Miracle-dz/UniFAR-FTUs huggingface dataset:
Oncologic Outcomes of Breast Cancer Patients Treated with Oncoplastic Surgery

Background: The impact of breast appearance after breast cancer surgical treatment on patients’ quality of life led to the development of the oncoplastic approach. However, studies reporting oncologic results associated with this treatment strategy are scarce. This cross-sectional study was designed to assess oncologic outcomes among patients who underwent oncoplastic surgery. Methods: A total of 190 breast cancer patients who underwent breast-conserving surgery were enrolled. Fifty of them underwent oncoplastic surgery and 140 had none breast reconstruction procedure (control group). All surgeries were performed by the same surgical team. Results: Groups were similar with regard to staging, histological type, grade of the tumor, presence of intraductal component, hormone receptors and nodal commitment. Patients in oncoplastic surgery group had larger tumors (ρ = 0.001) and more lymphovascular invasion (ρ = 0.047). Further, a higher proportion of them underwent chemotherapy (ρ = 0.030). Follow-up time of control group was longer (ρ = 0.05), and these patients also had a longer relapse-free survival time (ρ = 0.001). Local recurrence rate was 5.8% (11/190) and it was significantly greater in the oncoplastic surgery group (8/11, ρ = 0.001). Time to local recurrence after surgery was longer in oncoplastic surgery group (ρ = 0.002). Overall, patients in oncoplastic surgery group were younger (ρ = 0.001), but at the time of local recurrence, patients in oncoplastic surgery group were older than those in control group (ρ = 0.0002). Conclusions: Among the studied patients, local recurrence rate was greater in those who underwent oncoplastic surgery.
1-1-2011 Brain Activity Elicited by Positive and Negative Feedback in Preschool-Aged Children

To investigate the processing of positive vs. negative feedback in children aged 4–5 years, we devised a prize-guessing game that is analogous to gambling tasks used to measure feedback-related brain responses in adult studies. Unlike adult studies, the feedback-related negativity (FRN) elicited by positive feedback was as large as that elicited by negative feedback, suggesting that the neural system underlying the FRN may not process feedback valence in early childhood. In addition, positive feedback, compared with negative feedback, evoked a larger P1 over the occipital scalp area and a larger positive slow wave (PSW) over the right central-parietal scalp area. We believe that the PSW is related to emotional arousal and the intensive focus on positive feedback that is present in the preschool and early school years has adaptive significance for both cognitive and emotional development during this period. Citation: Mai X, Tardif T, Doan SN, Liu C, Gehring WJ, et al. (2011) Brain Activity Elicited by Positive and Negative Feedback in Preschool-Aged Children. PLoS ONE 6(4): e18774. doi:10.1371/journal.pone. 0018774 Editor: Sam Gilbert, University College London, United Kingdom Received February 1, 2011; Accepted March 9, 2011; Published April 19, 2011 Copyright: 2011 Mai et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by NSF grant SES-0527475 on Emotion Regulation as a Complex System, internal funding from the Center for Human Growth and Development to TT, and by NSFC (30930031), Ministry of Sci & Tech (973 Program, 2011CB711001), National Key Technologies R&D Program (2009BAI77B01) and Global Research Initiative Program, NIH, USA (1R01TW007897) to Y-JL. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: twila@umich.edu (TT); luoyj@bnu.edu. cn (Y-JL)
Lateral entrapment of sediment in tidal estuaries: an idealized model study

