Miracle-dz/UniFAR-FTUs huggingface dataset:
Recognition of native structure from complete enumeration of low‐resolution models with constraints

Complete sets of low‐resolution conformations are generated for eight small proteins by rotating the Cα‐Cα virtual bonds at selected flexible regions, while the remaining structural elements are assumed to move in rigid blocks. Several filtering criteria are used to reduce the ensemble size and to ensure the sampling of well‐constructed conformations. These filters, based on structure and energy constraints deduced from knowledge‐based studies, include the excluded volume requirement, the radius of gyration constraint, and the occurrence of sufficiently strong attractive inter‐residue potentials to stabilize compact forms. About 8,000 well‐constructed decoys or “probable folds” (PFs) are constructed for each protein. A correlation between root‐mean‐square (rms) deviations from X‐ray structure and total energies is observed, revealing a decrease in energy as the rms deviation decreases. The conformation with the lowest energy exhibits an rms deviation smaller than 3.0 Å, in most of the proteins considered. The results are highly sensitive to the choice of flexible regions. A strong tendency to assume native state rotational angles is revealed for some flexible bonds from the analysis of the distributions of dihedral angles in the PFs, suggesting the formation of foldons near these locally stable regions at early folding pathway. Proteins 32:211–222, 1998. © 1998 Wiley‐Liss, Inc.
MOSIS - A gateway to silicon

The MOSIS Service, a low-cost prototyping service for standard-cell and full-custom VLSI circuit development, is discussed. MOSIS (an acronym for MOS Implementation System) has developed a methodology that allows the merging of many different projects from various organizations onto one wafer. This cost-sharing gives designers opportunities that might be prohibitive at regular commercial prices. Since designs are combined on a single mask set. MOSIS users pay for only the fraction of the silicon that they use. Runs are scheduled on a regular basis for 3.0-, 2.0-, 1.6-, and 1.2- mu m double-metal CMOS/bulk technologies. MOSIS quality control and access to MOSIS are described. <<ETX>>
(R)-Methyl {[(2-carboxybicyclo[2.2.2]octan-1-yl)ammonio]methyl}phosphonate dichloromethane 0.25-solvate

The carboxylic acid molecule of the title compound, C11H20NO5P·0.25CH2Cl2, exists as a zwitterion with the H atom of the phosphonate group being transferred to the imine N atom. In the asymmetric unit, there are two crystallographically independent acid molecules adopting the same absolute configuration and differing slightly in their geometrical parameters. In each molecule, the imino and carboxyl groups are connected via an intramolecular N—H⋯O hydrogen bond. Intermolecular O—H⋯O and N—H⋯O hydrogen bonds induce the formation of layers parallel to the ab plane. The dichloromethane solvent molecule, with a site occupancy of 0.5, is located between the layers.
Training Software Engineers Using Open-Source Software: The Professors' Perspective

Traditional Software Engineering (SE) courses often prioritize methodologies and concepts in small, controlled environments: naive projects used as a proof of concept instead of full-fledged real software systems. Although this strategy has clear benefits, it does not place enough care in training students to face complex, non-trivial legacy software projects. To bridge this gap, novel SE courses are leveraging the rich variety of open-source software (OSS) projects to illustrate how these methodologies and concepts are applied to existing, non-trivial software systems. To better understand the benefits, challenges, and opportunities of this transition, in this paper, we interview seven SE professors that changed their academic setting to aspire students to comprehend, maintain, and evolve OSS systems as part of their SE course. We found that there are different ways to make use of OSS projects in SE courses in terms of project choice, assessment, and learning goals. Moreover, we evidence clear benefits of this approach, including improving students’ social and technical skills, and helping students enhancing their resume. Also, we observed that this strategy comes with costs: the activity demands effort and time from the professor and the barrier for one getting involved with and, therefore, placing a meaningful contribution, in an OSS community is often high.
Formal Specification and Analysis of Software Architectures Using the Chemical Abstract Machine Model

We are exploring an approach to formally specifying and analyzing software architectures that is based on viewing software systems as chemicals whose reactions are controlled by explicitly stated rules. This powerful metaphor was devised in the domain of theoretical computer science by Bana/spl circ/tre and Le Me/spl acute/tayer (1990) and then reformulated as the CHAM (CHemical Abstract Machine) by Berry and Boudol (1992). The CHAM formalism provides a framework for developing operational specifications that does not bias the described system toward any particular computational model. It also encourages the construction and use of modular specifications at different levels of detail. We illustrate the use of the CHAM for architectural description and analysis by applying it to two different architectures for a simple but familiar software system, the multiphase compiler. >
A hierarchical transaction concept for runtime adaptation in real-time, networked embedded systems

In this work, we consider reliable runtime adaptation in networked, embedded systems with tight real-time constraints. Specifically, we adapt the placement of software components on a multitude of hardware components and show the need for a hierarchical transaction concept in this context. We consider multiple adaptation steps under these hard system constraints and also introduce a model with undesired configurations, which cannot be maintained for an extended time period. Furthermore, we identify cases when adaptation steps can be performed in parallel. Our concept for adaptations is applied to realistic automotive examples, where the feasibility of adaptation in the inactive period of a software component is demonstrated.
Microsatellite multiplexing in fish.

