Miracle-dz/UniFAR-FTUs huggingface dataset:
Diagnosing Herpesvirus Infections by Real-Time Amplification and Rapid Culture

ABSTRACT Procedures using real-time technique were developed to demonstrate the presence of herpes simplex virus type 1 (HSV-1) and HSV-2, varicella zoster virus (VZV), and cytomegalovirus (CMV) in miscellaneous clinical specimens. The assays were compared to rapid culture using centrifugation followed by detection with monoclonal antibodies. A total of 711 consecutive samples were collected from different patient groups. Throat swabs were obtained from transplant patients; dermal or oral specimens were collected from patients suspected for VZV or HSV infection. Genital specimens were taken from patients who attended the Clinic for Sexually Transmitted Diseases at the Dijkzigt Hospital Rotterdam presenting with symptoms of a primary genital ulcer. Nucleic acid extraction was carried out using a MagnaPure LC instrument. The amplification steps were performed on the ABI Prism 7700 sequence detection system. To monitor the process of extraction and amplification, a universal control consisting of seal herpesvirus type 1 (PhHV-1) was added to the clinical specimens. By culture 127 of 668 (19%) samples were positive for HSV-1, 72 of 668 (10.8%) specimens were positive for HSV-2, and 17 of 366 (4.6%) were positive for VZV. Using real-time amplification the numbers of positive specimens were 143 of 668 (21.4%), 97 of 668 (14.5%), and 27 of 366 (7.4%), respectively. Eighty-six specimens were tested for CMV, 12 (14.0%) were positive by culture, and 17 (19.8%) were positive by real-time PCR. The clinical data of the patients with discrepant results were reviewed thoroughly. In all cases the patients with only real-time PCR-positive results could be considered as truly infected. We concluded that the real-time amplification technique is suitable for the detection of human herpesvirus infection. It offers a semiquantitative and reliable assay with a quick result that is more sensitive than rapid culture, especially for the diagnosis of HSV-2 and VZV infections.
Optimal Energy-Efficient Power Allocation for OFDM-Based Cognitive Radio Networks

This letter investigates the energy-efficient power allocation for orthogonal frequency division multiplexing (OFDM) based cognitive radio networks (CRNs). The problem is to maximize the energy-efficiency measured using the "throughput per Joule" metric subject to the total transmit power and interference constraints. It is then transformed into an equivalent convex problem using parametric programming. Furthermore, an optimal iterative algorithm based on convex optimization theory and parametric programming is proposed. The numerical results show that the proposed optimal algorithm can achieve higher energy-efficiency than that obtained by solving the original problem directly because of its non-convexity. Energy-efficiency maximization can also achieve a good tradeoff between capacity and energy in CRNs.
Exploring Undergraduates' Understanding of Photosynthesis Using Diagnostic Question Clusters

We present a diagnostic question cluster (DQC) that assesses undergraduates' thinking about photosynthesis. This assessment tool is not designed to identify individual misconceptions. Rather, it is focused on students' abilities to apply basic concepts about photosynthesis by reasoning with a coordinated set of practices based on a few scientific principles: conservation of matter, conservation of energy, and the hierarchical nature of biological systems. Data on students' responses to the cluster items and uses of some of the questions in multiple-choice, multiple-true/false, and essay formats are compared. A cross-over study indicates that the multiple-true/false format shows promise as a machine-gradable format that identifies students who have a mixture of accurate and inaccurate ideas. In addition, interviews with students about their choices on three multiple-choice questions reveal the fragility of students' understanding. Collectively, the data show that many undergraduates lack both a basic understanding of the role of photosynthesis in plant metabolism and the ability to reason with scientific principles when learning new content. Implications for instruction are discussed.
Gefitinib as first line therapy in Malaysian patients with EGFR mutation-positive non-small-cell lung cancer: A single-center retrospective study

