Miracle-dz/UniFAR-FTUs huggingface dataset:
A Corpus of Textual Revisions in Second Language Writing

This paper describes the creation of the first large-scale corpus containing drafts and final versions of essays written by non-native speakers, with the sentences aligned across different versions. Furthermore, the sentences in the drafts are annotated with comments from teachers. The corpus is intended to support research on textual revision by language learners, and how it is influenced by feedback. This corpus has been converted into an XML format conforming to the standards of the Text Encoding Initiative (TEI).
Plant MetGenMAP: An Integrative Analysis System for Plant Systems Biology1[W][OA]

The information and resources generated from diverse “omics” technologies provide opportunities for producing novel biological knowledge. It is essential to integrate various kinds of biological information and large-scale omics data sets through systematic analysis in order to describe and understand complex biological phenomena. For this purpose, we have developed a Web-based system, Plant MetGenMAP, which can comprehensively integrate and analyze large-scale gene expression and metabolite profile data sets along with diverse biological information. Using this system, significantly altered biochemical pathways and biological processes under given conditions can be retrieved rapidly and efficiently, and transcriptional events and/or metabolic changes in a pathway can be easily visualized. In addition, the system provides a unique function that can identify candidate promoter motifs associated with the regulation of specific biochemical pathways. We demonstrate the functions and application of the system using data sets from Arabidopsis (Arabidopsis thaliana) and tomato (Solanum lycopersicum), respectively. The results obtained by Plant MetGenMAP can aid in a better understanding of the mechanisms that underlie interesting biological phenomena and provide novel insights into the biochemical changes associated with them at the gene and metabolite levels. Plant MetGenMAP is freely available at http://bioinfo.bti. cornell.edu/tool/MetGenMAP.
Stabilizing factors in spatially structured food webs

Ecological models have problems showing the positive relationship between diversity and stability found in nature. Theory states that complex food webs have high extinction risks and low stability. However, persistent food webs found in nature are large and complex containing many interconnections between species. There are many possible mechanisms enabling persistent food webs such as; complex interaction patterns, asynchronous fluctuations of species densities, environmental fluctuations and spatial distribution. These factors have not been used in classical models. In this study, coloured environmental 1/f noise and dispersal between subpopulations were incorporated into a diamond shaped food web based on a model by Vasseur and Fox 2007. Contradictions between theoretical and empirical results regarding food webs can be resolved by detailed analyses of models, withholding stabilizing mechanisms. Weak environmental 1/f noise generated an increased coefficient of stability but the stabilizing effect of noise can be questioned because of a decreased mean food web biomass and reduced stabilizing effect when reddened. However, detailed studies of the food web revealed that noise can redistribute density proportions between species, evading lowest species density and thereby increase food web resistance to demographic stochasticity and catastrophes. Noise induced density proportion shifts imply that large population sizes are no insurance towards future increase in environmental variance. Synchrony of species environmental responses and dispersal between subpopulations can both have major influences on stability and extinction risk of smaller food webs indicating that spatial structure could be one of the dominating factors stabilizing complex food webs found in nature.
A corpus-based concatenative Mandarin singing voice synthesis system

A Mandarin singing voice synthesis (SVS) system is proposed in this paper. It generates a Mandarin song of an artificial singer based on the lyric and the music score information embedded in a MIDI file of the song. To get good quality of the song, two modules are presented, i.e., the synthesis unit selection module and the prosody and amplitude modification module. In the synthesis unit selection module, the corpus that complies with the lyric and closest to the music score information is selected. Then, an adaptive filter based prosody and amplitude modification algorithms are employed on the selected synthesis units. Through the proposed method, the system can synthesis any Mandarin singing voice on-the-fly by providing it the corpus of all syllables for male and female respectively. To increase the efficiency of the system, a preprocessing is also taken on the corpus. Finally, a subjective evaluation based on MOS is taken on the system and the synthesized sounds show good quality.
Is vulval erosive lichen planus a premalignant condition?

