Miracle-dz/UniFAR-FTUs huggingface dataset:
Cytogenetic comparison of Podocnemis expansa and Podocnemis unifilis: A case of inversion and duplication involving constitutive heterochromatin

Podocnemis expansa and P. unifilis present 2n = 28 chromosomes, a diploid number similar to those observed in other species of the genus. The aim of this study was to characterize these two species using conventional staining and differential CBG-, GTG and Ag-NOR banding. We analyzed specimens of P. expansa and P. unifilis from the state of Tocantins (Brazil), in which we found a 2n = 28 and karyotypes differing in the morphology of the 13th pair, which was submetacentric in P. expansa and telocentric in P. unifilis. The CBG-banding patterns revealed a heterochromatic block in the short arm of pair 13 of P. expansa and an interstitial one in pair 13 of P. unifilis, suggesting a pericentric inversion. Pair 14 of P. unifilis showed an insterstitial band in the long arm that was absent in P. expansa, suggesting a duplication in this region. Ag-NORs were observed in the first chromosome pair of both species and was associated to a secondary constriction and heterochromatic blocks.
The Cation Selectivity Filter of the Bacterial Sodium Channel, NaChBac

The Bacillus halodurans voltage-gated sodium-selective channel (NaChBac) (Ren, D., B. Navarro, H. Xu, L. Yue, Q. Shi, and D.E. Clapham. 2001b. Science. 294:2372–2375), is an ideal candidate for high resolution structural studies because it can be expressed in mammalian cells and its functional properties studied in detail. It has the added advantage of being a single six transmembrane (6TM) orthologue of a single repeat of mammalian voltage-gated Ca2+ (CaV) and Na+ (NaV) channels. Here we report that six amino acids in the pore domain (LESWAS) participate in the selectivity filter. Replacing the amino acid residues adjacent to glutamatic acid (E) by a negatively charged aspartate (D; LEDWAS) converted the Na+-selective NaChBac to a Ca2+- and Na+-permeant channel. When additional aspartates were incorporated (LDDWAD), the mutant channel resulted in a highly expressing voltage-gated Ca2+-selective conductance.
Mitotic Functions and Characters of KIF11 in Cancers

Mitosis mediates the accurate separation of daughter cells, and abnormalities are closely related to cancer progression. KIF11, a member of the kinesin family, plays a vital role in the formation and maintenance of the mitotic spindle. Recently, an increasing quantity of data have demonstrated the upregulated expression of KIF11 in various cancers, promoting the emergence and progression of cancers. This suggests the great potential of KIF11 as a prognostic biomarker and therapeutic target. However, the molecular mechanisms of KIF11 in cancers have not been systematically summarized. Therefore, we first discuss the functions of the protein encoded by KIF11 during mitosis and connect the abnormal expression of KIF11 with its clinical significance. Then, we elucidate the mechanism of KIF11 to promote various hallmarks of cancers. Finally, we provide an overview of KIF11 inhibitors and outline areas for future work.
From distributional to semantic similarity

Lexical-semantic resources, including thesauri and WORDNET, have been successfully incorporated into a wide range of applications in Natural Language Processing. However they are very difficult and expensive to create and maintain, and their usefulness has been severely hampered by their limited coverage, bias and inconsistency. Automated and semi-automated methods for developing such resources are therefore crucial for further resource development and improved application performance. Systems that extract thesauri often identify similar words using the distributional hypothesis that similar words appear in similar contexts. This approach involves using corpora to examine the contexts each word appears in and then calculating the similarity between context distributions. Different definitions of context can be used, and I begin by examining how different types of extracted context influence similarity. To be of most benefit these systems must be capable of finding synonyms for rare words. Reliable context counts for rare events can only be extracted from vast collections of text. In this dissertation I describe how to extract contexts from a corpus of over 2 billion words. I describe techniques for processing text on this scale and examine the trade-off between context accuracy, information content and quantity of text analysed. Distributional similarity is at best an approximation to semantic similarity. I develop improved approximations motivated by the intuition that some events in the context distribution are more indicative of meaning than others. For instance, the object-of-verb context wear is far more indicative of a clothing noun than get. However, existing distributional techniques do not effectively utilise this information. The new context-weighted similarity metric I propose in this dissertation significantly outperforms every distributional similarity metric described in the literature. Nearest-neighbour similarity algorithms scale poorly with vocabulary and context vector size. To overcome this problem I introduce a new context-weighted approximation algorithm with bounded complexity in context vector size that significantly reduces the system runtime with only a minor performance penalty. I also describe a parallelized version of the system that runs on a Beowulf cluster for the 2 billion word experiments. To evaluate the context-weighted similarity measure I compare ranked similarity lists against gold-standard resources using precision and recall-based measures from Information Retrieval,
A Family of Computationally Efficient and Simple Estimators for Unnormalized Statistical Models

