Miracle-dz/UniFAR-FTUs huggingface dataset:
13CFLUX2—high-performance software suite for 13C-metabolic flux analysis

Summary: 13C-based metabolic flux analysis (13C-MFA) is the state-of-the-art method to quantitatively determine in vivo metabolic reaction rates in microorganisms. 13CFLUX2 contains all tools for composing flexible computational 13C-MFA workflows to design and evaluate carbon labeling experiments. A specially developed XML language, FluxML, highly efficient data structures and simulation algorithms achieve a maximum of performance and effectiveness. Support of multicore CPUs, as well as compute clusters, enables scalable investigations. 13CFLUX2 outperforms existing tools in terms of universality, flexibility and built-in features. Therewith, 13CFLUX2 paves the way for next-generation high-resolution 13C-MFA applications on the large scale. Availability and implementation: 13CFLUX2 is implemented in C++ (ISO/IEC 14882 standard) with Java and Python add-ons to run under Linux/Unix. A demo version and binaries are available at www.13cflux.net. Contact: info@13cflux.net or k.noeh@fz-juelich.de Supplementary information: Supplementary data are available at Bioinformatics online.
What Principles of Communication Law Are Violated in Manipulation

The study investigates how manipulators and manipulation deviate from some law principles of communication. The research falls within a comprehensive framework of manipulation It starts from the four features of fraiming accredited by R. M. Entman (1993): define problem, diagnose causes, make moral judgments, and suggest remedies. Analytical, manipulation is framed as follows: a) manipulation is defined as influencing persuasive intervention, b) manipulation illicit causes consists of interests regarding the “other”; persuasive joints of manipulation are mostly unethical and consist of induction of toxic opinions, attitudes and behaviors; there are two remedies for manipulation: refusal manipulation and detection plus annihilation of manipulation. However, design the fundamental features of manipulation over raster of principles of the Communication Law. It is found that the manipulation violates the following principles of Communication Law: the principle of accountability and responsibility, the principle of truth, the principle of good faith, the principle of impartiality and objectivity.
Robustness and Evolvability in Living Systems

List of Figures ix Acknowledgments xiii Chapter 1: Introduction 1 PART I: ROBUSTNESS BELOW THE GENE LEVEL 13 Chapter 2: The Genetic Alphabet 15 Chapter 3: The Genetic Code 25 Chapter 4: RNA Structure 39 Chapter 5: Proteins and Point Mutations 62 Chapter 6: Proteins and Recombination 78 PART II: ROBUSTNESS ABOVE THE GENE LEVEL 91 Chapter 7: Regulatory DNA Regions and Their Reorganization in Evolution 93 Chapter 8: Metabolic Pathways 104 Chapter 9: Metabolic Networks 120 Chapter 10: Drosophila Segmentation and Other Gene Regulatory Networks 143 Chapter 11: Phenotypic Traits, Cryptic Variation, and Human Diseases 161 Chapter 12: The Many Ways of Building the Same Body 175 PART III: COMMON PRINCIPLES 193 Chapter 13: Neutral Spaces 195 Chapter 14: Evolvability and Neutral Mutations 217 Chapter 15: Redundancy of Parts or Distributed Robustness? 228 Chapter 16: Robustness as an Evolved Adaptation to Mutations 247 Chapter 17: Robustness as an Evolved Adaptation to Environmental Change and Noise 270 Chapter 18: Robustness and Fragility: Advantages to Variation and Trade-offs 281 PART IV: ROBUSTNESS BEYOND THE ORGANISM 295 Chapter 19: Robustness in Natural Systems and Self-Organization 297 Chapter 20: Robustness in Man-made Systems 310 Epilogue: Seven Open Questions for Systems Biology 321 Bibliography 323 Index 359
Measuring the Culture of C. P. Snow's Two Cultures

C. P. Snow's (1964) The Two Cultures has been controversial, and is still much cited in the literature of both the sciences and the humanities. However, there seem to have been no empirical studies of cultural and aesthetic activities in scientists and non-scientists. This study describes a questionnaire which measured 17 different cultural activities in a stratified survey of science and non-science students in London, UK. Science students showed a significantly lower level of activity on 12 of the 17 measures (and were significantly higher on none). Among the scientists, cultural activity overall was lowest in engineering and mathematics students, and highest in medical and biological science students. Cultural activity correlated significantly with the personality measure of Openness to Experience, although the correlation was weaker in scientists than in non-scientists.
Cross-Cultural Research as a Rosetta Stone for Discovering the Original Homelands of Protolanguage Groups

