Miracle-dz/UniFAR-FTUs huggingface dataset:
Loss of the tumor suppressor SMARCA4 in small cell carcinoma of the ovary, hypercalcemic type (SCCOHT)

Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT), is a rare and understudied cancer with a dismal prognosis. SCCOHT's infrequency has hindered empirical study of its biology and clinical management. However, we and others have recently identified inactivating mutations in the SWI/SNF chromatin remodeling gene SMARCA4 with concomitant loss of SMARCA4 protein in the majority of SCCOHT tumors.1–4 Here we summarize these findings and report SMARCA4 status by targeted sequencing and/or immunohistochemistry (IHC) in an additional 12 SCCOHT tumors, 3 matched germlines, and the cell line SCCOHT-1. We also report the identification of a homozygous inactivating mutation in the gene SMARCB1 in one SCCOHT tumor with wild-type SMARCA4, suggesting that SMARCB1 inactivation may also play a role in the pathogenesis of SCCOHT. To date, SMARCA4 mutations and protein loss have been reported in the majority of 69 SCCOHT cases (including 2 cell lines). These data firmly establish SMARCA4 as a tumor suppressor whose loss promotes the development of SCCOHT, setting the stage for rapid advancement in the biological understanding, diagnosis, and treatment of this rare tumor type.
A neutral terminology to define ‘invasive’ species

The use of simple terms to articulate ecological concepts can confuse ideological debates and undermine management efforts. This problem is particularly acute in studies of nonindigenous species, which alternatively have been called ‘exotic’, ‘introduced’, ‘invasive’ and ‘naturalised’, among others. Attempts to redefine commonly used terminology have proven difficult because authors are often partial to particular definitions. In an attempt to form a consensus on invasion terminology, we synthesize an invasional framework based on current models that break the invasion process into a series of consecutive, obligatory stages. Unlike previous efforts, we propose a neutral terminology based on this framework. This ‘stage‐based’ terminology can be used to supplement terms with ambiguous meanings (e.g. invasive, introduced, naturalized, weedy, etc.), and thereby improve clarity of future studies. This approach is based on the concept of ‘propagule pressure’ and has the additional benefit of identifying factors affecting the success of species at each stage. Under this framework, invasions can be more objectively understood as biogeographical, rather than taxonomic, phenomena; and author preferences in the use of existing terminology can be addressed. An example of this recommended protocol might be: ‘We examined distribution data to contrast the characteristics of invasive species (stages IVa and V) and noninvasive species (stages III and IVb)’.
Dynamically Partitionable Autoassociative Networks as a Solution to the Neural Binding Problem

An outstanding question in theoretical neuroscience is how the brain solves the neural binding problem. In vision, binding can be summarized as the ability to represent that certain properties belong to one object while other properties belong to a different object. I review the binding problem in visual and other domains, and review its simplest proposed solution – the anatomical binding hypothesis. This hypothesis has traditionally been rejected as a true solution because it seems to require a type of one-to-one wiring of neurons that would be impossible in a biological system (as opposed to an engineered system like a computer). I show that this requirement for one-to-one wiring can be loosened by carefully considering how the neural representation is actually put to use by the rest of the brain. This leads to a solution where a symbol is represented not as a particular pattern of neural activation but instead as a piece of a global stable attractor state. I introduce the Dynamically Partitionable AutoAssociative Network (DPAAN) as an implementation of this solution and show how DPANNs can be used in systems which perform perceptual binding and in systems that implement syntax-sensitive rules. Finally I show how the core parts of the cognitive architecture ACT-R can be neurally implemented using a DPAAN as ACT-R’s global workspace. Because the DPAAN solution to the binding problem requires only “flat” neural representations (as opposed to the phase encoded representation hypothesized in neural synchrony solutions) it is directly compatible with the most well developed neural models of learning, memory, and pattern recognition.
Effectiveness of Roundtable on Sustainable Palm Oil (RSPO) for reducing fires on oil palm concessions in Indonesia from 2012 to 2015

