Miracle-dz/UniFAR-FTUs huggingface dataset:
Accelerated Adaptive Evolution on a Newly Formed X Chromosome

Sex chromosomes originated from ordinary autosomes, and their evolution is characterized by continuous gene loss from the ancestral Y chromosome. Here, we document a new feature of sex chromosome evolution: bursts of adaptive fixations on a newly formed X chromosome. Taking advantage of the recently formed neo-X chromosome of Drosophila miranda, we compare patterns of DNA sequence variation at genes located on the neo-X to genes on the ancestral X chromosome. This contrast allows us to draw inferences of selection on a newly formed X chromosome relative to background levels of adaptation in the genome while controlling for demographic effects. Chromosome-wide synonymous diversity on the neo-X is reduced 2-fold relative to the ancestral X, as expected under recent and recurrent directional selection. Several statistical tests employing various features of the data consistently identify 10%–15% of neo-X genes as targets of recent adaptive evolution but only 1%–3% of genes on the ancestral X. In addition, both the rate of adaptation and the fitness effects of adaptive substitutions are estimated to be roughly an order of magnitude higher for neo-X genes relative to genes on the ancestral X. Thus, newly formed X chromosomes are not passive players in the evolutionary process of sex chromosome differentiation, but respond adaptively to both their sex-biased transmission and to Y chromosome degeneration, possibly through demasculinization of their gene content and the evolution of dosage compensation.
Vibes: A Platform-Centric Approach to Building Recommender Systems

Recommender systems have gained a lot of popularity as effective means of drawing repeat business, improving the navigability of web sites and generally in helping users and customers quickly locate items that are likely to be of interest. The rich literature of recommendation algorithms presents both opportunities and challenges. Clearly there are a wide variety of algorithmic tools available, but there are only a few that are suited for application to a broad variety of problem domains and even fewer that can scalably deal with very large data sets. In this paper we describe the architecture of the Vibes platform that is used to power recommendations across a wide range of Yahoo! properties including Shopping, Travel, Autos, Real Estate and Small Business. The design principles of Vibes stress ﬂexibility, re-usability, repeatability and scalability. The system can be broadly divided into the modeling component (“the brains”), the data processing component (“the torso”) and the serving component (“the arms”). Vibes can accommodate a number of techniques including afﬁnity based, attribute similarity based and collaborative ﬁltering based models. The data processing component enables the aggregation of data from users’ browse and purchase history logs after any required ﬁltering and joining with other data sources such as categorizer outputs and unitized search terms. We are currently working on moving the modeling and data processing components to the Hadoop grid computing platform to enable Vibes to take advantage of even larger data sets. Finally the serving infrastructure uses REST based web services APIs to provide quick and easy integration with other Yahoo! properties. The whole Vibes platform is designed to make it easy to extend and deploy new recommendation models (in most cases without having to write any custom code). We illustrate this point by using a case study of how Vibes was used to build recommendation systems for Yahoo! Shopping.
Vicarious Control: Exposure to Mastery and Perceived Self-Efficacy

We hypothesize and test that observing masterful performances of experts at difficult activities increases one’s perceptions of self-efficacy at those same activities. The exertion of control apparent in the masterful performance is vicariously experienced by the observers, and raises their expectations on their own ability to perform the same activity.
Collaborative Book Recommendation Based on Readers' Borrowing Records

Book recommendation is an important part and task for personalized services and educations provided by the academic libraries. Many libraries have the readers' borrowing records without the readers' rating information on books. And the collaborative filtering (CF) algorithms are not proper under this circumstance. To apply the CF algorithms in book recommendation, in this paper, we construct the ratings from the readers' borrowing records to enable the CF algorithms. And to evaluate the traditional CF algorithms, we show that linearly combining (blending) a set of CF algorithms increases the accuracy and outperforms any single CF algorithms. At last, we conduct the experiments based on the real world dataset and the results invalidate the efficiency of the blending methods.
Inorganic polyphosphate supports resistance and survival of stationary-phase Escherichia coli

