Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrating pre-integration into the shear-warp algorithm

The shear-warp volume rendering algorithm is one of the fastest algorithms for volume rendering, but it achieves this rendering speed only by sacrificing interpolation between the slices of the volume data. Unfortunately, this restriction to bilinear interpolation within the slices severely compromises the resulting image quality. This paper presents the implementation of pre-integrated volume rendering in the shear-warp algorithm for parallel projection to overcome this drawback. A pre-integrated lookup table is used during compositing to perform a substantially improved interpolation between the voxels in two adjacent slices.We discuss the design and implementation of our extension of the shear-warp algorithm in detail. We also clarify the concept of opacity and color correction, and derive the required sampling rate of volume rendering with postclassification. Furthermore, the modified algorithm is compared to the traditional shear-warp rendering approach in terms of rendering speed and image quality.
The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease

The Mouse Genome Database (MGD, http://www.informatics.jax.org) serves the international biomedical research community as the central resource for integrated genomic, genetic and biological data on the laboratory mouse. To facilitate use of mouse as a model in translational studies, MGD maintains a core of high-quality curated data and integrates experimentally and computationally generated data sets. MGD maintains a unified catalog of genes and genome features, including functional RNAs, QTL and phenotypic loci. MGD curates and provides functional and phenotype annotations for mouse genes using the Gene Ontology and Mammalian Phenotype Ontology. MGD integrates phenotype data and associates mouse genotypes to human diseases, providing critical mouse–human relationships and access to repositories holding mouse models. MGD is the authoritative source of nomenclature for genes, genome features, alleles and strains following guidelines of the International Committee on Standardized Genetic Nomenclature for Mice. A new addition to MGD, the Human–Mouse: Disease Connection, allows users to explore gene–phenotype–disease relationships between human and mouse. MGD has also updated search paradigms for phenotypic allele attributes, incorporated incidental mutation data, added a module for display and exploration of genes and microRNA interactions and adopted the JBrowse genome browser. MGD resources are freely available to the scientific community.
BAN Logic for Zero-Knowledge Identification Protocols

This paper is about verifying zero-knowledge identification protocols. First, we discuss the importance of identification, authentication and some of the techniques used to achieve this. Then we elaborate on the notion of zero-knowledge proofs of identity and give an example of the FFS. We review the notion of BAN logic and purpose that BAN logic is expressive enough to analyze zero-knowledge. Then, we set up some BAN constructs and postulates for analyzing the FFS. Further, we demonstrate with slight modification of BAN logic that the FFS zero-knowledge proof of identity can be analyzed using BAN.
Recommending under Threat of Manipulation 7 April

Collaborative filtering accomplishes automated personalized content recommendation but by relying on anonymous user feedback is vulnerable to manipulation. Taking measures to improve robustness to outliers seeks to increase resistance against such manipulation. However, this detrimentally impacts recommendation quality even in the absence of such attacks. By taking a competitive game perspective on collaborative filtering a strategy that strikes the desired trade-off between recommendation quality and resistance to manipulation can be found. Simulation on a 1M rating MovieLens dataset of varied size content push attacks is performed on a weighted alternating least squares recommender system running different levels of outlier trimming. These simulation results are used to assemble games where the utilities depend in addition on the weight the recommender puts on preventing manipulation compared to maintaining recommendation quality and how costly increasing attack size is to the attacker. The maxmin strategy for the recommender and present Nash Equilibria in these games are analysed. Results suggest that alternating recommendation between trimmed and non-trimmed methods serves to decrease the effectiveness of manipulation attacks while minimizing the impact on recommendation quality.
The basis of sharp spike onset in standard biophysical models

