Miracle-dz/UniFAR-FTUs huggingface dataset:
Setting up a Meta-Threading Pipeline for High-Throughput Structural Bioinformatics: eThread Software Distribution, Walkthrough and Resource Profiling

eThread, a meta-threading and machine learning-based approach, is designed to effectively identify structural templates for use in protein structure and function modeling from genomic data. This is an essential methodology for high-throughput structural bioinformatics and critical for systems biology, where extensive knowledge of protein structures and functions at the systems level is prerequisite. eThread integrates a diverse collection of algorithms, therefore its deployment on a large multi-core system necessarily requires comprehensive profiling to ensure the optimal utilization of available resources. Resource profiling of eThread and the single-threading component algorithms indicate as wide range of demands with respect to wall clock time and host memory. Depending on the threading algorithm used, the modeling of a single protein sequence of up to 600 residues in length takes minutes to hours. Full meta-threading of one gene product from E. coli proteome requires ~12h on average on a single state-of-the-art computing core. Depending on the target sequence length, the subsequent three-dimensional structure modeling using eThread/Modeller and eThread/TASSER-Lite takes additional 1-3 days of computing time. Using the entire proteome of E. coli, we demonstrate that parallel computing on a multi-core system follows Gustafson-Barsis' law and can significantly reduce the production time of eThread. Furthermore, graphics processor units can speedup portions of the calculations; however, to fully utilize this technology in protein threading, a substantial code development is required. eThread is freely available to the academic and non-commercial community as a user-friendly web-service at http://www.brylinski. org/ethread. We also provide source codes and step-by-step instructions for the local software installation as well as a case study demonstrating the complete procedure for protein structure modeling. We hope that genome-wide high-throughput structural bioinformatics using eThread will significantly expand our knowledge of protein structures and their molecular functions and contribute to the thriving area of systems biology.
Herd Behavior, the "Penguin Effect", and the Suppression of Informational Diffusion: An Analysis of Informational Externalities and Payoff Interdependency

This article analyzes a technology adoption process in which the effect of informational spillover interacts with network externalities. The interplay of informational externalities and payoff interdependency induces risk-averse and clustering behavior in the technology-adoption process. The analysis differs from the herd behavior literature in focusing on how the herd behavior of subsequent users influences the initial adoption decision. Moreover, herd behavior in this article stems from each agent's desire to inhibit the revelation of new information that can be used in a way detrimental to her, rather than from each agent's effort to free-ride on information contained in the decisions made by predecessors.
Two are Better than One: An Ensemble of Retrieval- and Generation-Based Dialog Systems

Open-domain human-computer conversation has attracted much attention in the field of NLP. Contrary to rule- or template-based domain-specific dialog systems, open-domain conversation usually requires data-driven approaches, which can be roughly divided into two categories: retrieval-based and generation-based systems. Retrieval systems search a user-issued utterance (called a query) in a large database, and return a reply that best matches the query. Generative approaches, typically based on recurrent neural networks (RNNs), can synthesize new replies, but they suffer from the problem of generating short, meaningless utterances. In this paper, we propose a novel ensemble of retrieval-based and generation-based dialog systems in the open domain. In our approach, the retrieved candidate, in addition to the original query, is fed to an RNN-based reply generator, so that the neural model is aware of more information. The generated reply is then fed back as a new candidate for post-reranking. Experimental results show that such ensemble outperforms each single part of it by a large margin.
Does the Spiritual Well-Being of Chronic Hemodialysis Patients Differ from that of Pre-dialysis Chronic Kidney Disease Patients?

Spiritual well-being is viewed as an essential component of health-related quality of life (HRQOL) in the modernized biopsychosocial-spiritual model of health. Understanding spiritual well-being should lead to better treatment plans from the patients’ point of view, and improved patient adherence. There are numerous studies of traditional HRQOL, physical, mental, and social well-being; however, studies of spiritual well-being in chronic kidney disease (CKD) patients are limited. Thus, this study compared spiritual well-being of chronic hemodialysis patients and pre-dialysis CKD patients. A total of 31 chronic hemodialysis and 63 pre-dialysis CKD patients were asked for consent and then interviewed for spiritual well-being using the Functional Assessment of Chronic Illness Therapy–Spiritual Well-Being (FACIT-Sp). Analysis of covariance was applied to compare FACIT-Sp scores between pre-dialysis CKD and chronic hemodialysis groups that were adjusted by patient characteristics. The FACIT-Sp scores of pre-dialysis CKD patients were non-significantly greater than those of chronic hemodialysis patients after adjustment for gender, age, and marital status. However, all FACIT-Sp scores of males were significantly lower than those of females [FACIT Meaning −1.59 (p = 0.024), FACIT Peace −2.37 (p = 0.004), FACIT Faith −2.87 (p = 0.001), FACIT Total Score −6.83 (p = 0.001)]. The spiritual well-being did not significantly differ by stages of chronic kidney disease; however, patient gender was associated with spiritual well-being instead. To improve spiritual well-being, researchers should consider patient gender as a significant factor.
Elliptic regularity and essential self-adjointness of Dirichlet operators on R