Fire is a common tool for land conversion and management associated with oil palm production. Fires can cause biodiversity and carbon losses, emit pollutants that deteriorate air quality and harm human health, and damage property. The Roundtable on Sustainable Palm Oil (RSPO) prohibits the use of fire on certified concessions. However, efforts to suppress fires are more difficult during El Niño conditions and on peatlands. In this paper, we address the following questions for oil palm concessions developed prior to 2012 in Sumatra and Kalimantan, the leading producers of oil palm both within Indonesia and globally: (1) for the period 2012–2015, did RSPO-certified concessions have a lower density of fire detections, fire ignitions, or ‘escaped’ fires compared with those concessions that are not certified? and (2) did this pattern change with increasing likelihood of fires in concessions located on peatland and in dry years? These questions are particularly critical in fuel-rich peatlands, of which approximately 46% of the area was designated as oil palm concession as of 2010. We conducted propensity scoring to balance covariate distributions between certified and non-certified concessions, and we compare the density of fires in certified and non-certified concessions using Kolmogorov–Smirnov tests based on moderate resolution imaging spectroradiometer Active Fire Detections from 2012–2015 clustered into unique fire events. We find that fire activity is significantly lower on RSPO certified concessions than non-RSPO certified concessions when the likelihood of fire is low (i.e., on non-peatlands in wetter years), but not when the likelihood of fire is high (i.e., on non-peatlands in dry years or on peatlands). Our results provide evidence that RSPO has the potential to reduce fires, though it is currently only effective when fire likelihood is relatively low. These results imply that, in order for this mechanism to reduce fire, additional strategies will be needed to control fires in oil palm plantations in dry years and on peatlands.
Association between RASSF1A Promoter Methylation and Prostate Cancer: A Systematic Review and Meta-Analysis

Prostate cancer (PCa) remains as one of the most common cause of cancer related death among men in the US. The widely used prostate specific antigen (PSA) screening is limited by low specificity. The diagnostic value of other biomarkers such as RAS association domain family protein 1 A (RASSF1A) promoter methylation in prostate cancer and the relationship between RASSF1A methylation and pathological features or tumor stage remains to be established. Therefore, a meta-analysis of published studies was performed to understand the association between RASSF1A methylation and prostate cancer. In total, 16 studies involving 1431 cases and 565 controls were pooled with a random effect model in this investigation. The odds ratio (OR) of RASSF1A methylation in PCa case, compared to controls, was 14.73 with 95% CI = 7.58–28.61. Stratified analyses consistently showed a similar risk across different sample types and, methylation detection methods. In addition, RASSF1A methylation was associated with high Gleason score OR=2.35, 95% CI: 1.56–3.53. Furthermore, the pooled specificity for all included studies was 0.87 (95% CI: 0.72–0.94), and the pooled sensitivity was 0.76 (95% CI: 0.55–0.89). The specificity in each subgroup stratified by sample type remained above 0.84 and the sensitivity also remained above 0.60. These results suggested that RASSF1A promoter methylation would be a potential biomarker in PCa diagnosis and therapy.
Clinical efficacy and survival with first-line inhaled iloprost therapy in patients with idiopathic pulmonary arterial hypertension.

AIMS To describe the long-term clinical efficacy of inhaled iloprost as first-line vasodilator mono-therapy in patients with idiopathic pulmonary arterial hypertension (IPAH). METHODS AND RESULTS Seventy-six IPAH patients were prospectively identified and treated with inhaled iloprost. Clinical, haemodynamic, and exercise parameters were obtained at baseline, after 3 and 12 months of therapy and yearly thereafter. Four endpoints were prospectively defined as follows: (i) death, (ii) transplantation, (iii) switch to intravenous (i.v.) therapy, or (iv) addition of or switch to other active oral therapy. During follow-up (535+/-61 days), 11 patients died, six were transplanted, 25 were switched to i.v. prostanoids, 16 received additional or other oral therapy, and 12 patients discontinued iloprost inhalation for other reasons. Event-free survival at 3, 12, 24, 36, 48, and 60 months was 81, 53, 29, 20, 17 and 13%, respectively. Among haemodynamic and exercise parameters, mixed venous oxygen saturation (P<0.001), right atrial pressure (P<0.001), and peak oxygen uptake (P=0.002) were associated with event-free survival. CONCLUSION In this study, only a minority of patients could be stabilized with inhaled iloprost mono-therapy during a follow-up period of up to 5 years. In the presence of multiple treatment options, chronic iloprost inhalation as mono-therapy appears to have a limited role.
Adaptive Scheduling Algorithm for Real-Time Multiprocessor Systems