This programmatic article describes how the two types of cross-cultural research (comparative ethnography and comparative archaeology) can provide a Rosetta stone to help us discover the original homelands of protolanguage groups. Here, the focus is on Proto-Afroasiatic and Proto-Indo-European. If words reconstructed by historical linguists for a protolanguage reflect cultural and environmental features, and if those features have material or archaeological indicators (which we can discover by the two types of cross-cultural research), then the archaeological record can be searched for sites that have the expected combinations of features. The likely homeland of the protolanguage should be the site or local region that has significantly more of those indicator features than other sites or local regions.
A suggested structure for a science of relationships

An attempt is made to sketch the structure of a science, in the sense of an ordered body of knowledge, of interpersonal relationships. The special properties of relationships are discussed. Relationships exist over time, involve properties beyond those of the constituent interactions, include both behavior and subjective experience, and exist in a social context. It is suggested that a science of human relationships will require three overlapping phases: (1) Description, listing 10 categories of dimensions potentially useful for ordering the data; (2) Principles of dynamics, which may concern external influences on the dyad, interchanges between the participants, or intrapsychic processes; and (3) The specification of the limits of applicability of those principles. In general, a balance must be found between the search for generalisations and recognition of the complexity of human relationships.
Experiences in Building a Tool for Navigating Association Rule Result Sets

Practical knowledge discovery is an iterative process. First, the experiences gained from one mining run are used to inform the parameter setting and the dataset and attribute selection for subsequent runs. Second, additional data, either incremental additions to existing datasets or the inclusion of additional attributes means that the mining process is reinvoked, perhaps numerous times. Reducing the number of iterations, improving the accuracy of parameter setting and making the results of the mining run more clearly understandable can thus significantly speed up the discovery process.In this paper we discuss our experiences in this area and present a system that helps the user to navigate through association rule result sets in a way that makes it easier to find useful results from a large result set. We present several techniques that experience has shown us to be useful. The prototype system -- IRSetNav -- is discussed, which has capabilities in redundant rule reduction, subjective interestingness evaluation, item and itemset pruning, related information searching, text-based itemset and rule visualisation, hierarchy based searching and tracking changes between data sets using a knowledge base. Techniques also discussed in the paper, but not yet accommodated into IRSetNav, include input schema selection, longitudinal ruleset analysis and graphical visualisation techniques.
A UNITED KINGDOM SURVEY OF ACCRED ITED COGNITIVE BEHAVIOUR THERAPISTS' ATTITUDES TOWARDS AND USE OF STRUCTURED SELF-HELP MATERIALS

Self-help materials can be offered to clients/patients either for use alone (unsupported self-help) or to support work with a health care practitioner (supported self-help). Structured self-help materials that use a Cognitive Behaviour Therapy (CBT) treatment approach have been shown to be clinically effective. We report a national survey of all 500 cognitive and behavioural psychotherapists registered with the British Association for Behavioural and Cognitive Psychotherapies, the lead organisation for CBT in the United Kingdom. A total of 265 therapists responded (53%). Self-help materials were used by 88.7% of therapists and were mostly provided as a supplement to individual therapy. Self-help was most frequently used to help patients experiencing depression, anxiety and obsessive compulsive disorder and was largely delivered using paper-based formats. The majority of self-help materials used a CBT approach. Only 36.2% of therapists had been trained in how to use self-help treatments, and those who had received training recommended self-help treatments to more clients/patients per week and rated self-help approaches as being significantly more helpful than those who had not received training.
A Galacturonic Acid–Containing Xyloglucan Is Involved in Arabidopsis Root Hair Tip Growth[W]

