Miracle-dz/UniFAR-FTUs huggingface dataset:
DNA Binding Specificity of Different STAT Proteins

STAT transcription factors are expressed in many cell types and bind to similar sequences. However, different STAT gene knock-outs show very distinct phenotypes. To determine whether differences between the binding specificities of STAT proteins account for these effects, we compared the sequences bound by STAT1, STAT5A, STAT5B, and STAT6. One sequence set was selected from random oligonucleotides by recombinant STAT1, STAT5A, or STAT6. For another set including many weak binding sites, we quantified the relative affinities to STAT1, STAT5A, STAT5B, and STAT6. We compared the results to the binding sites in natural STAT target genes identified by others. The experiments confirmed the similar specificity of different STAT proteins. Detailed analysis indicated that STAT5A specificity is more similar to that of STAT6 than that of STAT1, as expected from the evolutionary relationships. The preference of STAT6 for sites in which the half-palindromes (TTC) are separated by four nucleotides (N4) was confirmed, but analysis of weak binding sites showed that STAT6 binds fairly well to N3 sites. As previously reported, STAT1 and STAT5 prefer N3 sites; however, STAT5A, but not STAT1, weakly binds N4 sites. None of the STATs bound to half-palindromes. There were no specificity differences between STAT5A and STAT5B.
Optimal integrated maintenance strategy for parallel leased machines with warranty periods

This paper deals with an integrated production/maintenance problem of a manufacturing system considering a warranty and leasing constraints. The lessor may provide warranty periods to encourage the lessee to sign a lease contract with a longer lease period. The problem consists in a several parallel machines that have to satisfy a random demand over a finite time horizon under given service level and taking into account the warranty periods. First of all, to obtain an economical production planning, we minimize the total production and inventory cost. Secondly, we determine the optimal maintenance strategy for different machines according to the obtained production plan. The key of this study is to show the impact of the length of warranty periods on the optimal maintenance strategy. An analytical study and a numerical example are presented in order to prove the developed approach.
Microbial soil respiration and its dependency on carbon inputs, soil temperature and moisture

This experiment was designed to study three determinant factors in decomposition patterns of soil organic matter (SOM): temperature, water and carbon (C) inputs. The study combined field measurements with soil lab incubations and ends with a modelling framework based on the results obtained. Soil respiration was periodically measured at an oak savanna woodland and a ponderosa pine plantation. Intact soils cores were collected at both ecosystems, including soils with most labile C burnt off, soils with some labile C gone and soils with fresh inputs of labile C. Two treatments, dry‐field condition and field capacity, were applied to an incubation that lasted 111 days. Short‐term temperature changes were applied to the soils periodically to quantify temperature responses. This was done to prevent confounding results associated with different pools of C that would result by exposing treatments chronically to different temperature regimes. This paper discusses the role of the above‐defined environmental factors on the variability of soil C dynamics. At the seasonal scale, temperature and water were, respectively, the main limiting factors controlling soil CO2 efflux for the ponderosa pine and the oak savanna ecosystems. Spatial and seasonal variations in plant activity (root respiration and exudates production) exerted a strong influence over the seasonal and spatial variation of soil metabolic activity. Mean residence times of bulk SOM were significantly lower at the Nitrogen (N)‐rich deciduous savanna than at the N‐limited evergreen dominated pine ecosystem. At shorter time scales (daily), SOM decomposition was controlled primarily by temperature during wet periods and by the combined effect of water and temperature during dry periods. Secondary control was provided by the presence/absence of plant derived C inputs (exudation). Further analyses of SOM decomposition suggest that factors such as changes in the decomposer community, stress‐induced changes in the metabolic activity of decomposers or SOM stabilization patterns remain unresolved, but should also be considered in future SOM decomposition studies. Observations and confounding factors associated with SOM decomposition patterns and its temperature sensitivity are summarized in the modeling framework.
Methylation Status of Blood Leukocyte DNA and Risk of Gastric Cancer in a High-Risk Chinese Population

