gebhart/patrepeval huggingface dataset:
The catalytic domain of endoglucanase A from Clostridium cellulolyticum: effects of arginine 79 and histidine 122 mutations on catalysis (1992)

Sequence analysis of the endoglucanase EGCCA of Clostridium cellulolyticum indicates the existence of two domains: a catalytic domain extending from residue 1 to residue 376 and a reiterated domain running from residue 390 to 450. A small deletion in the C terminal end of the catalytic domain inactivated the protein. From the analysis of the sequences of 26 endoglucanases belonging to family A, we focused on seven amino acids which were totally conserved in all the catalytic domains compared. The roles of two of these, Arg-79 and His-122, were studied and defined on the basis of the mutants obtained by introducing various substitutions. Our findings suggest that Arg-79 is involved in the structural organization of the protein; the His-122 residue seems to be more essential for catalysis. The role of His-123, which is conserved only in subfamily A4, was also investigated.
Code coverage at Google (2019)

Code coverage is a measure of the degree to which a test suite exercises a software system. Although coverage is well established in software engineering research, deployment in industry is often inhibited by the perceived usefulness and the computational costs of analyzing coverage at scale. At Google, coverage information is computed for one billion lines of code daily, for seven programming languages. A key aspect of making coverage information actionable is to apply it at the level of changesets and code review. This paper describes Google’s code coverage infrastructure and how the computed code coverage information is visualized and used. It also describes the challenges and solutions for adopting code coverage at scale. To study how code coverage is adopted and perceived by developers, this paper analyzes adoption rates, error rates, and average code coverage ratios over a five-year period, and it reports on 512 responses, received from surveying 3000 developers. Finally, this paper provides concrete suggestions for how to implement and use code coverage in an industrial setting.
Chlamydia trachomatis: Its Role in Tubal Infertility (1985)

We compared the prevalence of antibody to Chlamydia trachomatis among 88 women undergoing an evaluation for infertility and 49 women attending an antenatal clinic. Demographic data regarding sexual behavior were also collected. Eighteen women had tubal infertility and 70 had infertility due to a variety of other reasons. In comparison with women who had other causes for infertility, women with tubal infertility began coitus sooner (17.7 +/- 2.2 years vs. 19.5 +/- 3.4 years, P less than .05) and had more lifetime sex partners (4.5 vs. 1.33, P less than .001). Women with tubal infertility had a higher prevalence of antibody to C. trachomatis (13 of 18) than did women with nontubal causes for infertility (6 of 70, P less than .0001) or pregnant women (11 of 49, P = .0003). This high prevalence of antibody to C. trachomatis among women with tubal infertility was independent of sexual experience. By immunoblot analysis, an antigen of approximately 57,000 Da was immunodominant in 11 of 13 seropositive subjects with tubal infertility vs. 2 of 6 seropositive subjects with nontubal infertility (P = .046) and 1 of 11 seropositive pregnant women (P = .0003). Thus, women with tubal infertility frequently have serological evidence of prior infection with C. trachomatis and have a distinctive antigen-specific humoral immune response. These results further support the etiologic role of infection with C. trachomatis in tubal infertility.
PAC-Bayesian Margin Bounds for Convolutional Neural Networks (2017)

Recently the generalization error of deep neural networks has been analyzed through the PAC-Bayesian framework, for the case of fully connected layers. We adapt this approach to the convolutional setting.
Joint interpretation of seismic and CSEM data using well log constraints: an example from the Luva Field (2009)

One of the hottest trends in geophysical exploration today is the integration of data from multiple sources to produce a geologically consistent, quantitative interpretation of seafloor rock and fluid properties. In this case study Peter Harris, Zhijun Du, Lucy MacGregor, Wiebke Olsen, Rone Shu and Richard Cooper present the application of a practical integration workflow to seismic, controlled source electromagnetic (CSEM), and well log data from the Luva gas field, offshore Norway.
The neocortical microcircuit as a <i>tabula rasa</i> (2005)

The neocortex has a high capacity for plasticity. To understand the full scope of this capacity, it is essential to know how neurons choose particular partners to form synaptic connections. By using multineuron whole-cell recordings and confocal microscopy we found that axons of layer V neocortical pyramidal neurons do not preferentially project toward the dendrites of particular neighboring pyramidal neurons; instead, axons promiscuously touch all neighboring dendrites without any bias. Functional synaptic coupling of a small fraction of these neurons is, however, correlated with the existence of synaptic boutons at existing touch sites. These data provide the first direct experimental evidence for a tabula rasa-like structural matrix between neocortical pyramidal neurons and suggests that pre- and postsynaptic interactions shape the conversion between touches and synapses to form specific functional microcircuits. These data also indicate that the local neocortical microcircuit has the potential to be differently rewired without the need for remodeling axonal or dendritic arbors.
Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community (2013)

