Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhancement of peri-implant bone formation via parathyroid hormone administration in a rat model at risk for medication-related osteonecrosis of the jaw

Purpose Dental implant-associated medication-related osteonecrosis of the jaw has been frequently reported in patients administered bisphosphonates (BPs) to prevent osteoporosis. The aim of this study was to investigate the effect of intermittent administration of parathyroid hormone (PTH) on peri-implant bone in the maxillae of ovariectomized rats systemically administered BPs. Methods Thirty 8-week-old female Sprague-Dawley rats were randomly divided into 3 groups. The OVX-ZP group included ovariectomized rats administered 60 µg/kg of zoledronate once a week for 6 weeks and 30 µg/kg PTH after implant installation. The OVX-Z group included ovariectomized rats administered 60 µg/kg of zoledronate once a week for 6 weeks and saline after implant installation, and the control group included rats that underwent a sham operation and were then administered saline. Rats were sacrificed 4 weeks after implant placement for histomorphometric and micro-computed tomography (CT) analyses. Results The average bone area percentage was greater in the OVX-ZP group than in the OVX-Z group (53.4%±4.0% vs. 28.9%±9.5%, P=0.01). The bone-to-implant contact ratio was 50.8%±1.4% in the OVX-ZP group and 16.9%±2.4% in the OVX-Z group (P=0.012). The average bone volume ratio as shown on micro-CT was 31.3%±19.8% in the OVX-ZP group and 19.4%±9.3% in the OVX-Z group (P=0.045). The OVX-ZP and OVX-Z groups displayed similar trabecular thickness (0.06±0.004 mm vs. 0.06±0.002 mm) (P>0.05) and trabecular separation (0.21±0.02 mm vs. 0.29±0.13 mm) (P>0.05). However, the number of trabeculae in the OVX-ZP group was significantly higher than that in the OVX-Z group (4.3±1.33/mm3 vs. 2.2±0.19/mm3) (P=0.024). Conclusions The present findings indicate that intermittently-administered PTH can promote peri-implant bone formation and suggest that PTH administration may aid in effective treatment for medication-related osteonecrosis of the jaw after dental implantation.
Fault-tolerant Event Boundary Detection in Wireless Sensor Networks

Event boundary detection is in and of itself a useful application in wireless sensor networks (WSNs). Typically, it includes the detection of a large-scale spatial phenomenon such as the transportation front line of a contamination or the diagnosis of network health. In this paper, we present FEBD, a fully distributed and light-weight Fault-tolerant Event Boundary Detection scheme. FEBD features an enhanced (nonparametric) statistical model that supports localized detection among neighboring nodes. To enhance detection accuracy, FEBD also introduces an error suppression technique prior to the determination of boundary nodes. The proposed scheme shows a much better detection accuracy and fault tolerance properties as compared to the previous models. The proposed FEBD is evaluated by extensive simulations, and presents very good detection accuracy, even when sensor fault probability is as high as 20%.
Supporting Social Network-Based Knowledge Creation

The nature of knowledge creation and innovation is complex. Whatpsilas more, the context in which an individual knowledge workers creates new knowledge often occurs within the construct of social interactions as opposed to in isolation. This research bases on the extant literature review in the domains of social networks and knowledge creation, continues to focus on knowledge creation and the social mechanism. Then the position of knowledge creation between social closure theory and structural hole theory is discussed. Finally this research looks at the relationship between several social network characteristics and knowledge creation and how to create knowledge through social network.
Some Issues in the Automatic Classification of U.S. Patents Working Notes for the AAAI-98 Workshop on Learning for Text Categorization