In most vertebrate neurons, spikes initiate in the axonal initial segment (AIS). When recorded in the soma, they have a surprisingly sharp onset, as if sodium (Na) channels opened abruptly. The main view stipulates that spikes initiate in a conventional manner at the distal end of the AIS, then progressively sharpen as they backpropagate to the soma. We examined the biophysical models used to substantiate this view, and we found that orthodromic spikes do no initiate through a local axonal current loop that propagates along the axon, but through a global current loop encompassing the AIS and soma, which forms an electrical dipole. Therefore, the phenomenon is not adequately modeled as the backpropagation of an electrical wave along the axon, since the wavelength would be as large as the entire system. Instead, in these models, we found that spike initiation rather follows the critical resistive coupling model proposed recently, where the Na current entering the AIS is matched by the axial resistive current flowing to the soma. Besides demonstrating it by examining the balance of currents at spike initiation, we show that the observed increase in spike sharpness along the axon is artifactual and disappears when an appropriate measure of rapidness is used; instead, somatic onset rapidness can be predicted from spike shape at initiation site. Finally, we reproduce the phenomenon in a two-compartment model, showing that it does not rely on propagation. In these models, the sharp onset of somatic spikes is therefore not an artifact of observing spikes at the incorrect location, but rather the signature that spikes are initiated through a global soma-AIS current loop forming an electrical dipole. Author summary In most vertebrate neurons, spikes are initiated in the axonal initial segment, next to the soma. When recorded at the soma, action potentials appear to suddenly rise as if all sodium channels opened at once. This has been previously attributed to the backpropagation of spikes from the initial segment to the soma. Here we demonstrate with biophysical models that backpropagation does not contribute to the sharpness of spike onset. Instead, we show that the phenomenon is due to the resistive coupling between the large somatodendritic compartment and the small axonal compartment, a geometrical discontinuity that leads to an abrupt variation in voltage.
Developmental Restriction of Embryonic Calvarial Cell Populations as Characterized by Their In Vitro Potential for Chondrogenic Differentiation

The mechanism(s) by which the cells within the calvaria tissue are restricted into the osteogenic versus the chondrogenic lineage during intramembranous bone formation were examined. Cells were obtained from 12‐day chicken embryo calvariae after tissue condensation, but before extensive osteogenic differentiation, and from 17‐day embryo calvariae when osteogenesis is well progressed. Only cell populations from the younger embryos showed chondrogenic differentiation as characterized by the expression of collagen type II. The chondrocytes underwent a temporal progression of maturation and endochondral development, demonstrated by the expression of collagen type II B transcript and expression of collagen type X mRNA. Cell populations from both ages of embryos showed progressive osteogenic differentiation, based on the expression of osteopontin, bone sialoprotein, and osteocalcin mRNAs. Analysis using lineage markers for either chondrocytes or osteoblasts demonstrated that when the younger embryonic cultures were grown in conditions that were permissive for chondrogenesis, the number of chondrogenic cells increased from ∼15 to ∼50% of the population, while the number of osteogenic cells remained almost constant at ∼35–40%. Pulse labeling of the cultures with BrdU showed selective labeling of the chondrogenic cells in comparison with the osteogenic cells. These data indicate that the developmental restriction of skeletal cells of the calvaria is not a result of positive selection for osteogenic differentiation but a negative selection against the progressive growth of chondrogenic cells in the absence of a permissive or inductive environment. These results further demonstrate that while extrinsic environmental factors can modulate the lineage progression of skeletal cells within the calvariae, there is a progressive restriction during embryogenesis in the number of cells within the calvaria with a chondrogenic potential. Finally, these data suggest that the loss of cells with chondrogenic potential from the calvaria may be related to the progressive limitation of the reparative capacity of the cranial bones.
Prognostic models to predict survival in patients with advanced non-small cell lung cancer treated with first-line chemo- or targeted therapy

