Miracle-dz/UniFAR-FTUs huggingface dataset:
Si tunneling transistors with high on-currents and slopes of 50 mV/dec using segregation doped Nisi2 tunnel junctions

Planar and nanowire (NW) tunneling field effect transistors (TFETs) have been fabricated on ultra thin strained and unstrained SOI with shallow doped Nickel disilicide (NiSi2) source and drain (S/D) contacts. We developed a novel, self-aligned process to form the p-i-n TFETs which greatly easies their fabrication by tilted dopant implantation using the high-k/metal gate as a shadow mask and dopant segregation. Two methods of dopant segregation are compared: Dopant segregation based on the “snow-plough” effect of dopants during silicidation and implantation into the silicide (IIS) followed by thermal outdiffusion. High drive currents of up to 60 μA/μm of planar p-TFETs were achieved indicating good silicide/silicon tunneling junctions. The non linear temperature dependence of the inverse subthreshold slope S indicates typical TFET behavior. Strained Si NW array n-TFETs with omega shaped HfO2/TiN gates showed high drive currents of 7 μA/μm @ 1V Vdd and steep inverse subthreshold slopes with minimum values of 50mV/dec due to the smaller band gap of strained Si and optimized electrostatics.
Construction of protein interaction network involved in lung adenocarcinomas using a novel algorithm

Studies that only assess differentially-expressed (DE) genes do not contain the information required to investigate the mechanisms of diseases. A complete knowledge of all the direct and indirect interactions between proteins may act as a significant benchmark in the process of forming a comprehensive description of cellular mechanisms and functions. The results of protein interaction network studies are often inconsistent and are based on various methods. In the present study, a combined network was constructed using selected gene pairs, following the conversion and combination of the scores of gene pairs that were obtained across multiple approaches by a novel algorithm. Samples from patients with and without lung adenocarcinoma were compared, and the RankProd package was used to identify DE genes. The empirical Bayesian (EB) meta-analysis approach, the search tool for the retrieval of interacting genes/proteins database (STRING), the weighted gene coexpression network analysis (WGCNA) package and the differentially-coexpressed genes and links package (DCGL) were used for network construction. A combined network was also constructed with a novel rank-based algorithm using a combined score. The topological features of the 5 networks were analyzed and compared. A total of 941 DE genes were screened. The topological analysis indicated that the gene interaction network constructed using the WGCNA method was more likely to produce a small-world property, which has a small average shortest path length and a large clustering coefficient, whereas the combined network was confirmed to be a scale-free network. Gene pairs that were identified using the novel combined method were mostly enriched in the cell cycle and p53 signaling pathway. The present study provided a novel perspective to the network-based analysis. Each method has advantages and disadvantages. Compared with single methods, the combined algorithm used in the present study may provide a novel method to analyze gene interactions, with increased credibility.
The Genetic Consequences of Spatially Varying Selection in the Panmictic American Eel (Anguilla rostrata)

Our understanding of the genetic basis of local adaptation has recently benefited from the increased power to identify functional variants associated with environmental variables at the genome scale. However, it often remains challenging to determine whether locally adaptive alleles are actively maintained at intermediate frequencies by spatially varying selection. Here, we evaluate the extent to which this particular type of balancing selection explains the retention of adaptive genetic variation in the extreme situation of perfect panmixia, using the American eel (Anguilla rostrata) as a model. We first conducted a genome scan between two samples from opposite ends of a latitudinal environmental gradient using 454 sequencing of individually tagged cDNA libraries. Candidate SNPs were then genotyped in 992 individuals from 16 sampling sites at different life stages of the same cohort (including larvae from the Sargasso Sea, glass eels, and 1-year-old individuals) as well as in glass eels of the following cohort. Evidence for spatially varying selection was found at 13 loci showing correlations between allele frequencies and environmental variables across the entire species range. Simulations under a multiple-niche Levene’s model using estimated relative fitness values among genotypes rarely predicted a stable polymorphic equilibrium at these loci. Our results suggest that some genetic-by-environment interactions detected in our study arise during the progress toward fixation of a globally advantageous allele with spatially variable effects on fitness.
A guide to uncertainty quantification and sensitivity analysis for cardiovascular applications