We introduce a new family of estimators for unnormalized statistical models. Our family of estimators is parameterized by two nonlinear functions and uses a single sample from an auxiliary distribution, generalizing Maximum Likelihood Monte Carlo estimation of Geyer and Thompson (1992). The family is such that we can estimate the partition function like any other parameter in the model. The estimation is done by optimizing an algebraically simple, well defined objective function, which allows for the use of dedicated optimization methods. We establish consistency of the estimator family and give an expression for the asymptotic covariance matrix, which enables us to further analyze the influence of the nonlinearities and the auxiliary density on estimation performance. Some estimators in our family are particularly stable for a wide range of auxiliary densities. Interestingly, a specific choice of the nonlinearity establishes a connection between density estimation and classification by nonlinear logistic regression. Finally, the optimal amount of auxiliary samples relative to the given amount of the data is considered from the perspective of computational efficiency.
ANALYSIS OF COMMUNITY KNOWLEDGE ON THE CONSERVATION OF WHITE-WINGED DUCK (Asarcornis Scutulata) IN WAY KAMBAS NATIONAL PARK

Indonesia is one of the countries that has a high diversity of birds, one of which is the White-winged Duck (Asarcornis scutulata) which is a protected bird. One of habitat white-winged duck habitat in Sumatra is Way Kambas National Park (WKNP). Declain of population the white-winged Duck requires efforts and community participation in its conservation. Community participation is influenced by the understanding of the community. The aims of research to analysis the community's understanding about conservation of white-winged duck in WKNP. Data collection used a interview method using a questionnaire with purposive sampling technique. Data analysis using a quantitative technique with a Likert scale and the indicators used are questions in the two answer categories, namely yes/know with a score of 2 and no/do not know with a score of 1. The result of community knowledge in buffer villages about conservation of white-winged duck have a value of 50.8 including good category. Community experience has a value of 53 including the medium category, and community knowledge of the benefits of white-winged duck is in the medium category with a value of 54.3. The communities of knowledge not the same about white-winged duck, but dominant shown interest in participating in conservation efforts. There is a need for activities that educate communities on white-winged duck conservation. The existence of good knowledge and experience of white-winged duck owned by the community, can influence in realizing white-winged duck conservation efforts in the natural habitat.
Analysis of Current Distribution in Driving Multiple Cold Cathode Fluorescent Lamps (CCFL)

Cold cathode fluorescent lamps (CCFLs) show complex characteristics, which make it difficult to drive them in parallel. In this paper, a backlight inverter, which can drive multiple CCFLs using single controller and single switching network, is presented. The analysis of the lamp current distribution is presented in detail. The current-balancing condition, under which the lamp currents are well balanced in the presence of the lamp voltage variation, is derived. The effect of the resonant component variation is also investigated. The analysis results are verified from experiments with two 720-mm/4-mm CCFLs for 32-in liquid crystal display televisions. Experimental results with eight CCFLs are also presented in the presence of the lamp voltage and the resonant component deviation
Spatial Agglomeration Dynamics

