One amphotropic MuLV DNA was cloned from supercoiled viral DNA at its unique EcoRI site in pBR322. Viral DNAs with one and two LTRs were isolated. After digestion with EcoRI, DNAs of both types were infectious. It is concluded that ecotropic and amphotropic MuLV's differ primarily in the region which encodes gp70.
Urine particle evaluation: a comparison between the UF-1000i and quantitative microscopy

Abstract Background: The study of urine particles plays a key role in the diagnosis of kidney diseases. In this study, the authors evaluated the correlation between the UF-1000i and quantitative manual microscopy. Methods: A total of 214 untreated urine samples were studied using the Sysmex UF-1000i and compared with results obtained from quantitative manual microscopy using the Fuchs-Rosenthal counting chamber. Results: Using Pearson statistics, we observed satisfactory correlation between the UF-1000i and quantitative microscopy: for red blood cells (RBCs) r was 0.98, for white blood cells (WBCs) r was 1.00, for epithelial cells (EC) r was 0.96, and for casts r was 0.69. Using linear regression statistics, we also observed satisfactory correlation between the UF-1000i and quantitative microscopy: for RBCs R2 was 0.95, for WBCs R2 was 0.99, for EC R2 was 0.92, and for casts R2 was 0.48. Conclusions: In our experience, automated urine particle analysis performed using the Sysmex UF-1000i analyzer is sufficiently precise and improves the workflow in a routine laboratory. Precision was satisfactory and concordance with the reference method is good for RBC, WBC and EC; for casts microscopic observation is required for flagged samples to discriminate hyaline from pathologic casts. Clin Chem Lab Med 2010;48:1107–11.
Perceived barriers to preventive dental care among Libyan dentists

Aim To explore the barriers to providing preventive dental care to patients, as perceived by Libyan dentists working in Benghazi. Settings and design A cross-sectional, questionnaire-based survey was conducted among dentists working in Benghazi, Libya. Materials and methods All dentists registered with the Dental Association of Benghazi and with 2 or more years of practice were invited to participate. The questionnaire collected information on participants’ demographic and professional characteristics as well as the patient-, practice- and dentist-related barriers to providing preventive dental care. Statistical analysis Scores for each type of barrier were compared by demographic and professional characteristics in bivariate and multivariate analyses. Results One hundred and seventy five dentists returned the questionnaires (response rate: 79%) and 166 had complete information on all the variables selected for analysis (75%). The majority were females (70%), aged between 23 and 34 years (85%), was working in the public health sector (43%), and had up to 5 years of service (46%). Patient-related barriers were scored the highest, followed by practice- and dentist-related barriers. Dentists with mixed practice reported lower scores on patient- and practice-related barriers than those in public or private practice. Conclusion Respondents were generally aware of the barriers to preventive dentistry and perceived the barriers as being more related to their patients than to their practices or themselves. However, these perceptions varied by practice sector.
Escaping from Flatland: clinical and biological aspects of human mammary duct anatomy in three dimensions

Accurate knowledge of breast duct anatomy in three dimensions is needed to understand normal breast development, how intraepithelial neoplasia may spread through a breast, and the potential for diagnostic and therapeutic access to breast parenchyma via the nipple. This paper reports three related exploratory studies. In study 1, the median number of milk‐collecting ducts in the nipple was determined in 72 breasts excised for cancer; in study 2, the volumes of all 20 complete duct systems (‘lobes’) in an autopsy breast were measured from 2 mm serial ‘subgross’ sections; and in study 3, a 3D digital model of all collecting ducts in a mastectomy nipple was made from 68 100 µm serial sections. The mastectomy nipples contained 11–48 central ducts (median 27, inter‐quartile range 21–30). In the autopsy breast, the largest ‘lobe’ drained 23% of breast volume; half of the breast was drained by three ducts and 75% by the largest six. Conversely, eight small duct systems together accounted for only 1.6% of breast volume. The 3D model of the nipple revealed three distinct nipple duct populations. Seven ducts maintained a wide lumen up to the skin surface (population A); 20 ducts tapered to a minute lumen at their origin in the vicinity of skin appendages (population B) on the apex of the nipple; and a minor duct population (C) arose around the base of the papilla. Major variations in duct morphology and extent define highly variable territories in which intraepithelial neoplasia could grow. While population A ducts appear accessible to duct endoscopy or lavage, population B and population C ducts may be less accessible. Copyright © 2004 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Impression Management and Non‐GAAP Disclosure in Earnings Announcements