ABSTRACT The processes and mechanisms of community assembly and its relationships to community functioning are central issues in ecology. Both deterministic and stochastic factors play important roles in shaping community composition and structure, but the connection between community assembly and ecosystem functioning remains elusive, especially in microbial communities. Here, we used microbial electrolysis cell reactors as a model system to examine the roles of stochastic assembly in determining microbial community structure and functions. Under identical environmental conditions with the same source community, ecological drift (i.e., initial stochastic colonization) and subsequent biotic interactions created dramatically different communities with little overlap among 14 identical reactors, indicating that stochastic assembly played dominant roles in determining microbial community structure. Neutral community modeling analysis revealed that deterministic factors also played significant roles in shaping microbial community structure in these reactors. Most importantly, the newly formed communities differed substantially in community functions (e.g., H2 production), which showed strong linkages to community structure. This study is the first to demonstrate that stochastic assembly plays a dominant role in determining not only community structure but also ecosystem functions. Elucidating the links among community assembly, biodiversity, and ecosystem functioning is critical to understanding ecosystem functioning, biodiversity preservation, and ecosystem management. IMPORTANCE Microorganisms are the most diverse group of life known on earth. Although it is well documented that microbial natural biodiversity is extremely high, it is not clear why such high diversity is generated and maintained. Numerous studies have established the roles of niche-based deterministic factors (e.g., pH, temperature, and salt) in shaping microbial biodiversity, the importance of stochastic processes in generating microbial biodiversity is rarely appreciated. Moreover, while microorganisms mediate many ecosystem processes, the relationship between microbial diversity and ecosystem functioning remains largely elusive. Using a well-controlled laboratory system, this study provides empirical support for the dominant role of stochastic assembly in creating variations of microbial diversity and the first explicit evidence for the critical role of community assembly in influencing ecosystem functioning. The results presented in this study represent important contributions to the understanding of the mechanisms, especially stochastic processes, involved in shaping microbial biodiversity.
Resource reservations with fuzzy requests (2006)

Abstract We present a scheme for reserving job resources with imprecise requests. Typical parameters such as the estimated runtime, the start time or the type or number of required CPUs need not be fixed at submission time but can be kept fuzzy in some aspects. Users may specify a list of preferences which guide the system in determining the best matching resources for the given job. Originally, the impetus for our work came from the need for efficient co‐reservation mechanisms in the Grid where rigid constraints on multiple job components often make it difficult to find a feasible solution. Our method for handling fuzzy reservation requests gives the users more freedom to specify the requirements and it gives the Grid Reservation Service more flexibility to find optimal solutions. In the future, we will extend our methods to process co‐reservations. We evaluated our algorithms with real workload traces from a large supercomputer site. The results indicate that our scheme greatly improves the flexibility of the solution process without having much affect on the overall workload of a site. From a user's perspective, only about 10% of the non‐reservation jobs have a longer response time, and from a site administrator's view, the makespan of the original workload is extended by only 8% in the worst case. Copyright © 2006 John Wiley & Sons, Ltd.
VERTEBRAL FRACTURES RESULTING FROM PROLONGED CORTISONE AND CORTICOTROPIN THERAPY (1954)

During the past year the authors have observed four male patients with rheumatoid arthritis in whom severe compression fractures of the vertebrae have developed during the administration of cortisone or corticotropin or both. Although demineralization of the skeleton is a recognized complication of cortisone therapy, these cases have prompted the authors to emphasize the importance of possible pathological fractures when prolonged treatment of this nature is used. Demartini, Grokoest, and Ragan,<sup>1</sup>in 1952, reported pathological fractures in five patients who had received intensive cortisone therapy. As these authors pointed out, however, other factors predisposing to osteoporosis were present in that all five patients were women (four had passed the menopause) and three had severe rheumatoid arthritis. In the same year Teicher and Nelson<sup>2</sup>reported the case of a young woman with pemphigus vulgaris who was treated for three years with cortisone, during which time pathological compression fractures from
A Computational Multiresolution BOLD fMRI Model (2011)

Blood oxygenation level-dependent (BOLD) functional magnetic resonance imaging (fMRI) is a widely used method for brain mapping. BOLD fMRI signal detection is based on an intravoxel dephasing mechanism. This model involves bulk nuclear spin precession in a BOLD-induced inhomogeneous magnetic field within a millimeter-resolution voxel, that is, BOLD signal formation spans a huge spatial scale range from Angstrom to millimeter. In this letter, we present a computational model for multiresolution BOLD fMRI simulation, which consists of partitioning the nuclear spin pool into spin packets at a mesoscopic scale (∼10(-6) m), and calculating multiresolution voxel signals by grouping spin packets at a macroscopic scale range (10(-5) to 10(-3) m). Under a small-angle approximation, we find that the BOLD signal intensity is related to its phase counterpart (or BOLD fieldmap) across two spatial resolution levels.
Chloride and potassium in the kraft chemical recovery cycle (1990)

