Miracle-dz/UniFAR-FTUs huggingface dataset:
A Novel Tumor Grading Scheme for Chromophobe Renal Cell Carcinoma: Prognostic Utility and Comparison With Fuhrman Nuclear Grade

Chromophobe renal cell carcinoma (RCC) is a histologic subtype of RCC that portends a favorable prognosis. It is controversial whether the Fuhrman nuclear grade of chromophobe RCC has prognostic utility. Irregular nuclei, prominent nucleoli, and nuclear pleomorphism are inherently present in chromophobe RCC. Hence, the Fuhrman nuclear grade is higher even though the majority of these tumors have a favorable outcome. In this study, the prognostic utility of a novel 3-tiered tumor grading system in which the innate nuclear atypia of chromophobe RCC was discounted, herein referred to as chromophobe tumor grade from a series of 124 chromophobe RCC, was compared with Fuhrman nuclear grade. Chromophobe tumor grade is based on the assessment of geographic nuclear crowding and anaplasia. The Fuhrman nuclear grade distribution between the tumors was grade 1 (1%), grade 2 (19%), grade 3 (74%), and grade 4 (6%), whereas the chromophobe tumor grade distribution was grade 1 (74%), grade 2 (16%), and grade 3 (10%). Neither Fuhrman nuclear grade nor chromophobe tumor grade was significantly associated with patient's age or sex and chromophobe RCC cell types, but both showed a significant association with tumor size. Both Fuhrman nuclear grade and chromophobe tumor grade showed statistically significant positive associations with broad alveolar growth, necrosis, vascular invasion, and with pathologic stage; however, all these associations tended to be dictated by tumors with sarcomatoid change. When tumors with sarcomatoid change were excluded, a strong positive association persisted between chromophobe tumor grade and pathologic stage. In contrast, there was no such association between Fuhrman nuclear grade and stage in nonsarcomatoid chromophobe RCCs. Characterizing aggressive chromophobe RCC with aggressive behavior with the time from surgery to first occurrence of metastasis, local recurrence, or death owing to disease, we found that both Fuhrman nuclear grade and chromophobe tumor grade were highly associated with adverse outcome. However, as with the pathologic stage, only a significant association between chromophobe tumor grade and outcome was retained among nonsarcomatoid chromophobe RCCs. Multivariable Cox regression analysis also tended to support chromophobe tumor grade rather than Fuhrman nuclear grade as an independent predictor of adverse outcome, controlling for other univariably significant risk factors [estimated relative hazard=3.68 (P=0.026) vs. 1.86 (P=0.42)]. In conclusion, the novel chromophobe tumor grading system proposed herewith provides superior prognostic value to that of the Fuhrman nuclear grade in chromophobe RCC and will potentially help stratify patients of chromophobe RCC who are at a greater risk of disease progression.
Multi-Task Cross-Lingual Sequence Tagging from Scratch

We present a deep hierarchical recurrent neural network for sequence tagging. Given a sequence of words, our model employs deep gated recurrent units on both character and word levels to encode morphology and context information, and applies a conditional random field layer to predict the tags. Our model is task independent, language independent, and feature engineering free. We further extend our model to multi-task and cross-lingual joint training by sharing the architecture and parameters. Our model achieves state-of-the-art results in multiple languages on several benchmark tasks including POS tagging, chunking, and NER. We also demonstrate that multi-task and cross-lingual joint training can improve the performance in various cases.
Lichen planus in children—a review of six cases

We present the features of six children who have been seen amongst 154 consecutive new patients with lichen planus in our outpatients clinic. All but one of the children had unusual forms of the disease and there was a family history of lichen planus in three. Lichen planus is rare in childhood and often assumes atypical clinical patterns.
Metronidazole-induced encephalopathy in a patient with Crohn's disease

