Miracle-dz/UniFAR-FTUs huggingface dataset:
Efficacy of Phosphorus Gettering and Hydrogenation in Multicrystalline Silicon

The emitter formation step (POCl3 diffusion) in p-type crystalline silicon solar cell processing includes many variables, e.g., peak temperature, gas flows, temperature ramps, which can be optimized in order to improve material quality. Diffusion parameters of an 80-Ω/L1 emitter are varied, and the resulting change in electronic quality of multicrystalline silicon is analyzed. A detailed gettering analysis of multicrystalline material, surface passivated with hydrogen-rich amorphous silicon, after POCl3 diffusion, and an additional gettering step combined with hydrogenation from SiNx:H is presented. The industrial-type diffusion leads to material of lower electronic quality than the extended reference diffusion. A major finding of this paper is the fact that results on different 5 × 5 cm2 samples out of one 15.6 × 15.6 cm2 wafer can vary significantly. Hence, conclusions about which diffusion is most efficient in gettering strongly depend on wafer position. An edge position close to crucible walls, for example, might improve less effectively than another position close to the crucible center. In fact, the opposite can also be shown, and samples originating from edge regions reach their highest lifetimes after gettering. This is explained by the different defect structure of the investigated samples. Structures exhibiting high gettering efficacy contain fewer recombination active grain boundaries and are predominantly free of extended defect clusters.
Mitogen-activated Protein Kinase Kinase 1 (MEK1) Stabilizes MyoD through Direct Phosphorylation at Tyrosine 156 During Myogenic Differentiation*

Previously, we reported that mitogen-activated protein kinase kinase 1 (MEK1) activated in the mid-stage of skeletal muscle differentiation promotes myogenic differentiation. To elucidate the molecular mechanism, we investigated an activity of MEK1 for MyoD. Activated MEK1 associates with MyoD in the nucleus of differentiating myoblasts. In vitro kinase assay using active MEK1, a 32P-labeled protein band corresponding to GST-MyoD was observed but not to mutant GST-MyoD-Y156F. Tyrosine phosphorylation of endogenous MyoD was detected with a specific anti-pMyoD-Y156 antibody; however, this response was blocked by PD184352, a MEK-specific inhibitor. These results indicate that activated MEK1 phosphorylates the MyoD-Y156 residue directly. Interestingly, the protein level of mutant MyoD-Y156F decreased compared with that of wild type but was recovered in the presence of lactacystin, a proteasome inhibitor. The protein level of MyoD-Y156E, which mimics phosphorylation at Tyr-156, was above that of wild type, indicating that the phosphorylation protects MyoD from the ubiquitin proteasome-mediated degradation. In addition, the low protein level of MyoD-Y156F was recovered over that of wild type by an additional mutation at Leu-164, a critical binding residue of MAFbx/AT-1, a Skp, Cullin, F-box (SCF) E3-ubiquitin ligase. The amount of MyoD co-precipitated with MAFbx/AT-1 also was reduced in the presence of active MEK1. Thus, these results suggested that the phosphorylation probably interrupts the binding of MAFbx/AT-1 to MyoD and thereby increases its stability. Collectively, our results suggest that MEK1 activated in differentiating myoblasts stimulates muscle differentiation by phosphorylating MyoD-Y156, which results in MyoD stabilization.
Mechanisms of HIV Receptor and Co-Receptor Down-Regulation by Prostratin: Role of Conventional and Novel PKC Isoforms

Prostratin is an unusual non-tumour promoting phorbol ester with potential as an inductive adjuvant therapy for highly active antiretroviral therapy (HAART) due to its ability to up-regulate viral expression from latent provirus. In addition, prostratin is also able to inhibit de novo HIV infection most probably because it induces down-regulation of HIV receptors from the surface of target cells. In this study, we investigate the mechanisms by which prostratin down-regulates HIV receptor and co-receptor surface expression in lymphocytic and monocytic cell lines. Our results indicate that prostratin induces down-regulation of surface expression of CD4 and CXCR4, but not CCR5, in various cell lines. Down-regulation of CD4 and CXCR4 by prostratin is achieved by internalization through receptor-mediated endocytosis and/or macropinocytosis, which is then followed by degradation of these molecules. Because prostratin is a protein kinase C (PKC) activator, we next examined the potential contribution of distinct PKC isoforms to down-regulate CD4 and CXCR4 in response to prostratin stimulation. Although exposure of cells to prostratin or phorbol-myristate-acetate (PMA) induces the translocation of several PKC isoforms to the plasma membrane, the use of specific PKC inhibitors revealed that novel PKCs are the main mediators of the prostratin-induced CD4 down-regulation, whereas both conventional and novel PKCs contribute to CXCR4 down-regulation. Altogether these results showed that prostratin, through the activation of conventional and/or novel PKC isoforms, rapidly reduces cell surface expression of CD4 and CXCR4, but not CCR5, by inducing their internalization and degradation.
A ganglion-cell-based primary image representation method and its contribution to object recognition