Abstract Microsatellite multiplexing is a powerful technique that can increase the productivity of genetic studies in fisheries biology. We review multiplexing methods and present an optimized and detailed protocol for microsatellite multiplexing that is specifically tailored for use with radioisotopes. The protocol can significantly reduce the cost associated with microsatellites and provides high polymerase chain reaction (PCR) fidelity and band resolution. Comparing three radioisotopes, we find that end labeling with 33P provides the highest resolution. We also present a quick and inexpensive DNA isolation protocol that is successful with fish larvae. Finally, we find that PCR fidelity depends on the quality of the DNA template, and we therefore review preservation and isolation methods specific to various fish tissue types. Together, these microsatellite multiplexing and DNA isolation protocols can significantly reduce the time and expense associated with genetic analyses in fish.
From UBGs to CFGs A practical corpus-driven approach

Abstract We present a simple and intuitive unsound corpus-driven approximation method for turning unification-based grammars, such as HPSG, CLE, or PATR-II into context-free grammars (CFGs). Our research is motivated by the idea that we can exploit (large-scale), hand-written unification grammars not only for the purpose of describing natural language and obtaining a syntactic structure (and perhaps a semantic form), but also to address several other very practical topics. Firstly, to speed up deep parsing by having a cheap recognition pre-flter (the approximated CFG). Secondly, to obtain an indirect stochastic parsing model for the unification grammar through a trained PCFG, obtained from the approximated CFG. This gives us an efficient disambiguation model for the unification-based grammar. Thirdly, to generate domain-specific subgrammars for application areas such as information extraction or question answering. And finally, to compile context-free language models which assist the acoustic model of a speech recognizer. The approximation method is unsound in that it does not generate a CFG whose language is a true superset of the language accepted by the original unification-based grammar. It is a corpus-driven method in that it relies on a corpus of parsed sentences and generates broader CFGs when given more input samples. Our open approach can be fine-tuned in different directions, allowing us to monotonically come close to the original parse trees by shifting more information into the context-free symbols. The approach has been fully implemented in JAVA.
Map generalization: Information theoretic approach to feature elimination

The present paper proposes an entropy based algorithm for the feature elimination in cartographic generalization. The methodology is tested on a map with 100 point symbols. The experiment demonstrates how the most con°icting map symbols are detected and eliminated from the map. The optimal symbol size can be computed from the entropy model. It is shown how to modify the entropy measure in such a way that the point elimination to a high degree preserves the point clusters.
The distal femoral anatomy of Australopithecus.

The anatomy of the distal femoral fragments from Sterkfontein is reviewed, including its orthopaedic and biomechanical implications with respect to locomotion pattern. Comparisons are made with other hominids and a number of quadrupedal primates. Items which are considered are the obliquity and robustness of the shaft, the anterior intercondylar groove, the intercondylar notch, and the contour of the medial and lateral articular surfaces. The distinctive hominid status of these specimens is shown by their extensive adaptation to bipedal locomotion. No feature is found which is not fully commensurate with completely bipedal locomotion; rather, their distinctive hominid character points to a need for a reanalysis of the gait pattern in these early Pleistocene hominids.
iAIML: a Mechanism to Treat Intentionality in AIML Chatterbots

This paper presents iAIML, a mechanism to treat intentional information based on AIML, a state-of-the-art technology in chatterbot development. Our main goal was to improve dialogues with AIML chatterbots. iAIML adds structure to AIML bases, incorporating intentions and rules used in sentence interpretation and generation. We adopted as linguistic base the conversational analysis theory (CAT), which considers intentionality in adjacent pairs in dialogue, facilitating the establishment of consistent dialogues between chatterbots and users. Tests with the implemented solution showed feasibility of the proposed approach. This is an original work with several contributions, such as the innovative and effective use of CAT, and a consistent modular structure of the iAIML base, favoring reuse and maintenance
Generation of a Sequence Characterized Amplified Region Probe for Authentication of Mainland Serow (Capricornis sumatraensis)

