Miracle-dz/UniFAR-FTUs huggingface dataset:
Effects of motion segment level, Pfirrmann intervertebral disc degeneration grade and gender on lumbar spine kinematics

MRI allows non‐invasive assessment of intervertebral disc degeneration with the added clinical benefit of using non‐ionizing radiation. What has remained unclear is the relationship between assessed disc degeneration and lumbar spine kinematics. Kinematic outcomes of 54 multi‐segment (L1‐Sacrum) lumbar spine specimens were calculated to discover if such an underlying relationship exists with degeneration assessed using the Pfirrmann grading system. Further analyses were also conducted to determine if kinematic outcomes were affected by motion segment level, gender or applied compressive preload. Range of motion, hysteresis, high flexibility zone size and rotational stiffness in flexion‐extension, lateral bending and axial rotation were the kinematic outcomes. Caudal intervertebral discs in our study sample were more degenerative than cranial discs. L5‐S1 discs had the largest flexion‐extension range of motion (p < 0.005) and L1‐L2 discs the lowest flexion high flexibility zone size (p < 0.013). No other strict cranial‐caudal differences in kinematic outcomes were found. Low flexibility zone rotational stiffness increased with disc degeneration grade in extension, lateral bending and axial rotation (p < 0.001). Trends towards higher hysteresis and lower range of motion with increased degeneration were observed in flexion‐extension and lateral bending. Applied compressive preload increased flexion‐extension hysteresis and augmented the effect of degeneration on hysteresis (p < 0.0005). Female specimens had about one degree larger range of motion in all rotational modes, and higher flexion extension hysteresis (p = 0.016). These results suggest that gender differences exist in lumbar spine kinematics. Additionally high disc loads, applied compressive preload or applied moment, are needed to kinematically distinguish discs with different levels of degeneration. © 2016 Orthopaedic Research Society. Published by Wiley Periodicals, Inc. J Orthop Res 34:1389–1398, 2016.
Framing justice: Taxpayer evaluations of personal tax burdens.

This study examines how taxpayers evaluate the distributive justice of personal income tax burdens. Using the concept of framing from behavioral decision theory, we suggest that taxpayers employ either an outcome-processing or a norm-processing frame of tax fairness evaluation. Framing is affected by substantive tax policies and the tax situations of individuals. Taxpayers who qualify for tax deductions and other tax preferences employ an outcome-processing frame and focus on perceived abuses of government power when evaluating fairness. Those unable to claim tax breaks employ a normprocessing frame and focus on vertical social comparisons and their inability to qualify for valued tax breaks. The findings suggest that tax avoidance policies have the net effect of increasing public perceptions of unfairness in the tax system.
Endothelial NO Synthase Gene Polymorphisms and Hypertension: A Meta-Analysis

Studies investigated the association between endothelial NO synthase gene polymorphisms and hypertension-reported contradicted or nonconclusive results. A meta-analysis of 35 genetic association studies that examined the relation between hypertension and the G894T, 4a/b, T786C, and G23T polymorphisms of the endothelial nitric oxide synthase gene was carried out. Subgroup analysis by ethnicity and potential sources of heterogeneity and bias were explored. The meta-analysis included genotype data on 7779/10 498, 2216/3222, 2491/3913, and 833/587 cases/controls for G894T, 4b/a, T786C, and G23T, respectively. For the 4b/a polymorphism, overall, the heterogeneity between studies was not significant (P =0.82), and the allele b was associated with a 15% decreased risk of hypertension relative to allele a (odds ratio: 0.85; 95% CI: 0.74 to 0.98). Overall and in whites, the recessive model for allele b produced significant results (odds ratios: 0.78; 95% CI: 0.68 to 0.90 and OR: 0.76 95% CI: 0.62 to 0.92, respectively), whereas the dominant model produced nonsignificant results. In studies involved East Asians and blacks, an association was not demonstrated. Regarding the G894T, T768C, and G23T polymorphisms, in no case (ie, overall, in whites, or in East Asians) was a statistically significant association and heterogeneity found. There was no substantial source of bias in the selected studies. In conclusion, there is evidence of association only between 4b/a polymorphism and hypertension; however, studies exploring combinations of the polymorphisms may help us better understand the genetics of hypertension.
Commonsense-based topic modeling

