Miracle-dz/UniFAR-FTUs huggingface dataset:
HtrA3 Is Downregulated in Cancer Cell Lines and Significantly Reduced in Primary Serous and Granulosa Cell Ovarian Tumors

Objective. The high temperature requirement factor A3 (HtrA3) is a serine protease homologous to bacterial HtrA. Four human HtrAs have been identified. HtrA1 and HtrA3 share a high degree of domain organization and are downregulated in a number of cancers, suggesting a widespread loss of these proteases in cancer. This study examined how extensively the HtrA (HtrA1-3) proteins are downregulated in commonly used cancer cell lines and primary ovarian tumors. Methods. RT-PCR was applied to various cancer cell lines (n=17) derived from the ovary, endometrium, testes, breast, prostate, and colon, and different subtypes of primary ovarian tumors [granulosa cell tumors (n=19), mucinous cystadenocarcinomas (n=6), serous cystadenocarcinomas (n=8)] and normal ovary (n = 9). HtrA3 protein was localized by immunohistochemistry. Results. HtrA3 was extensively downregulated in the cancer cell lines examined including the granulosa cell tumor-derived cell lines. In primary ovarian tumors, the HtrA3 was significantly lower in serous cystadenocarcinoma and granulosa cell tumors. In contrast, HtrA1 and HtrA2 were expressed in all samples with no significant differences between the control and tumors. In normal postmenopausal ovary, HtrA3 protein was localized to lutenizing stromal cells and corpus albicans. In serous cystadenocarcinoma, HtrA3 protein was absent in the papillae but detected in the mesenchymal cyst wall. Conclusion. HtrA3 is more extensively downregulated than HtrA1-2 in cancer cell lines. HtrA3, but not HtrA1 or HtrA2, was decreased in primary ovarian serous cystadenocarcinoma and granulosa cell tumors. This study provides evidence that HtrA3 may be the most relevant HtrA associated with ovarian malignancy.
MURAX: a robust linguistic approach for question answering using an on-line encyclopedia

Robust linguistic methods are applied to the task of answering closed-class questions using a corpus of natural language. The methods are illustrated in a broad domain: answering general-knowledge questions using an on-line encyclopedia. A closed-class question is a question stated in natural language, which assumes some definite answer typified by a noun phrase rather than a procedural answer. The methods hypothesize noun phrases that are likely to be the answer, and present the user with relevant text in which they are marked, focussing the user's attention appropriately. Furthermore, the sentences of matching text that are shown to the user are selected to confirm phrase relations implied by the question, rather than being selected solely on the basis of word frequency. The corpus is accessed via an information retrieval (IR) system that supports boolean search with proximity constraints. Queries are automatically constructed from the phrasal content of the question, and passed to the IR system to find relevant text. Then the relevant text is itself analyzed; noun phrase hypotheses are extracted and new queries are independently made to confirm phrase relations for the various hypotheses. The methods are currently being implemented in a system called MURAX and although this process is not complete, it is sufficiently advanced for an interim evaluation to be presented.
Illustrations and guidelines for selecting statistical methods for quantifying spatial pattern in ecological data

This paper aims to provide guidance to ecologists with limited experience in spatial analysis to help in their choice of techniques. It uses examples to compare methods of spatial analysis for ecological field data. A taxonomy of different data types is presented, including point- and area-referenced data, with and without attributes. Spatially and non-spatially explicit data are distinguished. The effects of sampling and other transformations that convert one data type to another are discussed; the possible loss of spatial information is considered. Techniques for analyzing spatial pattern, developed in plant ecology, animal ecology, landscape ecology, geostatistics and applied statistics are reviewed briefly and their overlap in methodology and philosophy noted. The techniques are categorized according to their output and the inferences that may be drawn from them, in a discursive style without formulae. Methods are compared for four case studies with field data covering a range of types. These are: 1) percentage cover of three shrubs along a line transect; 2) locations and volume of a desert plant in a 1 ha area; 3) a remotely-sensed spectral index and elevation from 105 km2 of a mountainous region; and 4) land cover from three rangeland types within 800 km2 of a coastal region. Initial approaches utilize mapping, frequency distributions and variance-mean indices. Analysis techniques we compare include: local quadrat variance, block quadrat variance, correlograms, variograms, angular correlation, directional variograms, wavelets, SADIE, nearest neighbour methods, Ripley's (t), and various landscape ecology metrics. Our advice to ecologists is to use simple visualization techniques for initial analysis, and subsequently to select methods that are appropriate for the data type and that answer their specific questions of interest. It is usually prudent to employ several different techniques.
The collaborative design platform protocol: a protocol for a mixed reality installation for improved incorporation of laypeople in architecture

