Miracle-dz/UniFAR-FTUs huggingface dataset:
Edematous Processes Within Kager Fat Pad: Magnetic Resonance Imaging, Gross Anatomical, and Histological Studies in Cadavers With Clinical Correlation

Objective: To demonstrate the anatomical features of Kager fat pad (KFP) and its fasciae using magnetic resonance imaging, gross anatomy, and histology in cadavers; and to correlate the data with image findings in patients. Methods: The KFP was analyzed in 10 fresh human cadavers and 152 clinical cases. The retrospective clinical study was institutional review board approved. The specimens were studied by magnetic resonance imaging and sectioned for anatomical/histological correlation. Clinical cases were selected to evaluate the frequency, distribution, and patterns of edema/inflammation in KFP. The square of the Pearson product moment correlation coefficient and Student t tests were performed. Results: Fasciae about KFP are double layered and derived from the union of the fascia of the leg and flexor and peroneal retinacula. Edema in KFP could be divided into diffuse, confined anteriorly, confined posteriorly, and confined externally. Confined patterns of edema were associated with paratenonitis and fluid in the Achilles bursae (P < 0.05). Conclusions: Four patterns of edema occur in KFP. Paratenonitis and bursal fluid were associated with confined edematous patterns. The double layer about KFP may contain edema that affects this region.
The solution structure of the ZnF UBP domain of USP33/VDU1

USP33/VDU1 is a deubiquitinating enzyme that binds to the von Hippel–Lindau tumor suppressor protein. It also regulates thyroid hormone activation by deubiquitinating type 2 iodothyronine deiodinase. USP33/VDU1 contains a ZF UBP domain, a protein module found in many proteins in the ubiquitin–proteasome system. Several ZF UBP domains have been shown to bind ubiquitin, and a structure of a complex of the ZF UBP domain of isoT/USP5 and ubiquitin is available. In the present work, the solution structure of the ZF UBP domain of USP33/VDU1 has been determined by NMR spectroscopy. The structure differs from that of the USP5 domain, which contains only one of the three Zn ions present in the USP33/VDU1 structure. The USP33/VDU1 ZnF UBP domain does not bind to ubiquitin.
CCMpred—fast and precise prediction of protein residue–residue contacts from correlated mutations

Motivation: Recent breakthroughs in protein residue–residue contact prediction have made reliable de novo prediction of protein structures possible. The key was to apply statistical methods that can distinguish direct couplings between pairs of columns in a multiple sequence alignment from merely correlated pairs, i.e. to separate direct from indirect effects. Two classes of such methods exist, either relying on regularized inversion of the covariance matrix or on pseudo-likelihood maximization (PLM). Although PLM-based methods offer clearly higher precision, available tools are not sufficiently optimized and are written in interpreted languages that introduce additional overheads. This impedes the runtime and large-scale contact prediction for larger protein families, multi-domain proteins and protein–protein interactions. Results: Here we introduce CCMpred, our performance-optimized PLM implementation in C and CUDA C. Using graphics cards in the price range of current six-core processors, CCMpred can predict contacts for typical alignments 35–113 times faster and with the same precision as the most accurate published methods. For users without a CUDA-capable graphics card, CCMpred can also run in a CPU mode that is still 4–14 times faster. Thanks to our speed-ups (http://dictionary.cambridge.org/dictionary/british/speed-up) contacts for typical protein families can be predicted in 15–60 s on a consumer-grade GPU and 1–6 min on a six-core CPU. Availability and implementation: CCMpred is free and open-source software under the GNU Affero General Public License v3 (or later) available at https://bitbucket.org/soedinglab/ccmpred Contact: johannes.soeding@mpibpc.mpg. de Supplementary information: Supplementary data are available at Bioinformatics online.
Functional Dissection of a HECT Ubiquitin E3 Ligase*S

