Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of naturopathic and nutritional supplement treatment on tumor response, control, and recurrence in patients with prostate cancer treated with radiation therapy.

OBJECTIVES Use of naturopathic and nutritional supplements (NNS) with antioxidant activity is controversial in patients receiving radiation therapy. The effects of concomitant use of NNS with antioxidant activity during radiation therapy for prostate cancer were investigated in terms of clinical tumor responsiveness, kinetics, and durability. MATERIALS AND METHODS A retrospective investigation was done of 134 patients treated with curative intent for limited-stage prostate cancer by radiation therapy. Patients self-selected to receive NNS as part of their treatment and maintenance during an extended post-treatment interval of at least 2 years. The outcome measures were the following: prostate-specific antigen (PSA) nadir; ≥24 months post-treatment PSA; time to reach nadir; and time to last follow-up were compared across +NNS and -NNS. RESULTS Sixty-nine (69) patients elected to receive NNS while 65 did not. Seventy-seven (77) (+NNS 39, -NNS 38) patients received hormone therapy while 57 (+NNS 30, -NNS 27) did not. In the nonhormone cohort, median pretreatment PSA, nadir, post-treatment PSA, time to reach nadir, and time to follow-up were 5.5 ng/mL, 0.56 ng/mL, 0.61 ng/mL, 25 months, and 39.7 months for the -NNS group and 5.1 ng/mL, 0.32 ng/mL, 0.44 ng/mL, 27 months, and 50.1 months for the +NNS group, respectively (p>0.05 for all). Similarly, no significant differences were observed between +NNS and -NNS in the hormone-receiving cohort. CONCLUSIONS The clinical tumor response to radiation therapy in patients with limited-stage prostate cancer is not inhibited by concomitant NNS based on the magnitude of the PSA response, the velocity of the PSA nadir, and the duration of PSA normalization.
A complex Xp11.22 deletion in a patient with syndromic autism: Exploration of FAM120C as a positional candidate gene for autism

We present a male patient with sporadic Aarskog syndrome, cleft palate, mild intellectual disability, and autism spectrum disorder (ASD). A submicroscopic discontiguous deletion was detected on chromosome Xp11.2 encompassing FGD1, FAM120C, and PHF8. That the deletion encompassed FGD1 (exons 2–8) explains the Aarskog features while the deletion of PHF8 most likely explains the cleft palate and mild intellectual disability. We identify FAM120C as a novel X‐linked candidate gene for autism for two reasons: first, a larger deletion encompassing FAM120C segregates with autism in a previously reported family and second, there is recent evidence that FAM120C interacts with CYFIP1, part of the FMRP (Fragile X Mental Retardation Protein) network. In the current study, resequencing of FAM120C in 87 Belgian male patients with autism spectrum disorder identified no novel mutations. Expression of Fam120c in mouse tissues showed enriched expression in pituitary, cerebellum, cortex, and pancreatic islets of Langerhans. Additionally, we found a cortical expression pattern of Fam120c similar to that of Fmr1. In conclusion, FAM120C is a novel candidate gene for autism spectrum disorder based on genetic evidence and the brain expression pattern. Thereby we highlight a role for FMRP network genes in ASD. © 2014 Wiley Periodicals, Inc.
Fear of cancer recurrence: a theoretical review and its relevance for clinical presentation and management

There is increasing recognition of the unique physical and psychosocial concerns of the growing population of cancer survivors. An emerging literature demonstrates that fear of cancer recurrence (FCR) is a problematic long‐term and late effect for cancer survivors. In fact, FCR is a top concern, and this article provides a necessary synthesis of the extant research evidence and theory.
Human Papovavirus (JC): Induction of Brain Tumors in Hamsters

Eighty-three percent of hamsters inoculated at birth with JC virus, a human papovavirus isolated from brain tissue of a case of progressive multifocal leukoencephalopathy, developed malignant gliomas within 6 months. Three brain tumors have been serially transplanted as subcutaneous tumors. JC virus was isolated from five of seven tumors tested. Cells from four tumors were cultivated in vitro. These cells contained an intranuclear antigen with the characteristics of a T antigen, and this antigen was antigenically related to SV40 T antigen. Although virus was not recovered from extracts of serially cultured tumor cells, JC virus was rescued when one tumor cell line was fused with permissive cells.
Real-time, continuous level of detail rendering of height fields