We present the conceptual design and implementation of the Collaborative Design Platform Protocol (CDPP), a communication protocol that offers the synchronisation of virtual worlds between two mixed reality peers. The CDPP is applied to connect the Collaborative Design Platform (CDP), a design tool which supports the architectural design process in an early stage, with the immersive Cave Automatic Virtual Environment (CAVE) display, where the design is visualised in life-size. This creates a prototype which enables a cost-efficient and easily comprehensible presentation of the early-staged design, and thus significantly simplifies the incorporation of laypeople in the early design process. By this means, the creative capabilities of laymen are exploited to a greater extent.
ADAPT_TCD: An Ontology-Based Context Aware Approach for Contextual Suggestion

In this paper we give an overview of the participation of the ADAPT Centre, Trinity College Dublin, Ireland, in both phases of the TREC 2016 Contextual Suggestion Track. We present our ontology-based approach that consists of three models that are based on an ontology that was extracted from the Four-square category hierarchy. The three models are: User Model, Document Model and Rule Model. In the User Model we build two models, one for each phase of the task, based upon the attractions that were rated in the user’s profile. The Document Model enriches documents with extra metadata from Foursquare and categories (concepts) from the ontology are attached to each document. The Rule model is used to tune the score for candidate suggestions based on how the context of the trip aligns with the rules in the model. The results of our submitted runs, in both phases, demonstrate the effectiveness of the proposed methods.
MOSFET aspect ratio optimization for minimized transistor mismatch at UDSM technology nodes

In this paper, we provide a comparative estimation of the W/L aspect ratio required to obtain a symmetric behavior of n-channel and p-channel MOS devices across ultradeep submicron (UDSM) technology nodes and various supply voltage ranges. This symmetric behavior is in terms of matching propagation delay during the pull-up (pMOS dependent) and pull-down (nMOS dependent) output transitions. To achieve this, mismatch in drain currents as well as threshold voltages for both devices is minimized through W/L ratio optimization, incorporating realistic variations from expected values. In doing so, significant deviations are observed in pMOS W/L ratio from the conventional values of 2-2.5 for obtaining identical transistor strength to nMOS in terms of on current. The ratio is seen to range from 1.3× to as high as 8.6× for superthreshold and subthreshold regimes respectively, depending on the specific technology node in use. Moreover, threshold voltages are matched for both devices through suitable sizing of channel lengths upto 1.09× to improve overall transistor matching. The optimal W/L values thus obtained can be suitably used for pre-design optimization depending on the choice of technology and supply voltage range.
Hydroxamic Acid-Based Histone Deacetylase (HDAC) Inhibitors Can Mediate Neuroprotection Independent of HDAC Inhibition