As we shift from population‐based medicine towards a more precise patient‐specific regime guided by predictions of verified and well‐established cardiovascular models, an urgent question arises: how sensitive are the model predictions to errors and uncertainties in the model inputs? To make our models suitable for clinical decision‐making, precise knowledge of prediction reliability is of paramount importance. Efficient and practical methods for uncertainty quantification (UQ) and sensitivity analysis (SA) are therefore essential. In this work, we explain the concepts of global UQ and global, variance‐based SA along with two often‐used methods that are applicable to any model without requiring model implementation changes: Monte Carlo (MC) and polynomial chaos (PC). Furthermore, we propose a guide for UQ and SA according to a six‐step procedure and demonstrate it for two clinically relevant cardiovascular models: model‐based estimation of the fractional flow reserve (FFR) and model‐based estimation of the total arterial compliance (CT). Both MC and PC produce identical results and may be used interchangeably to identify most significant model inputs with respect to uncertainty in model predictions of FFR and CT. However, PC is more cost‐efficient as it requires an order of magnitude fewer model evaluations than MC. Additionally, we demonstrate that targeted reduction of uncertainty in the most significant model inputs reduces the uncertainty in the model predictions efficiently. In conclusion, this article offers a practical guide to UQ and SA to help move the clinical application of mathematical models forward. Copyright © 2015 John Wiley & Sons, Ltd.
Image segmentation using a texture gradient based watershed transform

The segmentation of images into meaningful and homogenous regions is a key method for image analysis within applications such as content based retrieval. The watershed transform is a well established tool for the segmentation of images. However, watershed segmentation is often not effective for textured image regions that are perceptually homogeneous. In order to segment such regions properly, the concept of the "texture gradient" is introduced. Texture information and its gradient are extracted using a novel nondecimated form of a complex wavelet transform. A novel marker location algorithm is subsequently used to locate significant homogeneous textured or non textured regions. A marker driven watershed transform is then used to segment the identified regions properly. The combined algorithm produces effective texture and intensity based segmentation for application to content based image retrieval.
Cost-utility analysis of second-line hormonal therapy in advanced breast cancer: a comparison of two aromatase inhibitors to megestrol acetate

Randomized trials comparing the aromatase inhibitors, anastrozole and letrozole, to megestrol acetate (MA) in postmenopausal women with advanced breast cancer demonstrated that both agents are better tolerated than MA with comparable efficacy. In addition, one trial revealed that tumor response and time to treatment failure were significantly better with letrozole. Since oncologists are faced with a choice between three agents with at least comparable efficacy but different toxicity profiles and cost, a cost-utility analysis was conducted to quantify these differences and to determine if the new agents are more cost-effective than MA. In the absence of a randomized three-arm trial, a decision model was developed to simulate the most common therapeutic outcomes. The clinical data were obtained from an overview analysis of randomized trials. Total hospital resource consumption was collected from 87 patients with advanced disease that had failed second-line hormonal therapy. Utility estimates were obtained from interviewing a random sample of 25 women from the general public and 25 female health care professionals using the Time Trade-Off technique. The model suggested a similar duration of quality-adjusted progression-free survival between drugs (letrozole 150 days, anastrozole 153 days and MA 146 days). Letrozole had an overall cost of Can$2949 per patient which was comparable to MA at Can$2966 per patient. In contrast, anastrozole was slightly more costly than MA at $Can3149 per patient, respectively. The analysis revealed that letrozole has comparable overall costs relative to MA while providing at least equivalent quality-adjusted progression-free survival. These outcomes were largely related to its higher tumor response rate, which translated to a lower proportion of patients requiring chemotherapy. Anastrozole was slightly more costly than MA and did not demonstrate superiority in quality-adjusted progression-free survival in this palliative setting.
The effects of subchorionic hematoma on pregnancy outcome in patients with threatened abortion.