The classification of U.S. patents poses some special problems due to the enormous size of the corpus, the size and complex hierarchical structure of the classification system, and the size and structure of patent documents. The representation of the complex structure of documents has not received a great deal of previous attention, but we have found it to be an important factor in our work. We are exploring ways to use this structure and the hierarchical relations among patent subclasses to facilitate the classification of patents. Our approach is to derive a vector of terms and phrases from the most important parts of the patent to represent each document. We use both k-nearest-neighbor classifiers and Bayesian classifiers. The k-nearest-neighbor classifier allows us to represent the document structure using the query operators in the Inquery information retrieval system. The Bayesian classifiers can use the hierarchical relations among patent subclasses to select closely related negative examples to train more discriminating classifiers.
Modeling and Visualizing Power Amplification In Fiber Optic Cables

Transverse mode instability in fiber optic cables causes power amplification to exhibit chaotic behavior. Numerical modeling of fiber optic power amplification is extremely computationally expensive. In this paper I work through modeling similar behavior in a simpler system. I also visualize the three-dimensional phase portrait of the system in order to better understand the behavior and hopefully relate it to more well-understood problems.
Application of Convolutional Neural Network to Occurrence Prediction of Rainfall Events in Kyoto

A rainfall occurrence prediction model is developed based on the convolutional neural network algorithm, which is one of the representative machine learning algorithm in image recognition. As an image data, a spatiotemporal data array is created from the time series of related atmospheric variables from multiple ground gauge observation sites. By feeding the atmospheric data array to the CNN algorithm as an input, the algorithm is trained to classify whether there will be rain in a certain lead time, such as 30 minutes or 60 minutes ahead. The trained model shows promising results with 71% of the detection ratio and 0.40 of critical success index for 30-min of prediction lead time. The high false alarm ratio is a remaining task that should be improved in further research. This paper illustrates the basic concept of the developed model and the results from modeling tests with variant model structures and input data combinations.
Phenomena of Removal of Crystal Violet from Wastewater Using Khulays Natural Bentonite

The study investigates the phenomena involved in the crystal violet (CV) removal using the Khulays natural bentonite from the wastewater. The batch technique was utilized for performing the adsorption experiments. The operating systems were used for the investigation of the adsorption behaviour in the study, which included the initial CV concentration, time taken for shaking, the dosage of adsorbent, and the initial solution pH. The Freundlich isotherm framework and the Langmuir data were assessed in the experiment. The study outcome revealed that the equilibrium in the study was reached when shaking takes place for about 40 minutes. Additionally, the data of the sorption revealed that the enhancement of the CV concentration at the start mitigates the percentage of the CV removal as a result of which saturation integration in the Khulays bentonite dye occurs. The initial improvement in the solution pH led to improved CV adsorption. The data achieved at the isotherm adsorption were found adequate with the frameworks of Freundlich isotherm and Langmuir. Along with it, the model of pseudo-second-order kinetics was used to exhibit the adsorption of crystal violet with the Khulays natural bentonite. The Khulays natural bentonite adsorption of CV was demonstrated by the thermodynamic data exhibiting its spontaneous as well as endothermic nature. The study concludes that basic dyes can be effectively removed from the wastewater by the use of Khulays natural bentonite.
Fast and efficient mining for frequent patterns on biological sequence

Biological sequential frequent pattern mining is one of the important research fields in biological sequential data mining. In order to overcome the shortcomings of traditional algorithms, we proposed a fast algorithm SSPM here. We used longer patterns and prefix tree of primary frequent patterns for mining which avoided plenty of irrelevant patterns. The experimental results show that our algorithm could not only improve the performance but also achieve effective mining results.
Further Analysis of XCP Equilibrium Performance