The Escherichia coli mutant (ppk) lacking the enzyme polyphosphate kinase, which makes long chains of inorganic polyphosphate (poly P), is deficient in functions expressed in the stationary phase of growth. After 2 days of growth in a medium limited in carbon sources, only 7% of the mutants survived compared with nearly 100% of the wild type; the loss in viability of the mutant was even more pronounced in a rich medium. The mutant showed a greater sensitivity to heat, to an oxidant (H2O2), to a redox-cycling agent (menadione), and to an osmotic challenge with 2.5 M NaCl. After a week or so in the stationary phase, mutant survivors were far fewer in number and were replaced by an outgrowth of a small-colony-size variant with a stable genotype and with improved viability and resistance to heat and H2O2; neither polyphosphate kinase nor long-chain poly P was restored. Suppression of the ppk feature of heat sensitivity by extra copies of rpoS, the gene encoding the RNA polymerase sigma factor that regulates some 50 stationary-phase genes, further implicates poly P in promoting survival in the stationary phase.
Dimensioning of dynamic optical WDM networks under multi-hour traffic and soft QoS constraints

In this paper the problem of dimensioning dynamic optical WDM networks under multi-hour traffic and soft QoS constraints is studied. Unlike previous works, traffic matrices are generated according to a lognormal distribution, a more realistic model than the usual uniform approach. Additionally, instead of requiring hard QoS constraints (e.g. blocking probability under a given threshold 100% of time), soft QoS constraints that allow blocking to increase during some periods of time are considered. In multi-hour traffic, such soft QoS constraints seem to be a more natural way of dealing with customer SLAs. Results show that using lognormal traffic matrices and soft QoS constraints leads to a decrease in the number of wavelength requirements. In the studied cases, this decrease was about 10%.
Meet the walkers accelerating index traversals for in-memory databases

The explosive growth in digital data and its growing role in real-time decision support motivate the design of high-performance database management systems (DBMSs). Meanwhile, slowdown in supply voltage scaling has stymied improvements in core performance and ushered an era of power-limited chips. These developments motivate the design of DBMS accelerators that (a) maximize utility by accelerating the dominant operations, and (b) provide flexibility in the choice of DBMS, data layout, and data types. We study data analytics workloads on contemporary in-memory databases and find hash index lookups to be the largest single contributor to the overall execution time. The critical path in hash index lookups consists of ALU-intensive key hashing followed by pointer chasing through a node list. Based on these observations, we introduce Widx, an on-chip accelerator for database hash index lookups, which achieves both high performance and flexibility by (1) decoupling key hashing from the list traversal, and (2) processing multiple keys in parallel on a set of programmable walker units. Widx reduces design cost and complexity through its tight integration with a conventional core, thus eliminating the need for a dedicated TLB and cache. An evaluation of Widx on a set of modern data analytics workloads (TPC-H, TPC-DS) using full-system simulation shows an average speedup of 3.1× over an aggressive OoO core on bulk hash table operations, while reducing the OoO core energy by 83%.
Identification of Unprecedented Anticancer Properties of High Molecular Weight Biomacromolecular Complex Containing Bovine Lactoferrin (HMW-bLf)

With the successful clinical trials, multifunctional glycoprotein bovine lactoferrin is gaining attention as a safe nutraceutical and biologic drug targeting cancer, chronic-inflammatory, viral and microbial diseases. Interestingly, recent findings that human lactoferrin oligomerizes under simulated physiological conditions signify the possible role of oligomerization in the multifunctional activities of lactoferrin molecule during infections and in disease targeting signaling pathways. Here we report the purification and physicochemical characterization of high molecular weight biomacromolecular complex containing bovine lactoferrin (≥250 kDa), from bovine colostrum, a naturally enriched source of lactoferrin. It showed structural similarities to native monomeric iron free (Apo) lactoferrin (∼78–80 kDa), retained anti-bovine lactoferrin antibody specific binding and displayed potential receptor binding properties when tested for cellular internalization. It further displayed higher thermal stability and better resistance to gut enzyme digestion than native bLf monomer. High molecular weight bovine lactoferrin was functionally bioactive and inhibited significantly the cell proliferation (p<0.01) of human breast and colon carcinoma derived cells. It induced significantly higher cancer cell death (apoptosis) and cytotoxicity in a dose-dependent manner in cancer cells than the normal intestinal cells. Upon cellular internalization, it led to the up-regulation of caspase-3 expression and degradation of actin. In order to identify the cutting edge future potential of this bio-macromolecule in medicine over the monomer, its in-depth structural and functional properties need to be investigated further.
Quasi-cyclic LDPC-coded signal space diversity with precoding over fading channels