OBJECTIVE To assess the effects of ultrasonographically detected subchorionic hematomas on pregnancy outcomes in patients with vaginal bleeding within the first half of pregnancy. MATERIAL AND METHODS Patients diagnosed with threatened abortion due to painless vaginal bleeding and who were followed up in an in-patient service during the first vaginal bleeding between January 2009 and December 2010 were included in this retrospective cohort study. Patients were divided into two groups according to the presence of subchorionic hematoma. Miscarriage rates and pregnancy outcomes of ongoing pregnancies were compared between the groups. RESULTS There were no statistically significant differences between the groups regarding demographic parameters, including age, parity, previous miscarriage history, and gestational age at first vaginal bleeding. While 13 of 44 pregnancies (29.5%) with subchorionic hematoma resulted in miscarriage, 25 of 198 pregnancies (12.6%) without subchorionic hematoma resulted in miscarriage (p=.010). The gestational age at miscarriage and the duration between first vaginal bleeding and miscarriage were similar between the groups. The outcome measures of ongoing pregnancies, such as gestational week at delivery, birth weight, and delivery route, were also similar between the groups. CONCLUSION Ultrasonographically detected subchorionic hematoma increases the risk of miscarriage in patients with vaginal bleeding and threatened abortion during the first 20 weeks of gestation. However, it does not affect the pregnancy outcome measures of ongoing pregnancies.
The Impact of Common Planning Time on Middle Grades Students and Teachers.

AbstractThis descriptive study examines the practice of common planning time (CPT) for middle grades teachers who are members of interdisciplinary teams and the impact that this practice has on students' self-concepts and perceptions of their school climate and teachers' perceptions of their working environment. Instruments used were the Self-Description Questionnaire-II, Quality of School Life Scale, and Teacher Opinion Questionnaire. Results showed that students receiving instruction from teachers on interdisciplinary teams with CPT had higher overall self-concepts and more positive overall perceptions of their school climate than did students receiving instruction from teachers on interdisciplinary teams without CPT, organized departmentally. In addition, results of the study showed that teachers on interdisciplinary teams with CPT had more positive overall perceptions of their working environment than did teachers who were organized departmentally. The findings suggest that CPT for teachers on interdi.
RNA secondary structure regulates the translation of sxy and competence development in Haemophilus influenzae

The sxy (tfoX) gene product is the central regulator of DNA uptake by naturally competent γ-proteobacteria such as Haemophilus influenzae, Vibrio cholerae and probably Escherichia coli. However, the mechanisms regulating sxy gene expression are not understood despite being key to understanding the physiological role of DNA uptake. We have isolated mutations in H. influenzae sxy that greatly elevate translation and thus cause competence to develop in otherwise non-inducing conditions (hypercompetence). In vitro nuclease analysis confirmed the existence of an extensive secondary structure at the 5′ end of sxy mRNA that sequesters the ribosome-binding site and start codon in a stem-loop. All of the hypercompetence mutations reduced mRNA base pairing, and one was shown to cause a global destabilization that increased translational efficiency. Conversely, mutations engineered to add mRNA base pairs strengthened the secondary structure, resulting in reduced translational efficiency and greatly reduced competence for genetic transformation. Transfer of wild-type cells to starvation medium improved translational efficiency of sxy while independently triggering the sugar starvation regulator (CRP) to stimulate transcription at the sxy promoter. Thus, mRNA secondary structure is responsive to conditions where DNA uptake will be favorable, and transcription of sxy is simultaneously enhanced if CRP activation signals that energy supplies are limited.
Altered Folate Availability Modifies the Molecular Environment of the Human Colorectum: Implications for Colorectal Carcinogenesis