Metronidazole is a widely used antibiotic for the treatment of anaerobic bacterial infections. Metronidazole-induced encephalopathy (MIEP) is a rare but potentially reversible disease. The mechanism of MIEP remains unclear, and differences in the neurotoxic effects of oral versus intravenous (IV) metronidazole administration have not yet been determined. We report the case of a Crohn's disease (CD) patient who experienced encephalopathy immediately after a single IV dose of metronidazole following long-term exposure to the oral form of the drug. The 64-year-old man with intractable CD experienced a sudden change in mental status, aphasia, and muscle weakness after IV administration of metronidazole. He had previously taken metronidazole orally for 13 years and received intermittent IV metronidazole treatments for CD exacerbation. Brain magnetic resonance imaging (MRI) showed high-intensity signals in the bilateral medial thalamus and the midbrain and pontine tegmentum on fluid-attenuated inversion recovery images. After discontinuation of metronidazole, the high-intensity brain MRI signals resolved and the patient's mental status dramatically improved; however, the patient exhibited mild cognitive dysfunction 2 months after the onset of encephalopathy.
Recursive function data allocation to scratch-pad memory

This paper presents the first automatic scheme to allocate local (stack) data in recursive functions to scratch-pad memory (SPM) in embedded systems. A scratch-pad is a fast directly addressed compiler-managed SRAM memory that replaces the hardware-managed cache. It is motivated by its significantly lower access time, energy consumption, real-time bounds, area and overall runtime. Existing compiler methods for allocating data to scratch-pad are able to place only code, global, heap and non-recursive stack data in scratch-pad memory; stack data for recursive functions is allocated entirely in DRAM, resulting in poor performance. In this paper we present a dynamic yet compiler-directed allocation method for recursive function stack data that for the first time, is able to place a portion of recursive stack data in scratch-pad. It has almost no software-caching overhead, and is able to move recursive function data back and forth between scratch-pad and DRAM to better track the program's locality characteristics. With our method, all code, global, stack and heap variables can share the same scratch-pad. When compared to placing all recursive function data in DRAM and all other variables in scratch-pad, our results show that our method reduces the average runtime of our benchmarks by 29.3%, and the average power consumption by 31.1%, for the same size of scratch-pad fixed at5% of total data size. Furthermore,significant savings were observedwhen comparing our method against cache-based alternatives for SPM allocation. Finally, we show results that analyze the effects of profile variation on our allocation approach and present a modified version of our method which minimizes variation for profile-based allocations.
Displaced Acetabular Fractures

Displaced acetabular fractures occur primarily in young adults involved in high energy trauma and can lead to disabling posttraumatic arthritis. An initial roentgenographic evaluation with accurate delineation of all fracture lines provides the key to decisions about whether to give closed or open treatment. When open treatment is indicated, a surgical approach can be chosen that will almost always lead to reduction without the necessity of a second approach. The authors have found that the Kocher-Langenbeck, ilioinguinal, and extended iliofemoral approaches are the most useful. A fracture table and specialized reduction instruments aid fracture reduction and fixation. Satisfactory operative reduction of the fracture is the factor that correlates best with a satisfactory clinical result. The rate of satisfactory operative reductions improved gradually over the first 50 operations of a prospective study of 121 displaced acetabular fractures. Overall, there were 80% satisfactory clinical results in this series. Complications included a 3% infection rate and a 5% incidence of nerve palsy. Open reduction and internal fixation are indicated for the majority of displaced fractures. However, closed treatment can produce satisfactory results in selected patients.
Addiction in Parkinson's disease: Impact of subthalamic nucleus deep brain stimulation