ABSTRACT A visual stimulus is represented by the biological visual system at several levels: in the order from low to high levels, they are: photoreceptor cells, ganglion cells (GCs), lateral geniculate nucleus cells and visual cortical neurons. Retinal GCs at the early level need to represent raw data only once, but meet a wide number of diverse requests from different vision-based tasks. This means the information representation at this level is general and not task-specific. Neurobiological findings have attributed this universal adaptation to GCs' receptive field (RF) mechanisms. For the purposes of developing a highly efficient image representation method that can facilitate information processing and interpretation at later stages, here we design a computational model to simulate the GC's non-classical RF. This new image presentation method can extract major structural features from raw data, and is consistent with other statistical measures of the image. Based on the new representation, the performances of other state-of-the-art algorithms in contour detection and segmentation can be upgraded remarkably. This work concludes that applying sophisticated representation schema at early state is an efficient and promising strategy in visual information processing.
Rpph1 Upregulates CDC42 Expression and Promotes Hippocampal Neuron Dendritic Spine Formation by Competing with miR-330-5p

Alzheimer’s disease (AD) is a heterogeneous neurodegenerative disease. Recent studies employing microRNA-seq and genome-wide sequencing have identified some non-coding RNAs that are influentially involved in AD pathogenesis. Non-coding RNAs can compete with other endogenous RNAs by microRNA response elements (MREs) and manipulate biological processes, such as tumorigenesis. However, only a few non-coding RNAs have been reported in the pathogenesis of AD. In this study, we constructed the first competing endogenous RNA (ceRNA) network leveraging whole transcriptome sequencing and a previously studied microRNA-seq of APPswe/PS1ΔE9 transgenic mice. The underlying mechanisms for the involvement of ceRNA in AD were validated using the Dual Luciferase Reporter Assay, detection of transcription levels by quantitative RT-PCR and translation levels by Western blotting, and morphological examination in primary cultured neurons. In the ceRNA network, four lncRNAs (C030034L19Rik, Rpph1, A830012C17Rik, and Gm15477) and five miRNAs (miR-182-5p, miR-330-5p, miR-326-3p, miR-132-3p, and miR-484) are enriched in nine pathways and an AD-related gene pool. Among them, Ribonuclease P RNA component H1 (Rpph1) is upregulated in the cortex of APPswe/PS1ΔE9 mice compared to wild type controls. Rpph1 binds to miR326-3p/miR-330-5p and causes the release of their downstream target Cdc42, which leads to CDC42 upregulation. This effect was disrupted upon mutation of the MRE on Rpph1. Moreover, overexpression of Rpph1 increased dendritic spine density in primary cultured hippocampal pyramidal neurons, whereas knocking down of Rpph1 had the reverse effect. In conclusion, Rpph1 modulates CDC42 expression level in a ceRNA-dependent manner, which may represent a compensatory mechanism in the early stage of the AD pathogenesis.
Effects of Cardiac Rehabilitation Program on Right Ventricular Function after Coronary Artery Bypass Graft Surgery