Ubiquitination is one of the most prevalent protein post-translational modifications in eukaryotes, and its malfunction is associated with a variety of human diseases. Despite the significance of this process, the molecular mechanisms that govern the regulation of ubiquitination remain largely unknown. Here we used a combination of yeast proteome chip assays, genetic screening, and in vitro/in vivo biochemical analyses to identify and characterize eight novel in vivo substrates of the ubiquitinating enzyme Rsp5, a homolog of the human ubiquitin-ligating enzyme Nedd4, in yeast. Our analysis of the effects of a deubiquitinating enzyme, Ubp2, demonstrated that an accumulation of Lys-63-linked polyubiquitin chains results in processed forms of two substrates, Sla1 and Ygr068c. Finally we showed that the localization of another newly identified substrate, Rnr2, is Rsp5-dependent. We believe that our approach constitutes a paradigm for the functional dissection of an enzyme with pleiotropic effects.
Persistence of hybrid fibers in rat soleus after spinal cord transection

The effects of a chronic (up to 360 days) reduction in neuromuscular activity (defined as electrical activation and loading) on myosin heavy chain (MHC) isoform expression in the rat soleus muscle were studied. A complete mid‐thoracic (T7‐T8) spinal cord transection (ST) was used to induce a reduction in soleus muscle neuromuscular activity. Electrophoretic analyses revealed that MHC‐I was progressively decreased after ST, accounting for approx. 90% of the total soleus MHC in controls and only approx. 12% 1 year after ST. The reductions in the proportion of MHC‐I were countered by increases in MHC‐IIa and MHC‐IIx with the increase in MHC‐IIx preceding the increase in MHC‐IIa. Curiously, MHC‐IIb was expressed only at very low levels. Thus, a complete transformation from predominantly MHC‐I to MHC‐IIb did not occur. Many fibers (up to approx. 80%) contained multiple MHCs (hybrid fibers) after ST. The proportion of hybrid fibers was maintained at a high level (approx. 50%) 1 year after ST. These data suggest that: 1) a prolonged reduction in neuromuscular activity was not sufficient to induce high level MHC‐IIb expression by the soleus muscle; and 2) hybrid fibers were not simply transitional fibers. Thus, it appears that under appropriate conditions hybrid fibers may represent a “stable” fiber phenotype. Anat Rec 255:188–201, 1999. © 1999 Wiley‐Liss, Inc.
Savings in location management costs leveraging user statistics

The growth in the number of users in mobile communications networks and the rise in the traffic generated by each user, are responsible for the increasing importance of Mobility Management. Within Mobility Management, the main objective of Location Management is to enable the roaming of the user in the coverage area. In this paper, we analyze the savings in Location Management costs obtained leveraging the users' statistics, in comparison with the classical strategy. In particular, we introduce two novel algorithms to obtain the Beta parameters (useful terms in the calculation of location update costs for different Location Management strategies), utilizing a geographical study of relative positions of the cells within the location areas. Eventually, we discuss the influence of the different network parameters on the total Location Management costs savings for both the radio interface and the fixed network part, providing useful guidelines for the optimum design of the networks.
The neuropsychology of ecstasy (MDMA) use: a quantitative review

A growing number of empirical studies have found varying neuropsychological impairments associated with use of 3,4‐methylenedioxymethamphetamine (MDMA) use. We set out to determine to what extent neuropsychological abilities are impaired in MDMA users. To do so, meta‐analytical methods were used to determine the magnitude of neuropsychological impairment in MDMA users across pre‐specified cognitive domains. We found that cognitive impairment secondary to recreational drug use may result in what might be described as small‐to‐medium effects across all cognitive domains with learning and memory being most impaired. We also found that total lifetime ingestion of MDMA appears to be negatively associated with performance on tasks ranging from attention and concentration to learning and memory. Implications and limitations of these findings are discussed. Copyright © 2007 John Wiley & Sons, Ltd.
Thromboembolic events among adult patients with primary immune thrombocytopenia in the United Kingdom General Practice Research Database