Background We aimed to assess the prognostic role of neutrophilia, lymphocytopenia and the neutrophil-to-lymphocyte ratio (NLR), and to design models to define the prognosis of patients receiving first-line chemo- or targeted therapy for advanced non-small cell lung cancer (NSCLC). Materials and Methods We retrospectively analysed 401 consecutive patients with advanced NSCLC treated with first line chemo- or targeted therapy. Patients were stratified into two groups with pre-treatment NLR ≥ 3.7 (Group A) vs. < 3.7 (Group B). The best NLR cut-off was identified by ROC curve analysis. Results At baseline 264 patients had NLR≥3.7 (Group A), whilst 137 had lower NLR (Group B). Median OS was 10.8 months and 19.4 months in the two groups (p < 0.001), while median PFS was 3.6 months and 5.6 months, respectively (p = 0.012). At multivariate analysis, ECOG-PS≥2, stage IV cancer, non-adenocarcinoma histology, EGFR wild-type status and NLR were predictors of worse OS. Stage IV cancer, wild type EGFR status and NLR≥3.7 were independent prognostic factors for worse PFS. Patients were stratified according to the presence of 0-1 prognostic factors (8%), 2-3 factors (73%) and 4-5 factors (19%) and median OS in these groups was 33.7 months, 14.6 months and 6.6 months, respectively (p < 0.001). Similarly, patients were stratified for PFS based on the presence of 0-1 prognostic factor (15%), 2 factors (41%) and 3 factors (44%). The median PFS was 8.3 months, 4.6 months and 3.3 months respectively (p < 0.001). Conclusion Pre-treatment NLR is an independent prognostic factor for patients with advanced NSCLC treated with first-line therapies.
Using multiple measures to document change in English vowels produced by Japanese, Korean, and Spanish speakers: the case for goodness and intelligibility.

PURPOSE This study examined the effectiveness of using goodness ratings and intelligibility scores to document changes in vowel production following pronunciation training. The relationship between listener perceptions of goodness and intelligibility was also examined. METHOD Fifteen English language learner speakers (5 Japanese, 5 Korean, and 5 Spanish) participated in 16 sessions of vowel-focused pronunciation training. Pre- and posttraining judgments of 10 English vowels in /hVt/ context were conducted by 25 monolingual English speakers who served as listeners. Listeners judged vowel intelligibility using a 10-alternative forced-choice task and rated goodness using a 5-point Likert scale. RESULTS Goodness ratings and intelligibility scores captured improvement in the accuracy of several vowels following training. However, some vowels that received better mean intelligibility scores received poorer mean goodness ratings following training. The relationship between goodness ratings and intelligibility scores revealed that vowels such as /æ/ and /ʌ/ were more dependent on goodness for intelligibility than vowels such as /i/ and /e/, which were highly intelligible even when they received poor goodness ratings. CONCLUSION English vowels differ with respect to the importance of goodness for accurate identification by listeners. As such, clinicians should examine both goodness and intelligibility when measuring change following pronunciation training.
Contact allergy to petrolatums

Several pharmacopoeias set limits on the polycyclic aromatic hydrocarbon content in petrolatum. UV absorbance measurement of aromatic extracts of petrolatum sample has been shown to be a more reliable method than direct UV absorbance measurement as prescribed by several pharmacopoeias for the determination of that content, but the presence of allergenic polycyclic aromatic hydrocarbons does not always correlate with lower UV absorbance. Biological tests are ultimately the only certain method of detecting biologically active compounds. Polycyclic aromatic hydrocarbons can also be irritant and carcinogenic. Therefore, University uniform and very stringent limits should be set restricting their presence in pharmaceutical grade petrolatum.
Dispersion entropy for the analysis of resting-state MEG regularity in Alzheimer's disease