Funding: FCT-Foundation for Science and Technology in Portugal (grant nr. PTDC/EGE-GES/103770/2008), Spanish Ministry of Science and Innovation (grant nr. SEJ2007-67582-C02-02/ECON, ECO2010-19314), Ministerio de Economia y Competitividad (grant nr. 2014/00452/001), Comunidad Autonoma de Madrid (grant nr. SEJ2008-00059-003) and Nova Forum
Spirituality and Stress Management in Healthy Adults

The purposes of this longitudinal, descriptive pilot study were to (a) test the acceptability and feasibility of a 6-week spiritual intervention; (b) determine the relationship between spirituality and stress; (c) explore the effects of the intervention on measures of perceived stress, spiritual perspective, and spiritual well-being; and (d) explore the meaning of spirituality. The sample consisted of 27 community-dwelling adults. Six categories emerged from the qualitative data as descriptors of the meaning and significance of spirituality. The survey data indicated that there were significant negative correlations between perceived stress and spiritual well-being at three time intervals, a significant decline in the levels of perceived stress, and a significant increase in spiritual perspective from the pretest to the 6-week follow-up. There were no significant changes in spiritual well-being. The intervention proved effective in reducing stress in this healthy adult sample.
Average flow constraints and stabilizability in uncertain production-distribution systems

Consider multi-inventory systems in presence of uncertain demand and assume that demand is unknown but bounded in an assigned compact set and the control inputs (controlled flows) are subject to assigned constraints. Given a long-term average demand, we are interested in a control strategy that satisfies just one of the two requirements: i) meeting at each time all possible current demands (worst case stability) or ii) achieving a pre-defined nominal flow in the average (average flow constraints). We show that if we retain the average constraints and relax worst case stability requirement we can achieve stochastic stability. On the contrary, if we retain the worst case stability and relax the average flow constraints we can optimize the average linear flow cost. In the latter case we provide a tight bound for the cost.
Efficient low rank matrix approximation via orthogonality pursuit and ℓ2 regularization

Low rank matrix approximation, in the presence of missing data and outliers, has previously shown its significance as a theoretic foundation in a wide spectrum of tabulated information processing applications. To fit low rank models, minimizing the nuclear norm of matrices is a popular scheme, the computational load of which, however, is heavy. While bilinear factorization can largely mitigate the computational complexity. Unfortunately, without a known or precisely estimated target rank, this strategy often performs vulnerably when the given data is dirty. This paper attempts to simultaneously achieve the computational efficiency as well as the robustness to mild rank initialization and gross corruptions. Moreover, several Augmented Lagrange Multiplier based solvers and a heuristic rank estimator are customized to seek the optimal solution. Theoretical analysis on convergence and complexity, and experiments on both synthetic and real data are provided to reveal the efficacy of our method and show its superiority over the state-of-the-art alternatives.
Viewpoint Modelling with Emotions: A Case Study

In modern software development, considering the viewpoints of stakeholders is an important step in building the right system. Over the past decade, several authors have proposed solutions to capture and model these viewpoints. While these solutions have been successful, one viewpoint they have largely ignored is the emotional viewpoint of stakeholders. Considering the emotional needs of stakeholders is important, because users' perceptions of a product are influenced by emotion as much as cognition. Building on their recent work in modelling the emotional goals of stakeholders, the authors extend an existing viewpoint framework to capture emotional viewpoints, and to carry these from early-phase requirements to detailed software design. They demonstrate this with a case study of an emergency alarm system for older people, presenting the entire suite of models for this case study.
Apoptosis-inducing and apoptosis-preventing functions of poliovirus

Data showing that an apoptotic reaction (the exit into the cytoplasm and nucleolytic internucleosomal degradation of chromosomal DNA, compaction and fragmentation of chromatin, cellular shrinkage, and cytoplasmic blebbing) developed in a subline of HeLa-S3 cells upon nonpermissive poliovirus infection with either a guanidine-sensitive poliovirus in the presence of guanidine, a guanidine-dependent mutant in the absence of guanidine, or certain temperature-sensitive mutants at a restrictive temperature are presented. Essentially, no apoptotic reaction occurred upon permissive infection of these cells. Both permissive and nonpermissive infections resulted in the inhibition of host protein synthesis. Actinomycin D or cycloheximide also elicited a rapid apoptotic reaction in uninfected cells. However, preinfection or coinfection with poliovirus prevented the apoptotic response to the addition of actinomycin D, and preinfection blocked cycloheximide-induced apoptosis as well. These data fit a model in which the cells used are prepared to develop apoptosis, with their viability due to the presence of certain short-lived mRNA and protein species. Poliovirus infection turns on two oppositely directed sets of reactions. On the one hand, the balance is driven toward apoptosis, probably via the shutoff of host macromolecular synthesis. On the other hand, viral protein exhibits antiapoptotic activity, thereby preventing premature cell death. To our knowledge, this is the first description of an antiapoptotic function for an RNA virus.
Meta-analyses of therapies for postmenopausal osteoporosis. VIII: Meta-analysis of the efficacy of vitamin D treatment in preventing osteoporosis in postmenopausal women.