Topic modeling is a technique used for discovering the abstract 'topics' that occur in a collection of documents, which is useful for tasks such as text auto-categorization and opinion mining. In this paper, a commonsense knowledge based algorithm for document topic modeling is presented. In contrast to probabilistic models, the proposed approach does not involve training of any kind and does not depend on word co-occurrence or particular word distributions, making the algorithm effective on texts of any length and composition. 'Semantic atoms' are used to generate feature vectors for document concepts. These features are then clustered using group average agglomerative clustering, providing much improved performance over existing algorithms.
Letter to the 21st century botanist: “What is a flower?” The social science perspective

in representation. His theory was that the “culture of flowers” develops mostly where civilizations are highly elaborated and urbanized. This called for answers, and Mazrui (2014, see chapter 9) has questioned this “African gap”, raising in the process an interesting issue about the nature of flowers. The author underlines that African civilizations celebrate rather the end products (fruit, seeds). Flowers, in Africa, may not be recognized for their aesthetic value, but are indeed acknowledged for their instrumental value (medical uses, providing food). Moreover, when they are acknowledged, their scent or smell is privileged over their beauty, and hence over a visual appreciation. John C. Ryan in a recent work focused on the cultural aspects of interactions and interdependencies between human cultures and flowering plants in Australia (Ryan 2011). In the course of his field studies, one of his interviewees claimed that: “Our human appreciation is either aesthetic or edible. It’s the aesthetic beauty or whether it can be consumed. So that’s the major human perception of the plant. And so we forget that the only reason a plant has a flower is for its own reproduction. “ (Ryan 2011, 36). An anthropological survey of Saharan populations in southeast Morocco reveals a similar framework in yet another context (Gélard 2012). The author was investigating the rationale and values of the plastic China-made flowers in the homes of the local populations. These are used as decorations displayed solely on refrigerators and TV sets, and as a modern substitute for the traditional oleander (Nerium oleander L.) in wedding ceremonies. The women interviewed claimed that it was because the Saharan wilderness does not offer “true flowers” (i.e. polychrome), and because the other available flowers are those of vegetables or fruit trees, which it is totally excluded to pick because they are the premise of fruit, and so of food. A curious case along the same line is provided in a study of the classification of oil plants in Ethiopia. In this work, Strelcyn (1973) records a class of ṭeru ehel as “grains without flowers” (covering also wheat and barley), which serve as food. For these populations, the non-conspicuous flowers simply do not exist as flowers, and the flower is not considered a necessary stage in the formation of useful seeds and grains.
Rgtsp: a generalized top scoring pairs package for class prediction

SUMMARY A top scoring pair (TSP) classifier consists of a pair of variables whose relative ordering can be used for accurately predicting the class label of a sample. This classification rule has the advantage of being easily interpretable and more robust against technical variations in data, as those due to different microarray platforms. Here we describe a parallel implementation of this classifier which significantly reduces the training time, and a number of extensions, including a multi-class approach, which has the potential of improving the classification performance. AVAILABILITY AND IMPLEMENTATION Full C++ source code and R package Rgtsp are freely available from http://lausanne.isb-sib.ch/~vpopovic/research/. The implementation relies on existing OpenMP libraries.
Identification and characterization of a lysosomal transporter for small neutral amino acids