This Paper develops a model of economic growth and activity locating endogenously on a 3-dimensional featureless global geography. The same economic forces influence simultaneously growth, convergence, and spatial agglomeration and clustering. Economic activity is not concentrated on discrete isolated points but instead a dynamically-fluctuating, smooth spatial distribution. Spatial inequality is a Cass-Koopmans saddlepath, and the global distribution of economic activity converges towards egalitarian growth. Equality is stable but spatial inequality is needed to attain it.
Aspirin and Risk of Subarachnoid Hemorrhage: Systematic Review and Meta-Analysis

Background and Purpose— Recent studies have suggested that the use of low-dose aspirin may reduce the risk of aneurysmal subarachnoid hemorrhage (aSAH). We aimed to evaluate any association between aspirin use and risk of aSAH based on the literature, and whether this is influenced by duration or frequency of aspirin use. Methods— A search of electronic databases was done from inception to September 2016. For each study, data on risk of aSAH in aspirin versus nonaspirin users were used to generate odds ratios and 95% confidence intervals, and combined using inverse variance–weighted averages of logarithmic odds ratios in a random-effects models. Results— From 7 included studies, no significant difference was noted between aspirin use of any duration or frequency and nonaspirin users (odds ratio, 1.00; 95% confidence interval, 0.81–1.24; P=0.99). We found a significant association between short-term use of aspirin (<3 months) and the risk of aSAH (odds ratio, 1.61; 95% confidence interval, 1.20–2.18; P=0.002). No significant difference was found in terms of risk of aSAH for 3 to 12 months, 1 to 3 years, and >3 years of durations of use. No significant association was found between infrequent aspirin use (⩽2× per week) or frequent use (≥3× per week) with risk of aSAH. Conclusions— Current evidence suggests that short-term (<3 months) use of aspirin is associated with increased risk of aSAH. Limitations include substantial heterogenity of the included studies. The role of long-term aspirin in reducing risk of aSAH remains unclear and ideally should be addressed by an appropriately designed randomized controlled trial.
Bloch Oscillations of Atoms in an Optical Potential

Ultracold cesium atoms are prepared in the ground energy band of the potential induced by an optical standing wave. We observe Bloch oscillations of the atoms driven by a constant inertial force. We measure the momentum distribution of Bloch states and effective masses different from the mass of the free atom. {copyright} {ital 1996 The American Physical Society. }
Topology from the Simulated Sloan Digital Sky Survey

We measure the topology (genus curve) of the galaxy distribution in a very large cosmological simulation designed to resemble closely results from the upcoming Sloan Digital Sky Survey (SDSS). The mock survey is based on a large N-body simulation that uses 54,872,000 particles in a periodic cube 600 h-1 Mpc on a side. The adopted inflationary cold dark matter (CDM) model has parameters ΩCDM = 0.4, ΩΛ = 0.6, h = 0.6, b = 1.3. We "observe" this simulation to produce a simulated redshift catalog of ~106 galaxies over π steradians, mimicking the anticipated spectroscopic selection procedures of the SDSS in some detail. Sky maps, redshift slices, and three-dimensional contour maps of the mock survey reveal a rich and complex structure, including networks of voids and superclusters that resemble the patterns seen in the CfA redshift survey and the Las Campanas Redshift Survey (LCRS). The three-dimensional genus curve can be measured from the simulated catalog with superb precision; this curve not only has the general shape predicted for Gaussian, random phase initial conditions, but the error bars are small enough to demonstrate with high significance the subtle departures from this shape caused by nonlinear gravitational evolution on a 10 h-1 Mpc smoothing scale (where σgal = 0.4). These distortions have the form predicted by Matsubara's perturbative analysis, but they are smaller in amplitude. We also measure the three-dimensional genus curve of the radial peculiar velocity field measured by applying distance-indicator relations (with realistic errors) to the mock catalog. The genus curve is consistent with the Gaussian random phase prediction, though it is of relatively low precision because of the large smoothing length required to overcome noise in the measured velocity field. Finally, we measure the two-dimensional topology in redshift slices, similar to those which will become available early in the course of the SDSS and to those already observed in the LCRS. The genus curves of these slices are consistent with the observed genus curves of the LCRS, suggesting that our inflationary CDM model with ΩCDM ~ 0.4 is a good choice. Our mock redshift catalog is publicly available for the use of other researchers.
Genetic variation in KLK2 and KLK3 is associated with concentrations of hK2 and PSA in serum and seminal plasma in young men.