OBJECTIVE To review the effect of vitamin D on bone density and fractures in postmenopausal women. DATA SOURCE We searched MEDLINE and EMBASE from 1966 to 1999 and examined citations of relevant articles and proceedings of international meetings. We contacted osteoporosis investigators and primary authors to identify additional studies and to obtain unpublished data. STUDY SELECTION We included 25 trials that randomized women to standard or hydroxylated vitamin D with or without calcium supplementation or a control and measured bone density or fracture incidence for at least 1 yr. DATA EXTRACTION For each trial, three independent reviewers assessed the methodological quality and abstracted data. DATA SYNTHESIS Vitamin D reduced the incidence of vertebral fractures [relative risk (RR) 0.63, 95% confidence interval (CI) 0.45-0.88, P < 0.01) and showed a trend toward reduced incidence of nonvertebral fractures (RR 0.77, 95% CI 0.57-1.04, P = 0.09). Most patients in the trials that evaluated vertebral fractures received hydroxylated vitamin D, and most patients in the trials that evaluated nonvertebral fractures received standard vitamin D. Hydroxylated vitamin D had a consistently larger impact on bone density than did standard vitamin D. For instance, total body differences in percentage change between hydroxylated vitamin D and control were 2.06 (0.72, 3.40) and 0.40 (-0.25, 1.06) for standard vitamin D. At the lumbar spine and forearm sites, hydroxylated vitamin D doses above 50 microg yield larger effects than lower doses. Vitamin D resulted in an increased risk of discontinuing medication in comparison to control as a result of either symptomatic adverse effects or abnormal laboratory results (RR 1.37, 95% CI 1.01-1.88), an effect that was similar in trials of standard and hydroxylated vitamin D. CONCLUSIONS Vitamin D decreases vertebral fractures and may decrease nonvertebral fractures. The available data are uninformative regarding the relative effects of standard and hydroxylated vitamin D.
Effect Of Myplate Education On Overall Nutritional Knowledge At A Local Food Pantry And Resource Center In Watauga County, North Carolina

Recognizing and meeting the nutritional needs of a food pantry’s clientele may have a positive influence on overall diet and health outcomes. The purpose of this study was to assess the interests and needs for nutrition education and to create a sustainable nutrition education program that will increase nutritional knowledge of clients from the Hunger and Health Coalition in Boone, North Carolina. This study used a qualitative approach to creating an education series and examining beliefs and attitudes about self perceived health and nutrition of the rural Appalachian population. There was a statistically significant change (p=0.002) from pre-education knowledge to post-education knowledge using a paired samples t-test, as well as insights to the beliefs and attitudes about self- perceived health and nutrition of the rural Appalachian population. Future research should examine how to encourage participation through use of incentives and how to increase intervention duration to examine effects on health outcomes.
2014 European Guideline on HIV testing

Testing for HIV is one of the cornerstones in the fight against HIV spread. The 2014 European Guideline on HIV Testing provides advice on testing for HIV infection in individuals aged 16 years and older who present to sexually transmitted infection, genito-urinary or dermato-venereology clinics across Europe. It may also be applied in other clinical settings where HIV testing is required, particularly in primary care settings. The aim of the guideline is to provide practical guidance to clinicians and laboratories that within these settings undertake HIV testing, and to indicate standards for best practice.
Coordination in price setting and the zero lower bound: a global games approach

This paper constructs a two-period general equilibrium model with the effective lower bound of nominal interest rates and describes price competition among monopolistically competitive firms as a coordination game. While the model has multiple equilibria with different levels of inflation (positive or zero), the equilibrium selection in line with global games implies that the economy with high expected productivity growth moves into the positive inflation equilibrium. The policy analyses indicate that monetary policy measures such as an increase in the target inflation can prevent the economy from moving into the zero inflation equilibrium even with low productivity growth.
Loss of heterozygosity on chromosome 16q increases relapse risk in Wilms’ tumor: a meta-analysis