Low folate status increases colorectal cancer risk. Paradoxically, overly abundant folate supplementation, which is not uncommon in the United States, may increase risk. The mechanisms of these effects are unknown. We conducted two translational studies to define molecular pathways in the human colon altered either by folate supplementation or by dietary folate depletion (followed by repletion). In the first study, 10 healthy, at-risk volunteers (with documented stable/normal folate intake) received supplemental folic acid (1 mg/d) for 8 weeks. In the second study, 10 similar subjects were admitted to a hospital as inpatients for 12 weeks to study folate depletion induced by a low folate diet. A repletion regimen of folic acid (1 mg/d) was provided for the last 4 of these weeks. Both studies included an 8-week run-in period to ensure stabilized folate levels prior to intervention. We obtained 12 rectosigmoid biopsies (from 4 quadrants of normal-appearing mucosa 10–15 cm from the anal verge) at baseline and at measured intervals in both studies for assessing the primary endpoints: genome-wide gene expression, genomic DNA methylation, promoter methylation (depletion/repletion study only), and p53 DNA strand breaks. Serum and rectosigmoid folate concentrations accurately tracked all changes in folate delivery (P < 0.05). In the first study, gene array analysis revealed that supplementation upregulated multiple inflammation- and immune-related pathways in addition to altering several 1-carbon–related enzymes (P < 0.001). In the second study, folate depletion downregulated genes involved in immune response, inflammation, the cell cycle, and mitochondrial/energy pathways; repletion reversed most of these changes. However, changes in gene expression after repletion in the second study (involving immune response and inflammation) did not reach the levels seen after supplementation in the first study. Neither genomic nor promoter-specific DNA methylation changed during the course of the depletion/repletion protocol, and genomic methylation did not change with supplementation in the first study. p53 DNA strand breaks increased with depletion after 12 weeks. In sum, depletion downregulates, whereas repletion or supplementation upregulates pathways related to inflammation and immune response. These findings provide novel support to the concept that excessive folate supplementation might promote colorectal carcinogenesis by enhancing proinflammatory and immune response pathways. These results indicate that modest changes in folate delivery create substantial changes in the molecular milieu of the human colon. Cancer Prev Res; 4(4); 530–43. ©2011 AACR.
Reinforcement learning for dialog management using least-squares Policy iteration and fast feature selection

Reinforcement learning (RL) is a promising technique for creating a dialog manager. RL accepts features of the current dialog state and seeks to find the best action given those features. Although it is often easy to posit a large set of potentially useful features, in practice, it is difficult to find the subset which is large enough to contain useful information yet compact enough to reliably learn a good policy. In this paper, we propose a method for RL optimization which automatically performs feature selection. The algorithm is based on least-squares policy iteration, a state-of-the-art RL algorithm which is highly sampleefficient and can learn from a static corpus or on-line. Experiments in dialog simulation show it is more stable than a baseline RL algorithm taken from a working dialog system.
Music Therapy Using Singing Training Improves Psychomotor Speed in Patients with Alzheimer's Disease: A Neuropsychological and fMRI Study

Background/Aims: To investigate the effect of singing training on the cognitive function in Alzheimer's disease (AD) patients. Methods: Ten AD patients (mean age 78.1 years) participated in music therapy using singing training once a week for 6 months (music therapy group). Each session was performed with professional musicians using karaoke and a unique voice training method (the YUBA Method). Before and after the intervention period, each patient was assessed by neuropsychological batteries, and functional magnetic resonance imaging (fMRI) was performed while the patients sang familiar songs with a karaoke device. As the control group, another 10 AD patients were recruited (mean age 77.0 years), and neuropsychological assessments were performed twice with an interval of 6 months. Results: In the music therapy group, the time for completion of the Japanese Raven's Colored Progressive Matrices was significantly reduced (p = 0.026), and the results obtained from interviewing the patients' caregivers revealed a significant decrease in the Neuropsychiatric Inventory score (p = 0.042) and a prolongation of the patients' sleep time (p = 0.039). The fMRI study revealed increased activity in the right angular gyrus and the left lingual gyrus in the before-minus-after subtraction analysis of the music therapy intervention. Conclusion: Music therapy intervention using singing training may be useful for dementia patients by improving the neural efficacy of cognitive processing.
OATP and P-glycoprotein transporters mediate the cellular uptake and excretion of fexofenadine.