We present an algorithm for real-time level of detail reduction and display of high-complexity polygonal surface data. The algorithm uses a compact and efficient regular grid representation, and employs a variable screen-space threshold to bound the maximum error of the projected image. A coarse level of simplification is performed to select discrete levels of detail for blocks of the surface mesh, followed by further simplification through repolygonalization in which individual mesh vertices are considered for removal. These steps compute and generate the appropriate level of detail dynamically in real-time, minimizing the number of rendered polygons and allowing for smooth changes in resolution across areas of the surface. The algorithm has been implemented for approximating and rendering digital terrain models and other height fields, and consistently performs at interactive frame rates with high image quality.
Esthetic outcomes with porcelain-fused-to-ceramic and all-ceramic single-implant crowns: a randomized clinical trial.

OBJECTIVES the aim of this randomized-controlled clinical trial was to compare the objective and subjective esthetic outcomes of two types of screwed-retained single-implant crowns. MATERIALS AND METHODS participants were randomly assigned to the test (all-ceramic) and control [porcelain-fused-to-ceramic (PFM)] groups and were seen under investigation at baseline (B), crown insertion (CI), 1-year follow-up (1Y), and 2-year follow-up (2Y). Objective parameters were assessed by an intra-oral digital photograph (1:1 ratio), a study cast, a standardized radiograph, periodontal/peri-implant measurements, and questionnaires were obtained for the subjective parameters. In addition, pink esthetic score (PES) and white esthetic score (WES) were calculated for both groups. For the subjective evaluation, a visual analogue scale (VAS) questionnaire was used to assess the level of patient satisfaction regarding the esthetic outcome. Then, nine expert clinicians visually inspected and assessed subjective evaluation at the professional level. Statistical analysis was used to compare between groups and investigational appointments. RESULTS twenty patients were included in the study, 10 allocated to the all-ceramic group and 10 to the PFM group. No statistically significant differences were observed for the objective measurements comparing the test and control groups. Minor chipping of the ceramic veneering material was observed in the two patients of control group. The mean difference for all groups comparing objective parameters revealed an increase of papilla height between time points. A slight recession (0.26 mm) of the peri-implant mucosal margin at the implant site was observed between 1Y and 2Y. Mean values for PES and WES were 13.9 and 13.1 for the PFM group and for the all-ceramic group, respectively. These values were not statistically significant. Implant crown volume, outline, translucency, and characterization showed major discrepancies with the contra-lateral natural teeth. As for subjective parameters, VAS patients' responses regarding their perceptions of the esthetic outcome showed no statistical differences between groups and clinicians' accuracy scores were 50% and 47% for PFM and all-ceramic crowns, respectively. CONCLUSION PFM and all-ceramic single-implant restorations may be indistinguishable from each other regarding the objective/subjective assessment of esthetic integration. The material chosen for fabricating an implant crown per se does not ensure an optimal esthetic outcome if other esthetic parameters are not present.
Anti-retroviral therapy and cognitive function.

BACKGROUND The effect of anti-retroviral medications on the cognitive functions important in flying has not been determined. HYPOTHESIS Anti-retroviral medications have no effect on the cognitive performance of individuals at the CDC 4C2 (symptomatic HIV disease with no illness indicative of full-blown AIDS) stage of infection. METHODS A two-group study using a cross-sectional design was used. The participants in each group represented a sample of convenience obtained from a larger, naturalistic study. Each group consisted of 10 HIV+ males at the CDC 4C2 stage of infection. The two groups were found to be comparable on age, education, pre-morbid intelligence, and ethnicity. All members of the anti-retroviral medication group had been receiving medications for at least 3 mo. Those in the control group (no anti-retroviral medication) had received no anti-retroviral medications for at least 6 mo. Cognitive functioning was assessed using a computerized information processing battery that included test similar to those under consideration for inclusion in military pilot selection batteries and a neuropsychological battery. As part of the larger study, the participants were carefully and repetitively screened on factors known to affect performance on neuropsychological instruments. RESULTS The groups showed little difference in cognitive functioning. CONCLUSION Although more research is needed, anti-retroviral medication does not impair, and may improve, the cognitive processes of individuals with symptomatic HIV infection who do not have AIDS.
[Association between the interleukin 1B (C-31T) polymorphism and Helicobacter pylori infection in health checkup examinees].