A 58-year-old woman presented to the Vulval Dermatology Clinic with a 4-month history of vulval burning and irritation. Her quality of life was significantly affected: she reported pain while urinating, was unable to wear certain clothing, and experienced dyspareunia. Treatment for thrush using over-the-counter medications had resulted in worsening symptoms. Examination showed tender erythematous erosions with a white border, located at the vaginal introitus. These lesions were tender. Inspection of the oral cavity revealed bilateral lacy white plaques on the buccal mucosa. The oral lesions were asymptomatic. Biopsy from the edge of a vulval erosion was in keeping with the clinical diagnosis of erosive lichen planus. The patient was counseled about the possible risk of squamous cell carcinoma (SCC) of the vulva, which is associated with the condition. She asked about the magnitude of that risk, but we were unable to give an exact figure. This prompted our review of the literature. Erosive lichen planus is an uncommon, chronic inflammatory condition mainly affecting the mucosal surfaces of the mouth and genitalia. It is thought to be an autoimmune disorder with T cell–mediated damage to basal keratinocytes. Vulval erosive lichen planus (ELPV) causes painful erosions and scarring of the vulva and vagina. Some researchers have postulated on the basis of case reports that ELPV lesions may develop into SCC. However, ELPV is underresearched and evidence from larger-scale studies is lacking. This critically appraised topic aims to evaluate the evidence to determine whether ELPV is associated with an increased risk of vulval SCC.
BIFIDOBACTERIA AND LACTOBACILLI EXHIBITED DIFFERENT MITOGENIC ACTIVITY ON MURINE SPLENOCYTES

Forty-one strains of Bifidobacterium and Lactobacillus were tested for their ability to induce the proliferation of murine splenocytes using the MTT assay. The tested bifidobacteria induced the apparent proliferation of the murine splenocytes in a strain-dependent manner, while non of the tested lactobacilli showed any mitogenic activity. The bifidobacteria from allergic infants stimulated the proliferation of murine splenyoctes more than those from healthy subjects. On the otherhand, no significant differences were observed in the ability among the selected bifidobacteria and lactobacilli to alter Concanavalin A stimulated proliferation of murine splenyocytes. These results suggest that lactobacilli and bifidobacteria may, at least partly, posses a different potential in the way by which they can affect human immune responses.
Advanced physical optical model for simulating rainbows

It is difficult to get accurate phase functions of water drops for simulating rainbows in ray tracers. Sadeghi's model calculates the phase functions of drops based on geometric optics and does some extra work to match the prediction of Lorenz-Mie theory, which is the most accurate solution currently to predict phase function of small spherical particles. The model is applied to ellipsoidal drops, which are difficult for Lorenz-Mie theory. Inspired by this model, an advanced physical optical model for simulating rainbows is implemented on PBRT in this paper. In the original model, when the phase function of a water drop is simulated with insufficient rays, the performance near the rainbow angles is poor. Our proposed model improves it by replacing bilinear interpolation with triangle interpolation and improving the intensity algorithm, which are more accurate near the rainbow angles and more efficient. Even with relatively insufficient rays, the accuracies near the rainbow angles in our model are still acceptable to a certain extent. The experimental results demonstrate that our model outperforms the original model.
Effects of food availability and administration of orexigenic and anorectic agents on elevated ethanol drinking associated with drinking in the dark procedures.