Copyright Pulp & Paper Canada. Reprinted with permission from Annex Business Media.
Applications of Stable Isotopes to Pediatric Nutrition and Gastroenterology (1985)

The naturally occurring, nonradioactive, stable isotopes, 2H, 15N, 18O, and in particular, 13C, are valuable tracers in studies of pediatric nutrition and gastroenterology. Techniques using these isotopes have been developed for the measurement of digestion, absorption, utilization, and excretion of nutrients in premature and term infants, as well as in young children. Compounds labeled with 13C enable quantitative measurements of nutrient oxidation rates and percent nutrient malabsorption. Illustrations of these applications are presented in studies of simple and complex carbohydrate metabolism, of medium- and long-chain triglyceride absorption and malabsorption, and of bile salt conservation and loss in the neonate. Modular protocols for the determination of nutrient absorption, oxidation, and loss now can be applied in longitudinal studies which involve comparisons of diet or which monitor recovery following malnutrition or disease. Instrumentation to be available in the future will simplify isotope ratio determinations and create ready access to the methodologies described.
Relating variance in feedback effectiveness to learning styles (2017)

Introduction: Students consider feedback to be an important aspect of good teaching, and meta-analyses confirm its influence on academic achievement. Anecdotal observations in pharmacy practice workshops at our institution suggested variance in students' perceptions regarding the effectiveness of feedback. Aim: To explore reasons students perceive the effectiveness of feedback differently from each other. Methodology: As a conceptual paper, this article does not conform to the standard format of empirical research papers. Instead, it develops an argument by drawing on two established theories about the learning process, Vygotsky's theory of Social Constructivism and Learning Style theory. Results: The effectiveness of feedback may be influenced by factors other than quality. We propose an original model that links feedback preferences with learning styles, and make recommendations to pharmacy educators grounded in research findings. Conclusion: The Matched-Mismatched Feedback Model may account for some of the variation in feedback effectiveness. Further empirical research to explore the validity of our model is recommended.
Giant in-particle field concentration and Fano resonances at light scattering by high-refractive-index particles (2016)

We present the results of a detailed analytical study of light scattering by a particle with high refractive index $m+i\ensuremath{\kappa}$ and low losses ($m\ensuremath{\gg}1,\phantom{\rule{0.28em}{0ex}}0<\ensuremath{\kappa}\ensuremath{\ll}1$) based on the exact Mie solution. We show that there is a dramatic difference in the behavior of the electromagnetic field within the particle (inner problem) and outside it (outer problem). With an increase in $m$ at fixed values of the other parameters, the field within the particle asymptotically converges to a periodic function of $m$. The electric and magnetic type Mie resonances of different orders overlap substantially. It may lead to a giant concentration of the electromagnetic energy within the particle. At the same time, we demonstrate that the solution for the outer problem makes it possible to present each partial scattered wave as a sum of two partitions. One of them corresponds to the $m$-independent wave, scattered by a perfectly reflecting particle and plays the role of a background, while the other is associated with the excitation of a sharply $m$-dependent resonant Mie mode. The interference of the partitions brings about a typical asymmetric Fano profile. The profile is obtained from the exact Mie solution by means of identical transformations without any additional assumptions and/or fitting. It makes it possible to generalize rigorously the Fano theory to the case of finite dissipation. At an increase in $m$ the Fano resonances in the outer problem die out and the scattered field converges to the universal, $m$-independent profile. The behavior of the resonances at a fixed $m$ and varying particle size parameter $(x)$ is also discussed in detail. The similarities and differences of the two cases (fixed $x$, varying $m$ and fixed $m$, varying $x$) are disclosed. We also show that under certain very general conditions the scattering cross section of a large lossy sphere cannot be smaller than half its geometric cross section, while its absorption cross section cannot exceed three halves of the geometric one. Numerical estimates of most discussed effects for a gallium phosphide particle irradiated by the second harmonic of a Nd:YAG laser are presented as an example. In addition to purely academic interest, the obtained results may be employed to design new highly nonlinear heterogenic nanostructures and other metamaterials.
Speaker identification for security systems using reinforcement-trained pRAM neural network architectures (2001)