A unique galacturonic acidic–containing xyloglucan was identified in Arabidopsis root hair cell walls and characterized using genetic, biochemical, and chemical methods. Plants with a null mutation in a gene encoding a GT47 glycosyltransferase synthesize xyloglucan that lacks galacturonic acid and have short root hairs. These findings highlight a key role for acidic xyloglucan in root hair growth. Root hairs provide a model system to study plant cell growth, yet little is known about the polysaccharide compositions of their walls or the role of these polysaccharides in wall expansion. We report that Arabidopsis thaliana root hair walls contain a previously unidentified xyloglucan that is composed of both neutral and galacturonic acid–containing subunits, the latter containing the β-d-galactosyluronic acid-(1→2)-α-d-xylosyl-(1→ and/or α-l-fucosyl-(1→2)-β-d-galactosyluronic acid-(1→2)-α-d-xylosyl-(1→) side chains. Arabidopsis mutants lacking root hairs have no acidic xyloglucan. A loss-of-function mutation in At1g63450, a root hair–specific gene encoding a family GT47 glycosyltransferase, results in the synthesis of xyloglucan that lacks galacturonic acid. The root hairs of this mutant are shorter than those of the wild type. This mutant phenotype and the absence of galacturonic acid in the root xyloglucan are complemented by At1g63450. The leaf and stem cell walls of wild-type Arabidopsis contain no acidic xyloglucan. However, overexpression of At1g63450 led to the synthesis of galacturonic acid–containing xyloglucan in these tissues. We propose that At1g63450 encodes XYLOGLUCAN-SPECIFIC GALACTURONOSYLTRANSFERASE1, which catalyzes the formation of the galactosyluronic acid-(1→2)-α-d-xylopyranosyl linkage and that the acidic xyloglucan is present only in root hair cell walls. The role of the acidic xyloglucan in root hair tip growth is discussed.
A method for counting acid-fast bacteria.

A reliable, convenient, and accurate method for counting ac id-fast hacteria ( AFB) is essential for much work with Mycobacterium leprae. The procedure used , previously in the laboratory (~, 4 ) had two technical difficulties: (a) In order for the drops to spread satisfactorily the microscope slides had to have a uniform wetability of the correct degree; sometimes this requirement was difficult to sa tisfy and a satisfactory procedure for one batch of slides was sometimes unsatisfactory for the next batch. (b) There was a tendency for bacteria in suspensions devoid of tissue to concentrate in the periphery of the drop during drying. Consequently a new method was developed, and, after the tes ts described below, it was substituted for the previous method.
Performing the Global University

At a drama studies program review meeting, the chair wielded a fact sheet crafted by the program’s founders in the late 1960s emphasizing the importance of producing scholars and artists. As the question of form is integral to the production of knowledge or content in theater’s disciplinary structure, such an objective appears rather agreeable and necessary. But the bifurcation of form and content started to rear its ugly head when it became evident that reconfiguring the program would require diversifying the curriculum beyond its Eurocentric and practice-heavy focus. “But what about Ibsen and Chekhov? ” one senior faculty member cried, even though those playwrights were already duplicated in several classes. “The students need to know their own culture. ” That included Shakespeare, whose standing was so unshakeable it was simply a core requirement. With cursory acknowledgment of global frameworks, the small department voted in a class titled Non-Western Theater History and Practice as a kind of antidote for its Western bias, and reinforced offerings in playwriting, acting, and production based on the European and U.S.-American repertory. This performative encounter is the sine qua non of U.S. theater departments that profess to be “globalizing” but have a vested interest in what that means. In a rather striking way, it is also a version of the colonial scenario that designates knowledge and technique to the West. In such a scenario, the rest of the world and its theatrical forms are tokenized as illegible or irrelevant entities, while the logic of U.S. and European (artistic) exceptionalism is internalized as an unquestioned epistemology. The “need to know” argument is actually a mandate for all students to learn the theater history and vocabulary of Europe as their “own” culture. Excursions to the exotic non-West are often couched as exciting but nonessential supplements
A serologic survey of Mycoplasma spp. in farmed bison (Bison bison) herds in western Canada