BACKGROUND Drinking in the dark (DID) procedures have recently been developed to induce high levels of ethanol drinking in C57BL/6J mice, which result in blood ethanol concentrations reaching levels that have measurable affects on physiology and/or behavior. The present study determined if increased ethanol drinking associated with DID procedures may be motivated by caloric need rather than by the postingestive pharmacological effects of ethanol. To this end, food availability was manipulated or mice were given peripheral administration of orexigenic or anorectic agents during DID procedures. METHODS C57BL/6J had 2-hours of access to the 20% (v/v) ethanol solution beginning 3-hours into the dark cycle on days 1 to 3, and 4-hours of access to the ethanol bottle on day 4 of DID procedures. In Experiment 1, the effects of food deprivation on ethanol consumption during DID procedures was assessed. In Experiments 2 and 3, mice were given intraperitoneal (i.p.) injection of the orexigenic peptide ghrelin (0, 10 or 30 mg/kg) or the anorectic protein leptin (0 or 20 microg/g), respectively, before access to ethanol on day 4 of DID procedures. In Experiment 4, hourly consumption of food and a 0.05% saccharin solution were assessed over a period of hours that included those used with DID procedures. RESULTS Consistent with previous research, mice achieved blood ethanol concentrations (BECs) that ranged between 100 and 150 mg% on day 4 of DID experiments. Neither food deprivation nor administration of orexigenic or anorectic compounds significantly altered ethanol drinking with DID procedures. Interestingly, mice exhibited their highest level of food and saccharin solution consumption during hours that overlapped with DID procedures. CONCLUSIONS The present observations are inconsistent with the hypothesis that C57BL/6J mice consume large amounts of ethanol during DID procedures in order to satisfy a caloric need.
Check It, Change It: A Community-Based, Multifaceted Intervention to Improve Blood Pressure Control

Background—Although home blood pressure (BP) monitoring interventions have shown potential in selected populations, it is unclear whether such strategies can be generalized. We sought to determine whether a multifaceted BP control program that uses a web-based health portal (Heart360), community health coaches, and physician assistant guidance could improve hypertension control in a diverse community setting. Methods and Results—Between September 12, 2010, and November 11, 2011 Check It, Change It, a community-based hypertension quality improvement program, enrolled 1756 patients with hypertension from 8 clinics in Durham County, NC. The Check It, Change It community intervention was evaluated using a prepost study design without a concurrent control. Participants were stratified into 3 tiers according to their initial BP: tier 0 (BP <140/90 mm Hg)=51% of population, tier 1 (BP=140/90–159/99 mm Hg)=30% of total, and tier 2 (BP ≥159/99 mm Hg)=19% of total. Overall, median age was 59 years (interquartile range, 49–69), 67% were female, and 76% black. After 6 months, the mean overall systolic BP declined 4.7 mm Hg. Rates of achieving target BP control (<140/90) increased overall from 51% at baseline to 63% by 6 months, and 69% had either reached their BP target or had reduced their baseline systolic BP by 10 mm Hg or more. Conclusions—A multicomponent-tiered hypertension program was associated with improved BP control in a diverse community-based population.
Relative influence of surface topography and surface chemistry on cell response to bone implant materials. Part 2: Biological aspects

Abstract A current medical challenge is the replacement of tissue which can be thought of in terms of bone tissue engineering approaches. The key problem in bone tissue engineering lies in associating bone stem cells with material supports or scaffolds that can be implanted in a patient. Beside bone tissue engineering approaches, these types of materials are used daily in orthopaedics and dental practice as permanent or transitory implants such as ceramic bone filling materials or metallic prostheses. Consequently, it is essential to better understand how bone cells interact with materials. For several years, the current authors and others have developed in vitro studies in order to elucidate the mechanisms underlying the response of human bone cells to implant surfaces. This paper reviews the current state of knowledge and proposes future directions for research in this domain.
The effect of inflammation and its reduction on brain plasticity in multiple sclerosis: MRI evidence

Brain plasticity is the basis for systems‐level functional reorganization that promotes recovery in multiple sclerosis (MS). As inflammation interferes with plasticity, its pharmacological modulation may restore plasticity by promoting desired patterns of functional reorganization. Here, we tested the hypothesis that brain plasticity probed by a visuomotor adaptation task is impaired with MS inflammation and that pharmacological reduction of inflammation facilitates its restoration. MS patients were assessed twice before (sessions 1 and 2) and once after (session 3) the beginning of Interferon beta (IFN beta), using behavioural and structural MRI measures. During each session, 2 functional MRI runs of a visuomotor task, separated by 25‐minutes of task practice, were performed. Within‐session between‐run change in task‐related functional signal was our imaging marker of plasticity. During session 1, patients were compared with healthy controls. Comparison of patients' sessions 2 and 3 tested the effect of reduced inflammation on our imaging marker of plasticity. The proportion of patients with gadolinium‐enhancing lesions reduced significantly during IFN beta. In session 1, patients demonstrated a greater between‐run difference in functional MRI activity of secondary visual areas and cerebellum than controls. This abnormally large practice‐induced signal change in visual areas, and in functionally connected posterior parietal and motor cortices, was reduced in patients in session 3 compared with 2. Our results suggest that MS inflammation alters short‐term plasticity underlying motor practice. Reduction of inflammation with IFN beta is associated with a restoration of this plasticity, suggesting that modulation of inflammation may enhance recovery‐oriented strategies that rely on patients' brain plasticity. Hum Brain Mapp 37:2431–2445, 2016. © 2016 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.
The influence of local- and landscape-scale processes on spatial self-organization in estuarine ecosystems