PURPOSE Associations between Helicobacter pylori (HP) infection and lifestyle factors have been demonstrated by several studies, but there are very few reports on links with host factors, especially concerning genetic polymorphisms for inhabitants of large city. The present investigation was conducted to determine the HP infection rate with reference to the Interleukin-1 beta gene (IL-1B) polymorphism and assess the interactions with smoking reported for outpatients. METHOD The subjects were 468 participants in a health-check-up program of law of health for aged conducted by Nagoya Nishi Health Center. The participants were asked to permit use of their residual blood drawn during a health-check-up program and written informed consent was obtained for gene polymorphism tests. Data on smoking habit were obtained by self-administered questionnaire. The IL-1B C-to-T polymorphism at -31 was genotyped by PCR-CTPP (polymerase chain reaction with confronting two-pair primers) and an anti-HP IgG antibody test was used for detecting HP infection. Differences in values were assessed by a chi 2 test. An unconditional logistic model was applied for estimating odds ratios with the computer program STATA Version 6. This study was approved by the Ethical Committee at Aichi Cancer Center in 2000 before it was commenced (Ethical Committee Approval Number 11-12) RESULTS The HP infection rate was 52.6% (61/116) for the C/C genotype of IL-1B-31, 48.6% (89/183) for the C/T, and 63.2% (103/163) for T/T; the difference were not statistically significant. However, when non-current smokers were excluded, the rate were 47.8% (11/23), 52.9% (18/34), and 72.7% (16/22), respectively, indicating the T/T genotype to have a higher infection rate. The age-sex-smoking adjusted odds ratio (OR) relative to the C/C genotype were 0.97 (95% confidence interval, 0.59-1.57) for the T/C genotype and 1.73 (1.04-2.87) for the T/T genotype. Among current and former smokers the age-sex adjusted OR were 1.68 (0.50-5.71) for the T/C genotype and 5.29 (1.11-25.1) for the T/T genotype, suggesting a effect of this polymorphism prominent in smokers. CONCLUSION An association between the IL-1B-31 polymorphism and persistent HP infection was observed for inhabitants with a smoking habit, indicating that this polymorphism is one genetic trait conferring an increased likelihood of persistent HP infection.
An early decrease in serum HBeAg titre is a strong predictor of virological response to entecavir in HBeAg‐positive patients

Summary. Quantification of HBeAg levels has been found to be useful in monitoring and predicting the outcomes of interferon and lamivudine treatment in HBeAg‐positive patients. The aim of this study was to determine whether quantification of HBeAg at baseline and on treatment could predict which patients would achieve HBeAg seroconversion after 96 weeks of entecavir therapy. Sixty‐five HBeAg‐positive naïve chronic hepatitis B patients who were treated with entecavir at a dose of 0.5 mg once daily for 96 weeks were evaluated. Serum HBV DNA levels were assessed at baseline, week 24, 48 and 96; serum HBeAg levels were assessed at baseline, week 12, 24, 48, 72 and 96. Serum HBeAg levels were associated with a higher likelihood of HBeAg seroconversion to entecavir at weeks 96 than serum HBV DNA levels both at baseline and on treatment (at baseline: OR = 9.932, P = 0.003 vs OR = 5.045, P = 0.036; on treatment: OR = 112.5, P < 0.0001 vs OR = 47.782, P < 0.0001). A maintained reduction in HBeAg > 65% of pretreatment HBeAg values after 24 weeks of entecavir therapy is the strongest predictor for HBeAg seroconversion at week 96 (OR = 70.578, P < 0.0001). Quantification of HBeAg at the start and early during therapy showed a higher predictive value than that of HBV DNA for HBeAg seroconversion by entecavir. A significant decrease in serum HBeAg levels at week 24 may be a useful on‐treatment measurement in the early phase for predicting HBeAg seroconversion and identifying patients who will most likely benefit from finite entecavir treatment.
Mining until it hurts: automatic extraction of usability issues from online reviews compared to traditional usability evaluation