Background Cardiac rehabilitation has been recognized as one of the most effective strategies for managing cardiovascular indices as well as controlling the cardiovascular risk profile, in particular after coronary artery bypass graft surgery (CABG). However, the effect of this program on right ventricular function following CABG is unclear. The aim of this study was to evaluate the impact of cardiac rehabilitation on the right ventricular (RV) function in a cohort of patients who underwent CABG. Methods: A total of 28 patients who underwent CABG and participated consecutively in an 8-week cardiac rehabilitation program at Tehran Heart Center were studied. The control group consisted of 39 patients who refused to attend cardiac rehabilitation and only received postoperative medical treatment after registration in the Cardiac Rehabilitation Clinic. Two-dimensional and Doppler echocardiography was performed to assess the RV function in both groups at the three time points of before surgery, at the end of surgery, and at the end of the rehabilitation program. Results: Significant increase of RV function parameters were observed in both rehabilitation group (RG) and control group (CG) at the end of the rehabilitation program compared with post-CABG evaluation in terms of tricuspid annular plane systolic execution (RG: 12.50 mm to 14.18 mm; CG: 13.41 mm to 14.56 mm), tricuspid annular peak systolic velocity (RG: 8.55 cm/s to 9.14 cm/s; CG: 9.03 cm/s to 9.26 cm/s), and tricuspid annular late diastolic velocity (RG: 8.93 cm/s to 9.39 cm/s; CG: 9.26 cm/s to 9.60 cm/s). The parameters of the RV function did improve in both groups, but this improvement was not associated with participation in the complete cardiac rehabilitation program. Conclusion: The RV function parameters gradually improved after CABG; this progress, however, was independent of the exercise-based cardiac rehabilitation program.
Towards a hierarchy of loco-manipulation affordances

We propose a formalism for the hierarchical representation of affordances. Starting with a perceived model of the environment consisting of geometric primitives like planes or cylinders, we define a hierarchical system for affordance extraction whose foundation are elementary power grasp affordances. Higher-level affordances, e.g. bimanual affordances, result from combining lower-level affordances with additional properties concerning the underlying geometric primitives of the scene. We model affordances as continuous certainty functions taking into account properties of the environmental elements and the perceiving robot's embodiment. The developed formalism is regarded as the basis for the description of whole-body affordances, i.e. affordances associated with whole-body actions. The proposed formalism was implemented and experimentally evaluated in multiple scenarios based on RGB-D camera data. The feasibility of the approach is demonstrated on a real robotic platform.
Effects of grapefruit juice on the absorption of levothyroxine.

AIMS Our aim was to study the effect of grapefruit juice on the pharmacokinetics of levothyroxine. METHODS In a randomized cross-over study with two phases, 10 healthy subjects ingested 200 ml grapefruit juice or water (control) three times daily for 2 days. On day 3, a single 600 microg dose of levothyroxine was administered with 200 ml grapefruit juice or water, which was also ingested 1 h before and 1 h after levothyroxine. Serum concentrations of total thyroxine (T4) and thyroid-stimulating hormone (TSH) were measured up to 24 h. RESULTS Grapefruit juice decreased slightly (11%; P < 0.01) the maximal increase of T4 concentration after ingestion of levothyroxine from 66.4 nmol l(-1) to 59.4 nmol l(-1) (95% CI on the difference -11.3, -2.7). The incremental areas under the serum T4 concentration-time curve (dAUC) during the first 4 and 6 h were also decreased slightly: dAUC(0,4 h) by 13% (P < 0.05), from 195 nmol l(-1) h to 169 nmol l(-1) h (95% CI -51, -1) and dAUC(0,6 h) by 9% (P = 0.085), from 298 nmol l(-1) h to 271 nmol l(-1) h (95% CI -58, 4). The decrease in the serum concentration of TSH (1.25 mU l(-1)) measured 24 h after ingestion of levothyroxine, was not altered by grapefruit juice. CONCLUSIONS Grapefruit juice may slightly delay the absorption of levothyroxine, but it seems to have only a minor effect on its bioavailability. Accordingly, the clinical relevance of the grapefruit juice-levothyroxine interaction is likely to be small.
Phage Therapy and Photodynamic Therapy: Low Environmental Impact Approaches to Inactivate Microorganisms in Fish Farming Plants

Owing to the increasing importance of aquaculture to compensate for the progressive worldwide reduction of natural fish and to the fact that several fish farming plants often suffer from heavy financial losses due to the development of infections caused by microbial pathogens, including multidrug resistant bacteria, more environmentally-friendly strategies to control fish infections are urgently needed to make the aquaculture industry more sustainable. The aim of this review is to briefly present the typical fish farming diseases and their threats and discuss the present state of chemotherapy to inactivate microorganisms in fish farming plants as well as to examine the new environmentally friendly approaches to control fish infection namely phage therapy and photodynamic antimicrobial therapy.
Risk-dependent reward value signal in human prefrontal cortex