In Parkinson's disease, dopamine dysregulation syndrome (DDS) is characterized by severe dopamine addiction and behavioral disorders such as manic psychosis, hypersexuality, pathological gambling, and mood swings. Here, we describe the case of 2 young parkinsonian patients suffering from disabling motor fluctuations and dyskinesia associated with severe DDS. In addition to alleviating the motor disability in both patients, subthalamic nucleus (STN) deep brain stimulation greatly reduced the behavioral disorders as well as completely abolished the addiction to dopaminergic treatment. Dopaminergic addiction in patients with Parkinson's disease, therefore, does not constitute an obstacle to high‐frequency STN stimulation, and this treatment may even cure the addiction. © 2005 Movement Disorder Society
Superorbital variability of X-ray and radio emission of Cyg X-1 -II. Dependence of the orbital modulation and spectral hardness on the superorbital phase

We discover a pronounced dependence of the strength of the soft X-ray orbital modulation and the spectral hardness in Cyg X-1 in the hard state on its superorbital phase. We find, our results can be well modelled as a combination of two effects: the precession of the accretion disc (which appears to cause the superorbital flux modulation) and the orbital-phase dependent X-ray absorption in an accretion bulge, located at the accretion disc edge close to the supergiant companion but displaced from the line connecting the stars by about 25°. Our findings are supported by the distribution of the X-ray dips showing concentration towards zero superorbital phase, which corresponds to the bulge passing through the line of sight. We Fourier analyse our model, and find it explains the previous finding of asymmetric beat (between the orbital and superorbital modulations) frequencies in the observed power spectrum, provided the disc precession is prograde. On the other hand, we find no statistically significant changes of the orbital modulation with the superorbital phase in the 15-GHz radio data. This absence is consistent with the radio being emitted by a jet in the system, in which case the orbital modulation is caused by wind absorption far away from the disc. We also find that both the X-ray and radio fluxes of Cyg X-1 in the hard state on time-scales ≥10 4 s have lognormal distributions, which complements a previous finding of a lognormal flux distribution in the hard state on ∼1-s time-scales. We point out that the lognormal character of the flux distribution requires that flux logarithms rather than fluxes themselves should be used for averaging and error analysis. We also provide a correct formula for the uncertainty of rms of a light curve for the case when the uncertainty is higher than the measurement.
A Strongly Secure Certificateless Digital Signature Scheme in the Random Oracle Model

The main purpose of this paper is to provide a security proof for the certiﬁcateless digital signature scheme found in [Hassouna, Bashier, and Barry, A short certiﬁcateless digital signature scheme, International Conference of Digital Information Processing , Data Mining and Wireless Communications, 2015, pp. 120–127] in the random oracle model. Two types of attacks are considered: The ﬁrst type can be carried out by an outsider attacker and referred to as Type I, whereas the second one can be carried out by a malicious KGC and referred to as Type II. The possible oracles for each of the two types of attacks are discussed, and hence, the security of the proposed digital signature scheme was proved in the random oracle model.
Computationally Efficient Nonparametric Importance Sampling

The variance reduction established by importance sampling strongly depends on the choice of the importance sampling distribution. A good choice is often hard to achieve especially for high-dimensional integration problems. Nonparametric estimation of the optimal importance sampling distribution (known as “nonparametric importance sampling”) is a reasonable alternative to parametric approaches. In this article, nonparametric variants of both the self-normalized and the unnormalized importance sampling estimator are proposed and investigated. A common critique of nonparametric importance sampling is the increased computational burden compared with parametric methods. We solve this problem to a large degree by utilizing the linear blend frequency polygon estimator instead of a kernel estimator. Mean square error convergence properties are investigated, leading to recommendations for the efficient application of nonparametric importance sampling. Particularly, we show that nonparametric importance sampling asymptotically attains optimal importance sampling variance. The efficiency of nonparametric importance sampling algorithms relies heavily on the computational efficiency of the nonparametric estimator used. The linear blend frequency polygon outperforms kernel estimators in terms of certain criteria such as efficient sampling and evaluation. Furthermore, it is compatible with the inversion method for sample generation. This allows one to combine nonparametric importance sampling with other variance reduction techniques such as stratified sampling. Empirical evidence for the usefulness of the suggested algorithms is obtained by means of three benchmark integration problems. We show empirically that these methods may work in higher dimensions, at least up to dimension eight. As an application, we estimate the distribution of the queue length of a spam filter queuing system based on real data.
Local Structure Prediction with Local Structure-based Sequence Profiles