Fexofenadine, a nonsedating antihistamine, does not undergo significant metabolic biotransformation. Accordingly, it was hypothesized that uptake and efflux transporters could be importantly involved in the drug's disposition. Utilizing a recombinant vaccinia expression system, members of the organic anion transporting polypeptide family, such as the human organic anion transporting polypeptide (OATP) and rat organic anion transporting polypeptides 1 and 2 (Oatp1 and Oatp2), were found to mediate [(14)C]fexofenadine cellular uptake. On the other hand, the bile acid transporter human sodium taurocholate cotransporting polypeptide (NTCP) and the rat organic cation transporter rOCT1 did not exhibit such activity. P-glycoprotein (P-gp) was identified as a fexofenadine efflux transporter, using the LLC-PK1 cell, a polarized epithelial cell line lacking P-gp, and the derivative cell line (L-MDR1), which overexpresses P-gp. In addition, oral and i.v. administration of [(14)C]fexofenadine to mice lacking mdr1a-encoded P-gp resulted in 5- and 9-fold increases in the drug's plasma and brain levels, respectively, compared with wild-type mice. Also, a number of drug inhibitors of P-gp were found to be effective inhibitors of OATP. Because OATP transporters and P-gp colocalize in organs of importance to drug disposition such as the liver, their activity provides an explanation for the heretofore unknown mechanism(s) responsible for fexofenadine's disposition and suggests potentially similar roles in the disposition of other xenobiotics.
VISCOELASTIC MODEL FOR THERMOFORMING PROCESS OF THERMOPLASTIC COMPOSITE SHEETS

SUMMARY: An implicit finite element method is presented to analyze the thermoforming process of thermoplastic sheets reinforced with unidirectional continuous fibers. Unlike previous research works considering viscous or elastic behaviors for melted resin at the forming temperature, the reinforced laminates are regarded as an anisotropic viscoelastic material according to previous experimental studies. The transient reversible network theory is used to model the material behavior at the finite deformation. The kinematical constrains of material incompressibility and fiber inextensibility is considered in the finite element formulation. The present method is employed to analyze the pictureframe test of thermoplastic specimen reinforced with unidirectional fibers at forming temperature and the results are compared with the analytical solutions.
MiaB Protein Is a Bifunctional Radical-S-Adenosylmethionine Enzyme Involved in Thiolation and Methylation of tRNA*

The last biosynthetic step for 2-methylthio-N6-isopentenyl-adenosine (ms2i6A), present at position 37 in some tRNAs, consists of the methylthiolation of the isopentenyl-adenosine (i6A) precursor. In this work we have reconstituted in vitro the conversion of i6A to ms2i6A within a tRNA substrate using the iron-sulfur MiaB protein, S-adenosylmethionine (AdoMet), and a reducing agent. We show that a synthetic i6A-containing RNA corresponding to the anticodon stem loop of tRNAPhe is also a substrate. This study demonstrates that MiaB protein is a bifunctional system, involved in both thiolation and methylation of i6A. In this process, one molecule of AdoMet is converted to 5′-deoxyadenosine, probably through reductive cleavage and intermediate formation ofa5′-deoxyadenosyl radical as observed in other “Radical-AdoMet” enzymes, and a second molecule of AdoMet is used as a methyl donor as shown by labeling experiments. The origin of the sulfur atom is discussed.