Mainland serow is an endanged artiodactyl of southern Anhui province, China, that is often subject to poaching. To provide an easy, rapid and reliable marker for identification of bushmeat, skin and other tissues of the species, we developed a sequence characterized amplified region (SCAR) based on a species‐specific random amplified polymorphic DNA (RAPD) marker. Initially, a 1012‐bp species‐specific DNA fragment of mainland serow was detected by a RAPD primer S1193. Then, a serow‐specific primer pair (SCF/SCR) was designed according to the specific RAPD fragment, resulting in a 438‐bp SCAR for the species. Finally, the reliability of the SCAR primers was tested by a common multiplex polymerase chain reaction using the combination of the SCAR and cyt b universal primers. The results that all mainland serow samples presented two target bands but the others failed to produce the SCAR indicated that the designed primers were highly diagnostic. Therefore, the SCAR probe developed in this study will be useful for quick authentication of mainland serow tissue samples for conservation biology and bushmeat regulation.
On Constructing Interference-Aware k-Fault Resistant Topologies for Wireless Ad Hoc Networks

The most fundamental problem in wireless ad-hoc networks is to determine a connected communication subgraph that satisfies desirable topological propertiesby assigning appropriate transmission power to each node. Some of the properties considered by a vast majority of researchers include minimum-energy, fault tolerance, minimum interference, and bounded node degree. However preserving two or more combination of these properties at the same time is harder to achieve and often overlooked by the research community. In this paper, we propose a topology control algorithm that preserves connectivity and combines two other important properties, e.g, (a) minimum interference, and (b) fault tolerance. Interestingly, these two properti es create a fundamental tradeoff by running against each other. In one end, interference can be reduced by dropping links that create high interference. On the other end, dropp ing too many links make a network more susceptible to node failure/departure. Thus dropping high interference links while keeping the network significantly connected is a n important goal to achieve. We achieve such goal by formulating the problem of constructing minimum interference path preserving and fault tolerant wireless ad hoc networks under the same framework and then provide algorithms, both centralized and distributed with local information, to solve the problem. Moreover, for the first time in literature , we conceive the concept of fault tolerant interference spanner and provide a local a lgorithm to construct such spanner of a communication graph.
Lattice Boltzmann Simulations at Petascale on Multi-GPU Systems with Asynchronous Data Transfer and Strictly Enforced Memory Read Alignment

The lattice Boltzmann method is a well-established numerical approach for complex fluid flow simulations. Recently general-purpose graphics processing units have become accessible as high-performance computing resources at large-scale. We report on implementing a lattice Boltzmann solver for multi-GPU systems that achieves 0.69 PFLOPS performance on 16384 GPUs. In addition to optimizing the data layout on the GPUs and eliminating the halo sites, we make use of the possibility to overlap data transfer between the host CPU and the device GPU with computing on the GPU. We simulate flow in porous media and measure both strong and weak scaling performance with the emphasis being on a large scale simulation using realistic input data.
Three-dimensional Printing Technology in Surgery

Background: Three-dimensional printing has become an increasingly widespread technology, becoming more accessible to individuals, small businesses and organisations. It represents the ability to manufacture objects of various substrate material using computer aided 3D plans. This article aims to explore the various uses of this technology in medicine and surgery including future directions and applications Method: A generalised review of past and current articles was performed exploring the known uses of three-dimensional printing in medicine and surgery. Results: Broadly, the applications include; education for health professionals and patients, surgical planning and decisionmaking, custom prostheses, tissue scaffolds, and customised surgical instrument manufacturing. Future directions include bionic prostheses, live tissue grafts, and whole organ printing.
Multi-dimensional range queries in sensor networks

In many sensor networks, data or events are named by attributes. Many of these attributes have scalar values, so one natural way to query events of interest is to use a multi-dimensional range query. An example is: "List all events whose temperature lies between 50° and 60°, and whose light levels lie between 10 and 15. " Such queries are useful for correlating events occurring within the network.In this paper, we describe the design of a distributed index that scalably supports multi-dimensional range queries. Our distributed index for multi-dimensional data (or DIM) uses a novel geographic embedding of a classical index data structure, and is built upon the GPSR geographic routing algorithm. Our analysis reveals that, under reasonable assumptions about query distributions, DIMs scale quite well with network size (both insertion and query costs scale as O(√N)). In detailed simulations, we show that in practice, the insertion and query costs of other alternatives are sometimes an order of magnitude more than the costs of DIMs, even for moderately sized network. Finally, experiments on a small scale testbed validate the feasibility of DIMs.
Impaired Functional Recovery After Stroke in the Stroke-Prone Spontaneously Hypertensive Rat