The present retrospective, single-center study evaluated the objective response rate (ORR) and progression-free survival (PFS) of epidermal growth factor receptor (EGFR) mutation-positive Malaysian patients with advanced lung adenocarcinoma treated with gefitinib. During May 2008 to July 2013, 33 patients with Stage IV, EGFR mutation-positive non-small-cell lung cancer (NSCLC) were identified and received gefitinib (250 mg) as first line treatment. The primary and secondary end points were ORR, PFS and safety, respectively. A total of 18 (54.5%) and 2 (6.1%) patients achieved partial response (PR) and complete response (CR) to gefitinib therapy, respectively, yielding an ORR of 60.6% (95% CI, 42.1–77.1%). Patients with exon 20 or 21 mutations (n=6, 66.7%) tended to have better ORR compared with exon 19 (n=22, 59.1%). The median PFS was 8.9 months in Malaysian patients with EGFR mutation-positive NSCLC, treated with gefitinib. The majority of treatment-related toxicity was mild in nature. The most frequently reported adverse events included dry skin (39.4%), skin rash (27.2%), and dermatitis acneiform (15.2%). In conclusion, Malaysian patients with locally advanced and metastatic EGFR mutation-positive NSCLC responded favorably to gefitinib therapy in terms of ORR, median PFS, and tolerability, the results of which were consistent with those of the IPASS study conducted in an Asian population. Considering the efficacy and safety profile of gefitinib, it is a favorable option for the first-line treatment of Malaysian patients with EGFR mutation-positive NSCLC. However, future long-term studies in a larger population of Malaysian patients are required to support whether the prolonged PFS conferred by gefitinib will translate into prolonged overall survival.
Effect of Micronutrients on Insomnia in Adults

Insomnia is a debilitating condition causing psychological distress and frequently comorbid with other mental health conditions. This study examined the effect of 8 weeks of treatment by broad spectrum micronutrients (vitamins and minerals) on insomnia using a multiple-baseline-across-participants open-label trial design. Seventeen adults were randomized to 1-, 2-, or 3-week baseline periods (14 completed). Self-report measures were the Consensus Sleep Diary–Morning (CSD-M), the Pittsburgh Insomnia Rating Scale (PIRS), and the Depression, Anxiety, Stress Scale (DASS). Baselines were generally stable. Treatment completers reported reliable and clinically significant change in insomnia severity (PIRS), in depression, stress, and anxiety (DASS), and on at least two aspects of sleep measured by the CDS-M. All completers were treatment-compliant, and side effects were minimal. Nutritional supplementation is shown to be a novel, beneficial treatment for insomnia in adults. Follow-up research using placebo-controlled designs as well as comparisons to cognitive-behavioral and other treatments is recommended.
Iron Supplementation Alters Heme and Heme Oxygenase 1 (HO-1) Levels In Pregnant Women in Ghana.

BACKGROUND Iron supplementation is recommended for pregnant women to meet their iron requirement for a healthy pregnancy. The benefits and risks of universal iron supplementation during pregnancy in malaria endemic countries are currently being debated. As part of a broader study that focused on the effect of heme/HO-1 on pregnancy outcomes in malaria in pregnancy, we determined the association between iron supplementation and free heme levels in blood of pregnant women with and without malaria in Ghana. We hypothesized that pregnant women with malaria who took iron supplements will have higher levels of Heme/HO-1 than those who did not take iron supplements. METHODS A total of 337 women were recruited for this study. Blood samples were collected for malaria diagnosis and heme/HO-1 measurement. Quantification of heme was done using a heme colorimetric assay kit and HO-1 levels were performed using Enzyme-Linked Immunosorbent Assay (ELISA) on plasma samples. RESULTS Malaria positive iron supplemented women, in their third trimester, had significantly higher median levels of heme 59.3(43.1 - 60.4) than non-malaria iron supplemented women 35.7(33.0 - 62.2), p = 0.026. Also, malaria positive iron supplemented women had significant higher median levels of HO-16.2(IQR 4.9 - 8.1) than pregnant women who did not take iron supplements 2.9 (IQR 2.1 - 3.8), p = <0.001. CONCLUSION Although iron supplementation may be highly beneficial and improve pregnancy outcomes for iron deficient or anemic mothers, it is also likely that iron supplementation for pregnant women who are not iron deficient may put this group of women at risk for adverse pregnancy outcomes. Findings from this study sheds light on the effect of iron supplementation on malaria derived heme in pregnancy, which may inform how iron supplementation is recommended for pregnant women who are not iron deficient.
Disturbance Decoupling of Boolean Control Networks

