Miracle-dz/UniFAR-FTUs huggingface dataset:
Increased in vivo levels of neurotransmitters to trigeminal motoneurons: Effects on craniofacial bone and TMJ

The results of chronic, in vivo delivery of excitatory and inhibitory neurotransmitter substances upon the craniofacial skeleton are of ongoing interest to clinician and basic scientist alike. Our purpose was to document and compare the effects of biodegradable glycine, glutamate, and thyrotropin‐releasing hormone (TRH) microspheres upon the craniofacial skeleton and TMJ of actively growing rats. Glycine, glutamate, TRH, and blank microspheres were stereotactically implanted in proximity to motoneurons within the trigeminal motor nucleus in order to test the following null hypotheses: (1) neurotransmitter microspheres implanted near trigeminal motoneurons of growing rats have no significant effect on the craniofacial skeleton and temporomandibular joints of implanted animals, and (2) there are no significant differences between the relative effects of glutamate, TRH (excitatory to trigeminal motoneurons), and glycine (inhibitory to trigeminal motoneurons) implants upon the craniofacial skeleton and temporomandibular joint. Fifty male Sprague‐Dawley rats underwent stereotactic neurosurgery at 35 days; five rats each were killed at 14 and 21 days postoperative for data collection and comparison between glycine‐, glutamate‐, TRH‐, blank‐microsphere, and sham‐surgery rats. Glycine rats had significantly (P ≤ 0.05, 0.01) smaller implant‐side cranial dimensions and mandibular condyles, all glycine rats showed increased gracility of implant‐side bones, and deviation of their facial skeleton away from the implant‐side; this was in contrast to the generally larger implant‐side bony structures in both glutamate and TRH rats. The two null hypotheses were both rejected. Due to their inhibitory and excitatory effects upon trigeminal motoneurons, masticatory muscles, and their neuromuscular generation of biomechanical forces that affect bone, the neurotransmitter substances glycine, glutamate, and TRH appear to play an important role in the growth and development of the mammalian craniofacial skeleton and TMJ. Anat Rec 258:369–383, 2000. © 2000 Wiley‐Liss, Inc.
Planning Problems for Graph Structured Data in Description Logics

Motivation The complex structure and increasing size of information that has to be managed in today’s applications calls for flexible mechanisms for storing such information, making it easily and efficiently accessible, and facilitating its change and evolution over time. The paradigm of graph structured data (GSD) [5] has gained popularity recently as an alternative to traditional relational databases that provides more flexibility and thus can overcome the limitations of an a priori imposed rigid structure on the data. Indeed, differently from relational data, GSD do not require a schema to be fixed a priori. This flexibility makes them well suited for many emerging application areas such as managing Web data, information integration, persistent storage in object-oriented software development, or management of scientific data. Concrete examples of models for GSD are RDFS [2], object-oriented data models, and XML. Here we build on recent work that advocates the use of Description Logics (DLs) for managing change in GSD that happens as the result of (agents or users) executing actions [4]. We consider GSD understood in a broad sense, as information represented by means of a node and edge labeled graph, in which the labels convey semantic information. We identify GSD with the finite structures over which DLs are interpreted, and use DL knowledge bases as descriptions of constraints and properties of the data. We express actions using a specially tailored action language in which actions are finite sequences of (possibly conditional) insertions and deletions performed on the extensions of labels. For this setting, the static verification problem, which consists on deciding whether the execution of a given action will preserve some given integrity constraints on any possible GSD, has been studied in [4]. Here we discuss further problems that can be considered as variants of planning, such as deciding whether there is a sequence of actions that leads a given structure into a state where some property (either desired or not) holds, or whether a given sequence of actions leads every structure into a state where some property necessarily holds. We develop algorithms for variations of these problems, and characterize their computational complexity. We refer the reader to [1] for the extended version of this paper, which also includes an extensive discussion of related work.
Tracking the roots of cellulase hyperproduction by the fungus Trichoderma reesei using massively parallel DNA sequencing