Background The risk of thromboembolic events in adults with primary immune thrombocytopenia has been little investigated despite findings of increased susceptibility in other thrombocytopenic autoimmune conditions. The objective of this study was to evaluate the risk of thromboembolic events among adult patients with and without primary immune thrombocytopenia in the UK General Practice Research Database. Design and Methods Using the General Practice Research Database, 1,070 adults (≥18 years) with coded records for primary immune thrombocytopenia first referenced between January 1st 1992 and November 30th 2007, and having at least one year pre-diagnosis and three months post-diagnosis medical history were matched (1:4 ratio) with 4,280 primary immune thrombocytopenia disease free patients by age, gender, primary care practice, and pre-diagnosis observation time. The baseline prevalence and incidence rate of thromboembolic events were quantified, with comparative risk modelled by Cox’s proportional hazards regression. Results Over a median 47.6 months of follow-up (range: 3.0–192.5 months), adjusted hazard ratios of 1.58 (95% CI, 1.01–2.48), 1.37 (95% CI, 0.94–2.00), and 1.41 (95% CI, 1.04–1.91) were found for venous, arterial, and combined (arterial and venous) thromboembolic events, respectively, when comparing the primary immune thrombocytopenia cohort with the primary immune thrombocytopenia disease free cohort. Further event categorization revealed an elevated incidence rate for each occurring venous thromboembolic subtype among the adult patients with primary immune thrombocytopenia. Conclusions Patients with primary immune thrombocytopenia are at increased risk for venous thromboembolic events compared with patients without primary immune thrombocytopenia.
Organic anion–transporting polypeptide 1b2 (Oatp1b2) is important for the hepatic uptake of unconjugated bile acids: Studies in Oatp1b2‐null mice

The organic anion–transporting polypeptide 1b family (Oatp1b2 in rodents and OATP1B1/1B3 in humans) is liver‐specific and transports various chemicals into the liver. However, the role of the Oatp1b family in the hepatic uptake of bile acids (BAs) into the liver is unknown. Therefore, in Oatp1b2‐null mice, the concentrations of BAs in plasma, liver, and bile were compared with wild‐type (WT) mice. It was first determined that livers of the Oatp1b2‐null mice were not compensated by altered expression of other hepatic transporters. However, the messenger RNA of Cyp7a1 was 70% lower in the Oatp1b2‐null mice. Increased expression of fibroblast growth factor 15 in intestines of Oatp1b2‐null mice might be responsible for decreased hepatic expression of Cyp7a1 in Oatp1b2‐null mice. The hepatic concentration and biliary excretion of conjugated and unconjugated BAs were essentially the same in Oatp1b2‐null and WT mice. The serum concentration of taurine‐conjugated BAs was essentially the same in the two genotypes. In contrast, the serum concentrations of unconjugated BAs were 3‐45 times higher in Oatp1b2‐null than WT mice. After intravenous administration of cholate to Oatp1b2‐null mice, its clearance was 50% lower than in WT mice, but the clearance of taurocholate was similar in the two genotypes. Conclusion: This study indicates that Oatp1b2 has a major role in the hepatic uptake of unconjugated BAs. (HEPATOLOGY 2011.)
Transfer Learning for Improving Model Predictions in Highly Configurable Software

Modern software systems are built to be used in dynamic environments using configuration capabilities to adapt to changes and external uncertainties. In a self-adaptation context, we are often interested in reasoning about the performance of the systems under different configurations. Usually, we learn a black-box model based on real measurements to predict the performance of the system given a specific configuration. However, as modern systems become more complex, there are many configuration parameters that may interact and we end up learning an exponentially large configuration space. Naturally, this does not scale when relying on real measurements in the actual changing environment. We propose a different solution: Instead of taking the measurements from the real system, we learn the model using samples from other sources, such as simulators that approximate performance of the real system at low cost. We define a cost model that transform the traditional view of model learning into a multi-objective problem that not only takes into account model accuracy but also measurements effort as well. We evaluate our cost-aware transfer learning solution using real-world configurable software including (i) a robotic system, (ii) 3 different stream processing applications, and (iii) a NoSQL database system. The experimental results demonstrate that our approach can achieve (a) a high prediction accuracy, as well as (b) a high model reliability.
Neurofilament mRNA is reduced in Parkinson's disease substantia nigra pars compacta neurons