Disturbance decoupling problem (DDP) of Boolean control networks is considered. Using semi-tensor product of matrices and the matrix expression of logical functions, a working procedure is proposed to solve the problem. This procedure consists of two key design steps. First, how to convert a system into an output-friendly coordinate frame. An algorithm is provided to calculate the output-friendly subspaces. Secondly, it was shown how to find proper controllers to solve the problem if it is solvable. A state variable separation form is introduced to guide the design of controllers. Based on the design technique, necessary and sufficient conditions are obtained for the solvability of DDP.
Leukocyte DNA Methylation Signature Differentiates Pancreatic Cancer Patients from Healthy Controls

Pancreatic adenocarcinoma (PaC) is one of most difficult tumors to treat. Much of this is attributed to the late diagnosis. To identify biomarkers for early detection, we examined DNA methylation differences in leukocyte DNA between PaC cases and controls in a two-phase study. In phase I, we measured methylation levels at 1,505 CpG sites in treatment-naïve leukocyte DNA from 132 never-smoker PaC patients and 60 never-smoker healthy controls. We found significant differences in 110 CpG sites (false discovery rate <0.05). In phase II, we tested and validated 88 of 96 phase I selected CpG sites in 240 PaC cases and 240 matched controls (p≤0.05). Using penalized logistic regression, we built a prediction model consisting of five CpG sites (IL10_P348, LCN2_P86, ZAP70_P220, AIM2_P624, TAL1_P817) that discriminated PaC patients from controls (C-statistic = 0.85 in phase I; 0.76 in phase II). Interestingly, one CpG site (LCN2_P86) alone could discriminate resectable patients from controls (C-statistic = 0.78 in phase I; 0.74 in phase II). We also performed methylation quantitative trait loci (methQTL) analysis and identified three CpG sites (AGXT_P180_F, ALOX12_E85_R, JAK3_P1075_R) where the methylation levels were significantly associated with single nucleotide polymorphisms (SNPs) (false discovery rate <0.05). Our results demonstrate that epigenetic variation in easily obtainable leukocyte DNA, manifested by reproducible methylation differences, may be used to detect PaC patients. The methylation differences at certain CpG sites are partially attributable to genetic variation. This study strongly supports future epigenome-wide association study using leukocyte DNA for biomarker discovery in human diseases.
Impacts of Adelphophagic Development on Variation in Offspring Size, Duration of Development, and Temperature-Mediated Plasticity

Adelphophagic development, where embryos consume sibling embryos or nurse eggs, is particularly common in marine caenogastropods and some families of polychaetes. When exogenous nutrition is provided before hatching, egg size and hatching size can be uncoupled, but advantages and constraints of adelphophagic development compared to development from large eggs are unknown. Here we examine temperature-mediated plasticity in offspring size, brooding duration, and fecundity in the adelphophagic marine gastropod Crepidula cf. onyx. We use these data combined with previously published data on two planktotrophic Crepidula and two Crepidula species that develop from large eggs to test hypotheses about the consequences of adelphophagic development and patterns of variation in offspring size. In Crepidula cf. onyx, egg size shows no significant effect of temperature. Hatching size is significantly larger at 28 °C than at 23 °C but proceeds from fewer eggs per capsule at 28 °C. Hatching size is therefore decoupled from both egg size and the number of eggs per capsule. Although development is faster at the higher temperature, broods are produced roughly every 26–27 days at both temperatures. Increased rate of development has been cited as a potential advantage of adelphophagic development in muricids, but the adelphophagic C. cf. onyx did not develop more quickly than C. atrasolea or C. ustulatulina, species that produce similarly sized hatchlings from large eggs. Comparisons across calyptraeid species support the role of adelphophagy in increasing variance in offspring size. This increased variability is primarily expressed within broods or among broods from the same female, not among females.
Mood-state dependence in cognitive vulnerability to depression : The roles of positive and negative affect