Histone deacetylase (HDAC) inhibition improves function and extends survival in rodent models of a host of neurological conditions, including stroke, and neurodegenerative diseases. Our understanding, however, of the contribution of individual HDAC isoforms to neuronal death is limited. In this study, we used selective chemical probes to assess the individual roles of the Class I HDAC isoforms in protecting Mus musculus primary cortical neurons from oxidative death. We demonstrated that the selective HDAC8 inhibitor PCI-34051 is a potent neuroprotective agent; and by taking advantage of both pharmacological and genetic tools, we established that HDAC8 is not critically involved in PCI-34051's mechanism of action. We used BRD3811, an inactive ortholog of PCI-34051, and showed that, despite its inability to inhibit HDAC8, it exhibits robust neuroprotective properties. Furthermore, molecular deletion of HDAC8 proved insufficient to protect neurons from oxidative death, whereas both PCI-34051 and BRD3811 were able to protect neurons derived from HDAC8 knock-out mice. Finally, we designed and synthesized two new, orthogonal negative control compounds, BRD9715 and BRD8461, which lack the hydroxamic acid motif and showed that they stably penetrate cell membranes but are not neuroprotective. These results indicate that the protective effects of these hydroxamic acid-containing small molecules are likely unrelated to direct epigenetic regulation via HDAC inhibition, but rather due to their ability to bind metals. Our results suggest that hydroxamic acid-based HDAC inhibitors may mediate neuroprotection via HDAC-independent mechanisms and affirm the need for careful structure–activity relationship studies when using pharmacological approaches.
Using Real-World Reference to Improve Spoken Language Understanding

Humans understand spoken language in a continuous manner, incorporating complex semantic and contextual constraints at all levels of language processing on a word-by-word basis, but the standard paradigm for computational processing of language remains sentence-at-a-time, and does not demonstrate the tight integration of interpretations at various levels of processing that humans do. We introduce the fruit carts task domain, which has been specifically designed to elicit language that requires this sort of continuous understanding. A system architecture that incrementally incorporates feedback from a real-world reference resolution module into the parser is presented as a major step towards a continuous understanding system. A preliminary proof in principle shows that real-world knowledge can help resolve certain parsing ambiguities, thus improving accuracy, and that the efficiency of the parser, as measured by the number of constituents built, improves by upwards of 30% on certain example sentences with multiple attachment ambiguities. A 26% efficiency improvement was achieved for a dialogue transcript taken from those collected for the fruit carts task domain. We also argue that real-world reference information can help resolve ambiguities in speech recognition. Continuous Understanding of Spoken
Gaseous emissions from management of solid waste: a systematic review

The establishment of sustainable soil waste management practices implies minimizing their environmental losses associated with climate change (greenhouse gases: GHGs) and ecosystems acidification (ammonia: NH3). Although a number of management strategies for solid waste management have been investigated to quantify nitrogen (N) and carbon (C) losses in relation to varied environmental and operational conditions, their overall effect is still uncertain. In this context, we have analyzed the current scientific information through a systematic review. We quantified the response of GHG emissions, NH3 emissions, and total N losses to different solid waste management strategies (conventional solid storage, turned composting, forced aerated composting, covering, compaction, addition/substitution of bulking agents and the use of additives). Our study is based on a meta‐analysis of 50 research articles involving 304 observations. Our results indicated that improving the structure of the pile (waste or manure heap) via addition or substitution of certain bulking agents significantly reduced nitrous oxide (N2O) and methane (CH4) emissions by 53% and 71%, respectively. Turned composting systems, unlike forced aerated composted systems, showed potential for reducing GHGs (N2O: 50% and CH4: 71%). Bulking agents and both composting systems involved a certain degree of pollution swapping as they significantly promoted NH3 emissions by 35%, 54%, and 121% for bulking agents, turned and forced aerated composting, respectively. Strategies based on the restriction of O2 supply, such as covering or compaction, did not show significant effects on reducing GHGs but substantially decreased NH3 emissions by 61% and 54% for covering and compaction, respectively. The use of specific additives significantly reduced NH3 losses by 69%. Our meta‐analysis suggested that there is enough evidence to refine future Intergovernmental Panel on Climate Change (IPCC) methodologies from solid waste, especially for solid waste composting practices. More holistic and integrated approaches are therefore required to develop more sustainable solid waste management systems.
Marine Non-Glycosaminoglycan Sulfated Glycans as Potential Pharmaceuticals