Mycoplasma bovis is emerging as an important pathogen of farmed bison in North America and is associated with high morbidity and mortality in affected herds. We developed an in-house ELISA to detect antibodies against Mycoplasma spp. in bison sera. The aims of the study were to estimate the seroprevalence against Mycoplasma spp. in bison herds with or without past history of M. bovis–associated disease, and to determine potential risk factors for seropositivity to Mycoplasma spp. in farmed bison in western Canada. A total of 858 serum samples were collected from bison >1 y of age from 19 bison herds. The individual and herd-level seroprevalence of Mycoplasma spp. was 12% and 79%, respectively. The proportion of seropositive animals was 0–41% and 0–9% for herds with or without a history of M. bovis–associated disease, respectively. Mycoplasma spp. appear to be widespread in bison in Manitoba, Saskatchewan, and Alberta. Eight of 11 herds with no history of M. bovis–associated disease were seropositive for Mycoplasma spp. , which suggests that bison can be subclinically infected with Mycoplasma spp. , or that infection may be underdiagnosed. Although not specific to M. bovis, the in-house ELISA developed to detect antibodies against Mycoplasma spp. may prove to be a valuable herd-level screening tool, providing insight needed for the development of appropriate prevention and control measures for Mycoplasma-related disease in bison herds.
Embedded GPU Performance Estimation from Single-Threaded Applications 39 : 3 Global Memory ( DRAM ) Memory Interface Streaming Multiprocessor ( SMX ) L 2 Cache Streaming Multiprocessor ( SMX ) CUDA Cores Instruction Cache Warp Scheduler Warp Scheduler Warp Scheduler

Heterogeneous multiprocessor system-on-chip architectures are endowed with accelerators such as embedded GPUs and FPGAs capable of general-purpose computation. The application developers for such platforms need to carefully choose the accelerator with the maximum performance bene t. For a given application, usually, the reference code is speci ed in a high-level single-threaded programming language such as C. The performance of an application kernel on an accelerator is a complex interplay among the exposed parallelism, the compiler, and the accelerator architecture. Thus, determining the performance of a kernel requires its redevelopment into each accelerator-speci c language, causing substantial wastage of time and e ort. To aid the developer in this early design decision, we present an analytical framework CGPredict to predict the performance of a computational kernel on an embedded GPU architecture from un-optimized, single-threaded C code. The analytical approach provides insights on application characteristics which suggest further application-speci c optimizations. The estimation error is as low as 2.66% (average 9%) compared to the performance of the same kernel written in native CUDA code running on NVIDIA Kepler embedded GPU. This low performance estimation error enables CGPredict to provide an early design recommendation of the accelerator starting from C code.
GENETIC ALGORITHM LEARNING IN GAME PLAYING

The aim of this paper is to describe utilization of genetic algorithms for strategy evolution. In order to speed up the evolution process we have empowered our genetic algorithm by a kind of macromutation operator that is known to genetic programming community as so called headless chicken crossover. This approach has been tested on a game of Nim and our results are quite promising. We have managed to significantly speed up the evolutionary process and that is why we do believe that the results described here can be useful when tackling other problems where the suitable strategy goal
The Law of the Good Neighbor

This essay portrays the "law of the good neighbor" as the principle of the Warburg Library's collections—as the argument for their expansion and coherence, as well as the principle governing the scholarly practice inspired by the Warburg Institute and "Warburg school" of cultural analysis. The essay includes a tribute to Anne Marie Meyer (1919-2004), Warburg scholar and long-time affiliate of the Institute, with special emphasis on the question that she uniquely raised: "Exactly what was the relation between [Aby] Warburg's research on paganism in the Renaissance and his meditations and fears about Judaism (and Jews)? "
Lacto-N-fucopentaose III, a Pentasaccharide, Prolongs Heart Transplant Survival