Wilms’ tumor (WT) is the most frequent malignant renal tumor in children. The survival rate is lower in patients with recurrence, and the factors that influence relapse in WT are not fully understood. Loss of heterozygosity on chromosome 16q (LOH 16q) has been reported to be associated with the relapse in WT, but this remains controversial. We performed a meta-analysis to clarify this. PUBMED, EMBASE, and the Cochrane Library were searched up to March 17, 2017. Ten studies involving 3385 patients were ultimately included in the meta-analysis. The meta-analysis showed that LOH 16q was significantly associated with the relapse in WT (relative risk [RR] = 1.74, 95% confidence interval [CI] = 1.43–2.13, P < 0.00001; hazard ratio [HR] = 1.76, 95% CI = 1.38–2.24, P < 0.00001). No significant heterogeneity among studies or publication bias was found. Sensitivity analysis showed omitting one study in each turn could not change the results. Subgroup analysis based on two studies indicated LOH 16q was more effective on elevated replase risk in patients with favorable-histology WT (RR = 2.52, 95% CI = 1.68–3.78, P < 0.00001; HR = 2.99, 95% CI = 1.84–4.88, P < 0.0001) but further work are needed to confirm this. These findings confirm that LOH 16q increased the relapse risk in WT, but more studies are required to further assess the association between LOH 16q and WT relapse among different subgroups.
Microsatellite loci isolated from the tropical tree Hymenaea courbaril L. (Fabaceae)

We developed 11 microsatellite markers for Hymenaea courbaril for the purpose of studying spatial genetic structure and gene flow. The microsatellite loci were screened in 44 trees from two populations. All loci were polymorphic, exhibiting between two and 16 alleles, and levels of expected heterozygosity from 0.174 to 0.909. Departures from Hardy–Weinberg equilibrium were detected for all loci in one population. The estimated null allele frequency is low or moderate. No locus combinations exhibited linkage disequilibrium.
Analytic common spatial pattern and adaptive classification for multiclass motor imagery-based BCI

This paper focuses on the classification of motor imagery tasks from electroencephalogram (EEG) for brain computer interfaces (BCI). A new processing algorithm based on filter bank common spatial pattern (FBCSP) is presented. Analytic common spatial pattern (ACSP) and adaptive classification are introduced to investigate whether they can improve the performance. Four versions of FBCSP, namely, common spatial pattern (CSP) and ACSP with static or adaptive classification are studied. The session-to-session performances of the proposed approaches are evaluated on a 4-class problem posed in the BCI Competition IV dataset 2a. Our results demonstrate the effectiveness of the proposed methods in comparison to the winner of the BCI Competition IV Dataset 2a as well as other more recent studies using this dataset. Adaptive classification yields a higher kappa value of 0.61 compared to 0.57 for multiclass FBCSP algorithm. ACSP further improves the performance achieving a mean kappa of 0.63.
Variation of Virulence and Other Properties among Sendai Virus Strains

The virulence of five Sendai virus strains (MN, Z, KN, Mol, and Hm) isolated from laboratory rodents was compared, using 3‐week‐old female Jcl‐ICR mice. The virulence of the strains was Mol, MN, KN, Z, and Hm in decreasing order. The 50% lethal dose and 50% lung consolidation inducing dose of the highest virulent strain differed by the order of more than 103 and 106, respectively, from those of the lowest virulent one. Other properties such as the growth rate in LLC‐MK2 cells, neuraminidase activities, and molecular weights of structural proteins also differed among the virus strains. These results indicate that Sendai virus prevailing in laboratory rodents is not homogenous with respect to virulence and some other properties.
Use of everolimus in liver transplantation

In recent years, the use of mammalian target of rapamycin inhibitors has gained traction in their use as alternative or adjunct immunosuppressants in the post-liver transplantation (LT) setting. The efficacy of everolimus (EVR) in de novo LT is established and a reasonable time to initiate EVR is 30 d from LT surgery. Initiating EVR early post-LT allows for calcineurin inhibitor (CNI) reduction, thus reducing nephrotoxicity in LT recipients. However, data is inadequate on the appropriate timing for conversion from CNI to EVR maintenance in order to achieve optimal renoprotective effect without compromising drug efficacy. Adverse effects of proteinuria, hypercholesterolemia and hyperlipidemia are significantly higher as compared to standard CNI and long-term implications on graft and patient survival in LT is still unclear. Future research to explore strategies to minimise EVR adverse effects will be crucial for the success of EVR as an important alternative or adjunct immunosuppressive therapy in LT.