BACKGROUND Genetic variants in KLK2 and KLK3 have been associated with increased serum concentrations of their encoded proteins, human kallikrein-related peptidase 2 (hK2) and prostate-specific antigen (PSA), and with prostate cancer in older men. Low PSA concentrations in seminal plasma (SP) have been associated with low sperm motility. To evaluate whether KLK2 and KLK3 genetic variants affect physiological prostatic secretion, we studied the association of SNPs with hK2 and PSA concentrations in SP and serum of young, healthy men. METHODS Leukocyte DNA was extracted from 303 male military conscripts (median age 18.1 years). Nine SNPs across KLK2-KLK3 were genotyped. We measured PSA and hK2 in SP and serum using immunofluorometric assays. The association of genotype frequencies with hK2 and PSA concentrations was tested with the Kruskal-Wallis test. RESULTS Four KLK2 SNPs (rs198972, rs198977, rs198978, and rs80050017) were strongly associated with hK2 concentrations in SP and serum, with individuals homozygous for the major alleles having 3- to 7-fold higher concentrations than the intermediate concentrations found in other homozygotes and heterozygotes (all P < 0.001). Three of these SNPs were significantly associated with percentage of free PSA (%fPSA) in serum (all P < 0.007). Three KLK3 SNPs showed associations with PSA in SP, and the rs1058205 SNP was associated with total PSA in serum (P = 0.001) and %fPSA (P = 0.015). CONCLUSIONS Associations observed in young, healthy men between the SP and serum concentrations of hK2 and PSA and several genetic variants in KLK2 and KLK3 could be useful to refine models of PSA cutoff values in prostate cancer testing.
SERF: schema evolution through an extensible, re-usable and flexible framework

With current database technology trends, there is an increasing need to specify and handle complex schema changes. The existing support for schema evolution in current OODB systems is limited to a pre-defined taxonomy of schema evolution operations with fixed semantics. Given the variety of types, complexity, and semantics of transformations, it is sheer impossible to a-priori provide a complete set of all complex changes that are going to meet all user’s needs. This paper is the first effort to successfully address this open problem by providing an extensible framework for schema transformations. Our proposed SERF framework succeeds in giving the user the flexibility to define the semantics of their choice, the extensibilty of defining new complex transformations, and the power of re-using these transformations through the notion of templates. To verify the feasibility of our SERF approach we have implemented one realization of our concepts in a working prototype system, called OQL-SERF, based on OQL, ODMG MetaData and Java’s binding of ODL. We have also conducted a thorough case study demonstrating that our SERF approach can handle all the schema evolution operations we identified from the literature to validate the completeness of our approach.
Efficient and Resilient Backbones for Multihop Wireless Networks

We consider the problem of finding "backbones" in multihop wireless networks. The backbone provides end-to-end connectivity, allowing nonbackbone nodes to save energy since they do not have to route nonlocal data or participate in the routing protocol. Ideally, such a backbone would be small, consist primarily of high capacity nodes, and remain connected even when nodes are mobile or fail. Unfortunately, it is often infeasible to construct a backbone that has all of these properties; e.g., a small optimal backbone is often too sparse to handle node failures or high mobility. We present a parameterized backbone construction algorithm that permits explicit trade-offs between backbone size, resilience to node movement and failure, energy consumption, and path lengths. We prove that our scheme can construct essentially best possible backbones (with respect to energy consumption and backbone size) when the network is relatively static. We generalize our scheme to build more robust structures better suited to networks with higher mobility. We present a distributed protocol based upon our algorithm and show that this protocol builds and maintains a connected backbone in dynamic networks. Finally, we present detailed packet-level simulation results to evaluate and compare our scheme with existing energy-saving techniques. Our results show that, depending on the network environment, our scheme increases network lifetimes by 20 percent to 220 percent without adversely affecting delivery ratio or end-to-end latency.
Lack of Predictivity of the Rat Lethality (LD50) Test for Ecological and Human Health Effects