Recent theory and research suggests that cognitive differences between depression-prone and non vulnerable individuals are only apparent under priming conditions, such as dysphoric mood. For example, Miranda and Persons (1988 ; Miranda, Persons, & Byers, 1990) found that dysfunctional attitudes correlate with dysphoric affect in remitted depressives, but not in never depressed subjects. The current study replicated and extended this research by examining a wider variety of cognitive constructs (dysfunctional attitudes, automatic positive and negative thoughts, self-esteem), as well as testing the roles of low positive affect (PA) and high negative affect (NA) as mood primes, separately and combined. Consistent with previous findings, results indicated that NA was more strongly associated with negativity on all measured cognitive constructs in remitted dysphorics, than in never dysphoric subjects. In contrast, low PA and the combination of high NA and low PA did not demonstrate this differential pattern of correlation.
Melanoma During Pregnancy

Melanoma is the most malignant cutaneous tumor. The incidence of melanoma accounts for the sixth place among malignant diseases, 5% of malignancies among men and 4% of malignancies among women; it stands for 1.4% of deaths caused by malignant disease (Fisher et al., 2008). The incidence of malignant melanoma has constantly been increasing and it has reached 3% per year in the last several years. At the beginning of the 20th century, the population risk for malignant melanoma was in the ratio 1:500 but today 1:73 of women and 1:49 of men are at risk (Fisher et al., 2008). It is anticipated that there will be 68,130 newly diagnose cases of melanoma and approximately 8,700 deaths from the disease in the USA (Jamal et al., 2010). Among the population aged between 20 to 39 years malignant melanoma is on the second place by incidence. Although the disease is more frequent among men, its incidence during the reproductive period is higher among women. In Great Britain, the third of all diagnosed melanomas arise before 50 years of age and about 30% to 35% develop during the reproductive period of women (Anonymus, 2003; Cancer Research UK 2006). The actual incidence of melanoma during pregnancy is unknown. Smith and Randall (Smith RS & Randall, 1969) gave the first reports based on the source documents of a small non-reference Plattsburg Air Force Base Hospital, New York. The incidence of melanoma was 2.8 per 1000 deliveries but studies that are more recent showed that it is between 2.8 and 5 per 100,000 of pregnancies; the registry of German Dermatological Society shows that 1% of female patients affected with melanoma is pregnant (Dillman et al., 1996; Garbe, 1993). A group of Swedish authors analyzed the period from 1973 to 1984 and reported that melanoma is the most common cancer appearing in pregnancy and accounts for 24.5% of cancer cases in pregnant women (Matthiasen & Berg, 1989). From 1958 to 1999, 19,337 women with melanoma were included in the most extensive epidemiology study based on Swedish and regional registries; 0.9% of malignant melanomas were diagnosed during the pregnancy. Of all included patients, 5,533 of women were in reproductive age and 185 (3.3%) of them were diagnosed with melanoma during the pregnancy (Lens et al., 2004.). The prognostic features for melanoma depend on the stage it has been diagnosed. Although the 5-year survival for stage IV melanoma is still less than 5%, overall mortality from melanoma has a decreasing tendency (Rigel et al., 1996). The effect of pregnancy to the course of melanoma has been a researching issue for years. The results of uncontrolled studies conducted from 1950 to 1980 show that pregnancy is an unfavorable prognostic factor in
Flat Feline Faces: Is Brachycephaly Associated with Respiratory Abnormalities in the Domestic Cat (Felis catus)?