Trichoderma reesei (teleomorph Hypocrea jecorina) is the main industrial source of cellulases and hemicellulases harnessed for the hydrolysis of biomass to simple sugars, which can then be converted to biofuels such as ethanol and other chemicals. The highly productive strains in use today were generated by classical mutagenesis. To learn how cellulase production was improved by these techniques, we performed massively parallel sequencing to identify mutations in the genomes of two hyperproducing strains (NG14, and its direct improved descendant, RUT C30). We detected a surprisingly high number of mutagenic events: 223 single nucleotides variants, 15 small deletions or insertions, and 18 larger deletions, leading to the loss of more than 100 kb of genomic DNA. From these events, we report previously undocumented non-synonymous mutations in 43 genes that are mainly involved in nuclear transport, mRNA stability, transcription, secretion/vacuolar targeting, and metabolism. This homogeneity of functional categories suggests that multiple changes are necessary to improve cellulase production and not simply a few clear-cut mutagenic events. Phenotype microarrays show that some of these mutations result in strong changes in the carbon assimilation pattern of the two mutants with respect to the wild-type strain QM6a. Our analysis provides genome-wide insights into the changes induced by classical mutagenesis in a filamentous fungus and suggests areas for the generation of enhanced T. reesei strains for industrial applications such as biofuel production.
Coordinated activation of premotor and ventromedial prefrontal cortices during vicarious reward

The vicarious reward we receive from watching likable others obtaining a positive outcome is a pervasive phenomenon, yet its neural correlates are poorly understood. Here, we conducted a series of functional magnetic resonance imaging experiments to test the hypothesis that the brain areas responsible for action observation and reward processing work in a coordinated fashion during vicarious reward. In the first experiment (manipulation phase), the participant was instructed to cheer for a particular player in a two-player competitive game (Rock–Paper–Scissors). This manipulation made participants feel more unity with that player and resulted in unity-related activation in the premotor area during action observation. In the following main experiment, the participant witnessed the previously cheered-for or non-cheered-for player succeed in a new solitary game (a stopwatch game). The ventromedial prefrontal cortex (vmPFC) was activated when the cheered-for player succeeded in the game but not when the other player did. Interestingly, this vmPFC activation was functionally connected with premotor activation only during the cheered-for player’s success. These results suggest that vicarious reward is processed in the vmPFC-premotor network, which is activated specifically by the success of the other person with whom the individual feels unity and closeness.
ADOLESCENT MEDICINE

A disturbing observation is the recent increase in the use of LSD and other hallucinogens by younger adolescents. Almost 90% of high school seniors in 1992 reported some experience with alcohol in the past. In 1991, some of the highest rates of gonorrhea were among adolescents aged 15 to 19 years.
A Formalization of Kant's Second Formulation of the Categorical Imperative

We present a formalization and computational implementation of the second formulation of Kant's categorical imperative. This ethical principle requires an agent to never treat someone merely as a means but always also as an end. Here we interpret this principle in terms of how persons are causally affected by actions. We introduce Kantian causal agency models in which moral patients, actions, goals, and causal influence are represented, and we show how to formalize several readings of Kant's categorical imperative that correspond to Kant's concept of strict and wide duties towards oneself and others. Stricter versions handle cases where an action directly causally affects oneself or others, whereas the wide version maximizes the number of persons being treated as an end. We discuss limitations of our formalization by pointing to one of Kant's cases that the machinery cannot handle in a satisfying way.
Fault-tolerant control for a class of non-linear systems with dead-zone

In this paper, a fault-tolerant control scheme is proposed for a class of single-input and single-output non-linear systems with the unknown time-varying system fault and the dead-zone. The non-linear state observer is designed for the non-linear system using differential mean value theorem, and the non-linear fault estimator that estimates the unknown time-varying system fault is developed. On the basis of the designed fault estimator, the observer-based fault-tolerant tracking control is then developed using the backstepping technique for non-linear systems with the dead-zone. The stability of the whole closed-loop system is rigorously proved via Lyapunov analysis and the satisfactory tracking control performance is guaranteed in the presence of the unknown time-varying system fault and the dead-zone. Numerical simulation results are presented to illustrate the effectiveness of the proposed backstepping fault-tolerant control scheme for non-linear systems.
A Multithickness Sea Ice Model Accounting for Sliding Friction

A multithickness sea ice model explicitly accounting for the ridging and sliding friction contributions to sea ice stress is developed. Both ridging and sliding contributions depend on the deformation type through functions adopted from the Ukita and Moritz kinematic model of floe interaction. In contrast to most previous work, the ice strength of a uniform ice sheet of constant ice thickness is taken to be proportional to the ice thickness raised to the 3/2 power, as is revealed in discrete element simulations by Hopkins. The new multithickness sea ice model for sea ice stress has been implemented into the Los Alamos “CICE” sea ice model code and is shown to improve agreement between model predictions and observed spatial distribution of sea ice thickness in the Arctic.
Microsatellite Repeat Instability Fuels Evolution of Embryonic Enhancers in Hawaiian Drosophila