In eukaryotic cells, lysosomes represent a major site for macromolecule degradation. Hydrolysis products are eventually exported from this acidic organelle into the cytosol through specific transporters. Impairment of this process at either the hydrolysis or the efflux step is responsible of several lysosomal storage diseases. However, most lysosomal transporters, although biochemically characterized, remain unknown at the molecular level. In this study, we report the molecular and functional characterization of a lysosomal amino acid transporter (LYAAT-1), remotely related to a family of H+-coupled plasma membrane and synaptic vesicle amino acid transporters. LYAAT-1 is expressed in most rat tissues, with highest levels in the brain where it is present in neurons. Upon overexpression in COS-7 cells, the recombinant protein mediates the accumulation of neutral amino acids, such as γ-aminobutyric acid, l-alanine, and l-proline, through an H+/amino acid symport. Confocal microscopy on brain sections revealed that this transporter colocalizes with cathepsin D, an established lysosomal marker. LYAAT-1 thus appears as a lysosomal transporter that actively exports neutral amino acids from lysosomes by chemiosmotic coupling to the H+-ATPase of these organelles. Homology searching in eukaryotic genomes suggests that LYAAT-1 defines a subgroup of lysosomal transporters in the amino acid/auxin permease family.
Image contrast enhancement using classified virtual exposure image fusion

In our daily life, digital cameras and smart phones have been widely used to take pictures. However, digital cameras and smart phones have a limited dynamic range, which is much lower than that human eyes can perceive. Thus, the photographs taken in high dynamic range scenes often exhibit under-exposure or over-exposure artifacts in shadow or highlight regions. In this study, an image fusion based approach, called classified virtual exposure image fusion (CVEIF), is proposed for image enhancement. First, a function imitating the F-stop concept in photography is designed to generate several virtual images having different intensity. Then, a classified image fusion method, which blends pixels in distinct luminance classes using different fusion functions, is proposed to produce a fused image in which every image region is well exposed. Experimental results on four different kinds of generic images, including a normal image, a low-contrast images, a backlight image, and a dark scene image, have shown that the proposed CVEIF approach produced more pleasingly enhanced images than other methods.
Connections of higher order visual relays in the thalamus: A study of corticothalamic pathways in cats

Axonal markers injected into layers 5 and 6 of cortical areas 17, 18, or 19 labeled axons going to the lateral geniculate nucleus (LGN), the lateral part of the lateralis posterior nucleus (LPl), and pulvinar (P). Area 19 sends fine axons (type 1, Guillery [ 1966 ] J Comp Neurol 128:21–50) to LGN, LPl, and P, and thicker, type 2 axons to LPl and P. Areas 17 and 18 send type 1 axons to LGN, and a few type 1, but mainly type 2 axons to LPl and P. Type 1 and 2 axons from a single small cortical locus distribute to distinct, generally nonoverlapping parts of LP and P; type 1 axons have a broader distribution than type 2 axons. Type 2 axons, putative drivers of thalamic relay cells (Sherman and Guillery [ 1998 ] Proc Natl Acad Sci USA 95:7121–7126; Sherman and Guillery [ 2001 ] Exploring the thalamus. San Diego: Academic Press), supply small terminal arbors (100‐ to 200‐μm diameter) in LPl and P, and then continue into the midbrain. Each thalamic type 2 arbor contains two terminal types. One, at the center of the arbor, is complex and multilobulated; the other, with a more peripheral distribution, is simpler and may contribute to adjacent arbors. Type 2 arbors from a single injection are scattered around and along “isocortical columns” in LPl, (i.e., columns that represent cells having connections to a common cortical locus). Evidence is presented that the connections and consequently the functional properties of cells in LP change along these isocortical columns. Type 2 driver afferents from a single cortical locus can, thus, be seen as representing functionally distinct, parallel pathways from cortex to thalamus. J. Comp. Neurol. 438:66–85, 2001. © 2001 Wiley‐Liss, Inc.
OCME: Out-of-Core Mesh Editing Made Practical

OCME (Out-of-Core Mesh Editing) comprises a novel data structure and related algorithms for out-of-core editing of large meshes. Triangles are inserted in a multigrid on the basis of their size in average constant time. OCME maintains no explicit hierarchy, so inserting, modifying, or deleting data doesn't require costly refitting.
Demonstration of Software-Reconfigurable Real-Time FEC-Enabled 4/16/64-QAM-OFDM Signal Transmission in an X-Band RoF System