Lewy bodies are filamentous neuronal inclusions characteristic of Parkinson's disease, and neurofilament triplet proteins are the major components of the filaments in Lewy bodies. Since the neurofilament proteins found in Lewy bodies are abnormally phosphorylated and partially degraded, the formation of Lewy bodies may be due to the defective metabolism of these proteins, and this could lead to impairments in the structure and function of neurofilament rich neuronal processes (i.e., large caliber axons). To gain further insights into the metabolism of neurofilaments in Parkinson's disease, we evaluated neurofilament mRNA levels by semiquantitative in situ hybridization histochemistry in postmorten tissues from Parkinson's disease and control subjects. Substantia nigra pars compacta neurons were examined with digoxigenin‐UTP labeled cRNA probes to the heavy and light neurofilament mRNAs. The relative abundance of these mRNAs was measured by videodensitometric image analysis of chromogenic reaction product. Using this approach, we demonstrated that the levels of both heavy and light neurofilament mRNAs were reduced in Parkinson's disease substantia nigra pars compacta neurons. Additionally, the levels of heavy neurofilament mRNA were lowest in Lewy body containing neurons in the Parkinson's disease cases. These results suggest that the formation of neurofilament‐rich Lewy bodies in substantia nigra pars compacta neurons is associated with reduced levels of the heavy and light neurofilament mRNAs in Parkinson's disease. Thus, it is possible that the accumulation of abnormal neurofilament proteins in Lewy bodies and diminished neurofilament mRNAs contribute to the degeneration of substantia nigra pars compacta neurons in Parkinson's disease. © 1993 Wiley‐Liss, Inc.
The Issue-Adjusted Ideal Point Model

We develop a model of issue-specific voting behavior. This model can be used to explore lawmakers' personal voting patterns of voting by issue area, providing an exploratory window into how the language of the law is correlated with political support. We derive approximate posterior inference algorithms based on variational methods. Across 12 years of legislative data, we demonstrate both improvement in heldout prediction performance and the model's utility in interpreting an inherently multi-dimensional space.
Standard platform for sensor fusion on advanced driver assistance system using Bayesian Network

In this paper, a new architecture for sensor fusion for advanced driver assistant system (ADAS) is proposed. This architecture is based on Bayesian Network and plays the role of a platform for integrating various sensors such as Lidar, Radar and Vision sensors into sensor fusion systems. This architecture has the following 3 major advantages: (1) It makes structure and signal flow of the complicated fusion systems easy to understand (2) It increases the reusability of the sensor algorithm modules (3) It achieves easy integration of various sensors with different specifications. These advantages are confirmed by vehicle test.
The Role of Patient Activation in Preferences for Shared Decision Making: Results From a National Survey of U.S. Adults

Studies investigating preferences for shared decision making (SDM) have focused on associations with sociodemographic variables, with few investigations exploring patient factors. We aimed to investigate the relationship between patient activation and preferences for SDM in 6 common medical decisions among a nationally representative cross-sectional survey of American adults. Adults older than 18 were recruited online (n = 2,700) and by telephone (n = 700). Respondents completed sociodemographic assessments and the Patient Activation Measure. They were also asked whether they perceived benefit (yes/no) in SDM in 6 common medical decisions. Nearly half of the sample (45.9%) reached the highest level of activation (Level 4). Activation was associated with age (p < .001), higher income (p = .001), higher education (p = .010), better self-rated health (p < .001), and fewer chronic conditions (p = .050). The proportion of people who agreed that SDM was beneficial varied from 53.1% (deciding the necessity of a diagnostic test) to 71.8% (decisions associated with making lifestyle changes). After we controlled for participant characteristics, higher activation was associated with greater perceived benefit in SDM across 4 of the 6 decisions. Preferences for SDM varied among 6 common medical scenarios. Low patient activation is an important barrier to SDM that could be ameliorated through the development of behavioral interventions.
Equivalent circuit modeling of coupled resonator filters