Alzheimer's disease (AD) is a progressive degenerative brain disorder affecting memory, thinking, behaviour and emotion. It is the most common form of dementia and a big social problem in western societies. The analysis of brain activity may help to diagnose this disease. Changes in entropy methods have been reported useful in research studies to characterize AD. We have recently proposed dispersion entropy (DisEn) as a very fast and powerful tool to quantify the irregularity of time series. The aim of this paper is to evaluate the ability of DisEn, in comparison with fuzzy entropy (FuzEn), sample entropy (SampEn), and permutation entropy (PerEn), to discriminate 36 AD patients from 26 elderly control subjects using resting-state magnetoencephalogram (MEG) signals. The results obtained by DisEn, FuzEn, and SampEn, unlike PerEn, show that the AD patients' signals are more regular than controls' time series. The p-values obtained by DisEn, FuzEn, SampEn, and PerEn based methods demonstrate the superiority of DisEn over PerEn, SampEn, and PerEn. Moreover, the computation time for the newly proposed DisEn-based method is noticeably less than for the FuzEn, SampEn, and PerEn based approaches.
Open Repairs for the Treatment of Anterior Shoulder Instability

Successful treatment of anterior instability of the shoulder requires a balance between restoring joint stability and minimizing loss of glenohumeral motion. The choice of treatment should be individualized on the basis of the patient's occupation and level of participation in sports, as well as on the degree of instability of the shoulder. Despite discussions to the contrary, there is no single “essential lesion,” as proposed by Bankart, that is responsible for recurrent anterior shoulder instability, although the Bankart lesion is by far the most important. The choice of operative treatment must be tailored to correct the abnormality that is identified at the time of surgery. A variety of promising arthroscopic techniques have been developed for the treatment of anterior shoulder instability; however, open stabilization remains the standard, especially for severe instabilities, revision procedures, and for athletes who participate in contact sports. This article will review the open surgical techniques used for treatment of anterior instability of the shoulder. Both current and historical operations will be discussed. Regardless of which procedure is chosen by a surgeon, the treatment should follow the guidelines taught by Rowe: anatomic dissection at the time of surgery, identification and repair of the lesions responsible for the instability, returning tissues to their anatomic locations, and early postoperative range of motion. By following these guidelines, the results of treatment of anterior instability of the shoulder can be optimized.
Telomerase: A Target for Therapeutic Effects of Curcumin and a Curcumin Derivative in Aβ1-42 Insult In Vitro

This study was designed to investigate whether telomerase was involved in the neuroprotective effect of curcumin and Cur1. Alzheimer's disease is a consequence of an imbalance between the generation and clearance of amyloid-beta peptide in the brain. In this study, we used Aβ1-42 (10 µg/ml) to establish a damaged cell model, and curcumin and Cur1 were used in treatment groups. We measured cell survival and cell growth, intracellular oxidative stress and hTERT expression. After RNA interference, the effects of curcumin and Cur1 on cells were verified. Exposure to Aβ1–42 resulted in significant oxidative stress and cell toxicity, and the expression of hTERT was significantly decreased. Curcumin and Cur1 both protected SK-N-SH cells from Aβ1–42 and up-regulated the expression of hTERT. Furthermore, Cur1 demonstrated stronger protective effects than curcumin. However, when telomerase was inhibited by TERT siRNA, the neuroprotection by curcumin and Cur1 were ceased. Our study indicated that the neuroprotective effects of curcumin and Cur1 depend on telomerase, and thus telomerase may be a target for therapeutic effects of curcumin and Cur1.
Two separate genes involved in sulphate transport in Escherichia coli K12.

SUMMARY: In the course of the experiments described above it became clear that the two cys mutations used were not identical. The cysA471 mutation was isolated by Tully (1976) as conferring resistance to chromate, the cysZ474 mutation arose spontaneously and simultaneously with a ptsI mutation, (it may be the result of an inversion with ends in these two genes). The mapping of the genes (see above, Table 3) shows that cysA and cysZ lie on opposite sides of ptsI. We therefore investigated the biochemical nature of the mutations.
SMT-Based Bounded Model Checking for Embedded ANSI-C Software