When making choices under uncertainty, people usually consider both the expected value and risk of each option, and choose the one with the higher utility. Expected value increases the expected utility of an option for all individuals. Risk increases the utility of an option for risk-seeking individuals, but decreases it for risk averse individuals. In 2 separate experiments, one involving imperative (no-choice), the other choice situations, we investigated how predicted risk and expected value aggregate into a common reward signal in the human brain. Blood oxygen level dependent responses in lateral regions of the prefrontal cortex increased monotonically with increasing reward value in the absence of risk in both experiments. Risk enhanced these responses in risk-seeking participants, but reduced them in risk-averse participants. The aggregate value and risk responses in lateral prefrontal cortex contrasted with pure value signals independent of risk in the striatum. These results demonstrate an aggregate risk and value signal in the prefrontal cortex that would be compatible with basic assumptions underlying the mean-variance approach to utility.
Extra-Anatomic Ascending Aorta to Abdominal Aorta Bypass in Takayasu Arteritis Patients with Mid-Aortic Syndrome

Background We evaluated the operative outcomes of an extra-anatomic bypass from the ascending aorta to the abdominal aorta in patients with type II or III Takayasu arteritis (TA) with mid-aortic syndrome. Methods From 1988 to 2014, 8 patients with type II (n=2) or III (n=6) TA underwent an ascending aorta to abdominal aorta bypass. The mean patient age was 43.5±12.2 years and the mean peak pressure gradient between the upper and lower extremities was 54.8±39.0 mm Hg. The median follow-up duration was 54.4 months (range, 17.8 to 177.4 months). Results There were no cases of operative mortality. The mean peak pressure gradient significantly decreased to −2.4±32.3 mm Hg (p=0.017 compared to the preoperative value). Late death occurred in 2 patients. The symptoms of upper extremity hypertension and claudication improved in all patients. The bypass grafts were patent at 47.1±58.9 months in 7 patients who underwent follow-up imaging studies. Conclusion An extra-anatomic ascending aorta to abdominal aorta bypass could be an effective treatment option for severe aortic steno-occlusive disease in patients with type II or III TA, with favorable early and long-term outcomes.
Force Modeling in Single Point Incremental Forming of Variable Wall Angle Components

Prediction of forming forces in Incremental Sheet Forming (ISF) is specially important in the case of using adapted machinery not designed for the process. Moreover, forming force is an important indicator that can be monitored on-line and utilized for real time process control. Besides experimentation, simulations based on the Finite Element Method (FEM) have been utilized as a reliable source of process force data. Nevertheless, the long solution times required to simulate ISF renders difficult its inclusion into a process optimization chain. In consequence, models that predict the forces required to manufacture simple parts have appeared. This work begins with a review of forming force models available for Single Point Incremental Forming (SPIF). Then, an equation recently proposed in the literature is compared with published experimental results of SPIF under different working conditions. The same data is employed to verify our own FEM simulations. Finally, the above-mentioned formula and FEM simulation were applied to predict the forming force of Variable Wall Angle (VWA) geometries where available force information is limited. Besides the applicability assessment of the equation, results will supplement a future experimental campaign focused in modeling geometries of intermediate complexity level by means of Computational Intelligence methods.
Long-Term Nonprogressor and Elite Controller Patients Who Control Viremia Have a Higher Percentage of Methylation in Their HIV-1 Proviral Promoters than Aviremic Patients Receiving Highly Active Antiretroviral Therapy

ABSTRACT Several factors are involved in the control of HIV transcription/replication, including epigenetic modifications at the promoter level. Analysis of the HIV long terminal repeat (LTR) methylation status in infected patients controlling viremia is scarce. Herein, we show a higher degree of DNA methylation in the 5′-LTR of long-term nonprogressor and elite controller (LTNP/EC) versus progressor patients and a positive correlation with time of infection, indicating a certain contribution of HIV LTR silencing in reducing the number of replicating viruses which may account for a delayed progression.
Results of the Randomized Danish Lung Cancer Screening Trial with Focus on High-Risk Profiling.