MOTIVATION A large body of experimental and theoretical evidence suggests that local structural determinants are frequently encoded in short segments of protein sequence. Although the local structural information, once recognized, is particularly useful in protein structural and functional analyses, it remains a difficult problem to identify embedded local structural codes based solely on sequence information. RESULTS In this paper, we describe a local structure prediction method aiming at predicting the backbone structures of nine-residue sequence segments. Two elements are the keys for this local structure prediction procedure. The first key element is the LSBSP1 database, which contains a large number of non-redundant local structure-based sequence profiles for nine-residue structure segments. The second key element is the consensus approach, which identifies a consensus structure from a set of hit structures. The local structure prediction procedure starts by matching a query sequence segment of nine consecutive amino acid residues to all the sequence profiles in the local structure-based sequence profile database (LSBSP1). The consensus structure, which is at the center of the largest structural cluster of the hit structures, is predicted to be the native state structure adopted by the query sequence segment. This local structure prediction method is assessed with a large set of random test protein structures that have not been used in constructing the LSBSP1 database. The benchmark results indicate that the prediction capacities of the novel local structure prediction procedure exceed the prediction capacities of the local backbone structure prediction methods based on the I-sites library by a significant margin. AVAILABILITY All the computational and assessment procedures have been implemented in the integrated computational system PrISM.1 (Protein Informatics System for Modeling). The system and associated databases for LINUX systems can be downloaded from the website: http://www.columbia. edu/~ay1/.
On message lengths for noisy network coding

Quantize-map-forward (QMF) and noisy network coding (NNC) differ primarily from compress-forward relaying in that relays do not hash their quantization bits. Two further differences are that source nodes use “long”-message repetitive encoding and destination nodes use simultaneous joint decoding. Recent work has shown that classic “short”-message encoding combined with backward decoding achieves the same rates as QMF and NNC. A simplified proof of this result is given.
Development of the biologically active Guglielmi detachable coil for the treatment of cerebral aneurysms. Part II: an experimental study in a swine aneurysm model.

BACKGROUND AND PURPOSE Ion implantation is a surface-modification technology that creates a borderless surface on protein-coated platinum; this change in physical and chemical properties on the surface of Guglielmi detachable coils (GDCs) appears to enhance cell proliferation and adhesion. Our purpose was to evaluate the effect of ion implantation on GDCs in an experimental aneurysm model. METHODS GDCs were coated with either type I collagen, fibronectin, vitronectin, laminin, or fibrinogen. Using He+ or Ne+ 1 x 10(14-15) ions/cm2, ion implantation was performed on these protein-coated GDCs (GDC-Is). A total of 56 experimental aneurysms were constructed microsurgically in the common carotid arteries of 28 swine. These experimental aneurysms were embolized with standard GDCs (n = 23), collagen GDC-Is (n = 11), vitronectin GDC-Is (n = 6), laminin GDC-Is (n = 4), fibrinogen GDC-Is (n = 6), and fibronectin GDC-Is (n = 6). The animals were sacrificed at day 14 after coil embolization. The physical properties of the new coils (friction on delivery, deployment into aneurysms, trackability, etc) and the development of tissue scarring and neoendothelium across the aneurysm's orifice were evaluated macroscopically and microscopically. RESULTS No evidence of increased coil friction/stiffness was observed during delivery of GDC-Is through microcatheters in this aneurysm model. A more intense scar formation and neoendothelium at the neck of aneurysms were observed macroscopically when treated with GDC-Is. Significant differences in the proportion of neck coverage between standard GDCs (48.3% +/- 20.5%) and all GDC-I groups were observed (collagen GDC-I-89.4% +/- 14.9%, P < .01; vitronectin GDC-I-71.5% +/- 7.0%, P < .05; laminin GDC-I-76.5% +/- 11.0%, P < .05; fibrinogen GDC-I-74.8% +/- 13.9%, P < .05; fibronectin GDC-I-87.5% +/- 15.0%, P < .01). Light microscopy showed a well-organized fibrous tissue bridging the aneurysm's neck when using GDC-Is, whereas only a fibrin-like thin layer covered the standard GDC surfaces. CONCLUSION GDC-Is indicated a more intense inflammatory response in the aneurysm body and dome and faster re-endothelial coverage of the neck of the aneurysm. This accelerated histologic response may decrease the chances of coil compaction and aneurysm recanalization. This technology may improve anatomic and clinical outcomes in patients harboring intracranial aneurysms.
Partial loss of Tip60 slows mid-stage neurodegeneration in a spinocerebellar ataxia type 1 (SCA1) mouse model