Two physical mechanisms leading to lateral accumulation of sediment in tidally dominated estuaries are investigated, involving Coriolis forcing and lateral density gradients. An idealized model is used that consists of the three? dimensional shallow water equations and sediment mass balance. Conditions are assumed to be uniform in the along? estuary direction. A semidiurnal tidal discharge and tidally averaged density gradients are prescribed. The erosional sediment flux at the bed depends both on the bed shear stress and on the amount of sediment available in mud reaches for resuspension. The distribution of mud reaches over the bed is selected such that sediment transport is in morphodynamic equilibrium, that is, tidally averaged erosion and deposition of sediment at the bed balance. Analytical solutions are obtained by using perturbation analysis. Results suggest that in most estuaries lateral density gradients induce more sediment transport than Coriolis forcing. When frictional forces are small (Ekman number E 0.02), the lateral density gradient mechanism dominates and entraps sediment in areas with fresher water. Results also show that the lateral sediment transport induced by the semidiurnal tidal flow is significant when frictional forces are small (E ? 0.02). Model predictions are in good agreement with observations from the James River estuary.
Molecular Dynamics of µ Opioid Receptor Complexes with Agonists and Antagonists

Opioid receptors like other G-protein-coupled receptors undergo specific rearrangements of structure upon ac- tivation by agonists. Such processes proceed via several steps ruled by different molecular switches. In order to reveal the first steps of receptor activation concurrent with ligand binding, we investigated μ opioid receptor complexes with an- tagonists - naltrexone and ￻-FNA, and two closely related agonists - morphine and N-methyl-morphine. The molecular dynamics simulations revealed distinct binding modes of analyzed antagonists and agonists. They all interacted with D3.32 on TM3 but while the antagonists formed a bond with Y3.33 (TM3) the agonists bound H6.52 (TM6). Furthermore, it was possible to observe a break of a hydrogen bond D3.32-Y7.43 between TM3 and TM7 (3-7 lock) during simulations of agonist complexes but not those of antagonist. Interdependence between the 3-7 lock and the rotamer toggle switch of W6.48 is proposed based on simulation of the naltrexone complex restrained to force an agonistic action.
Use of a Tissue Engineered Human Skin Model to Investigate the Effects of Wounding and of an Anti-Inflammatory on Melanoma Cell Invasion

An increasing number of studies suggest inflammation stimulates tumour invasion. In melanoma, despite recent advances in targeted therapy and immunomodulatory therapies, this cancer remains difficult to treat. Our previous studies show melanoma cells interact with skin cells in their invasion into tissue engineered skin and suggest inflammation stimulates invasion. The aim of this study was to investigate the use of an anti-inflammatory on melanoma invasion. To do this we developed a wounded and inflamed in vitro 3D melanoma model in which to investigate the use of an anti-inflammatory on melanoma invasion. The tissue engineered skin model was based on human de-epidermised acellular dermis to which keratinocytes, fibroblasts and three different melanoma cell lines were added in various combinations. A simple incisional wound was made in the model and TNF-α and fibrin were added to simulate conditions of inflammation. Topical ibuprofen in a hydrogel was added and the extent of melanoma invasion into the dermis was assessed under the various conditions. The results showed that penetration of two of the cell lines (HBL and A375SM) into the tissue engineered skin was exacerbated by wounding and ibuprofen significantly decreased invasion of A375SM cells and slightly reduced invasion of HBL cells. A third cell line, C8161, was aggressively invasive under all conditions to an extent that was not influenced by wounding, TNF-α or the addition of ibuprofen. In summary, the results for one these cell lines (and a trend for a second cell line) support the hypothesis that a wound environment is conducive to melanoma invasion but the local addition of an anti-inflammatory drug such as ibuprofen may attenuate invasion.
Donor‐Derived Trypanosoma cruzi Infection in Solid Organ Recipients in the United States, 2001–2011

Although Trypanosoma cruzi, the parasite that causes Chagas disease, can be transmitted via organ transplantation, liver and kidney transplantation from infected donors may be feasible. We describe the outcomes of 32 transplant recipients who received organs from 14 T. cruzi seropositive donors in the United States from 2001 to 2011. Transmission was confirmed in 9 recipients from 6 donors, including 3 of 4 (75%) heart transplant recipients, 2 of 10 (20%) liver recipients and 2 of 15 (13%) kidney recipients. Recommended monitoring posttransplant consisted of regular testing by PCR, hemoculture, and serology. Thirteen recipients had no or incomplete monitoring; transmission was confirmed in five of these recipients. Four of the five recipients had symptomatic disease and all four died although death was directly related to Chagas disease in only one. Nineteen recipients had partial or complete monitoring for T. cruzi infection with weekly testing by PCR, hemoculture and serology; transmission was confirmed in 4 of 19 recipients with no cases of symptomatic disease. Our results suggest that liver and kidney transplantation from T. cruzi seropositive donors may be feasible when the recommended monitoring schedule for T. cruzi infection is followed and prompt therapy with benznidazole can be administered.
THE DISTRIBUTION OF PRICE CHANGES WORKING PAPER 99 / 2015