Using the stacked crystal filter (SCF) concept, a coupled resonator filter (CRF) can be interpreted as a device in which 2 piezoresonators are stacked on top of each other in such a way that a certain degree of acoustic interaction occurs. The work presented in this paper reports a novel all-electrical model for the CRF. The model associates acoustical coupling with an equivalent electrical coupling between resonators. The resulting equivalent circuit makes it possible to apply classical filter synthesis techniques directly based on the coupling control between resonators. It complements with a synthesis approach the analysis approach of the Mason model.
Measurement of 7-methylguanine as an estimate of the amount of dimethylnitrosamine formed following administration of aminopyrine and nitrite to rats.

We have demonstrated that there is a dose-related increase in the excretion of 7-[methyl-14C]methylguanine ( [14C]m7Gua) following p.o. administration of di[methyl-14C]methylnitrosamine to rats. Urine was collected for 24 hr after di[methyl-14C]methylnitrosamine administration, and the purines were precipitated from an aliquot of the urine with silver nitrate. Purines were released from the precipitate with HCl, and [14C]m7Gua was quantified by chromatography on an Aminex A-6 column. The excretion of [14C]m7Gua increased linearly with the dose of dimethylnitrosamine. This relationship was used to estimate the amount of di[methyl-14C]methylnitrosamine formed in the reaction of [14C]aminopyrine with sodium nitrite in rats gavaged with these compounds. The dose of dimethylnitrosamine was also estimated from the amount of alkylation of liver DNA in the same animals. These estimates usually differed by less than a factor of 2. [14C]aminopyrine and sodium nitrite were administered. The possibility of using this assay to obtain data on nitrosation in humans is discussed.
An Assessment of Relationship Between Growth and Inequality Using Micro Data from Thailand

Applying comprehensive decomposition analyses to the micro data from Thailand, this paper shows that growth and income distribution dynamics are closely linked through occupation, financial intermediation, and education. The compositional change of these characteristics accounts for more than half of the Thai inequality increase while it contributed to nearly forty percent of the Thai growth and poverty reduction between 1976 and 1996, which not only validates the empirical importance of the relationship between growth and income inequality that Kuznets (1955) speculated on, but also identifies the key factors through which they are linked. This study thus lays a cornerstone on the works searching for the relevant specification of underlying mechanisms of growth and inequality and the scope of potential policies for equity-enhancing growth. The orders of magnitudes of the compositional effects on growth are similar over these characteristics but their effects on income distribution dynamics sharply contrast. Financial deepening and educational expansion contributed to increase in inequality while occupational transformation did not so much contributed to inequality increase as to poverty alleviation. However, the effect of diverging income levels across income-status groups on inequality is most remarkable via occupation, suggesting the importance of a rise in skill premia on inequality dynamics along growth, which is the main factor together with the occupational transformation that shapes the aggregate inequality dynamics along growth as an inverted-U curve.
Faster Parallel Traversal of Scale Free Graphs at Extreme Scale with Vertex Delegates

At extreme scale, irregularities in the structure of scale-free graphs such as social network graphs limit our ability to analyze these important and growing datasets. A key challenge is the presence of high-degree vertices (hubs), that leads to parallel workload and storage imbalances. The imbalances occur because existing partitioning techniques are not able to effectively partition high-degree vertices. We present techniques to distribute storage, computation, and communication of hubs for extreme scale graphs in distributed memory supercomputers. To balance the hub processing workload, we distribute hub data structures and related computation among a set of delegates. The delegates coordinate using highly optimized, yet portable, asynchronous broadcast and reduction operations. We demonstrate scalability of our new algorithmic technique using Breadth-First Search (BFS), Single Source Shortest Path (SSSP), K-Core Decomposition, and Page-Rank on synthetically generated scale-free graphs. Our results show excellent scalability on large scale-free graphs up to 131K cores of the IBM BG/P, and outperform the best known Graph500 performance on BG/P Intrepid by 15%.