Miracle-dz/UniFAR-FTUs huggingface dataset:
High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.
Phenomenology of Implantation: The Liminal Body and the Implantable Cardioverter Defibrillator

To prevent sudden cardiac death as a result of fatal arrhythmias, over 1155 implantable cardioverter defibrillators (ICD) were implanted in Australians, in 2001. This represents an increase of 125% in the number of ICDs used in Australia since the previous survey, conducted in 1997. This rapidly expanding biotechnology remains poorly understood by recipients, their family members and by health professionals. Studies of both the effectiveness of ICDs, and their acceptability to patients, have provided equivocal results. Insufficient in-depth research exists to provide direction to health professionals involved in ICD implantation or to provide assistance to recipients and their family members in their decision-making. This study focused on the phenomenon of implantation of a person’s heart with a permanent bioelectronic ICD. Implantation was explored through the existential perspectives of participants from four groups: recipients of ICDs, family members of recipients; cardiac nurses and paramedical personnel; and cardiologists. Hermeneutical phenomenology was considered an appropriate methodology through which to explore the research question because of the humanistic approach that locates implantation within the context of the human Being. Methods of inquiry included unstructured in-depth dialogue, thematic analysis of participants’ lived-through experience, and interpretation by drawing on literature, poetry, art, and idiomatic usage of words relating to the heart. Six themes emerged from the dialogue of the key players in heart implantation with an ICD: implantation as body-liminality; implantation as body-temporality/time; implantation as body-spatiality/movement; implantation as body-emotionality; implantation as body-sexuality/gender; and implantation as body-relationality. After intensive reflection on the existential themes in this study it was necessary to move into a higher level of analysis that would complete the phenomenological journey. The phenomenological journey extended from exploring the phenomenon of heart implantation with an ICD to an understanding of the phenomenon as liminal-Being.
Morphometry of the Human Lung

results of many experiments with much discussion as to their meaning, the questions were of the "I should like to ask Dr. X why he said so and so" variety. In contrast, the questions following the sessions in which the short communications predominated were of the "I should like to present the results of a recent experiment performed in my laboratory" variety. Most interesting among those articles in which the author's recent work is presented is Bullough's paper, in which he discussed his recent experiments with a substance he has isolated from epidermis and which in complex with adrenalin seems to inhibit mitosis in mouse epidermis. He calls this substance "chalone". Also notable was the contribution of Feldman, et al., in which their experiments were described demonstrating the failure of thymectomized mice subjected to total body X-irradiation to reject tumor transplants unless they received regrafts of intact thymuses from either newborn mice or one month old donors. Throughout this volume the reader finds lip service being paid to "Jacob and Monod" (no less than 20 references), "induction and repression," "operon", "derepression", etc. The last section of Prof. Kaplan's closing paper is entitled, "Can we propose testable molecular mechanisms for the neoplastic transformation? " Instead of answering this question directly, Prof. Kaplan proceeds to present an elaborate Jacob and Monod-type model consisting of a "Differentiation Operon" and a "Replication Operon," each induced and repressed by a complex system of interacting inducers, effectors, and repressors. No mention is made of an essentially identical model invoked by Bullough earlier in the conference in his excellent paper on chalone. Although this sort of Model-building is great sport, one would have hoped that Prof. Kaplan and others at this conference would have instead, devoted some thought to the problem of the experimental demonstration of Jacob and Monod's model (documented by them for B-galactosidase in E. coli) in higher organisms. There are, however, no more than numerous invocations of the operon model with no consideration of the monumental difficulties involved in applying this model to mammalian tissues and demonstrating it experimentally. It is difficult at this time to see any useful purpose in publishing such mental gymnastics. This collection of papers probably contains little that is new or useful to the experienced investigator. The review papers should prove of value to the student interested in molecular biology and carcinogenesis. There is a danger, however, that those unfamiliar …
The Effect of Inverse Document Frequency Weights on Indexed Sequence Retrieval