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A General Stochastic Model for Nucleation and Linear Growth

The model considered here has arisen in a number of completely separate contexts: release of neurotransmitter at neuro-muscular synapses, unravelling of strands of DNA, diierentiation of cells into heterocysts in algae and growth of crystals. After a shear transformation the model becomes a Markov process, based on a Poisson process on the upper half plane, homogeneous in the horizontal (time) direction, which increases at unit rate except for occasional \drops". By considering the process separately when it is above or below a given \level", for any interval on the time axis, we obtain in particular exact moment results and prove asymptotic normality for long time intervals for the number of downcrossings in the interval, the total time in the interval when the process is below the speciied level and the number of drops in the interval. Limit distributions as the length of interval tends to innnity are obtained for the level at which the interval is \covered". It is shown that several problems considered in the literature have analytic solutions as special cases of the general model. The numerical results from one special case are compared to statistics obtained from experimental data from neurobiology.
Z-Measures on Partitions, Robinson-Schensted-Knuth Correspondence, and beta=2 Random Matrix Ensembles

We suggest an hierarchy of all the results known so far about the connection of the asymptotics of combinatorial or representation theoretic problems with ``beta=2 ensembles'' arising in the random matrix theory. We show that all such results are, essentially, degenerations of one general situation arising from so-called generalized regular representations of the infinite symmetric group.
An Empirical Study on the Use of Team Building Criteria in Software Projects

The goal of this article is to identify criteria used in industrial practice to select members of a software project team, and to look for relationships between these criteria and project success. Initially, using semi-structured interviews for data collection and qualitative methods for data analysis and synthesis, a set of team building criteria was identified from project managers in industry. Then, using this set of criteria and a method to evaluate software project success, a survey questionnaire was created to investigate the relationship between the consistent use or application of the criteria and project success. A cross-sectional survey collected data from 48 projects in 24 software companies and the data was analyzed for internal reliability using statistical methods. The findings show that the consistent use of the set of criteria correlated significantly with project success, and the criteria related to human factors present the strongest correlations.
IMPACTS OF SUBSIDIES ON THE COSTS OF URBAN PUBLIC TRANSPORT

As transit subsidies have increased by a factor of 15 in the United States during the 1970s, the article argues that subsidies have increased problems of productivity and cost in mass transit thus undermining the potential benefits of subsidies. The discussion reviews nationwide trends in subsidies, compares them with changes in productivity and cost indices, and then uses multiple regression analysis on a pooled cross-section sample of 77 transit systems in 1979 and 135 systems in 1980 to measure separate impacts of subsidies on costs. Recommendations are made concerning revisions in the subsidy programme likely to encourage more efficient use of subsidy funds.
Sticky Rebates: Target Rebates Induce Non-Rational Loyalty in Consumers

Competition policy often relies on the assumption of a rational consumer, although other models may better account for people’s decision behavior. In three experiments, we investigate the influence of loyalty rebates on consumers based on the alternative Cumulative Prospect Theory (CPT), both theoretically and experimentally. CPT predicts that loyalty rebates could harm consumers by impeding rational switching from an incumbent to an outside option (e.g., a market entrant). In a repeated trading task, participants decided whether or not to enter a loyalty rebate scheme and to continue buying within that scheme. Meeting the condition triggering the rebate was uncertain. Loyalty rebates considerably reduced the likelihood that participants switched to a higher-payoff outside option later. We conclude that loyalty rebates may inflict substantial harm on consumers and may have an underestimated potential to foreclose consumer markets.
Predictive factors for flexible ureterorenoscopy requirement after rigid ureterorenoscopy in cases with renal pelvic stones sized 1 to 2 cm

Purpose To evaluate the outcomes of rigid ureterorenoscopy (URS) for renal pelvic stones (RPS) sized 1 to 2 cm and to determine the predictive factors for the requirement for flexible URS (F-URS) when rigid URS fails. Materials and Methods A total of 88 patients were included into the study. In 48 patients, the RPS were totally fragmented with rigid URS and F-URS was not required (group 1). In 40 patients, rigid URS was not able to access the renal pelvis or fragmentation of the stones was not completed owing to stone position or displacement and F-URS was utilized for retrograde intrarenal surgery (RIRS) (group 2). The predictive factors for F-URS requirement during RIRS for RPS were evaluated. Both groups were compared regarding age, height, sex, body mass index, stone size, stone opacity, hydronephrosis, and previous treatments. Results The mean patient age was 48.6±16.5 years and the mean follow-period was 39±11.5 weeks. The overall stone-free rate in the study population was 85% (75 patients). In groups 1 and 2, the overall stone-free rates were 83% (40 patients) and 87% (35 patients), respectively (p>0.05). The independent predictors of requirement for F-URS during RIRS were male gender, patient height, and higher degree of hydronephrosis. Conclusions Rigid URS can be utilized in selected patients for the fragmentation of RPS sized 1 to 2 cm with outcomes similar to that of F-URS. In case of failure of rigid URS, F-URS can be performed successfully in this group of patients.
The Valuation Effect of LIFO's Repeal on High Pricing Power Firms