In this paper, to the best of our knowledge, this is the first time that the generation and reception of online software-reconfigurable real-time 4/16/64-quadrature amplitude modulation (QAM)-encoded and forward error correction (FEC)-enabled orthogonal frequency-division multiplexing (OFDM) signals over X-band fiber-over-radio-based upstream links has been demonstrated. A Reed-Solomon code, i.e., RS (288, 256), with symbol interleaving/deinterleaving is applied to enhance bit-error-rate (BER) performance. The experimental results show that the 4/16/64-QAM-OFDM signals with net data rates of 1.6/3.2/4.8-Gb/s after 1.5-m wireless and 2.26-km SMF-28 transmission with BERs below the hard-decision FEC threshold of 3.8e-3 can be successfully achieved without using FEC. With the help of symbol-interleaved RS code, a post-FEC BER below 1e-8 can be observed when the pre-FEC BER is around 1e-3.
Modeling and Verifying Active XML Artifacts

Towards a data-centric workflow approach, we introduce an artifact model to capture data and workflow management activities in distributed settings. The model is built on Active XML, i.e., XML trees including Web service calls. The model captures the essential features of business artifacts as described informally in the paper Nigam & Caswell 2003. We also show how to verify temporal properties for this model.
Taxol (paclitaxel): mechanisms of action.

Paclitaxel, an antitumor drug that is demonstrating encouraging activity in human malignancies, is likely to play a major role in cancer chemotherapy. Paclitaxel has an unusual chemical structure--it is a complex diterpene having a taxane ring with a four-membered oxetane ring and an ester side chain at position C-13--and a unique mechanism of action. In vitro, paclitaxel enhances the polymerization of tubulin to stable microtubules and also interacts directly with microtubules, stabilizing them against depolymerization by cold and calcium, which readily depolymerize normal microtubules. The fact that the drug has a specific binding site on the microtubule polymer makes it unique among chemotherapeutic agents, and the ability of paclitaxel to polymerize tubulin in the absence of cofactors like guanosine triphosphate and microtubule-associated proteins is unusual. When paclitaxel and microtubule protein are irradiated with ultraviolet light, the drug preferentially binds covalently to the beta-subunit of tubulin. Paclitaxel binds to cells in a specific and saturable manner with a single set of high-affinity binding sites. The microtubule cytoskeleton is reorganized in the presence of paclitaxel and extensive parallel arrays or stable bundles of microtubules are formed in cells growing in tissue culture. Paclitaxel blocks cells in the G2/M phase of the cell cycle and such cells are unable to form a normal mitotic apparatus. (ABSTRACT TRUNCATED AT 250 WORDS)
WAR MEMORIALS AS POLITICAL MEMORY

War memorials acquire their landscape definition from sentiment, utility, social purposes, and historical interpretations. Social purposes of identity and service can be used to express sacred and nonsacred sentiment for war memory, but honor and humanitarianism are used only to symbolize the sacred in memorials. When physical settings, forms of sentiment, and social purpose are combined in memorials, war memory socially becomes either a part of everyday life or a celebration of the past. Forms of meaning in war memorials are influenced by reinterpretations of political history that enhance, contradict, or deemphasize the status of past wars.
Combined effects of landscape composition and heterogeneity on farmland avian diversity