Summary: The IDF (Inverse Document Frequency) weight is a method to calculate a relative weighting factor for words used in natural language text indexing. The purpose of these experiments was to determine the effect of this technique when applied to retrieval of genomic sequences. This paper reports the results of an implementation of the IDF on the NCBI “nt” nucleotide data base and compares the results with other sequence retrieval systems. The implementation discussed here consists of a collection of open-source, C++ programs written for Linux that (1) build an inverted index of all sequences in a data base; (2) calculate a relative weight for each possible tuple of length k; (3) and retrieve, score, and rank, sequences from the data base in response to queries. Retrieval speeds are based primarily on query length rather than data base size.
A Critique of Konrad Lorenz's Theory of Instinctive Behavior

BE EGINNING about 1931, Konrad Lorenz, with his students and collaborators (notably N. Tinbergen), has published numerous behavioral and theoretical papers on problems of instinct and innate behavior which have had a widespread influence on many groups of scientific workers (Lorenz, 1931, 1932, 1935, 1937a; Lorenz and Tinbergen, 1938; Lorenz, 1939; Tinbergen, 1939; Lorenz, 1940, 1941; Tinbergen, 1942, 1948a, 1950; Lorenz, 1950; Tinbergen, 1951). Lorenz's influence is indicated in the founding of the Zeitschrift fur Tierpsychologie in 1937 and in its subsequent development, and also in the journal Behaviour, established in 1948 under the editorship of an international board headed by Tinbergen. Lorenz's theory of instinctive and innate behavior has attracted the interest of many investigators, partly because of its diagrammatic simplicity, partly because of its extensive use of neurophysiological concepts, and partly because Lorenz deals with behavior patterns drawn from the life cycle of the animals discussed, rather than with the laboratory situations most often found in American comparative psychology. These factors go far toward accounting for the great attention paid to the theory in Europe, where most students of animal behavior are zoologists, physiologists, zoo curators or naturalists, unlike the psychologists who constitute the majority of American students of animal behavior (Schneirla, 1945). In recent years Lorenz's theories have attracted more and more attention in the United States as well, partly because of a developing interest in animal behavior among American zoologists and ecologists, and partly through the receptive audience provided for Lorenz and his colleague, Tinbergen, by American ornithologists. The ornithologists were interested from the start, especially because a great part of the material on which Lorenz based his system came from studies of bird behavior, but the range of interest in America has widened considerably. Lorenz and his theories were recently the subject of some discussion at a conference in New York at which zoologists and comparative psychologists were both represented (Riess, 1949), and are prominently represented in the recent symposium on animal behavior of the Society of Experimental Biologists (Armstrong, 1950; Baerends, 1950; Hartley, 1950; Koehler, 1950; Lorenz, 1950; Tinbergen, 1950), and extensively used in several chapters of a recent American handbook of experimental psychology which will be a standard sourcebook for some years to come (Beach, 1951a; Miller, 1951; Nissen, 1951). Because Lorenz's ideas have gained wide attention, and in particular because a critical discussion
Immunotherapy for Lung Cancers

Lung cancer is the leading cause of cancer-related deaths worldwide. Although treatment methods in surgery, irradiation, and chemotherapy have improved, prognosis remains unsatisfactory and developing new therapeutic strategies is still an urgent demand. Immunotherapy is a novel therapeutic approach wherein activated immune cells can specifically kill tumor cells by recognition of tumor-associated antigens without damage to normal cells. Several lung cancer vaccines have demonstrated prolonged survival time in phase II and phase III trials, and several clinical trials are under investigation. However, many clinical trials involving cancer vaccination with defined tumor antigens work in only a small number of patients. Cancer immunotherapy is not completely effective in eradicating tumor cells because tumor cells escape from host immune scrutiny. Understanding of the mechanism of immune evasion regulated by tumor cells is required for the development of more effective immunotherapeutic approaches against lung cancer. This paper discusses the identification of tumor antigens in lung cancer, tumor immune escape mechanisms, and clinical vaccine trials in lung cancer.
Mechanism of magnetism in stacked nanographite: Theoretical study

Antiferromagnetism in stacked nanographite is investigated with using the Hubbard-type model. The A-B stacking is favorable for the hexagonal nanographite with zigzag edges, in order that magnetism appears. Next, we find that the open shell electronic structures can be origins of the decreasing magnetic moment with the decrease of the inter-graphene distance, as experiments on adsorption of molecules suggest.
Studying Neonates’ Language and Memory Capacities with Functional Near-Infrared Spectroscopy