Large amounts of data available on the web, for example reviews, tweets, and forum postings, contain user narratives on interaction with products. Finding usability issues in such user narratives offers an interesting alternative to traditional usability testing. To leverage such data for identifying usability issues, we (I) devise a methodology for building automated extraction tools for usability issues; (II) perform empirical assessment of such tools by training a number of classifiers to extract sentences describing usability issues for two digital cameras and a children's tablet; (III) perform quantitative and qualitative comparisons between the usability issues identified by the classifiers and those identified and assessed by two traditional methods: heuristic evaluation and think aloud testing. Our results show that it is possible to build and train algorithms for extracting actionable usability issues, but raise serious concerns about the practical future prospects for supplementing traditional evaluation methods with automated extraction algorithms.
Comparing individual means in the analysis of variance.

The practitioner of the analysis of variance often wants to draw as many conclusions as are reasonable about the relation of the true means for individual "treatments," and a statement by the F-test (or the z-test) that they are not all alike leaves him thoroughly unsatisfied. The problem of breaking up the treatment means into distinguishable groups has not been discussed at much length, the solutions given in the various textbooks differ and, what is more important, seem solely based on intuition. After discussing the problem on a basis combining intuition with some hard, cold facts about the distributions of certain test quantities (or "statistics") a simple and definite procedure is proposed for dividing treatments into distinguishable groups, and for determining that the treatments within some of these groups are different, although there is not enough evidence to say "which is which. " The procedure is illustrated on examples.
Structural evolution of an open source system: a case study

Software evolution empirical studies are made possible only when data is available and easily collectable. Open source software provides a good opportunity for observing software products in various phases of their evolution, growth and maturity. One of the aspects that have not been analyzed yet through empirical studies is the relation that exists between code components growth and the evolving code structure. In this paper, we look at the growth of code elements by measuring the total number of files per release and also by visualizing the folder structure as a tree. Both, the number of files and the shape of the folder tree structure offer proxies to study the evolving complexity of the system. In this study, a number of hypotheses about the evolutionary patterns in the size of files and folders, in the folder tree structure, reflecting common assumptions on software engineering and open source are tested against empirical data reflecting the evolution of the ARLA system. We also relate some of the observed patterns to the arrival rate of new developers. Results show that the number of code components (files and folders) over releases can be interpreted as a linear trend with a superimposed ripple. We also describe the more apparent characteristics of the evolution of the folder tree structure. Furthermore, we observe that the average size of files and folders tends to stabilize over releases. The cumulative number of people who have been involved as developers of the system follows a trend which resembles that of the size in files over releases, suggesting that the latter could provide a good indicator for rate of work and productivity. There was no apparent relation between the arrival rate of developers and the changes observed in the code structure.
The middle Eocene climatic optimum (MECO): A multiproxy record of paleoceanographic changes in the southeast Atlantic (ODP Site 1263, Walvis Ridge)