RATIONALE As of April 2015, participants in the Danish Lung Cancer Screening Trial had been followed for at least 5 years since their last screening. OBJECTIVES Mortality, causes of death, and lung cancer findings are reported to explore the effect of computed tomography (CT) screening. METHODS A total of 4,104 participants aged 50-70 years at the time of inclusion and with a minimum 20 pack-years of smoking were randomized to have five annual low-dose CT scans (study group) or no screening (control group). MEASUREMENTS AND MAIN RESULTS Follow-up information regarding date and cause of death, lung cancer diagnosis, cancer stage, and histology was obtained from national registries. No differences between the two groups in lung cancer mortality (hazard ratio, 1.03; 95% confidence interval, 0.66-1.6; P = 0.888) or all-cause mortality (hazard ratio, 1.02; 95% confidence interval, 0.82-1.27; P = 0.867) were observed. More cancers were found in the screening group than in the no-screening group (100 vs. 53, respectively; P < 0.001), particularly adenocarcinomas (58 vs. 18, respectively; P < 0.001). More early-stage cancers (stages I and II, 54 vs. 10, respectively; P < 0.001) and stage IIIa cancers (15 vs. 3, respectively; P = 0.009) were found in the screening group than in the control group. Stage IV cancers were nonsignificantly more frequent in the control group than in the screening group (32 vs. 23, respectively; P = 0.278). For the highest-stage cancers (T4N3M1, 21 vs. 8, respectively; P = 0.025), this difference was statistically significant, indicating an absolute stage shift. Older participants, those with chronic obstructive pulmonary disease, and those with more than 35 pack-years of smoking had a significantly increased risk of death due to lung cancer, with nonsignificantly fewer deaths in the screening group. CONCLUSIONS No statistically significant effects of CT screening on lung cancer mortality were found, but the results of post hoc high-risk subgroup analyses showed nonsignificant trends that seem to be in good agreement with the results of the National Lung Screening Trial. Clinical trial registered with www.clinicaltrials. gov (NCT00496977).
Comparative Effectiveness Research: An Empirical Study of Trials Registered in ClinicalTrials.gov

Background The $1.1 billion investment in comparative effectiveness research will reshape the evidence-base supporting decisions about treatment effectiveness, safety, and cost. Defining the current prevalence and characteristics of comparative effectiveness (CE) research will enable future assessments of the impact of this program. Methods We conducted an observational study of clinical trials addressing priority research topics defined by the Institute of Medicine and conducted in the US between 2007 and 2010. Trials were identified in ClinicalTrials.gov. Main outcome measures were the prevalence of comparative effectiveness research, nature of comparators selected, funding sources, and impact of these factors on results. Results 231 (22.3%; 95% CI 19.8%–24.9%) studies were CE studies and 804 (77.7%; 95% CI, 75.1%–80.2%) were non-CE studies, with 379 (36.6%; 95% CI, 33.7%–39.6%) employing a placebo control and 425 (41.1%; 95% CI, 38.1%–44.1%) no control. The most common treatments examined in CE studies were drug interventions (37.2%), behavioral interventions (28.6%), and procedures (15.6%). Study findings were favorable for the experimental treatment in 34.8% of CE studies and greater than twice as many (78.6%) non-CE studies (P<0.001). CE studies were more likely to receive government funding (P = 0.003) and less likely to receive industry funding (P = 0.01), with 71.8% of CE studies primarily funded by a noncommercial source. The types of interventions studied differed based on funding source, with 95.4% of industry trials studying a drug or device. In addition, industry-funded CE studies were associated with the fewest pediatric subjects (P<0.001), the largest anticipated sample size (P<0.001), and the shortest study duration (P<0.001). Conclusions In this sample of studies examining high priority areas for CE research, less than a quarter are CE studies and the majority is supported by government and nonprofits. The low prevalence of CE research exists across CE studies with a broad array of interventions and characteristics.
A Numerical Model for Brownian Particles Fluctuating in Incompressible Fluids

We present a numerical method that consistently implements thermal fluctuations and hydrodynamic interactions to the motion of Brownian particles dispersed in incompressible host fluids. In this method, the thermal fluctuations are introduced as random forces acting on the Brownian particles. The hydrodynamic interactions are introduced by directly resolving the fluid motions with the particle motion as a boundary condition to be satisfied. The validity of the method has been examined carefully by comparing the present numerical results with the fluctuation–dissipation theorem whose analytical form is known for dispersions of a single spherical particle. Simulations are then performed for more complicated systems, such as a dispersion composed of many spherical particles and a single polymeric chain in a solvent.