The measurement of newborns’ brain hemodynamic activity has improved our understanding of early cognitive processes, in particular of language acquisition. In this paper, we describe two experimental protocols adapted to study neonates’ speech-processing capacities using functional near-infrared spectroscopy (fNIRS): the block design and the familiarization-recognition design. We review some of their benefits and disadvantages, and refer to research issues that can be explored by means of these protocols. We also illustrate the use of the two experimental designs through representative fNIRS studies that reveal specific patterns of activation of the newborn brain during speech perception, learning of repetition structures, and word recognition.
The Major Research Themes of Big Data Literature: From 2001 to 2016

The paper adopts a citation-based analysis to survey the big data relevant literature from 2001 to 2016 to identify the major research themes over the past decade. Databases of Web of Science (WOS) and Scopus are used to retrieve the relevant articles. The edge-betweenness clustering technique is applied to the citation network that is built from the retrieved data. The major research groups in the big data field are identified via the clustering. A word clouding is used to extract the major research themes of each group by calculating the frequencies of words used in the titles of articles. Eleven major and minor research themes are identified: "cloud computing", "data mining", "MapReduce", "privacy", "social media", "healthcare", "ethics and legal", "surveillance", "geography", "business intelligence", and "bioinformatics". The approaches presented in this paper can also be applied to any scientific or technological field.
Response to: Comment on “Efficacy of 7-Day and 14-Day Triple Therapy Regimens for the Eradication of Helicobacter pylori: A Comparative Study in a Cohort of Romanian Patients”

Objective. This study compared the eradication rates of of Helicobacter pylori (HP) infection by a 7-day and 14-day anti-HP regimen. Materials and Methods. An open, randomized, prospective study was performed to evaluate the response to anti-HP treatment in adult HP-positive patients following a 7-day course (Regimen A) of a proton pump inhibitor in association with clarithromycin and amoxicillin compared to a 14-day course (Regimen B). Gastric biopsies were performed at baseline and two months after anti-HP treatment. Results. Seventy-eight patients aged 18-64 years (28 males, 50 females) diagnosed with HP infection were included. Fifty-two (66.7%) patients received Regimen B and 26 (33.3%) Regimen A. The overall eradication rate was 70.5%. Better treatment response (p < 0.01) was seen in Regimen B (44/52, 84.2% versus 11/26, 42.3%). Significant improvement in histological features was seen in regimen B. There has been significant overall reduction in endoscopic aspects of gastric and duodenal lesions in both regimens. Younger patients ≤35 years had a better response to Regimen B. Better treatment response was seen in women, urban residents, and those with tertiary level of education in both groups. Conclusion. 14-day anti-HP regimen offered a significant better overall eradication of HP in study population.
Self-Assembly of Hydrogels From Elastin-Mimetic Block Copolymers

Abstract : Triblock copolymers have traditionally been synthesized with conventional organic components. However, triblock copolymers could be synthesized by the incorporation of two incompatible protein-based polymers. The polypeptides would differ in their hydrophobicity and confer unique physiochemical properties to the resultant materials. One protein-based polymer, based on a sequence of native elastin, that has been utilized in the synthesis of biomaterials is poly (Valine-Proline-Glycine-Valine- Glycine) or poly(VPGVG) 1. This polypeptide has been shown to have an inverse temperature transition that can be adjusted by non-conservative amino acid substitutions in the fourth position 2. By combining polypeptide blocks with different inverse temperature transition values due to hydrophobicity differences, we expect to produce amphiphilic polypeptides capable of self-assembly into hydrogels. Our research examines the design, synthesis and characterization of elastin-mimetic block copolymers as functional biomaterials. The methods that are used for the characterization include variable temperature 1D and 2D High-Resolution-NMR, cryo-High Resolutions Scanning Electron Microscopy and Differential Scanning Calorimetry.
Time-dependent Transformation of Episodic Memories