Purpose - – The aim of the study is to provides a timely examination of the valuation effect of current initiatives to repeal LIFO by analyzing the valuation impact of the potential repeal of LIFO conditional on the pricing power of the firm. Design/methodology/approach - – Using the methodology from prior research for all LIFO companies, we use price levels regressions to empirically test the potential tax effect of LIFO’s repeal on the value of the firm. To evaluate the robustness of these results, we also use event study methodology to estimate abnormal returns around the House Bill H. R. 3970. Findings - – Results show a favorable (unfavorable) valuation effect for high (low) pricing power firms that are able (unable) to recover tax payments by reducing costs and/or charging higher prices. These findings are robust to alternative measures of valuation (price and returns), as well as long and short event windows and suggest that certain firms may be able to offset post-LIFO repeal increased tax payments by increasing sales-output prices and or decreasing cost-input prices. Originality/value - – The primary contribution of this paper is to provide relevant and new empirical evidence regarding the potential valuation effects of the currently proposed political and regulatory initiatives to abolish LIFO.
The great risk shift : the assault on American jobs, families, health care, and retirement and how you can fight back

America's leaders say the economy is strong and getting stronger. But ordinary Americans aren't buying it. They see what the rosy statistics hide: We are all struggling under the weight of terrifying economic instability. No matter how well educated and hard working we are, we know that the bottom can fall out at any moment. Meanwhile, the safety net that once protected us is fast unraveling. With retirement plans in growing jeopardy while health coverage erodes, more and more economic risk is shifting from government and business onto the fragile shoulders of the American family. In The Great Risk Shift, Jacob S. Hacker lays bare this unsettling new economic climate, showing how it has come about, what it is doing to our families, and how we can fight back. Behind this shift, he contends, is the Personal Responsibility Crusade, eagerly embraced by corporate leaders and Republican politicians who speak of a nirvana of economic empowerment, an "ownership society" in which Americans are free to choose. But as Hacker reveals, the result has been quite different: a harsh new world of economic insecurity, in which far too many Americans are free to lose. The book documents how two great pillars of economic security--the family and the workplace--guarantee far less financial stability than they once did. The final leg of economic support--the public and private benefits that workers and families get when economic disaster strikes--has dangerously eroded as political leaders and corporations increasingly cut back protections of our health care, our income security, and our retirement pensions. Hacker concludes by advocating an "insurance and opportunity society" that would safeguard economic security and expand economic opportunity, ensuring that all Americans have the basic financial security they need to reach for and achieve the American Dream. Jacob Hacker brings into focus as never before the pressures that the Great Risk Shift exerts on our pocketbooks and on our lives. Blending powerful human stories, big-picture analysis, and compelling ideas for reform, this remarkable volume will hit a nerve, serving as a rallying point in the vital struggle for economic security in an increasingly uncertain world.
Inhibition of Bacterial Growth, Enterotoxin Production, and Spore Outgrowth in Strains of Bacillus cereus by Bacteriocin AS-48

ABSTRACT Bacteriocin AS-48 showed high bactericidal activity for mesophilic and psychrotrophic strains of Bacillus cereus over a broad pH range. AS-48 inhibition of the enterotoxin-producing strain LWL1 was enhanced by sodium nitrite, sodium lactate, and sodium chloride. The latter also enhanced AS-48 activity against strain CECT 131. Bacterial growth and enterotoxin production by strain LWL1 were completely inhibited at bacteriocin concentrations of 7.5 μg/ml. At subinhibitory bacteriocin concentrations, enterotoxin production decreased markedly and sporulation was delayed. Intact spores were resistant to AS-48 but became gradually sensitive to AS-48 during the course of germination.
Finance, Saving and Accumulation

This paper analyzes the interaction between financial and real variables in different time frames and monetary regimes. Firms finance investment through retained earnings, new issues, or bank loans, and households' desired portfolio of financial assets is related to current income flows. The average saving propensity becomes an endogenous variable determined jointly by household and firm decisions and it is shown that changes in the basic parameters give rise to both saving and valuation effects. Contrary to standard Keynesian results, an increase in a saving parameter may be expansionary if the valuation effect dominates the saving effect. Copyright 1988 by Oxford University Press.
A study on the use of semaphoric gestures to support secondary task interactions