EDF (Earliest Deadline First) has been proved to be optimal scheduling algorithm for single processor real-time system. It also performs well for multiprocessor system. Limitation of EDF is that its performance decreases exponentially when system becomes slightly overloaded. ACO (Ant Colony Optimization) based scheduling algorithm performs well in both underloaded and overloaded conditions. But its limitation is that it takes more time for execution compared to EDF. In this paper, an adaptive algorithm for multiprocessor real-time system is proposed, which is combination of both of these algorithms. The proposed algorithm along with EDF and ACO based algorithm is simulated for real-time multiprocessor system and the results are obtained. The performance is measured in terms of Success Ratio (SR) and Effective CPU Utilization (ECU). Execution Time taken by each scheduling algorithm is also measured. From analysis and experiments, it reveals that the proposed algorithm is fast as well as efficient in both underloaded and overloaded conditions for real-time multiprocessor systems.
The active site residue Valine 867 in human telomerase reverse transcriptase influences nucleotide incorporation and fidelity

Human telomerase reverse transcriptase (hTERT), the catalytic subunit of human telomerase, contains conserved motifs common to retroviral reverse transcriptases and telomerases. Within the C motif of hTERT is the Leu866-Val867-Asp868-Asp869 tetrapeptide that includes a catalytically essential aspartate dyad. Site-directed mutagenesis of Tyr183 and Met184 residues in HIV-1 RT, residues analogous to Leu866 and Val867, revealed that they are key determinants of nucleotide binding, processivity and fidelity. In this study, we show that substitutions at Val867 lead to significant changes in overall enzyme activity and telomere repeat extension rate, but have little effect on polymerase processivity. All Val867 substitutions examined (Ala, Met, Thr) led to reduced repeat extension rates, ranging from ∼20 to 50% of the wild-type rate. Reconstitution of V867M hTERT and telomerase RNAs (TRs) with mutated template sequences revealed the effect on extension rate was associated with a template copying defect specific to template A residues. Furthermore, the Val867 hTERT mutants also displayed increased nucleotide incorporation fidelity, implicating Val867 as a determinant of telomerase fidelity. These findings suggest that by evolving to have a valine at position 867, the wild-type hTERT protein may have partially compromised polymerase fidelity for optimal and rapid repeat synthesis.
A Low Phase-Noise Multi-Phase LO Generator for Wideband Demodulators Based on Reconfigurable Sub-Harmonic Mixers

The advent of wideband systems, e.g., software defined radios, cognitive radios and UWB technology, motivates research for new transceiver architectures and circuit topologies to arrive at compact and low power solutions. Reference frequency generation in wideband CMOS receivers is usually power and area hungry. In this paper a wide band quadrature demodulator, based on mixers reconfigurable between fundamental and sub-harmonic operation modes is presented. The technique allows covering an RF bandwidth three times larger than the frequency covered by the synthesizer. Multiple local oscillator phases are required for the proposed architecture. For low phase noise and fast settling time, they are generated by means of a multi-stage injection locked ring oscillator. This solution proves very accurate and power efficient and may find applications in other communication systems requiring multiple phase references. A demodulator test chip tailored to WiMedia UWB groups 1, 3, 4 (3.1-9.5 GHz), and comprising mixers and frequency synthesizer, has been realized in a 65 nm CMOS technology. Experimental results show 10 dB of conversion gain with 2.3 nV/sqrt(Hz) equivalent input noise voltage spectral density. IIP2 and IIP3, with interferers in the GSM and WLAN bands, are 40 dBm and 11 dBm respectively. The synthesizer displays maximum spurs level of -43 dBc, a state of the art phase noise of -128 dBc/Hz@10 MHz offset and a settling time of less than 6 ns with 43 m W only.
Arabic document similarity analysis using n-grams and singular value decomposition