For ∼30 million years, the eggs of Hawaiian Drosophila were laid in ever-changing environments caused by high rates of island formation. The associated diversification of the size and developmental rate of the syncytial fly embryo would have altered morphogenic gradients, thus necessitating frequent evolutionary compensation of transcriptional responses. We investigate the consequences these radiations had on transcriptional enhancers patterning the embryo to see whether their pattern of molecular evolution is different from non-Hawaiian species. We identify and functionally assay in transgenic D. melanogaster the Neurogenic Ectoderm Enhancers from two different Hawaiian Drosophila groups: (i) the picture wing group, and (ii) the modified mouthparts group. We find that the binding sites in this set of well-characterized enhancers are footprinted by diverse microsatellite repeat (MSR) sequences. We further show that Hawaiian embryonic enhancers in general are enriched in MSR relative to both Hawaiian non-embryonic enhancers and non-Hawaiian embryonic enhancers. We propose embryonic enhancers are sensitive to Activator spacing because they often serve as assembly scaffolds for the aggregation of transcription factor activator complexes. Furthermore, as most indels are produced by microsatellite repeat slippage, enhancers from Hawaiian Drosophila lineages, which experience dynamic evolutionary pressures, would become grossly enriched in MSR content.
Impact of the supplementation of kidney mass on blood pressure and progression of kidney disease.

BACKGROUND To test the hypothesis that nephron mass is an independent determinant of arterial pressure, the effects of augmenting renal mass by isograft transplantation were studied in the model of secondary hypertension. METHODS The effects of isograft transplantation or sham operation on blood pressure, proteinuria, remnant kidney mass, glomerular filtration rate and glomerulosclerosis were assessed in 5/6 nephrectomized (5/6 NPX) rats. RESULTS Systolic blood pressure was lowered on average by approximately 35 mmHg and glomerular hyperfiltration was attenuated in the remnant kidneys of transplant recipients. Markedly lower urinary protein excretion rates and glomerulosclerosis scores in the remnant kidney accompanied these supplemental transplants to values roughly one-third of those from sham-operated rats. CONCLUSIONS The data show that reduced renal mass per se is the major factor in the development and maintenance of arterial hypertension and glomerular injury in 5/6 NPX rats and these changes can be reversed by supplementing renal mass. The data provide strong support for the notion that renal mass is a significant, independent determinant of arterial pressure.
Kollector: transcript-informed, targeted de novo assembly of gene loci

Motivation: Despite considerable advancements in sequencing and computing technologies, de novo assembly of whole eukaryotic genomes is still a time‐consuming task that requires a significant amount of computational resources and expertise. A targeted assembly approach to perform local assembly of sequences of interest remains a valuable option for some applications. This is especially true for gene‐centric assemblies, whose resulting sequence can be readily utilized for more focused biological research. Here we describe Kollector, an alignment‐free targeted assembly pipeline that uses thousands of transcript sequences concurrently to inform the localized assembly of corresponding gene loci. Kollector robustly reconstructs introns and novel sequences within these loci, and scales well to large genomes—properties that makes it especially useful for researchers working on non‐model eukaryotic organisms. Results: We demonstrate the performance of Kollector for assembling complete or near‐complete Caenorhabditis elegans and Homo sapiens gene loci from their respective, input transcripts. In a time‐ and memory‐efficient manner, the Kollector pipeline successfully reconstructs respectively 99% and 80% (compared to 86% and 73% with standard de novo assembly techniques) of C.elegans and H.sapiens transcript targets in their corresponding genomic space using whole genome shotgun sequencing reads. We also show that Kollector outperforms both established and recently released targeted assembly tools. Finally, we demonstrate three use cases for Kollector, including comparative and cancer genomics applications. Availability and Implementation: Kollector is implemented as a bash script, and is available at https://github.com/bcgsc/kollector Contact: ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.
First-principles study of He effects in a bcc Fe grain boundary: site preference, segregation and theoretical tensile strength

We perform a first-principles calculation to investigate the effects of He in an Fe Σ5(310)/[001] grain boundary (GB) with the SIESTA code, for which the reliability of the pseudopotential and the basis set are systematically tested. We calculate the formation and segregation energies for different substitutional and interstitial cases in order to determine the site preference and the segregation properties of He in the Fe GB. It is demonstrated that the He segregation either breaks (substitution) or weakens (interstitial) the surrounding interfacial Fe–Fe bonds, leading to the GB tensile strength reduction.
Timing of subduction initiation, arc formation, ophiolite obduction and India–Asia collision in the Himalaya