The middle Eocene climatic optimum (MECO, ~40 Ma) was a transient period of global warming that interrupted the secular Cenozoic cooling trend. We investigated the paleoceanographic, paleoenvironmental, and paleoecological repercussions of the MECO in the southeast Atlantic subtropical gyre (Ocean Drilling Program Site 1263). TEX86 and δ18O records support an ~4°C increase in surface and deepwater temperatures during the MECO. There is no long-term negative carbon isotope excursion (CIE) associated with the early warming, consistent with other sites, and there is no short-term negative CIE (~50 kyr) during the peak of the MECO, in contrast to what has been observed at some sites. This lack of a CIE during the peak of the MECO at Site 1263 could be due to poor sediment recovery or geographic heterogeneity of the δ13C signal. Benthic and planktic foraminiferal mass accumulation rates markedly declined during MECO, indicating a reduction of planktic foraminiferal production and export productivity. Vertical δ13C gradients do not indicate major changes in water column stratification, and there is no biomarker or micropaleontological evidence that hypoxia developed. We suggest that temperature dependency of metabolic rates could explain the observed decrease in foraminiferal productivity during warming. The kinetics of biochemical reactions increase with temperature, more so for heterotrophs than for autotrophs. Steady warming during MECO may have enhanced heterotroph (i.e., foraminiferal) metabolic rates, so that they required more nutrients. These additional nutrients were not available because of the oligotrophic conditions in the region and the lesser response of primary producers to warming. The combination of warming and heterotroph starvation altered pelagic food webs, increased water column recycling of organic carbon, and decreased the amount of organic carbon available to the benthos.
Asp433 in the closing gate of ASIC1 determines stability of the open state without changing properties of the selectivity filter or Ca2+ block

A constriction formed by the crossing of the second transmembrane domains of ASIC1, residues G432 to G436, forms the narrowest segment of the pore in the crystal structure of chicken ASIC1, presumably in the desensitized state, suggesting that it constitutes the “desensitization gate” and the “selectivity filter. ” Residues Gly-432 and Asp-433 occlude the pore, preventing the passage of ions from the extracellular side. Here, we examined the role of Asp-433 and Gly-432 in channel kinetics, ion selectivity, conductance, and Ca2+ block in lamprey ASIC1 that is a channel with little intrinsic desensitization in the pH range of maximal activity, pH 7.0. The results show that the duration of open times depends on residue 433, with Asp supporting the longest openings followed by Glu, Gln, or Asn, whereas other residues keep the channel closed. This is consistent with residue Asp-433 forming the pore’s closing gate and the properties of the side chain either stabilizing (hydrophobic amino acids) or destabilizing (Asp) the gate. The data also show residue 432 influencing the duration of openings, but here only Gly and Ala support long openings, whereas all other residues keep channels closed. The negative charge of Asp-433 was not required for block of the open pore by Ca2+ or for determining ion selectivity and unitary conductance. We conclude that the conserved residue Asp-433 forms the closing gate of the pore and thereby determines the duration of individual openings while desensitization, defined as the permanent closure of all or a fraction of channels by the continual presence of H+, modulates the on or off position of the closing gate. The latter effect depends on less conserved regions of the channel, such as TM1 and the extracellular domain. The constriction made by Asp-433 and Gly-432 does not select for ions in the open conformation, implying that the closing gate and selectivity filter are separate structural elements in the ion pathway of ASIC1. The results also predict a significantly different conformation of TM2 in the open state that relieves the constriction made by TM2, allowing the passage of ions unimpeded by the side chain of Asp-433.
The Natural Antioxidants, Pomegranate Extract and Soy Isoflavones, Favourably Modulate Canine Endothelial Cell Function

Cardiovascular disease, preceded by vascular endothelial dysfunction, is a prominent cause of death in dogs. L-carnitine and taurine, well known for their antioxidative capacity, beneficially affect cardiovascular disease as well as certain dog cardiomyopathies. It is well established that vascular endothelial dysfunction precedes cardiovascular disease and that “vasoprotective factors” (NO and antioxidants) prevent apoptosis, whereas “risk factors” such as oxidized LDL, hyperglycemia, and free fatty acids trigger it in cultured human vascular endothelial cells. Whereas human vascular cell in vitro models are widely established and used for the characterisation of potential vasoprotective substances, such models are not available for canine endothelial cells. In the present study we therefore developed an in vitro model, which allows the testing of the effects of different substances on proliferation and apoptosis in canine aortic endothelial cells. This model was used to test L-carnitine, taurine, pomegranate extract, and Soy Isoflavones in comparison to reference substances (glutathione and pioglitazone) previously shown to modulate human endothelial cell function. L-carnitine and taurine neither exhibited antiproliferative nor antiapoptotic activities in the context of this study. However extracts from pomegranate and soy isoflavones dramatically reduced proliferation and apoptosis in a dose dependent fashion, being in line with a vasoprotective activity in dogs.