Background. Lacto-N-fucopentaose III (LNFPIII) is a pentasaccharide containing the LewisX trisaccharide that is found on schistosome eggs and in breast milk. LNFPIII conjugates suppress host immune responses and have therapeutic efficacy in mouse models of psoriasis and type 1 diabetes. Methods. We used nonvascularized neonatal ear-heart transplantation and heterotopic vascularized heart transplantation models to evaluate immunosuppressive effects of LNFPIII and subsequently analyzed the mechanism. Results. We found that administration of LNFPIII conjugates prolonged median graft survival by 80% when 1-day-old DBA/2 hearts were transplanted into ears of B6 mice. A similar graft prolongation was observed in a fully vascularized heterotopic heart transplantation model (DBA/2 into B6), No prolongation was observed with carrier protein (human serum albumin [HSA] or dextran) alone. We found increased programmed death ligand 1 (PD-L1) expression on F4/80+ macrophages, CD4+ T cells, and CD11b+ CD11c+ (myeloid) dendritic cells, and increased arginase1 and Ym1 expression, typical of alternatively activated macrophages, in the draining (cervical) lymph node cells. We found accumulation of Foxp3+ regulatory T cells (Tregs) in the lymph nodes draining donor hearts, suggesting a possible role of Treg induction in graft prolongation. Anti-PD-L1 antibody treatment abrogated LNFPIII-mediated the graft survival benefit and Treg accumulation. LNFPIII-treated macrophages had increased PD-L1 expression and significantly prolonged DBA/2 allograft survival when injected intraperitoneally into B6 recipient mice. Conclusions. LNFPIII prolongs fully allogeneic graft survival in both vascularized and nonvascularized allograft transplantation models. The mechanism of graft prolongation seems to involve both alternatively activated PDL-1+ macrophages and recruitment of Foxp3+ Treg cells.
Constraint Integration and Violation Handling for BPEL Processes

Autonomic, i.e. dynamic and fault-tolerant Web service composition is a requirement resulting from recent developments such as on-demand services. In the context of planning-based service composition, multiagent planning and dynamic error handling are still unresolved problems. Recently, business rule and constraint management has been looked at for enterprise SOA to add business flexibility. This paper proposes a constraint integration and violation handling technique for dynamic service composition. Higher degrees of reliability and fault-tolerance, but also performance for autonomously composed WS-BPEL processes are the objectives.
Randomized, double-blind, placebo-controlled trial of an iron-fortified food product in female soldiers during military training: relations between iron status, serum hepcidin, and inflammation.

BACKGROUND Iron status degrades in female soldiers during military training. Inflammation-mediated up-regulation of hepcidin, a key mediator of iron homeostasis, may be a contributing factor. OBJECTIVE We measured the efficacy of an iron-fortified food product for maintaining iron status in female soldiers during basic combat training (BCT) and examined relations between iron status, serum hepcidin concentrations, and inflammation. DESIGN A randomized, double-blind, placebo-controlled trial was conducted. Volunteers received an iron-fortified food product (total dose = 56 mg Fe/d) or a placebo twice daily during the 9-wk BCT course. Iron-status indicators, serum hepcidin concentrations, and markers of inflammation were measured pre- and post-BCT. RESULTS BCT affected iron status; serum ferritin concentrations decreased (P < or = 0.05), and concentrations of soluble transferrin receptor (sTfR) and hemoglobin and the red cell distribution width increased (P < or = 0.05). Consumption of the iron-fortified food product attenuated declines in iron status in iron-deficient anemic soldiers; a group-by-time interaction was observed for hemoglobin and sTfR concentrations (P < or = 0.05). Serum hepcidin concentrations were not affected by BCT; however, hepcidin concentrations were lower in iron-deficient anemic soldiers than in those with normal iron status (P < or = 0.05) and were positively associated with serum ferritin (P < or = 0.05) and C-reactive protein (P < or = 0.05) concentrations pre- and post-BCT. CONCLUSIONS Twice-daily consumption of an iron-fortified food product improved iron status in iron-deficient anemic soldiers but not in iron-normal or iron-deficient nonanemic soldiers. Serum hepcidin concentrations were not affected by training but were associated with iron status and inflammation pre- and post-BCT. This trial was registered at clinicaltrials.gov as NCT01100905.
Caution: Classroom under observation

In this article, it is argued that there are serious difficulties in observing someone else teach for the purpose of providing evaluation or corrective feedback on their teaching. The article reports on responses from a group of teacher educators who watched a videotaped classroom lesson. Their written critiques were surprisingly contradictory, so much so as to call into question the reliability of lesson critiques. It is suggested that, where observation and critique of classroom teaching are used, summative judgements be avoided, and that a major goal of observations be to stimulate debate about different teaching styles and individual and cooperative reflection. Most importantly, observers must acknowledge the variety of intentions and perspectives of classroom teachers.