Signal space diversity (SSD) has been viewed as a very efficient method to increase the diversity order and the reliability of wireless transmission over fading channels. The LDPC code can provide powerful error protection. The quasi cyclic structure which has significant advantage for memory efficiency, facilitates encoder and decoder implementation through shift register based circuits. The combination of quasi-cyclic LDPC codes and SSD is an effective technique to improve the performance of communication system for fading channel. This paper discusses a signal space diversity with a precoder by adding a simple encoder before applying the rotation matrix that can be viewed as a SSD with rate below 1. We propose three design criteria and two implementation method. And we further consider a quasi-cyclic LDPC-coded signal space diversity with precoding and their rate reallocation between channel coding and SSD. The simulation results show that our scheme outperforms the conventional coded-SSD over the fading channel when we get a better rate allocation that depends on the specific channel coding.
Using Gratitude to Promote Positive Change: A Series of Meta-Analyses Investigating the Effectiveness of Gratitude Interventions

ABSTRACT Gratitude interventions have been proposed as beneficial practices for improving myriad positive outcomes, and are promoted in self-help literature. The current work examined gratitude interventions’ effects with meta-analytic techniques to synthesize findings of thirty-eight studies, totaling 282 effect sizes. Fifty-six separate meta-analyses examined outcome effects for: gratitude versus neutral comparison at postintervention and delayed follow-up; gratitude versus negative comparison at post and follow-up; and gratitude versus positive comparison at post and follow-up. Results show that gratitude interventions can lead to improvements for numerous outcomes, including happiness, but do not influence others. Their unique benefits may be overemphasized in the literature.
On a Simple Superconductivity Model and New Superconducting Material

In this paper, we establish a simple superconductivity model based on virtual photons exchange mechnisim. It shows that this simple model can be used to explain the supercondutivity mechanism for some superconductive materials by comparing the theoretical prediction with the experimental data. On this basis, we propose new possible structures that can produce high temperature superconductors.
The perceptual foundation of linguistic context

Context plays a ubiquitous role in language processing. For the most part, work in language processing investigates the effects of context without investigating questions about what determines a context. For example, interpretation of any referential expression must take into account the notion of a referential domain. Here we investigate the influence of perceptual cues in establishing a referential domain, or linguistic context. We demonstrate that people use perceptual cues to establish a linguistic context; the influence of perceptual cues is gradient with respect to cue magnitude; and the contribution of a perceptual cue in constructing a linguistic context is not an effect of attention or salience. We provide these results as a first step toward developing a formal model for the establishment of linguistic context.
Automatic utterance type detection using suprasegmental features

The goal of the work presented here is to automatically predict the type of an utterance in spoken dialogue by using automatically extracted suprasegmental information. For this task, we present and compare three stochastic algorithms: hidden Markov models, artificial neural nets, and classification and regression trees. These models are easily trainable, reasonably robust and fit into the probabilistic framework required for speech recognition. Utterance type detection is dependent on the assumption that different types of utterances have different suprasegmental characteristics. The categorisation of utterance types is based on the theory of conversation games and consists of 12 move types (e.g. reply to a question, wh-question, acknowledgement). This utterance type detector is used in an automatic speech recognition system to reduce the word error rate.
Preliminary Results for Detection of Partially Occluded Humans in Video Sequences