Abstract Reconstruction of the Western Himalaya requires three subduction systems operating beneath the Spong arc, Dras–Kohistan arc and the Asian continent during the Late Cretaceous–Paleocene. The timing of the closure of the Neo-Tethys Ocean along the Indus Suture Zone (ISZ) in Ladakh and south Tibet has been proposed to be as old as c. 65 Ma and as young as c. 37 Ma. The definition of the India–Asia collision can span >15 myr from the first touching of Indian continental crust with Asian crust to the final marine sedimentation between the two plates. There is good geological evidence for a Late Cretaceous–Early Paleocene phase of folding, thrusting and crustal thickening of Indian Plate shelf carbonates associated with obduction of ophiolites. There is no geological evidence of any oceanic ‘Greater Indian Basin’ separating the northern Tethyan and Greater Himalaya from India. There is clear evidence to support final ending of marine sedimentation along the ISZ at 50 Ma (planktonic foraminifera zone P7–P8). There is no evidence for diachroneity of collision along the Pakistan–Ladakh–South Tibet Himalaya. The timing of ultrahigh-pressure metamorphism cannot be used to constrain India–Asia collision, and the timing of high-grade kyanite- and sillimanite-grade metamorphism along the Greater Himalaya can only give a minimum age of collision.
Effects of Fishing and Fishing Closures on Beach Clams: Experimental Evaluation across Commercially Fished and Non-Fished Beaches before and during Harvesting

Management responses to reconcile declining fisheries typically include closed areas and times to fishing. This study evaluated this strategy for a beach clam fishery by testing the hypothesis that changes in the densities and size compositions of clams from before to during harvesting would differ between commercially fished and non-fished beaches. Sampling was spatially stratified across the swash and dry sand habitats on each of two commercially fished and two non-fished beaches, and temporally stratified across three six-week blocks: before, early and late harvesting. Small-scale spatio-temporal variability in the densities and sizes of clams was prevalent across both habitats and the components of variation were generally greatest at the lowest levels examined. Despite this, differences in the densities and sizes of clams among individual beaches were evident, but there were few significant differences across the commercially fished versus non-fished beaches from before to during harvesting. There was no evidence of reduced densities or truncated size compositions of clams on fished compared to non-fished beaches, contrasting reports of some other organisms in protected areas. This was probably due to a combination of factors, including the current levels of commercial harvests, the movements and other local-scale responses of clams to ecological processes acting independently across individual beaches. The results identify the difficulties in detecting fishing-related impacts against inherent levels of variability in clam populations. Nevertheless, continued experimental studies that test alternate management arrangements may help refine and determine the most suitable strategies for the sustainable harvesting of beach clams, ultimately enhancing the management of sandy beaches.
Graph Data Management: Techniques and Applications

Graph Data Management: Techniques and Applications is a central reference source for different data management techniques for graph data structures and their application. This book discusses graphs for modeling complex structured and schemaless data from the Semantic Web, social networks, protein networks, chemical compounds, and multimedia databases and offers essential research for academics working in the interdisciplinary domains of databases, data mining, and multimedia technology.
A Hybrid Approach to Chinese Word Segmentation around CRFs

In this paper, we present a Chinese word segmentation system which is consisted of four components, i.e. basic segmentation, named entity recognition, error-driven learner and new word detector. The basic segmentation and named entity recognition, implemented based on conditional random fields, are used to generate initial segmentation results. The other two components are used to refine the results. Our system participated in the tests on open and closed tracks of Beijing University (PKU) and Microsoft Research (MSR). The actual evaluation results show that our system performs very well in MSR open track, MSR closed track and PKU open track.
A multitheoretical approach for solving trust problems in B2C e-commerce

Trust has been identified as a major barrier in online shopping, especially in the B2C e-commerce model. It has been studied for several years, but there is no indicator that a satisfactory solution for trust in online shopping has been achieved. A trust model is proposed in this paper in order to address this issue. It is uniquely based on five current issues (cybercrime, security, control, web interface, and a trusted third party) that impact trust, guided by four supportive theories: Semiotics, Trust in Signs, Simmelian Model of Trust and Trustworthiness. The research was accomplished with an online survey to collect data from online shoppers around the world. Structural Equation Modelling (SEM) was used to validate the trust model revealing that privacy and security of information are most important factors affecting trust in B2C e-commerce followed by web interface and control.