Background: To evaluate the relationship between methylation status of blood leukocyte DNA and risk of gastric cancer, a population-based study was conducted in Linqu County. Methods: Methylation levels of IGFII and N33 were determined by quantitative methylation-specific PCR. The temporal trend of methylation levels during gastric cancer development was investigated in 133 gastric cancer cases from two cohorts with pre– and/or post–gastric cancer samples. As the references of pre-GCs, 204 intestinal metaplasia (IM) or dysplasia (DYS) subjects who did not progress to gastric cancer during the follow-up period were selected. Meanwhile, 285 subjects with superficial gastritis/chronic atrophic gastritis (SG/CAG) were also selected as controls. Results: IGFII median methylation level was significantly higher in gastric cancer cases than those with SG/CAG (61.47% vs. 49.73%; P < 0.001). IGFII and N33 methylation levels were elevated at least 5 years ahead of clinical gastric cancer diagnosis comparing with SG/CAG (63.38% vs. 49.73% for IGFII, 9.12% vs. 5.70% for N33; all P < 0.001). Furthermore, the frequency of hypermethylated IGFII was markedly increased in IM or DYS subjects who progressed to gastric cancer in contrast to those who remained with IM and DYS, and adjusted ORs were 12.52 [95% confidence interval (CI), 3.81–41.15] for IM and 10.12 (95% CI, 2.68–38.22) for DYS. Similar results were also found for N33 in subjects with IM (OR, 3.77; 95% CI, 1.20–11.86). Conclusions: Our findings suggested that hypermethylated IGFII and N33 in blood leukocyte DNA were associated with risk of gastric cancer in a Chinese population. Impact: IGFII and N33 methylation status may be related to gastric carcinogenesis. Cancer Epidemiol Biomarkers Prev; 23(10); 2019–26. ©2014 AACR.
A new class of nondiffracting pulses based on focusing leaky waves

In this work, we propose an azimuthally-invariant periodic leaky-wave radiator for the generation of Bessel beams and X-waves by means of backward cylindrical leaky waves at millimeter wavelengths. A rigorous framework is first outlined to understand the theoretical constraints of such novel design. A specific attention is devoted to the impact of the attenuation constant on the focusing properties of the device. On this basis, a practical design is then proposed to meet the previous requirements. Numerical results confirm the interesting capabilities of the considered structure, paving the way for the first generation of focusing leaky waves.
The role of the paracrine/autocrine mediator endothelin‐1 in regulation of cardiac contractility and growth

Endothelin‐1 (ET‐1) is a critical autocrine and paracrine regulator of cardiac physiology and pathology. Produced locally within the myocardium in response to diverse mechanical and neurohormonal stimuli, ET‐1 acutely modulates cardiac contractility. During pathological cardiovascular conditions such as ischaemia, left ventricular hypertrophy and heart failure, myocyte expression and activity of the entire ET‐1 system is enhanced, allowing the peptide to both initiate and maintain maladaptive cellular responses. Both the acute and chronic effects of ET‐1 are dependent on the activation of intracellular signalling pathways, regulated by the inositol‐trisphosphate and diacylglycerol produced upon activation of the ETA receptor. Subsequent stimulation of protein kinases C and D, calmodulin‐dependent kinase II, calcineurin and MAPKs modifies the systolic calcium transient, myofibril function and the activity of transcription factors that coordinate cellular remodelling. The precise nature of the cellular response to ET‐1 is governed by the timing, localization and context of such signals, allowing the peptide to regulate both cardiomyocyte physiology and instigate disease.
Validity of the Mind Monitoring System as a Mental Health Indicator