This paper presents a method for detection of humans in video sequences. The intended application of the method is outdoor surveillance. In such an uncontrolled environment, the appearance of humans varies hugely due to clothing, identity, occluding accessories (such as briefcases, shopping bags). Also we can have partial human appearances in video sequences. We are developing a system that can detect humans which are partially occluded in video sequences. Here we present some preliminary results.
Author ' s personal copy Multi-scale stacked sequential learning

Sequential learning is the discipline of machine learning that deals with dependent data such that neighboring labels exhibit some kind of relationship. The paper main contribution is two-fold: first, we generalize the stacked sequential learning, highlighting the key role of neighboring interactions modeling. Second, we propose an effective and efficient way of capturing and exploiting sequential correlations that takes into account long-range interactions. We tested the method on two tasks: text lines classification and image pixel classification. Results on these tasks clearly show that our approach outperforms the standard stacked sequential learning as well as state-of-the-art conditional random fields. & 2011 Elsevier Ltd. All rights reserved.
Self-organization , ergodicity breaking , phase transition and synchronization in two-dimensional traffic-flow model

Analytical investigation is made on the two-dimensional traffic-flow model with alternative movement and exclude-volume effect between right and up arrows [Phys. Rev. A 46 R6124 (1992)]. Several exact results are obtained, including the upper critical density above which there are only jamming configurations, and the lower critical density below which there are only moving configurations. The observed jamming transition takes place at another critical density pc(N), which is in the intermidiate region between the lower and upper critical densities. It is derived that pc(N) = CN , where C and α are determined to be respectively 0.76 and −0.14 from previous numerical simulation. This transition is suggested to be a second-order phase transition, the order parameter is found. The nature of self-organization, ergodicity breaking and synchronization are discussed, Comparison with the sandpile model is made. PACS numbers: 05.70. Ln, 64.60. Cn, 64.60. Ak, 89.40. +k
Epidemiology of virus-induced asthma exacerbations: with special reference to the role of human rhinovirus

Viral respiratory infections may be associated with the virus-induced asthma in adults as well as children. Particularly, human rhinovirus is strongly suggested a major candidate for the associations of the virus-induced asthma. Thus, in this review, we reviewed and focused on the epidemiology, pathophysiology, and treatment of virus-induced asthma with special reference on human rhinovirus. Furthermore, we added our preliminary data regarding the clinical and virological findings in the present review.
GRB 080913 AT REDSHIFT 6.7

We report on the detection by Swift of GRB 080913, and subsequent optical/near-infrared follow-up observations by GROND, which led to the discovery of its optical/NIR afterglow and the recognition of its high-z nature via the detection of a spectral break between the i′ and z′ bands. Spectroscopy obtained at the ESO-VLT revealed a continuum extending down to λ = 9400 Å, and zero flux for 7500 Å<λ < 9400 Å, which we interpret as the onset of a Gunn–Peterson trough at z = 6.695± 0.025 (95.5% confidence level), making GRB 080913 the highest-redshift gamma-ray burst (GRB) to date, and more distant than the highest-redshift QSO. We note that many redshift indicators that are based on promptly available burst or afterglow properties have failed for GRB 080913. We report on our follow-up campaign and compare the properties of GRB 080913 with bursts at lower redshift. In particular, since the afterglow of this burst is fainter than typical for GRBs, we show that 2 m class telescopes can identify most high-redshift GRBs.
How is open source affecting software development?

The open source movement is affecting software development products and processes. Software products benefit from reusable elements' increased availability and flexibility but might suffer from tighter coupling and more complex dependencies between reused components. The software development process is gaining from the widespread availability and use of sophisticated open source development platforms and tools, and the adoption of corresponding development and coding practices by the programmer community. In addition, code as literature is helping the meaningful education of programmers. However, process integration and the coevolution of multiple open source and proprietary projects are still open problems.
Prediction of fluid responsiveness by a continuous non-invasive assessment of arterial pressure in critically ill patients: comparison with four other dynamic indices.