Low analyzes the equilibrium performance of the recently developed eXplicit Control Protocol (XCP) by applying the derived window-based dynamical model. However, Low's window-based dynamic model is too complicated to be used easily. In our previous works, a simple rate-based model is proposed for analyzing XCP's equilibrium performance. Most results that appeared in Low's paper can be easily reproduced by applying our simple dynamic model. Furthermore, we prove that the shuffling parameter γ is no more than the parameter α to achieve high link utilization. In this paper, we derive stringent lower and upper bounds of link utilization provided with the new constraint γ ≤ α . F urther- more, to study the equilibrium performance of networks with the compensation policy, we use the simplest topology of two links in chains. The sufficient conditions of the compensation policy are proposed, and the link utilization with the compensation policy is derived as a root of a cubic equation. Simulation results are used to verify our results. Low's paper. However, the derived window-based dynamic model is so complicated that it can not be used easily. In our previous works (9), a simple rate-based model is proposed for analyzing XCP's equilibrium performance. Most results that appeared in Low's paper can be easily reproduced by applying our simple dynamic model. Furthermore, we prove that the shuffling parameter γ is no more than the parameter α to achieve high link utilization. In this paper, we derive a stringent lower and upper bound of link utilization provided with the new constraint γ ≤ α. Furthermore, to study the equilibrium performance of net- works with the compensation policy, we use the simplest topology of two links in chains. The sufficient conditions of the compensation policy are proposed, and the link utilization with the compensation policy is derived as a root of a cubic equation. Simulation results are used to verify our results. The remainder of the paper is structured as follows. In the next section, XCP, and our previous works are introduced briefly. In Section III, we derive stringent bounds of link utilization based on the constraint γ ≤ α. Then, we study the compensation policy for the network with two links. In section IV, simulations are used to verify our results. Finally, we conclude in Section V.
In Sickness and in Health: Health Care Experiences of Korean Immigrant Older Adults

Author(s): Juhn, Erica | Advisor(s): Kagawa-Singer, Marjorie | Abstract: The purpose of this study was to document the health care experiences of Korean immigrant older adults, 65 years of age or older, living in Los Angeles County, who have health care access through Medicare and/or Medi-Cal, access to a large Korean ethnic enclave, and a diverse social support network. Twelve Korean immigrant older adults were recruited through word-of-mouth via community contacts. Semi-structured qualitative interviews were conducted with individual seniors, with the help of a bilingual, bicultural interpreter. Translated transcripts of the interviews were coded, and domains were identified via a "grounded theory" approach. The themes that emerged were: 1) ambivalence toward Korean primary care doctors, 2) limited health care choices, 3) dependence on a diverse social support network, 4) personal responsibility for one's health, and 5) the idea of enduring difficulties in life and expected health challenges "old age. " Implications of the findings are discussed for service and policy, with attention to the importance of language and culture for this population.
Towards a weighted voting system for Q&A sites

Version: Accepted for publication in the Proceedings of the International Conference on Software Maintenance (ICSM), 2013, IEEE Computer Society. Doi: http://dx.doi. org/10.1109/ICSM.2013. 49 Q&A sites have become popular to share and look for valuable knowledge. Users can easily and quickly access high quality answers to common questions. The main mechanism to label good answers is to count the votes per answer. This mechanism, however, does not consider whether other answers were present at the time when a vote is given. Consequently, good answers that were given later are likely to receive less votes than they would have received if given earlier. In this paper we present a Weighted Votes (WV) metric that gives different weights to the votes depending on how many answers were present when the vote is performed. The idea behind WV is to emphasize the answer that receives most of the votes when most of the answers were already posted. Mining the Stack Overflow data dump we show that the WV metric is able to highlight between 4.07% and 10.82% answers that differ from the most voted ones.
Usefulness of altmetrics for measuring the broader impact of research: A case study using data from PLOS (altmetrics) and F1000Prime (paper tags)