We have been developing a method to evaluate the mental health condition of a person by the sound of his or her voice. Now, we have applied this technology as a system to create a smartphone app. Since using voice to measure one's mental health condition is a non-invasive method and as it could be used continually through the smartphone, one carries, unlike a routine checkup, it could be used for monitoring on a daily basis. The purpose of this study is to compare this vitality score and the widely used BDI (Beck Depression Inventory) and evaluate its validity. This experiment was conducted at COI (Center of Innovation) Program of the University of Tokyo with a total of 50 employees of multiple corporations as subjects between early December 2015 and early February 2016. The test subjects were each lent a smartphone with our app recording their voices automatically during calls, and in addition to it, we had them read and record a fixed phrase daily. BDI test was conducted at the beginning of the experiment period. The vitality score was calculated based on the voice data collected during the first two weeks of the experiment and considered it the vitality score of the time BDI was conducted. When these two indicators were compared, we found there was a negative correlation between BDI and the vitality score. Additionally, it was a useful method to identify a test subject with a high BDI score.
Multiplicative Characters, the Weil Bound, and Polyphase Sequence Families With Low Correlation

Power residue and Sidelnikov sequences are polyphase sequences with low correlation and variable alphabet sizes, represented by multiplicative characters. In this paper, sequence families constructed from the shift and addition of the polyphase sequences are revisited. Initially, ψ(0)=1 is assumed for multiplicative characters ψ to represent power residue and Sidelnikov sequences in a simple form. The Weil bound on multiplicative character sums is refined for the assumption, where the character sums are equivalent to the correlations of sequences represented by multiplicative characters. General constructions of polyphase sequence families that produce some of known families as the special cases are then presented. The refined Weil bound enables the efficient proofs on the maximum correlation magnitudes of the sequence families. From the constructions, it is shown that M-ary known sequence families with large size can be partitioned into (M+1) disjoint subsequence families with smaller maximum correlation magnitudes. More generalized constructions are also considered by the addition of multiple cyclic shifts of power residue and Sidelnikov sequences.
The Long-Term Impact of Education on Diabetes for Older People: A Systematic Review

Background: Although enthusiasm is growing for diabetic education programs for older people, data regarding their effectiveness and their long-term impact on self-management were neglected. Purpose: To systematically review diabetes mellitus education that has long-term effects on the self-management of older diabetic people. Data Sources: The authors searched multiple sources dated through September 2012, including the Cochrane Library, MEDLINE, PsycINFO, Nursing and Allied Health databases, and the bibliographies of 50 previous reviews. Methods and Data Extraction: Electronic databases were searched for controlled studies in English, published from 1987 to 2012, assessing the effects of long-term education for older people. Reviewers extracted study data using a structured abstraction form. Aggregated information about the effects of long-term education programs on older people with diabetes was used for making adjustments in the review. Results: The pooled estimate of the long-term effects of education was a 0.5 percentage point reduction (95% confidence interval), modest but significant improvement. The evidence also supports that long-term education is beneficial for improving diabetic patient self-care management in terms of glycemic control.
On Secure and Usable Program Obfuscation: A Survey

Program obfuscation is a widely employed approach for software intellectual property protection. However, general obfuscation methods (e.g., lexical obfuscation, control obfuscation) implemented in mainstream obfuscation tools are heuristic and have little security guarantee. Recently in 2013, Garg et al. have achieved a breakthrough in secure program obfuscation with a graded encoding mechanism and they have shown that it can fulfill a compelling security property, i.e., indistinguishability. Nevertheless, the mechanism incurs too much overhead for practical usage. Besides, it focuses on obfuscating computation models (e.g., circuits) rather than real codes. In this paper, we aim to explore secure and usable obfuscation approaches from the literature. Our main finding is that currently we still have no such approaches made secure and usable. The main reason is we do not have adequate evaluation metrics concerning both security and performance. On one hand, existing code-oriented obfuscation approaches generally evaluate the increased obscurity rather than security guarantee. On the other hand, the performance requirement for model-oriented obfuscation approaches is too weak to develop practical program obfuscation solutions.
Energetic components VirD4, VirB11 and VirB4 mediate early DNA transfer reactions required for bacterial type IV secretion