BACKGROUND We evaluated the ability of an infrared photoplethysmography arterial waveform (continuous non-invasive arterial pressure, CNAP) to estimate arterial pulse pressure variation (PPV). We compared the ability of non-invasive PPV to predict fluid responsiveness with invasive PPV, respiratory variation of pulse contour-derived stroke volume, and changes in cardiac index induced by passive leg raising (PLR) and end-expiratory occlusion (EEO) tests. METHODS We measured the responses of cardiac index (PiCCO) to 500 ml of saline in 47 critically ill patients with haemodynamic failure. Before fluid administration, we recorded non-invasive and invasive PPVs, stroke volume variation, and changes in cardiac index induced by PLR and by 15 s EEO. Logistic regressions were performed to investigate the advantage of combining invasive PPV, stroke volume variation, PLR, and EEO when predicting fluid responsiveness. RESULTS In eight patients, CNAP could not record arterial pressure. In the 39 remaining patients, fluid increased cardiac index by ≥15% in 17 'responders'. Considering the 195 pairs of measurements, the bias (sd) between invasive and non-invasive PPVs was -0.6 (2.3)%. The areas under the receiver operating characteristic (ROC) curves for predicting fluid responsiveness were 0.89 (95% confidence interval, 0.78-1.01) for non-invasive PPV compared with 0.89 (0.77-1.01), 0.84 (0.70-0.96), 0.95 (0.88-1.03), and 0.97 (0.91-1.03) for invasive pulse pressure, stroke volume variations, PLR, and EEO tests (no significant difference). Combining multiple tests did not significantly improve the area under the ROC curves. CONCLUSIONS Non-invasive assessment of PPV seems valuable in predicting fluid responsiveness.
Resolving Ellipsis in Clarification

We offer a computational analysis of the resolution of ellipsis in certain cases of dialogue clarification. We show that this goes beyond standard techniques used in anaphora and ellipsis resolution and requires operations on highly structured, linguistically heterogeneous representations. We characterize these operations and the representations on which they operate. We offer an analysis couched in a version of Head-Driven Phrase Structure Grammar combined with a theory of information states (IS) in dialogue. We sketch an algorithm for the process of utterance integration in ISs which leads to grounding or clarification.
Response option for attacks detected by intrusion detection system

In past decades, we have seen that the increasing speed of the network attacks compromising computer system functionality and degrading network performance. The security of these systems has attracted a lot of research in the field of intrusion detection and response system to reduce the effect of these attacks. Response is a major part of intrusion detection system. Intrusion detection system without a timely response is not considered good even they detect threat and generate alarms. Optimum response is based on the selection of proper response option. In this paper, we categorize the attacks and propose some response option to thwart these attacks.
Podocytes in childhood minimal change nephrotic syndrome

8 REVIEW OF THE LITERATURE.11 1. NORMAL GLOMERULAR FILTRATION . 11 1.1 PHYSIOLOGY . 11 1.2 ANATOMY . 13 1.2.1 Endothelium . 13 1.2.2 Glomerular basement membrane (GBM) . 14 1.2. 3 Visceral epithelium (podocytes). 14 1.2. 4 Slit diaphragm (SD) . 16 1.2. 5 Foot process cytoskeleton . 19 2. PROTEINURIA . 20 2.1 GBM AND PROTEINURIA . 21 2.2 PODOCYTES AND PROTEINURIA . 22 2.2.1 Foot process effacement and the filtration pores.23 2.2. 4 Foot process detachment . 24 2.2. 5 Disruption of the SD . 25 3. NEPHROTIC KIDNEY DISEASES IN CHILDREN.26 3.1 CONGENITAL NEPHROTIC SYNDROME OF THE FINNISH TYPE (NPHS1, CNF) . 27 3.2 FOCAL AND SEGMENTAL GLOMERULOSCLEROSIS (FSGS) . 28 3.3 MINIMAL CHANGE NEPHROTIC SYNDROME (MCNS) . 29 3.3.1 Pathogenesis . 30 3.3.2 Clinical features.30 3.3.3 Long term outcome . 31 AIMS OF THE STUDY.33