This study shows that replacing the traditional measure of asymmetry that is skewness in the inflation forecasting model with an alternative asymmetry measure that captures the joint influence of both skewness and variance on inflation significantly improves the forecast at various horizons. The empirical evidence suggests that it is more appropriate to use such measure of asymmetry in inflation forecast model as it has edge over simple measure of skewness in predicting inflation. These findings are consistent with the prediction of menu cost model that the variance of cross sectional distribution of relative price changes amplifies the impact of skewness on inflation.
Eliminating Stop-Points in the Installation and Use of Anonymity Systems: a Usability Evaluation of the Tor Browser Bundle

Broad-based participation in anonymizing technology can be hindered by a lack of usability. Since systems such as Tor give 1 n anonymity, the existence of stop-points is of particular concern because wider adoption of Tor equals better anonymity for all users of the system. Stop points are places in an interface at which an individual is at risk from being presented with a situation which may prevent them from moving forward with installation or use. Sixty four percent of users in our study encountered at least one stop-point while using the Tor Browser Bundle. While each stop-point may be minor in isolation, the cumulative effect is great and has the potential to harm the overall anonymity of the system. In this paper we enumerate these stop points and detail speciﬁc design changes that may address them. We also provide more generic but generalizable recommendations for the design of anonymity systems. Taken together, these suggestions may enhance usability and thus anonymity of individual users as well as system level anonymity.
Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing

Reduced representation bisulfite sequencing (RRBS) has been used to profile DNA methylation patterns in mammalian genomes such as human, mouse and rat. The methylome of the zebrafish, an important animal model, has not yet been characterized at base-pair resolution using RRBS. Therefore, we evaluated the technique of RRBS in this model organism by generating four single-nucleotide resolution DNA methylomes of adult zebrafish brain. We performed several simulations to show the distribution of fragments and enrichment of CpGs in different in silico reduced representation genomes of zebrafish. Four RRBS brain libraries generated 98 million sequenced reads and had higher frequencies of multiple mapping than equivalent human RRBS libraries. The zebrafish methylome indicates there is higher global DNA methylation in the zebrafish genome compared with its equivalent human methylome. This observation was confirmed by RRBS of zebrafish liver. High coverage CpG dinucleotides are enriched in CpG island shores more than in the CpG island core. We found that 45% of the mapped CpGs reside in gene bodies, and 7% in gene promoters. This analysis provides a roadmap for generating reproducible base-pair level methylomes for zebrafish using RRBS and our results provide the first evidence that RRBS is a suitable technique for global methylation analysis in zebrafish.
Pathobiologic Markers of the Ewing Sarcoma Family of Tumors: State of the Art and Prediction of Behaviour

Over the past three decades, the outcome of Ewing sarcoma family tumor (ESFT) patients who are nonmetastatic at presentation has improved considerably. The prognosis of patients with metastatic disease at the time of diagnosis and recurrence after therapy remains dismal. Drug-resistant disease at diagnosis or at relapse remains a major cause of mortality among patients diagnosed with ESFT. In order to improve the outcome for patients with potential relapse, there is an urgent need to find reliable markers that either predict tumor behaviour at diagnosis or identify therapeutic molecular targets at the time of recurrence. An improved understanding of the cell of origin and the molecular pathways that regulate tumorigenicity in ESFT should aid us in the search for novel therapies for ESFT. The purpose of this paper is thus to outline current concepts of sarcomagenesis in ESFT and to discuss ESFT patterns of differentiation and molecular markers that might affect prognosis or direct future therapeutic development.
An approach to improve apriori algorithm based on association rule mining