Speaker identification may be employed as part of a security system requiring user authentication. In this case, the claimed identity of the user is known from a magnetic card and PIN number, for example, and an utterance is requested to confirm the identity of the user. A fast response is necessary in the confirmation phase and a fast registration process for new users is desirable. The time encoded signal processing and recognition (TESPAR) digital language is used to preprocess the speech signal. A speaker cannot be identified directly from the single TESPAR vector since there is a highly nonlinear relationship between the vector's components such that vectors are not linearly separable. Therefore the vector and its characteristics suggest that classification using a neural network will provide an effective solution. Good classification performance has been achieved using a probabilistic RAM (pRAM) neuron. Four probabilistic pRAM neural network architectures are presented. A performance of approximately 97% correct classifications has been obtained, which is similar to results obtained elsewhere (M. Sharma and R.J. Mammone, 1996), and slightly better than a MLP network. No speech recognition stage was used in obtaining these results, so the performance relates only to identifying a speaker's voice and is therefore independent of the spoken phrase. This has been achieved in a hardware-realizable system which may be incorporated into a smart-card or similar application.
Nerve Growth Factor from Cobra Venom (1970)

The chemical and biological properties of the nerve growth factor isolated from Naja naja venom are described. The nerve growth promoting activity appears to be distinct from the most commonly known enzymes and toxins present in the venom. The purified nerve growth factor from cobra venom has properties remarkably similar to those of the nerve growth factor isolated from mouse submaxillary gland. These findings are discussed in connection with the problem of the physiological function of this unique protein in the two species.
Parallel operation control technique of voltage source inverters in UPS (1999)

The control technique of a parallel operation system of voltage source inverters with other inverters or with utility source has been applied in many fields, especially in uninterruptible power supply (UPS). The multi-module UPS can flexibly implement expansion of power system capacities. Furthermore, it can be used to build up a parallel redundant system in order to improve the reliability of whole power system operation. This paper analyses voltage and current status of a voltage source inverter in parallel, as well as the principle of parallel redundant system. Several control strategies according to the load-sharing problem in parallel control systems are also presented, from which the research of distributed-logic-control to realize parallel operation of four 3 kVA UPSs based on TMS320F240, a kind of real time digital signal processor (DSP), is discussed and proposed in detail.
Medulloblastoma Exosome Proteomics Yield Functional Roles for Extracellular Vesicles (2012)

Medulloblastomas are the most prevalent malignant pediatric brain tumors. Survival for these patients has remained largely the same for approximately 20 years, and our therapies for these cancers cause significant health, cognitive, behavioral and developmental sequelae for those who survive the tumor and their treatments. We obviously need a better understanding of the biology of these tumors, particularly with regard to their migratory/invasive behaviors, their proliferative propensity, and their abilities to deflect immune responses. Exosomes, virus-sized membrane vesicles released extracellularly from cells after formation in, and transit thru, the endosomal pathway, may play roles in medulloblastoma pathogenesis but are as yet unstudied in this disease. Here we characterized exosomes from a medulloblastoma cell line with biochemical and proteomic analyses, and included characterization of patient serum exosomes. Further scrutiny of the proteomic data suggested functional properties of the exosomes that are relevant to medulloblastoma tumor biology, including their roles as proliferation stimulants, their activities as attractants for tumor cell migration, and their immune modulatory impacts on lymphocytes. Aspects of this held true for exosomes from other medulloblastoma cell lines as well. Additionally, pathway analyses suggested a possible role for the transcription factor hepatocyte nuclear factor 4 alpha (HNF4A); however, inhibition of the protein's activity actually increased D283MED cell proliferation/clonogenecity, suggesting that HNF4A may act as a tumor suppressor in this cell line. Our work demonstrates that relevant functional properties of exosomes may be derived from appropriate proteomic analyses, which translate into mechanisms of tumor pathophysiology harbored in these extracellular vesicles.
SPECIFICATION AND IMPLEMENTATION OF A BELIEF-DESIRE-JOINT-INTENTION ARCHITECTURE FOR COLLABORATIVE PROBLEM SOLVING (1993)

Systems composed of multiple interacting problem solvers are becoming increasingly pervasive and have been championed in some quarters as the basis of the next generation of intelligent information systems. If this technology is to fulfill its true potential then it is important that the systems which are developed have a sound theoretical grounding. One aspect of this foundation, namely the model of collaborative problem solving, is examined in this paper. A synergistic review of existing models of cooperation is presented, their weaknesses are highlighted and a new model (called joint responsibility) is introduced. Joint responsibility is then used to specify a novel high-level agent architecture for cooperative problem solving in which the mentalistic notions of belief, desire, intention and joint intention play a central role in guiding an individual’s and the group’s problem solving behaviour. An implementation of this high-level architecture is then discussed and its utility is illustrated for the real-world domain of electricity transportation management.
On the Synthesis of Finite-State Machines from Samples of Their Behavior (1972)

The Nerode realization technique for synthesizing finite-state machines from their associated right-invariant equivalence relations is modified to give a method for synthesizing machines from finite subsets of their input-output behavior. The synthesis procedure includes a parameter that one may adjust to obtain machines that represent the desired behavior with varying degrees of accuracy and that consequently have varying complexities. We discuss some of the uses of the method, including an application to a sequential learning problem.