Bacteria use type IV secretion systems (T4SS) to translocate DNA (T‐DNA) and protein substrates across the cell envelope. By transfer DNA immunoprecipitation (TrIP), we recently showed that T‐DNA translocates through the Agrobacterium tumefaciens VirB/D4 T4SS by forming close contacts sequentially with the VirD4 receptor, VirB11 ATPase, the inner membrane subunits VirB6 and VirB8 and, finally, VirB2 pilin and VirB9. Here, by TrIP, we show that nucleoside triphosphate binding site (Walker A motif) mutations do not disrupt VirD4 substrate binding or transfer to VirB11, suggesting that these early reactions proceed independently of ATP binding or hydrolysis. In contrast, VirD4, VirB11 and VirB4 Walker A mutations each arrest substrate transfer to VirB6 and VirB8, suggesting that these subunits energize this transfer reaction by an ATP‐dependent mechanism. By co‐immunoprecipitation, we supply evidence for VirD4 interactions with VirB4 and VirB11 independently of other T4SS subunits or intact Walker A motifs, and with the bitopic inner membrane subunit VirB10. We reconstituted substrate transfer from VirD4 to VirB11 and to VirB6 and VirB8 by co‐synthesis of previously identified ‘core’ components of the VirB/D4 T4SS. Our findings define genetic requirements for DNA substrate binding and the early transfer reactions of a bacterial type IV translocation pathway.
Publisher Placement Algorithms in Content-Based Publish/Subscribe

Many publish/subscribe systems implement a policy for clients to join to their physically closest broker to minimize transmission delays incurred on the clients' messages. However, the amount of delay reduced by this policy is only the tip of the iceberg as messages incur queuing, matching, transmission, and scheduling delays from traveling across potentially long distances in the broker network. Additionally, the clients' impact on system load is totally neglected by such a policy. This paper proposes two new algorithms that intelligently relocate publishers on the broker overlay to minimize both the overall end-to-end delivery delay and system load. Both algorithms exploit live publication distribution patterns but with different optimization metrics and computation methodologies to determine the best relocation point. Evaluations on PlanetLab and a cluster testbed show that our algorithms can reduce the average input load of the system by up to 68%, average broker message rate by up to 85%, and average delivery delay by up to 68%.
A Creative Lifecycle Model for Internetware Based Software Development

While culture being the "software" controlling human mind, computer software development becomes one of the most creative activities that human undertake since the civilisation began. The only limitation in software creation is human imagination, and that limit is often self-imposed. The "Internetware", refers to a software paradigm, aims to satisfy the need of human kind using Internet as an integrated development and execution platform. Such software systems composed of entities distributed through the Internetwork, allowing connections that would be impossible or difficult to make otherwise. This paper gear towards the tasks for the Internetware is to accommodate creativity. In particular, we propose a six-step approach to Internetware development, an approach suggests essential difference to traditional methods. The six steps in this approach are search, ideation, specification, coding, testing, and operation. For each of these steps, we suggest a set of techniques to carry out the step in practice. The proposed developmental model asks researchers and practitioners of the Internetware paradigm to better understand human creativity and to formulate an algorithmic perspective on creative behavior in human, to design programs that can enhance human creativity without necessarily being creative themselves.
Duties Beyond Borders

Perhaps Hoffmann's quarter of a century residence in the U.S., explains some of the tics in this provocative and yet frustrating book. The author was born in Vienna and educated in France, where he was a student of Raymond Aron, an interpretor of Gaullism, and spiritual father of the well-known In Search of France. He knows how to turn theory against supposed pragmatists while brandishing a tactical realism in the face of Utopian naiveté. As a Harvard professor, on the other hand, he is more relaxed and dialogues mainly with his contemporaries (whom he supposes well known and worthy of attention).
Sex differences and plasticity in dehydration tolerance: insight from a tropical liverwort.