Apriori algorithm is a popular and a classical algorithm in data mining. The main idea of this approach is to find a useful pattern in various sets of data. The algorithm suffers from many drawbacks. This paper deals with the apriori algorithm, and various techniques that were proposed to improve the apriori algorithm. The paper discusses about various approaches use to overcome the drawback of the apriori algorithm as to improve its efficiency. It also discusses about the new proposed model for improvement of apriori algorithm. The novel algorithm decreases pruning operation of candidate itemset. A new and improved model to handle dataset and to find an association between them is given. The new algorithm reduces storage space, improves efficiency and accuracy of the algorithm.
Dietary Arsenic Exposure in Bangladesh

Background Millions of people in Bangladesh are at risk of chronic arsenic toxicity from drinking contaminated groundwater, but little is known about diet as an additional source of As exposure. Methods We employed a duplicate diet survey to quantify daily As intake in 47 women residing in Pabna, Bangladesh. All samples were analyzed for total As, and a subset of 35 samples were measured for inorganic arsenic (iAs) using inductively coupled plasma mass spectrometry equipped with a dynamic reaction cell. Results Median daily total As intake was 48 μg As/day [interquartile range (IQR), 33–67) from food and 4 μg As/day (IQR, 2–152) from drinking water. On average, iAs comprised 82% of the total As detected in dietary samples. After adjusting for the estimated inorganic fraction, 34% [95% confidence interval (CI), 21–49%] of all participants exceeded the World Health Organization’s provisional tolerable daily intake (PTDI) of 2.1 μg As/kg-day. Two of the 33 women who used a well with < 50 μg As/L exceeded this recommendation. Conclusions When drinking water concentrations exceeded the Bangladesh drinking water standard of 50 μg As/L, ingested water was the dominant source of exposure. However, as drinking water As concentrations decrease, the relative contribution of dietary As sources becomes more important to ingested dose. The combined intake from both diet and drinking water can cause some individuals to exceed the PTDI in spite of using a tube well that contains < 50 μg As/L.
Stress Effects on Multiple Memory System Interactions

Extensive behavioural, pharmacological, and neurological research reports stress effects on mammalian memory processes. While stress effects on memory quantity have been known for decades, the influence of stress on multiple memory systems and their distinct contributions to the learning process have only recently been described. In this paper, after summarizing the fundamental biological aspects of stress/emotional arousal and recapitulating functionally and anatomically distinct memory systems, we review recent animal and human studies exploring the effects of stress on multiple memory systems. Apart from discussing the interaction between distinct memory systems in stressful situations, we will also outline the fundamental role of the amygdala in mediating such stress effects. Additionally, based on the methods applied in the herein discussed studies, we will discuss how memory translates into behaviour.
Localization for Wireless Sensor Networks: A Neural Network Approach

As Wireless Sensor Networks are penetrating into the industrial domain, many research opportunities are emerging. One such essential and challenging application is that of node localization. A feed-forward neural network based methodology is adopted in this paper. The Received Signal Strength Indicator (RSSI) values of the anchor node beacons are used. The number of anchor nodes and their configurations has an impact on the accuracy of the localization system, which is also addressed in this paper. Five different training algorithms are evaluated to find the training algorithm that gives the best result. The multi-layer Perceptron (MLP) neural network model was trained using Matlab. In order to evaluate the performance of the proposed method in real time, the model obtained was then implemented on the Arduino microcontroller. With four anchor nodes, an average 2D localization error of 0.2953 m has been achieved with a 12-12-2 neural network structure. The proposed method can also be implemented on any other embedded microcontroller system.
Does mandatory adoption of International Accounting Standards reduce the cost of equity capital