Sulfated fucans (SFs) and sulfated galactans (SGs) are currently the marine non-glycosaminoglycan (GAG) sulfated glycans most studied in glycomics. These compounds exhibit therapeutic effects in several pathophysiological systems such as blood coagulation, thrombosis, neovascularization, cancer, inflammation, and microbial infections. As analogs of the largely employed GAGs and due to some limitations of the GAG-based therapies, SFs and SGs comprise new carbohydrate-based therapeutics available for clinical studies. Here, the principal structural features and the major mechanisms of action of the SFs and SGs in the above-mentioned pathophysiological systems are presented. Discussion is also given on the current challenges and the future perspectives in drug development of these marine glycans.
Advances in Brief Apoptosis Induction by the Photosensitizer Verteporfin : Identification of Mitochondrial Adenine Nucleotide Translocator as a Critical Target 1

We report that the photosensitizer verteporfin kills lymphoma cells by an apoptotic process involving a dissipation of the mitochondrial inner transmembrane potential (DCm). Light-activated verteporfininduced apoptosis was abolished by transfection with Bcl-2, a procedure reported to inhibit the mitochondrial permeability transition pore complex (PTPC). Verteporfin triggered the DCm loss in isolated mitochondria in vitro, and this effect was suppressed by bongrekic acid and cyclosporin A. Verteporfin plus light also permeabilized proteoliposomes containing the semipurified PTPC or the purified PTPC component adenine nucleotide translocator (ANT), yet had no effect on protein-free control liposomes. Verteporfin phototoxicity on ANT proteoliposomes was mediated by reactive oxygen species and was prevented by recombinant Bcl-2 or the adenine nucleotides ATP and ADP. In conclusion, verteporfin belongs to a class of clinically used chemotherapeutic agents acting on PTPC and ANT.
Serum Dioxin, Testosterone, and Subsequent Risk of Benign Prostatic Hyperplasia: A Prospective Cohort Study of Air Force Veterans

Background Operation Ranch Hand veterans were involved in spraying herbicides, including Agent Orange, during the Vietnam War in 1962–1971; Agent Orange was contaminated with 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). It has been hypothesized that dioxins may be partially responsible for an increase of male reproductive tract disorders such as testicular cancer, cryptorchidism, and hypospadias. Objectives In this study, our objective was to assess the effect of serum TCDD concentration on the risk of development of benign prostatic hyperplasia (BPH) and on serum testosterone levels. Methods This study was a longitudinal, prospective cohort study made up of U.S. Air Force veterans involved in Operation Ranch Hand. Other Air Force veterans who did not spray herbicides were included as comparisons. BPH was determined by medical record review and by medical examinations conducted during the study. Data were available for 971 Ranch Hand and 1,266 comparison veterans. We investigated the relationship between BPH and serum TCDD level using the Cox proportional hazards models adjusted for testosterone levels, body mass index (BMI), and the percentage change in BMI per year. Results In univariate and multivariate analyses, the risk of BPH decreased with increasing serum TCDD in the comparison group. The multivariate risk ratio for BPH in the comparison group was 0.84 (95% confidence interval, 0.73–0.98). Excluding men with prostate cancer, inflammatory or other prostatic diseases did not substantially alter the association. Serum testosterone levels were inversely associated with serum TCDD levels in both Ranch Hand and comparison groups. Conclusions TCDD exposure at general population levels is associated with a decreasing risk of BPH with higher exposure levels. TCDD exposure is also negatively associated with serum testosterone levels.
A Methodology Using Partial Swarm Optimization and Kriging to Ship Multidisciplinary Design Optimization

Ship optimization design is a complex multidisciplinary process due to determining ship configuration variables that satisfy a set of mission requirements. In this paper A Monte Carlo method (MCM) is employed to explore the design space and to sample data for covering the design space. Particularly in ship multidisciplinary design optimization, we investigate the use of kriging sampling methods for constructing global approximations and fit model to facilitate multidisciplinary design optimization (MDO). In this search (MDO) are used to computational expense and organizational complexity, Partial Swarm Optimization (PSO) adopt as a feasible alternative to the existing sizing and optimization methods and to illustrate the appropriate design result in approach through (MDO) process, the objective of this search to minimum ship running cost which it subjected to constraints in performance, geometric parameters, power of population and voyage. Finally, the validity of the proposed methodology is proven by a case study of a bulk carrier.
Current era survival of patients with pulmonary arterial hypertension associated with congenital heart disease: a comparison between clinical subgroups.