Although there has been over a century of research on memory and consolidation, there remains no consensus with respect to the nature of episodic memories over time. This study tests two prominent theories (Standard Consolidation Theory and Trace Transformation Hypothesis), which make opposing predictions as to the quality of remote episodic memory, by investigating memories for film clips. Using true/false questions to test recall immediately, 3 days, and 7 days after encoding, these experiments demonstrate that details (both perceptual and story-line details) are lost, while the gist of memories is maintained over time. These data also suggest that gist and detail may be maintained independently in the brain. These results broaden our understanding of recent and remote memory, and provide support for the transformation view of consolidation. In the future, the transfer of this paradigm to neuroimaging will allow us to investigate the neural basis of episodic memory over time.
The effect of cooperative learning on social networking with creative problem solving process on creative problem solving ability and teamwork skills of pre-service teachers

The purpose of this article is to compare the cooperative learning outcomes on social networking with the creative problem solving process which affected creative problem solving ability and teamwork skills. With the purposive sampling method, 25 pre-service teachers were divided into 5 groups according to three levels of their learning ability clever, medium, and weak. Each group learned by means of cooperative learning on social networking in order to brainstorm and give some suggestions for solving problems to the researcher. Teamwork skills used as research instruments were as follows; solving problem activities and treatment skilled evaluation test. Samples were asked to evaluation themselves and their team after their learning through social networking. The questionnaires, pre-test and post-test were used in this research with the analysis of Arithmetic means, standard deviation and t-test. The result of this research indicated that learners engaged in cooperative learning with creative problem solving method could succeed after having some problems solving. This group of learners all got the higher scores in post-test compared with pre-test showing statistically significant at the . 05 level. Students who engaged in teamwork skills over social networking with creative problem solving ability have statistically significantly higher score than the previous test at 0.5 level.
Pitfalls in Ultralightweight Authentication Protocol Designs

This article introduces prudent engineering practices and offers recommendations to follow, together with typical mistakes to avoid, when designing new ultralightweight authentication protocols. This work can help, as a sanity check, designers of RFID, NFC, and sensor networks based security solutions to improve the security, reliability, and longevity of ultralightweight authentication protocol designs. Additionally, it aims to help reviewers to quickly distinguish what is really new and worthy in a research area that has been flooded lately with proposals of dubious quality.
Datenbanken und Artificial Intelligence BDD-based Dynamic Programming on Tree Decompositions DBAI-TR-2016-95

Dynamic programming on tree decompositions is a well-studied approach for solving computationally hard problems efficiently – given that the input exhibits small treewidth. Usually, implementations rely on tables for storing information, and algorithms specify how tuples are manipulated during traversal of the decomposition. However, a bottleneck of such table-based algorithms is relatively high memory consumption. Binary Decision Diagrams (BDDs) and related concepts have been shown to be very well suited to store information efficiently. In this report we illustrate BDD-based dynamic programming on tree decompositions. We first show algorithms for several well-known NP-complete problems that are fixed-parameter tractable w.r. t treewidth. These algorithms are specified on a logical level in form of set-based formula manipulation operations that are executed directly on the underlying BDD data structure. We then extend our approach to Quantified Boolean Formula (QBF) solving. Since the corresponding decision problem (QSAT) is PSPACE-complete, we require additional machinery. The data structure is extended to nestings of BDDs, which account for quantifier alternations of the QBF instance. Additionally, several algorithm optimizations, including heuristic data structure compression, delayed variable removal and intermediate unsatisfiability checks, are introduced. We develop the prototypical QBF solver dynQBF, that shows to be useful in practice for instances with few quantifier alternations and where the treewidth of the propositional formula does not exceed 50. Compared to state-of-the-art solvers, our system performs well on 2-QBF instances, and we even identify classes of instances that are uniquely solved by dynQBF. 1Institute for Information Systems 184/2, Technische Universität Wien, Favoritenstrasse 9-11, 1040 Vienna, Austria. E-mail: {gcharwat,woltran}@dbai.tuwien. ac.at Acknowledgements: This work has been supported by the Austrian Science Fund (FWF): Y698, P25607, P25518. The authors would like to thank Michael Abseher for his effort on the very efficient htd tree decomposition library. Copyright c © 2016 by the authors Technical Report DBAI-TR-2016-95 2