Abstract Conserving biodiversity on farmland is an essential element of worldwide efforts for reversing the global biodiversity decline. Common approaches involve improving the natural component of the landscape by increasing the amount of natural and seminatural habitats (e.g., hedgerows, woodlots, and ponds) or improving the production component of the landscape by increasing the amount of biodiversity‐friendly crops. Because these approaches may negatively impact on economic output, it was suggested that an alternative might be to enhance the diversity (compositional heterogeneity) or the spatial complexity (configurational heterogeneity) of land cover types, without necessarily changing composition. Here, we develop a case study to evaluate these ideas, examining whether managing landscape composition or heterogeneity, or both, would be required to achieve conservation benefits on avian diversity in open Mediterranean farmland. We surveyed birds in farmland landscapes of southern Portugal, before (1995–1997) and after (2010–2012) the European Union's Common Agricultural Policy (CAP) reform of 2003, and related spatial and temporal variation in bird species richness to variables describing the composition, and the compositional and configurational heterogeneity, of the natural and production components of the landscape. We found that the composition of the production component had the strongest effects on avian diversity, with a particularly marked effect on the richness of farmland and steppe bird species. Composition of the natural component was also influential, mainly affecting the richness of woodland/shrubland species. Although there were some effects of compositional and configurational heterogeneity, these were much weaker and inconsistent than those of landscape composition. Overall, we suggest that conservation efforts in our area should focus primarily on the composition of the production component, by striving to maximize the prevalence of biodiversity‐friendly crops. This recommendation probably applies to other areas such as ours, where a range of species of conservation concern is strongly associated with crop habitats.
A design methodology for automotive component manufacturing systems

This thesis proposes a design methodology for manufacturing processes in automotive component plants. Included is a proposed set of analysis tools to be developed to aid the manufacturing engineer in designing new manufacturing lines. The intended users of this methodology are manufacturing engineers designing or facilitating the design of a new process. The proposed methodology utilizes Quality Function Deployment to identify the requirements of a new manufacturing line, and to facilitate both a system level and detailed level design of the new process. The methodology is used to develop the new process in terms of the plant, operators, customers, supply chain, product design, and line design requirements. The relationship between the purchasing organization and the equipment suppliers is studied to identify the incentives in the existing purchasing system. This thesis also describes examples of how the methodology can be used, including an application for an electronics assembly line, and three ex-post analyses to show the benefits of a structured methodology. In an increasingly competitive environment, the use of a structured methodology can help an automotive supplier to develop more efficient processes while bringing products to market in less time. The use of analysis tools facilitates the design process, allowing manufacturing engineers to make better decisions faster. Thesis supervisors: Stephen Graves, Professor of Management Science Daniel Whitney, Senior Research Scientist
Genetic ablation of N‐linked glycosylation reveals two key folding pathways for R345W fibulin‐3, a secreted protein associated with retinal degeneration

An R345W mutation in the N‐glycoprotein, fibulin‐3 (F3), results in inefficient F3 folding/secretion and higher intracellular F3 levels. Inheritance of this mutation causes the retinal dystrophy malattia leventinese. N‐Linked glycosylation is a common cotranslational protein modification that can regulate protein folding efficiency and energetics. Therefore, we explored how N‐glycosylation alters the protein homeostasis or proteostasis of wild‐type (WT) and R345W F3 in ARPE‐19 cells. Enzymatic and lectin binding assays confirmed that WT and R345W F3 are both primarily N‐glycosylated at Asn249. Tunicamycin treatment selectively reduced R345W F3 secretion by 87% (vs. WT F3). Genetic elimination of F3 N‐glycosylation (via an N249Q mutation) caused R345W F3 to aggregate intracellularly and adopt an altered secreted conformation. The endoplasmic reticulum (ER) chaperones GRP78 (glucose‐regulated protein 78) and GRP94 (glucose‐regulated protein 94), and the ER lectins calnexin and calreticulin were identified as F3 binding partners by immunoprecipitation. Significantly more N249Q and N249Q/R345W F3 interacted with GRP94, while substantially less N249Q and N249Q/R345W interacted with the ER lectins than their N‐glycosylated counterparts. Inhibition of GRP94 ATPase activity reduced only N249Q/R345W F3 secretion (by 62%), demonstrating this variant's unique reliance on GRP94 for secretion. These observations suggest that R345W F3, but not WT F3, requires N‐glycosylation to acquire a stable, native‐like structure. —Hulleman, J. D. , Kelly, J. W. Genetic ablation of N‐linked glycosylation reveals two key folding pathways for R345W fibulin‐3, a secreted protein associated with retinal degeneration. FASEB J. 29, 565‐575 (2015). www.fasebj. org