The computerized methods for document similarity estimation (or plagiarism detection) in natural languages, evolved during the last two decades, have focused on English language in particular and some other languages such as German and Chinese. On the other hand, there are several language-independent methods, but the accuracy of these methods is not satisfactory, especially with morphological and complicated languages such as Arabic. This paper proposes an innovative content-based method for document similarity analysis devoted to Arabic language in order to bridge the existing gap in such software solutions. The proposed method is based on modeling the relation between documents and their n-gram phrases. These phrases are generated from the normalized text, exploiting Arabic morphology analysis and lexical lookup. Resolving possible morphological ambiguity is carried out through applying Part-of-Speech (PoS) tagging on the examined documents. Text indexing and stop-words removal are performed, employing a new method based on text morphological analysis. The examined documents' TF-IDF model is constructed using Heuristic based pair-wise matching algorithm, considering lexical and syntactic changes. Then, the hidden associations between the unique n-gram phrases and their documents are investigated using Latent Semantic Analysis (LSA). Next, the pairwise document subset and similarity measures are derived from the Singular Value Decomposition (SVD) computations. The performance of the proposed method was confirmed through experiments with various data sets, exhibiting promising capabilities in estimating literal and some types of intelligent similarities. Finally, the results of the proposed method was compared to that of Plagiarism-Checker-X, and the proposed method outperformed Plagiarism-Checker-X, especially for the intelligent similarity cases with syntactic changes.
Determinants of Inpatient Mental Health Use In a Heavily Insured Population

This paper estimates a model of the demand for hospital inpatient mental health services. It uses data on enrollees who were in the Blue Cross and Blue Shield Association Federal Health Benefits Plan from 1979 to 1981. The econometric analysis focuses on the impact of increased copayments and deductibles in the high-option plan. The results provide evidence that increases in outpatient copayments and deductibles reduce the utilization of both inpatient and outpatient mental health services. Of interest is the negative income elasticity of demand for hospital inpatient services and the positive association between the relative availability of mental health providers and the demand for mental health care.
Hepatic phosphatidylcholines: evidence for synthesis in the rat by extensive reutilization of endogenous acylglycerides.

Studies were performed to compare the extent of fatty acid incorporation into liver phosphatidylcholines (PCs) by acyl remodeling and by de novo synthesis. To this end, isolated rat livers were first perfused with palmitoleic acid (16:1) and [2-3H]glycerol and then with 17:1 fatty acid and nonradiolabeled glycerol that resulted in the formation of new molecular species of radiolabeled PCs containing 16:1 and 17:1 acyl groups. The specific activities of newly formed molecular species of the de novo precursors of acylglyceride synthesis, phosphatidic acids (PAs) and diglycerides (DGs), and the products of synthesis, PCs and triglycerides (TGs), were measured at periods during both the labeling period of perfusion with 16:1 (first 15 min) and the more prolonged chase period with 17:1 (up to 120 min). At the end of the labeling period, the specific activity of all the 16:1-containing PAs, DGs, and 16:1-16:1-16:1 and 16:1-16:1-18:2 TGs were the same and were much higher than any molecular species that did not contain 16:1. The specific activities of these molecular species are indicative of the specific activity of molecular species synthesized exclusively by de novo synthesis (i.e., by acylation of glycerol 3-phosphate) during the labeling period. In contrast, the specific activity of 16:1-16:1 PC was only 2/3 that of the other 16:1-16:1 glycerides, and the specific activities of the other 16:1-containing PCs were only about 1/3 that of the corresponding 16:1-containing PAs, DGs, and 16:1-16:1 TGs. After the labeling period and during the chase period with perfusion of 17:1 and nonradiolabeled glycerol, the specific activities of major 16:1 PCs exceeded the specific activities of their corresponding PAs and DGs and remained considerably higher than these precursors of de novo synthesis for the duration of perfusions. However, during this period, the specific activities of major 16:1 PCs were less than their corresponding molecular species of TGs. During the chase period, new 17:1 molecular species of PCs were formed that were also radiolabeled. The specific activity of 16:1-17:1 PC, the 17:1 PC with the highest specific activity, always exceeded its corresponding PA and DG precursors. During the chase period, non-16:1 and non-17:1 molecular species of PCs that comprised the bulk of hepatic PCs were also radiolabeled and the specific activities of these molecular species progressively increased during this period. (ABSTRACT TRUNCATED AT 400 WORDS)
The Ties That Divide: Ethnic Politics, Foreign Policy, and International Conflict