The relationship between acute toxicity in rats (LD50 values) and indicators of potential health hazards in humans was investigated, based on a chemical population-based paradigm (i.e. the “chemical diversity approach”). These structure–activity relationship-based analyses indicate that high toxicity in rats (i.e. a low LD50 value) is not a good predictor of health effects in humans. In fact, it was found that high acute toxicity to minnows, as well as toxicity to cultured cells, showed significantly greater associations with the potential for health effects than rat LD50 values.
3D Constrained Local Model for rigid and non-rigid facial tracking

We present 3D Constrained Local Model (CLM-Z) for robust facial feature tracking under varying pose. Our approach integrates both depth and intensity information in a common framework. We show the benefit of our CLM-Z method in both accuracy and convergence rates over regular CLM formulation through experiments on publicly available datasets. Additionally, we demonstrate a way to combine a rigid head pose tracker with CLM-Z that benefits rigid head tracking. We show better performance than the current state-of-the-art approaches in head pose tracking with our extension of the generalised adaptive view-based appearance model (GAVAM).
Changes in corneal endothelium cell characteristics after cataract surgery with and without use of viscoelastic substances during intraocular lens implantation

Purpose To evaluate whether the use of balanced salt solution (BSS) or an ophthalmic viscoelastic device (OVD) during hydrophilic acrylic intraocular lens (IOL) implantation variously impacts corneal endothelial cell characteristics in eyes undergoing uneventful phacoemulsifications. Methods Prospective nonrandomized observational clinical trial. Patients were assigned either to the BSS plus® or to the OVD Z-Celcoat™ group depending on the substance used during IOL implantation. Corneal endothelium cell characteristics were obtained before, 1 week, and 6 weeks after surgery. Intraoperative parameters (eg, surgery time, phacoemulsification energy) were recorded. Results Ninety-seven eyes were assigned to the BSS plus and 86 eyes to the Z-Celcoat group. Preoperative corneal endothelium cell density (ECD) and endothelium cell size were 2,506±310 cells/mm2/2,433±261 cells/mm2 and 406±47 µm2/416±50 µm2 (P=0.107/P=0.09). After 1 and 6 weeks, ECD decreased and endothelium cell size increased significantly in both groups (each P<0.001) without significant differences between both groups (each P>0.05). Irrigation–aspiration suction time (30.3±16.6 versus 36.3±14.5 seconds) and overall surgical time (7.2±1.2 versus 8.0±1.4 minutes) were significantly longer in the OVD Z-Celcoat group (each P<0.001). No complications or serious side effects occurred. Conclusion Implantation of a hydrophilic acrylic IOL under BSS infusion seems to be a useful and faster alternative in experienced hands without generating higher ECD loss rates.
Identification of prognostic signatures in breast cancer microarray data using Bayesian techniques

We apply a new Bayesian data analysis technique (latent process decomposition) to four recent microarray datasets for breast cancer. Compared to hierarchical cluster analysis, for example, this technique has advantages such as objective assessment of the optimal number of sample or gene clusters in the data, penalization of overcomplex models fitting to noise in the data and a common latent space of explanatory variables for samples and genes. Our analysis provides a clearer insight into these datasets, enabling assignment of patients to one of four principal processes, each with a distinct clinical outcome. One process is indolent and associated with under-expression across a number of genes associated with tumour growth. One process is associated with over expression of GRB7 and ERBB2. The most aggressive process is associated with abnormal expression of transcription factor genes, including members of the FOX family of transcription factor genes.