Spinocerebellar ataxia type 1 (SCA1) is one of nine dominantly inherited neurodegenerative diseases caused by polyglutamine tract expansion. In SCA1, the expanded polyglutamine tract is in the ataxin-1 (ATXN1) protein. ATXN1 is part of an in vivo complex with retinoid acid receptor-related orphan receptor alpha (Rora) and the acetyltransferase tat-interactive protein 60 kDa (Tip60). ATXN1 and Tip60 interact directly via the ATXN1 and HMG-box protein 1 (AXH) domain of ATXN1. Moreover, the phospho-mimicking Asp amino acid at position 776, previously shown to enhance pathogenesis, increases the ability of ATXN1 to interact with Tip60. Using a genetic approach, the biological relevance of the ATXN1/Tip60 interaction was assessed by crossing ATXN1[82Q] mice with Tip60+/−animals. Partial Tip60 loss increased Rora and Rora-mediated gene expression and delayed ATXN1[82]-mediated cerebellar degeneration during mid-stage disease progression. These results suggested a specific, temporal role for Tip60 during disease progression. We also showed that genetic background modulated ATXN1[82Q]-induced phenotypes. Of interest, these latter studies showed that some phenotypes are enhanced on a mixed background while others are suppressed.
Managing Price Risk in a Multimarket Environment

In a competitive electricity market, a generation company (Genco) can manage its trading risk through trading electricity among multiple markets such as spot markets and contract markets. The question is how to decide the trading proportion of each market in order to maximize the Genco's profit and minimize the associated risk. Based on the mean-variance portfolio theory, this paper proposes a sequential optimization approach to electric energy allocation between spot and contract markets, taking into consideration the risks of electricity price, congestion charge, and fuel price. Especially, the impact of the fuel market on electric energy allocation is analyzed and simulated with historical data in respect of the electricity market and other fuel markets in the U.S. Simulation results confirm that the proposed analytic approach is consistent with intuition and therefore reasonable and feasible for a Genco to make a trading plan involving risks in an electricity market
Strategic outsourcing for competing OEMs that face cost reduction opportunities

This paper explores production and outsourcing decisions for two Original Equipment Manufacturers (OEMs) who produce partially substitutable products and have opportunities to invest in reducing the manufacturing cost. In such an environment, competition drives both OEMs to set lower prices and invest more than would maximize their combined profits, particularly when product substitutability is high. However, outsourcing provides a mechanism by which the two OEMs can credibly signal that they will not overinvest in cost reduction, mitigating a mutually destructive cost competition. Our paper explores the role that an external supplier(s) can play in dampening competition between the OEMs when there are opportunities to invest in cost reduction. In particular, we characterize the conditions under which a supplier can profitably enter the market by inducing the OEMs to outsource production. We first examine a basic model of two identical OEMs in which there is a single common supplier and a single component that is a candidate for outsourcing. Later, we extend the basic model to allow for market asymmetry, two suppliers, and more than one component that might be outsourced.