Acknowledgements1. Introduction: The Problem-Why do States Take Sides in Ethnic Conflicts? 2. Explaining the International Relations of Ethnic Conflict3. Understanding the Congo Crisis, 1960-19634. Religious Ties and the Nigerian Civil War, 1967-19705. The International Relations of Yugoslavia's Demise, 1991-19956. Quantitative Analyses of Ethnic Conflict's International Relations7. Findings, Future Directions and Policy Dilemmas
First Identification and Description of Rickettsioses and Q Fever as Causes of Acute Febrile Illness in Nicaragua

Background Rickettsial infections and Q fever present similarly to other acute febrile illnesses, but are infrequently diagnosed because of limited diagnostic tools. Despite sporadic reports, rickettsial infections and Q fever have not been prospectively studied in Central America. Methodology/Principal Findings We enrolled consecutive patients presenting with undifferentiated fever in western Nicaragua and collected epidemiologic and clinical data and acute and convalescent sera. We used ELISA for screening and paired sera to confirm acute (≥4-fold rise in titer) spotted fever and typhus group rickettsial infections and Q fever as well as past (stable titer) infections. Characteristics associated with both acute and past infection were assessed. Conclusions/Significance We enrolled 825 patients and identified acute rickettsial infections and acute Q fever in 0.9% and 1.3%, respectively. Clinical features were non-specific and neither rickettsial infections nor Q fever were considered or treated. Further study is warranted to define the burden of these infections in Central America.
A New Coarse-Grained Reconfigurable Architecture with Fast Data Relay and Its Compilation Flow

In this paper we propose a Fast Data Relay (FDR) mechanism and the supporting compiler techniques to enhance exist ing CGRA. Our results on FDR-based CGRA are compared with two other works in this field: ADRES and RCP. Experimental results for various multimedia applications show that FDR combined with a routing based resource conflict solver enables us to delive r up to 29% and 21% higher performance than ADRES and RCP, respecti vely.
Characterizing Latent User Interests on Enterprise Networks

We present a methodology for promoting situational awareness of an enterprise network using only network artifacts discernible from network protocol logs. We utilized latent Dirichlet allocation (LDA) over two corpora, the first composed of search queries and the second composed of external domain names issued by enterprise users through the network proxy of a mid-sized enterprise network. We not only quantitatively demonstrate that the LDA topic modeling approach achieves superior fit to the data than do naive models, but we also demonstrate that a topic modeling approach yields qualitative business analytic information.
A landscape metaphor for visualization of software projects

Software project management involves assessing the software system risks and costs, establishing a master schedule, integrating the various engineering specialities and design groups, maintaining configuration control and continuously auditing the effort to ensure that cost and schedule are met and the technical requirements objectives are satisfied. This paper presents a new graphical representation model for controlling and managing a project development process using metaphors and visual representation techniques.
Adaptive Join Plan Generation in Hadoop For CPS 296 . 1 Course Project

Joins in Hadoop has always been a problem for its users: the Map/Reduce framework seems to be specifically designed for group-by aggregation tasks rather than across-table operations; on the other hand, join operation in distributed database systems was never an easy task because data location and skewness makes join strategies harder to optimize. Fragment-replicate join (map join) may be a clever step towards good performance in some cases, but it can be a dangerous move under certain circumstances. This paper introduces some new techniques used in map join to tackle these issues, and proposes a plan generator for the join types that we currently have.