Propositional bounded model checking has been applied successfully to verify embedded software but is limited by the increasing propositional formula size and the loss of structure during the translation. These limitations can be reduced by encoding word-level information in theories richer than propositional logic and using SMT solvers for the generated verification conditions. Here, we investigate the application of different SMT solvers to the verification of embedded software written in ANSI-C. We have extended the encodings from previous SMT-based bounded model checkers to provide more accurate support for variables of finite bit width, bit-vector operations, arrays, structures, unions and pointers. We have integrated the CVC3, Boolector, and Z3 solvers with the CBMC front-end and evaluated them using both standard software model checking benchmarks and typical embedded software applications from telecommunications, control systems, and medical devices. The experiments show that our approach can analyze larger problems and substantially reduce the verification time.
miR‐20a Promotes Prostate Cancer Invasion and Migration Through Targeting ABL2

The aberrant expression of microRNAs (miRNAs) has been found in various types of cancer. The present study found miR‐20a was significantly up‐regulated in prostate cancer compared with normal prostate tissues. Patients with a higher miR‐20a expression had a Gleason score of 7–10 and shorter survival time. The transwell and wound healing assays revealed that blocking expression of miR‐20a by miR‐20a ASO suppresses the invasion and migration of PC‐3 and DU145 cells in vitro and also inhibits tumor growth in vivo. Furthermore, we identified miR‐20a directly targets the ABL family non‐receptor tyrosine kinases ABL2 and negatively regulates the phosphorylation of its downstream gene p190RhoGAP. Knockdown of ABL2 promoted cell invasion and migration and we identified miR‐20a‐induced cell invasion and migration can be rescued by ABL2. In conclusion, our findings show that miR‐20a significantly contributes to the progression of prostate cancer by targeting ABL2. J. Cell. Biochem. 115: 1269–1276, 2014. © 2014 Wiley Periodicals, Inc.
A remarkable identity for lengths of curves

In this thesis we will prove the following new identity Σγ 1/(1 + exp |γ|) = 1/2, where the sum is over all closed simple geodesics γ on a punctured torus with a complete hyperbolic structure, and |γ| is the length of γ. Although it is well known that there are relations between the lengths of simple geodesics on a hyperbolic surface (for example the Fricke trace relations and the Selberg trace formula) this identity is of a wholly different character to anything in the literature. Our methods are purely geometric; that is, the techniques are based upon the work of Thurston and others on geodesic laminations rather than the analytic approach of Selberg. The first chapter is intended as an exposition of some relevant theory concerning laminations on a punctured surface. Most important of these results is that a leaf of a compact lamination cannot penetrate too deeply into a cusp region. Explicit bounds for the maximum depth are given; in the case of a torus a simple geodesic is disjoint from any cusp region whose bounding curve has length less than 4, and this bound is sharp. Another significant result is that a simple geodesic which enters a small cusp region is perpendicular to the horocyclic foliation of the cusp region. The second chapter is concerned with Gcusp, the set of ends of simple geodesics with at least one end up the cusp. A natural metric on Gcusp is introduced so that we can discuss approximation theory. We divide the geodesics of Gcusp into three classes according to the behaviour of their ends; each class also has a characterisation in terms of how well any member geodesic can be approximated. An example is given to demonstrate how this classification generalises some ideas in the classical theory of Diophantine approximation. The first class consists of geodesics with both ends up the cusp. Restricting to the punctured torus it is shown that for such a geodesic, γ, there is a portion of the cusp region surrounding each end which is disjoint from all other geodesics in Gcusp. We call such a portion a gap. The geometry of the gaps attached to γ is described and their area computed by elementary trigonometry. The area is a function of the length of the unique closed simple geodesic disjoint from γ. Next we consider the a generic geodesic in Gcusp, that is, a geodesic with a single end up the cusp and another end spiralling to a minimal compact lamination which is not a closed geodesic. We show that such a geodesic is the limit from both the right and left of other geodesics in Gcusp. Finally we give a technique for approximating a geodesic with a single end up the cusp and the other end spiralling to a closed geodesic. Essentially we repeatedly Dehn twist a suitable geodesic in Gcusp round this closed geodesic. The results of this chapter are then combined with a theorem of J. Birman and C. Series to yield the identity.