BACKGROUND AND AIMS Adaptations allowing plants to cope with drying are particularly relevant in the light of predicted climate change. Dehydration tolerance (DhT, also dehydration-tolerant) is one such adaptation enabling tissue to survive substantial drying. A great deal of work has been conducted on highly DhT species. However, bryophytes showing less intense and variable DhT are understudied, despite the potential for these species to provide an informative link between highly tolerant and sensitive species. In this study, we tested the degree to which DhT varies across populations and the sexes of a species expected to exhibit a moderate DhT phenotype. METHODS To test predicted patterns of tolerance we assessed DhT in males and females of Marchantia inflexa from two distinct habitat types that differ in water availability. Both common garden and field-collected tissue was subjected to drying assays at multiple intensities and recovery was monitored by chlorophyll florescence. Verification studies were conducted to confirm the level of dehydration, the rate of drying and the associated changes in photosynthetic physiology. KEY RESULTS We confirmed our expectation that M. inflexa is able to tolerate moderate dehydration. We also found that females exhibited higher DhT than males, but populations did not differ in DhT when cultured in a common garden. However, field-collected samples exhibited differences in DhT corresponding to environmental dryness, suggesting plasticity in DhT. CONCLUSIONS By studying a less extreme DhT phenotype we gained insight into how more sensitive (yet still tolerant) organisms cope with dehydration. Additionally, the identified sex-specific variation in DhT may explain ecological patterns such as female-biased sex ratios. Furthermore, plasticity in DhT has the potential to inform management practices aimed at increasing tolerance to drought conditions.
An Analysis of Public Interest Reporting: The Case of General Motors in South Africa

The purpose of this paper is to examine General Motors Corpora tions^ (GM) use of a specific social responsibility disclosure device, the General Motors Public Interest Report, to explain and defend its pro duction and marketing operations in South Africa from 1971 through 1986. In order to analyze GM's management of its position on South African investment, first we studied each GM report published during that period. Afterward, we evaluated GM's discussions in light of share-holder, government and activist pressures for GM to defend and/ or change its policies toward South Africa. Our longitudinal analysis provides new information about the dynamic nature of a firm's social responsiveness strategy and about the use of a disclosure mechanism that is supplemental to corporate annual reports. Thus, our study ad vances the stream of corporate social performance research concerned with "corporate social responsiveness" (Wood, 1991). The remainder of our paper is organized as follows. First, we discuss society's changing expectations of business during the 1970s and activist groups' confrontations with U.S. multinational corporations over foreign human rights issues. Appealing to prior research, we then dis cuss the concept of corporate social responsiveness. Next, apartheid in South Africa as a corporate social responsibility issue is discussed. In presenting a detailed account of the content of General Motors Public Interest Reports from 1971 through 1987 concerning the corporation's South African business practices and policies, we evaluate GM's dis closure trends and present some overall conclusions.
Module Selection and Supply Chain Optimization for Customized Product Families Using Redundancy and Standardization

In this paper, we study the problem of configuring a product family which has to satisfy diversified customer requirements. Modular design strategies allow a bill of materials to be generated for various finished products from a limited subset of modules. Simultaneously, a production location must be selected for the manufacture of each module. From a product point-of-view, the strategies adopted are often extreme, proposing either the manufacturing of the total diversity (all possible products) or a limited set of standardized products (only a few products are proposed). The objective of this paper is to investigate intermediate cases on this continuum, in order to better understand the potential for profit. Our comparison is based on the product family configuration (selection of the best modules) that minimizes production and transportation costs under time constraints.
Work Overload, Work-Family Conflict, Family-Work Conflict and Their Effects on Job Embeddedness: The Moderating Role of Coworker Support

The study was intended to find out the impact of work overload, work-family conflict and family-work conflict on job embeddedness. For the analysis of the study an aggregate of 250 responses were chosen. Analysis was made through Simple, multiple and moderating regression. Results have shown a substantial influences of work overload and family-work conflict towards job embeddedness. Support of coworker could not moderate any of the proposed relationships.