Background and Purpose— To identify if the stroke-prone spontaneously hypertensive rat (SHRSP) exhibits impaired functional recovery after stroke compared with its normotensive reference strain, the Wistar Kyoto rat (WKY). Methods— In study 1, a 2-mm distal middle cerebral artery occlusion (middle cerebral artery occlusion) was performed in both strains and recovery assessed using a 33-point neurological score. Because SHRSPs displayed much larger infarcts than WKYs, study 2 and study 3 involved extending the length of middle cerebral artery (MCA) occlusion in the WKY to increase the volume and distribution of infarction to comparable levels with SHRSP. Animals were assessed with the neurological score, tapered beam walk, and cylinder tests. Results— In study 1, infarct volume (expressed as a percent of contralateral hemisphere) was WKY 13.1±3% and SHRSP 19.8±1%. Initial neurological deficit was greater (WKY 25±1, SHRSP 22±1, out of a possible 33) and subsequent recovery was poorer in SHRSP. In studies 2 and 3, infarct volume and distribution (study 2, WKY 21.8±1.3%, SHRSP 22.9±3%; study 3, WKY 17.2±2%, SHRSP 16.5±3%) and initial neurological deficit at 2 hours after middle cerebral artery occlusion (study 2 WKY 23±1, SHRSP 22±2; study 3 WKY 25±1 and SHRSP 23±1; mean±SEM) were comparable between strains. However, whereas WKY recovered toward normal scores, SHRSP scored significantly lower 2 weeks (study 2) and 4 weeks (study 3) after middle cerebral artery occlusion. Beam walk data revealed long-term impairment in SHRSP contralateral limb use, compared with WKY, at days 3, 7, and 28 (P<0.05). Conclusions— SHRSP exhibit impaired functional recovery after stroke compared with WKY.
Competing interpretations of computer supported co-operative work.

This paper will investigate the competing discourses between empowerment and control that surrounded the use of Lotus Notes in the UK selling division of a pharmaceuticals company called Compound UK. We will suggest that managing and using Notes in Compound UK was itself a rhetorical accomplishment, and that by focusing on rhetoric we can illuminate some of the contradictions that surround the management and use of the technology. We will also show how the political and normative context is deeply implicated in the reproduction of these competing interpretations. Finally, we will suggest that the introduction of the discourse of empowerment is implicated in changes in the work practices in Compound UK, at least to a minimal degree.
The Cross Product of Interconnection Networks

We study the cross product as a method for generating and analyzing interconnection network topologies for multiprocessor systems. Consider two interconnection graphs G/sub 1/ and G/sub 2/ each with some established properties such as symmetry, low degree and diameter, scalability, simple optimal routing, recursive structure (partitionability), fault tolerance, existence of node-disjoint paths, low cost embedding, and efficient broadcasting. We investigate and evaluate the corresponding properties for the cross product of G/sub 1/ and G/sub 2/ based on the properties of G/sub 1/ and those of G/sub 2/. We also give a mathematical characterization of product families of graphs which are closed under the cross product operation. This investigation is useful in two ways. On one hand, it gives a new tool for further studying some of the known interconnection topologies, such as the hypercube and the mesh, which can be defined using the cross product operation. On the other hand, it can be used in defining and evaluating new interconnection graphs using the cross product operation on known topologies.
Activation of Adenosine 1 Receptors Induces Antidepressant-Like , Anti-Impulsive Effects on Differential Reinforcement of Low-Rate 72s Behavior in Rats

Stress and psychiatric illness have been associated with a dysregulation of glutamatergic neurotransmission. Recently, positive allosteric modulators (PAMs) of the metabotropic glutamate 2 (mGlu2) receptor have been found to exert antidepressant-like activity in rats performing under a differential reinforcement of low rate (DRL) 72-s schedule. An autoreceptor role at glutamatergic synapses is the most salient physiological role played by the mGlu2 receptor. Adenosine A1 receptors play a heteroreceptor role at many of the same forebrain synapses where mGlu2 autoreceptors are found. Agonists and/or PAMs of mGlu2 receptors act similarly to adenosine A1 receptor agonists with respect to a wide range of electrophysiological, biochemical, and behavioral responses mediated by limbic circuitry thought to play a role in the pathophysiology of neuropsychiatric disease and to mediate therapeutic drug effects. Therefore, the role of adenosine A1 receptor activation on rat DRL 72-s behavior was explored to provide preclinical evidence consistent or inconsistent with potential antidepressant effects. The adenosine A1 receptor agonist N -cyclohexyladenosine (CHA) increased the reinforcement rate, decreased the response rate, and induced a rightward shift in inter-response time distributions in a dose-dependent fashion similar to most known antidepressant drugs. The adenosine A1 receptor antagonist 8-cyclopentyl-1,3-dipropylxanthine (DPCPX) blocked these antidepressant-like effects. These novel observations with CHA and DPCPX suggest that activation of adenosine A1 receptors could contribute to antidepressant effects, in addition to previous preclinical reports of anxiolytic and antipsychotic effects. By implication, targeting a dysregulated glutamatergic system may be an important principle in discovering novel antidepressant agents that may also possess anti-impulsive activity.