AIMS This study compared the clinical, functional, and haemodynamic characteristics and current era survival of subgroups of patients with pulmonary arterial hypertension associated with congenital heart disease (PAH-CHD): Eisenmenger syndrome (ES); PAH-CHD associated with systemic-to-pulmonary shunts (SPs); PAH with small defects (SDs); and PAH after defect correction (CDs). METHODS AND RESULTS Data from consecutive PAH-CHD patients referred to our centre from 1 January 1998 to 31 May 2011 were collected. A contemporary group of idiopathic PAH patients was utilized for comparison. Treatment was per PAH guidelines, including combination therapy, with approved PAH-specific drugs. Survival was assessed with Kaplan-Meier analysis from the first invasive haemodynamic confirmation of PAH and compared across subgroups by log-rank test. Of 192 patients (mean age 41 ± 17 years; 61% female), 90 had ES (aged 41 ± 16 years); 48 SP (aged 47 ± 18 years); 10 SD (aged 25 ± 21 years); and 44 CD (aged 36 ± 17 years). Patients with ES had the highest baseline pulmonary vascular resistance and the lowest exercise capacity. Seventy-eight per cent were treated with approved PAH-specific drugs, and 44% were treated with combination therapy. Kaplan-Meier survival estimates (95% confidence interval) at 20 years for ES, SP, and CD were 87% (77-93%), 86% (60-96%), and 36% (12-72%, P = 0.0001 vs. ES; P = 0.004 vs. SP), respectively, and at 15 years for SD was 66% (16-91%, P = 0.015 vs. ES; P = 0.016 vs. SP). The survival of the 278 patients with idiopathic PAH appeared to be worse when compared with the PAH-CHD subgroups. CONCLUSION Relevant clinical, functional, haemodynamic, and survival differences were observed among subgroups. In particular, patients with CD and SD had the worst survival. These findings should be considered when planning medical or interventional treatment strategies in PAH-CHD patients.
Image restoration using L1 norm penalty function

The process of estimating an original image from a given blurred and noisy image is known as image restoration. It is an ill-posed inverse problem, since one of the ways of solving it requires finding a solution to a Fredholm integral equation of convolution type in two-dimensional space. The focus of the article is to achieve a quality edge preserving image restoration using a less expensive (fast) regularization technique with L1 norm penalty function. L1 norm based approaches do not penalize edges or high frequency contents in the restored image compared to L2 norm based approaches. Total variation (TV) is an established L1 norm regularization approach that performs edge preserving image restoration, but at a high computational cost. TV regularization requires linearization of a highly nonlinear penalty term, which increases the restoration time considerably for large scale images. In order to reduce the computational cost, we extend least absolute shrinkage and selection operator (LASSO), an L1 norm minimization statistical modeling technique to image restoration. The penalty function of LASSO is an identity matrix so it is computationally fast. The metrics, like, residual error, peak signal to noise ratio (PSNR), restoration time, edge map of the restored image, and subjective visual evaluation are used to assess the performances of both methods. Based on our experimental results, we show that LASSO achieves similar quality of edge preserving restoration as TV regularization, and is approximately two times faster in computation compared to TV regularization on the same set of images. We also analyze the impact of the different degree of blurring caused by point spread functions (PSFs) corrupted by different signal to noise ratios (SNRs) on image restoration.
CipherCard: Enhancing Security on Common Touchscreen Devices using Two-factor Authentication

We present CipherCard, a physical token that defends against shoulder-surfing attacks on user authentication on touchscreen devices. Placed over a touchscreen pin-pad, CipherCard remaps a user's touch points on the physical token to different locations on the pin-pad (i.e. as a substitution cipher). It translates a visible user password into a different system password received by a touchscreen, hiding the system password from observers. CipherCard enhances authentication security through Two-Factor Authentication (TFA), in that both the correct user password and a specific card are needed for authentication. We explore the design space of CipherCard, and describe three implemented variations each with unique capabilities. Based on user feedback, we discuss the security and usability implications of CipherCard, and describe several avenues for continued exploration.