Purpose: Whereas citation counts allow the measurement of the impact of research on research itself, an important role in the measurement of the impact of research on other parts of society is ascribed to altmetrics. The present case study investigates the usefulness of altmetrics for measuring the broader impact of research. Methods: This case study is essentially based on a dataset with papers obtained from F1000. The dataset was augmented with altmetrics (such as Twitter counts) which were provided by PLOS (the Public Library of Science). In total, the case study covers a total of 1,082 papers. Findings: The F1000 dataset contains tags on papers which were assigned intellectually by experts and which can characterise a paper. The most interesting tag for altmetric research is "good for teaching". This tag is assigned to papers which could be of interest to a wider circle of readers than the peers in a specialist area. Particularly on Facebook and Twitter, one could expect papers with this tag to be mentioned more often than those without this tag. With respect to the "good for teaching" tag, the results from regression models were able to confirm these expectations: Papers with this tag show significantly higher Facebook and Twitter counts than papers without this tag. This association could not be seen with Mendeley or Figshare counts (that is with counts from platforms which are chiefly of interest in a scientific context). Conclusions: The results of the current study indicate that Facebook and Twitter, but not Figshare or Mendeley, can provide indications of papers which are of interest to a broader circle of readers (and not only for the peers in a specialist area), and seem therefore be useful for societal impact measurement.
SEMANTICAL CONSIDERATIONS ON FLOYD-HOARE LOGIC

This paper deals with logics of programs. The objective is to formalize a notion of program description and to give both plausible (semantic) and effective (syntactic) criteria for the notion of truth of a description. A novel feature of this treatment is the development of the mathematics underlying Floyd-Hoare axiom systems independently of such systems. Other directions that such research might take are also considered. This paper grew out of, and is intended to be usable as, class notes for an introductory semantics course. The three sections of the paper are: 1) A frame work for the logic of programs. Programs and their partial correctness theories are treated as binary relations on states and formulae respectively. Truth-values are assigned to partial correctness assertions in a plausible (Tarskian) but not directly usable way. 2) Particular Programs. Effective criteria for truth are established for some programs using the Tarskian criteria as a benchmark. This leads directly to a sound, complete, effective axiom system for the theories of these programs. The difficulties involved in finding such effective criteria for other programs are explored. 3) Variations and extensions of the framework. Alternatives to binary relations for both programs and theories are speculated on, and their possible roles in semantics are considered. We discuss a hierarchy of varieties of programs and the importance of this hierarchy to the issues of definability and describability. Modal logic is considered as a first-order alternative to Floyd-Hoare logic. We give an appropriate axiom system which is complete for loop-free programs and also puts conventional predicate calculus in a different light by lumping quantifiers with non-logical assignments rather than treating them as logical concepts.
Revealing the functions of supra-temporal and insular auditory responsive areas in humans

The human auditory sensory area, which includes primary and non-primary auditory cortices, has been considered to locate in the supra-temporal lobe for more than a century. Recently, accumulating evidence shows that the posterior part of insula responses to sounds under non-task states with relevant short latencies. However, whether posterior insula (InsP) contribute to forming auditory sensation remains unclear. Here we addressed this issue by recording and stimulation directly on the supra-temporal and insular areas via intracranial electrodes from 53 epileptic patients. During passive listening to a non-speech sound, the high-γ (60-140 Hz) active rate of InsP (68.8%) was approximate to the non-primary auditory areas (72.4% and 79.0%). Moreover, we could not distinguish InsP from supra-temporal subareas by either activation, latency, temporal pattern or lateral dominance of sound induce high-γ. On the contrary, direct electrical stimulation evoked auditory sensations effectively on supra-temporal subareas (> 65%), while sparsely on InsP (9.49%). The results of cortico-cortical evoked potentials (CCEPs) showed strong bidirectional connectivity within supra-temporal areas, but weak connectivity between supra-temporal areas and InsP. These findings suggest that even the InsP has similar basic auditory response properties to the primary or non-primary cortex, it may not directly participate in the formation of auditory perception.
Thiol efflux mediated by an ABCC-like transporter participates for Trypanosoma cruzi adaptation to environmental and chemotherapeutic stresses