This paper examines whether the mandatory adoption of International Accounting Standards (IAS) in the European Union (EU) in 2005 reduces the cost of equity capital. Using a sample of 6,456 firm-year observations of 1,084 EU companies during the period of 1995 to 2006, I find evidence that mandatory introduction of IAS, on average, significantly reduces the cost of equity for mandatory adopters by 48 basis points. I also find that this reduction is present only in countries with strong enforcement systems and that both increased disclosure and enhanced information comparability help explain why IAS reduces the cost of equity. Taken together, these findings suggest that mandatory IAS adoption benefits shareholders, but that the benefits depend critically on the strength of the countries’ enforcement systems. 1 This paper is based on my dissertation at the University of Southern California. I am grateful to my dissertation committee, especially my co-chairs, Mark DeFond and Mingyi Hung, for their invaluable guidance and support. I am also thankful to Robert Trezevant and Biqin Xie for their helpful comments and suggestions. This work is supported in part by U.S. Department of Education Title V1-B funds administered by USC’s Center for International Business, Education, and Research.
Symptomatic Effects of Exposure to Diluted Air Sampled from a Swine Confinement Atmosphere on Healthy Human Subjects

Aerial emissions from a swine house at North Carolina State University’s field laboratory were diluted to a level that could occur at varying distances downwind from a confined animal feeding operation (CAFO) both within and beyond the property line, and these emissions were delivered to an environmental exposure chamber. The study design consisted of two 1-hr sessions, one in which 48 healthy human adult volunteers were exposed to diluted swine air and another in which they were exposed to clean air (control). Objective measures of blood pressure, temperature, heart rate, respiratory rate, lung function, nasal inflammation, secretory immunity, mood, attention, and memory were correlated with objective measures of air quality. Ratings of perceived (self-reported) health symptoms were also obtained. The mean levels of airborne constituents in the swine air condition were hydrogen sulfide (24 ppb), ammonia (817 ppb), total suspended particulates (0.0241 mg/m3), endotoxin (7.40 endotoxin units/m3), and odor (57 times above odor threshold). No statistical differences on objective measures of physical symptoms, mood, or attention resulted from the 1-hr exposure to swine emissions in the environmental chamber when compared with clean air for healthy human volunteers. However, subjects were 4.1 (p = 0.001) times more likely to report headaches, 6.1 (p = 0.004) times more likely to report eye irritation, and 7.8 (p = 0.014) times more likely to report nausea in the swine air (experimental) condition than in the control condition. These results indicate that short-term exposure in an environmental chamber to malodorous emissions from a swine house at levels expected downwind can induce clinically important symptoms in healthy human volunteers.
Molecular model of SARS coronavirus polymerase: implications for biochemical functions and drug design

The causative agent of severe acute respiratory syndrome (SARS) is a previously unidentified coronavirus, SARS-CoV. The RNA-dependent RNA polymerase (RdRp) of SARS-CoV plays a pivotal role in viral replication and is a potential target for anti-SARS therapy. There is a lack of structural or biochemical data on any coronavirus polymerase. To provide insights into the structure and function of SARS-CoV RdRp, we have located its conserved motifs that are shared by all RdRps, and built a three-dimensional model of the catalytic domain. The structural model permits us to discuss the potential functional roles of the conserved motifs and residues in replication and their potential interactions with inhibitors of related enzymes. We predict important structural attributes of potential anti-SARS-CoV RdRp nucleotide analog inhibitors: hydrogen-bonding capability for the 2′ and 3′ groups of the sugar ring and C3′ endo sugar puckering, and the absence of a hydrophobic binding pocket for non-nucleoside analog inhibitors similar to those observed in hepatitis C virus RdRp and human immunodeficiency virus type 1 reverse transcriptase. We propose that the clinically observed resistance of SARS to ribavirin is probably due to perturbation of the conserved motif A that controls rNTP binding and fidelity of polymerization. Our results suggest that designing anti-SARS therapies can benefit from successful experiences in design of other antiviral drugs. This work should also provide guidance for future biochemical experiments.