We present results of a study that considers (a) gestures outside the context of a specific implementation and (b) their use in supporting secondary, rather than primary tasks in a multitasking environment. The results show semaphoric gestures offer significant benefits over function keys in such interactions, and how our findings can be used to extend models of design and evaluation for ubiquitous computing environments that support multitasking.
Slack-based global multiprocessor scheduling of aperiodic tasks in parallel embedded real-time systems

We provide a constant time schedulability test and priority assignment algorithm for an on-line multiprocessor server handling aperiodic tasks. Dhall's effect is avoided by dividing tasks in two priority classes based on their utilization: heavy and light. The improvement in this paper is due to assigning priority of light tasks based on slack - not on deadlines. We prove that if the load on the multiprocessor stays below (3 - radic5)/2 ap 38.197%, the server can accept an incoming aperiodic task and guarantee that the deadlines of all accepted tasks will be met. This is better than the current state-of- the-art algorithm where the priorities of light tasks are based on deadlines (the corresponding bound is in that case 35.425%).
Waste plastic as a stabilizing additive in Stone Mastic Asphalt

The present study investigates the benefits of stabilizing the stone mastic asphalt (SMA) mixture in flexible pavement with shredded waste plastic. Conventional (without plastic) and the stabilized SMA mixtures were subjected to performance tests including Marshall Stability, tensile strength and compressive strength tests. Triaxial tests were also conducted with varying percentage bitumen by weight of mineral aggregate (6% to 8%) and by varying percentage plastic by weight of mix (6% to 12% with an increment of 1%). Plastic content of 10% by weight of bitumen is recommended for the improvement of the performance of Stone Mastic Asphalt mixtures. 10% plastic content gives an increase in the stability, split tensile strength and compressive strength of about 64%, 18% and 75% respectively compared to the conventional SMA mix. Triaxial test results show a 44% increase in cohesion and 3% decrease in angle of shearing resistance showing an increase in the shear strength. The drain down value decreases with an increase in plastic content and the value is only 0.09 % at 10% plastic content and proves to be an effective stabilizing additive in SMA mixtures.
Gauging by numbers: A first attempt to measure the quality of public finances in the EU

Ensuring high quality of public finances (QPF) with a view to supporting long-term economic growth has gained new urgency as the room for fiscal manoeuvre has shrunk in light of the current crisis. To more systematically analyse QPF and compare developments across countries and over time, a greater focus on identifying and developing comparable QPF indicators is needed. This paper provides a first attempt in this respect. Based on the view that QPF is a multi-dimensional concept, it creates composite indicators for twelve areas of public finances that are linked to long-term economic growth. While the proposed alternative calculation methods yield relatively robust results and findings are in line with conventional wisdom, due to data problems the composite indicators should only be seen as a useful starting point for identifying a country's main strengths and weaknesses in QPF. This would need to be complemented by qualitative analysis that also accounts for country and other specificities. JEL classification: E62, H11, H50, H52, H60
Multilocus Sequence Typing and Further Genetic Characterization of the Enigmatic Pathogen, Staphylococcus hominis

Staphylococcus hominis is a commensal resident of human skin and an opportunistic pathogen. The species is subdivided into two subspecies, S. hominis subsp. hominis and S. hominis subsp. novobiosepticus, which are difficult to distinguish. To investigate the evolution and epidemiology of S. hominis, a total of 108 isolates collected from 10 countries over 40 years were characterized by classical phenotypic methods and genetic methods. One nonsynonymous mutation in gyrB, scored with a novel SNP typing assay, had a perfect association with the novobiocin-resistant phenotype. A multilocus sequence typing (MLST) scheme was developed from six housekeeping gene fragments, and revealed relatively high levels of genetic diversity and a significant impact of recombination on S. hominis population structure. Among the 40 sequence types (STs) identified by MLST, three STs (ST2, ST16 and ST23) were S. hominis subsp. novobiosepticus, and they distinguished between isolates from different outbreaks, whereas 37 other STs were S. hominis subsp. hominis, one of which was widely disseminated (ST1). A modified PCR assay was developed to detect the presence of ccrAB4 from the SCCmec genetic element. S. hominis subsp. novobiosepticus isolates were oxacillin-resistant and carriers of specific components of SCCmec (mecA class A, ccrAB3, ccrAB4, ccrC), whereas S. hominis subsp. hominis included both oxacillin-sensitive and -resistant isolates and a more diverse array of SCCmec components. Surprisingly, phylogenetic analyses indicated that S. hominis subsp. novobiosepticus may be a polyphyletic and, hence, artificial taxon. In summary, these results revealed the genetic diversity of S. hominis, the identities of outbreak-causing clones, and the evolutionary relationships between subspecies and clones. The pathogenic lifestyle attributed to S. hominis subsp. novobiosepticus may have originated on more than one occasion.