The protozoan Trypanosoma cruzi is the etiologic agent for Chagas disease, which affects 6-7 million people worldwide. The parasite presents high biological diversity, reflecting on the inefficiency of benznidazole in chronic or older patients. ABC superfamily proteins contain active transporters involved in the xenobiotic and endobiotic efflux and overexpressed in MDR cells. An ABCC-like transport was identified in the T. cruzi Y strain, being able to extrude thiol-conjugated compounds. As non-protein thiols represent prime line of defense towards reactive species, ABCC-like activity could participate in the regulation of mediators implicated in responses to cellular stress arising from a variety of stimuli, as environmental or chemotherapeutic. This study shows that T. cruzi ABCC-like protein transports GSH, GSSG and ceramides, all implicated in cellular stress. Hemin, representative from the hematophagous feeding of the vector, was transported as well, suggesting a role for ABCC as a metal-thiol transporter. In addition, all strains evaluated showed ABCC-like activity, while no ABCB1-like activity was detected. Also, results suggest that ABCC-like does not associate to natural resistance to benznidazole, considering that the sensitive strains CL Brener and Berenice showed higher ABCC-like activity than the resistant strains Y and Colombiana. Instead, ABCC-like efflux increased after continuous exposure of Y strain to benznidazole. Moreover, ABCC does not perform direct efflux of drug and its participation in the machinery of protection against stress depends on the efflux of metabolites in conjugation to or in cotransport with thiol.
Implicit modeling of the impact of adsorption on solid surfaces for protein mechanics and activity with a coarse-grain representation

Surface immobilized enzymes play a key role in numerous biotechnological applications such as biosensors, biofuel cells or biocatalytic synthesis. As a consequence, the impact of adsorption on the enzyme structure, dynamics and function needs to be understood on the molecular level as it is critical for the improvement of these technologies. With this perspective in mind, we used a theoretical approach for investigating protein local flexibility on the residue scale that couples a simplified protein representation with an elastic network and Brownian Dynamics simulations. The protein adsorption on a solid surface is implicitly modeled via additional external constraints between the residues in contact with the surface. We first performed calculations on a redox enzyme, bilirubin oxidase (BOD) from M. verrucaria, to study the impact of adsorption on its mechanical properties. The resulting rigidity profiles show that, in agreement with the available experimental data, the mechanical variations observed in the adsorbed BOD will depend on its orientation and its anchor residues (i.e. residues that are in contact with the functionalized surface). Additional calculations on ribonuclease A and nitroreductase shed light on how seemingly stable adsorbed enzymes can nonetheless display an important decrease in their catalytic activity resulting from a perturbation of their mechanics and internal dynamics.
Biophysical characterization of the SARS-CoV-2 spike protein binding with the ACE2 receptor and implications for infectivity

SARS-CoV-2 is a novel highly virulent pathogen which gains entry to human cells by binding with the cell surface receptor – angiotensin converting enzyme (ACE2). We computationally contrasted the binding interactions between human ACE2 and coronavirus spike protein receptor binding domain (RBD) of the 2002 epidemic-causing SARS-CoV-1, SARS-CoV-2, and bat coronavirus RaTG13 using the Rosetta energy function. We find that the RBD of the spike protein of SARS-CoV-2 is highly optimized to achieve very strong binding with human ACE2 (hACE2) which is consistent with its enhanced infectivity. SARS-CoV-2 forms the most stable complex with hACE2 compared to SARS-CoV-1 (23% less stable) or RaTG13 (11% less stable) while occupying the greatest number of residues in the ATR1 binding site. Notably, the SARS-CoV-2 RBD out-competes the angiotensin 2 receptor type I (ATR1) which is the native binding partner of ACE2 by 35% in terms of the calculated binding affinity. Strong binding is mediated through strong electrostatic attachments with every fourth residue on the N-terminus alpha-helix (starting from Ser19 to Asn53) as the turn of the helix makes these residues solvent accessible. By contrasting the spike protein SARS-CoV-2 Rosetta binding energy with ACE2 of different livestock and pet species we find strongest binding with bat ACE2 followed by human, feline, equine, canine and finally chicken. This is consistent with the hypothesis that bats are the viral origin and reservoir species. These results offer a computational explanation for the increased infectivity of SARS-CoV-2 and allude to therapeutic modalities by identifying and rank-ordering the ACE2 residues involved in binding with the virus.