There has been little research into brachycephalism and associated disorders in cats. A questionnaire aimed at cat owners was used to determine the relationship between feline facial conformation and owner-reported cat management requirements and respiratory abnormalities. Owner-submitted photographs of cats were used to develop novel measures of skull conformation. One thousand valid questionnaires were received. Within these there were 373 valid photographs that allowed measurement of muzzle ratio (M%) and 494 that allowed nose position ratio (NP%). The data included 239 cats for which both measurements were available. Owners reported lifestyle factors (e.g. feeding type, grooming routine, activity level), physical characteristics (e.g. hair length) and other health characteristics of their cat (e.g. tear staining, body condition score). A composite respiratory score (RS) was calculated for each cat using their owner’s assessment of respiratory noise whilst their cat was asleep and then breathing difficulty following activity. Multivariate analyses were carried out using linear models to explore the relationship between RS and facial conformation, and lifestyle risk factors. The results showed that reductions in NP% and M% were significantly associated with RS (P < 0.001 and P = 0.026, respectively) and that the relationship was significantly negatively correlated (r = -0.56, P < 0.001 for both). Respiratory score was also significantly associated with increased presence of tear staining (P < 0.001) and a sedentary lifestyle (P = 0.01). This study improves current knowledge concerning cats with breeding-related alterations in skull confirmation and indicates that brachycephalism may have negative respiratory implications for cat health and welfare, as has been previously shown in dogs.
Numerical Models for the Simulation of Flexible Artificial Heart Valves: Part I - Computational Methods

Abstract A numerical model of the coupled motion of a flexing surface in a high Reynolds number flow is presented for the simulation of flexible polyurethane heart valves in the aortic position. This is achieved by matching a Lagrangian dynamic leaflet model with a panel method based flow solver. The two models are coupled via the time-dependent pressure field using the unsteady Bernoulli equation. Incorporation of sub-cycling in the dynamic model equations and fast pre conditioning techniques in the panel method solver yields efficient convergence and near real-time simulations of valve motion. The generality of dynamic model allows different material properties and/or geometries to be studied easily and interactively. This interactivity is realized by embedding the models within a design environment created using the software IRIS Explorer TM. Two flow domains are developed, an infinite domain and an internal domain using conformal mapping theory. In addition bending stress on the valve is computed using a simple stress model based on spline and circle equation techniques.
Development of the hippocampal region in the rat I. Neurogenesis examined with 3H‐thymidine autoradiography

Neurogenesis in the rat hippocampal region was examined with 3H‐thymidine autoradiography. The rats in the prenatal groups were the offspring of pregnant females given two injections of 3H‐thymidine on consecutive days in an overlapping series: embryonic (E) day E13+E14, E14+E15,…, E21+E22. The rats in the postnatal (P) groups were injected in two nonoverlapping series: first, the day of birth (PO) and P1, P2+P3,…, P18+P19; second, P0–P3, P4–P7,…, P16–P19. On 60 days of age, the percentage of labelled cells and the proportion of cells added during each day of formation were determined at several anatomical levels within each structure of the hippocampal region (entorhinal cortex, parasubiculum, presubiculum, subiculum, Ammon's horn, and the dentate gyrus) and the hippocampal rudiment (tenia tecta, indusium griseum). The neurons in each structure arise in overlapping, but still significantly different, waves: the hippocampal rudiment between E16–E17; the entorhinal cortex between E15–E17; the para‐ and presubiculum between E16–E19; the subiculum between E16–E18; large cells in strata oriens, radiatum, lacunosum‐moleculare of Ammon's horn between E15–E17; Ammon's horn pyramidal cells between E17–E19; large cells in the dentate hilus and molecular layer between E15–E19. Dentate granule cells begin to originate on E17, and 10% of the population forms after P18.