Summary Complexity theory proposes that spatial self-organization, the process whereby small-scale, localized interactions among the components of a system generate complex spatial structures at large spatial scales, explains the formation of autogenic spatial patterns in ecosystems. We question this premise by reviewing three estuarine ecosystems – mussel beds, mudflats and salt marshes – where self-organization has been put forward to explain spatial patterns. Our review highlights that these self-organized estuarine systems are shaped by the combination of small-scale interactions between ecological and physical processes on the one hand, and large-scale physical forcing on the other. More specifically, local interactions generate patchiness at small spatial scales, whereas landscape forcing determines the shape and orientation of these patches in the landscape. We present a framework that illustrates how self-organized ecosystems are shaped by interactions between organisms and physical processes occurring at multiple spatial scales. Moreover, the present review of estuarine systems underlines that scale-dependent feedbacks are capable of explaining spatial patterns that are much more complex than the regular patterns to which they have been applied so far.
Lie Algebra-Based Kinematic Prior for 3D Human Pose Tracking

We propose a novel kinematic prior for 3D human pose tracking that allows predicting the position in subsequent frames given the current position. We first define a Riemannian manifold that models the pose and extend it with its Lie algebra to also be able to represent the kinematics. We then learn a joint Gaussian mixture model of both the human pose and the kinematics on this manifold. Finally by conditioning the kinematics on the pose we are able to obtain a distribution of poses for subsequent frames that which can be used as a reliable prior in 3D human pose tracking. Our model scales well to large amounts of data and can be sampled at over 100,000 samples/second. We show it outperforms the widely used Gaussian diffusion model on the challenging Human3.6M dataset.
Treatment discontinuation and clinical outcomes in the 1-year naturalistic treatment of patients with schizophrenia at risk of treatment nonadherence

Background: This study aimed to improve physicians’ understanding of the treatment circumstances and needs of outpatients with schizophrenia at risk of nonadherence, by naturalistically assessing antipsychotic treatment patterns, clinical outcomes, and health care service use in this little-studied patient population. Methods: In this one-year, prospective, multicenter, noninterventional, observational study, patients considered at risk of nonadherence by their physicians were switched from their primary oral antipsychotic to another oral or a depot antipsychotic at study entry. All cause treatment discontinuation (antipsychotic switch, augmentation, or discontinuation) during the study was assessed using Kaplan–Meier survival analyses and descriptive statistics. Patients’ illness severity, quality of life, attitude towards medication, patient-reported adherence, and health care resource utilization were assessed during the study. Results: Of the 406 enrolled patients, 43 (10.6%) were switched to depot and 363 (89.4%) were switched to oral antipsychotics at study entry. During the study, 99 (24.4%) patients switched, augmented, or discontinued their antipsychotic (all cause treatment discontinuation). Of the 99 patients who switched, augmented, or discontinued their antipsychotic, 8 (18.6%) were taking depot and 91 (25.0%) were taking oral antipsychotics. These patients were switched to either depot (n = 15) or oral (n = 78) antipsychotics, or discontinued their antipsychotic medication (n = 6). Inadequate response was the most frequently reported reason for medication discontinuation. During the study, patients’ clinical and functional status improved significantly and service use was low. Most patients considered themselves to be adherent at study entry, and this favorable self-perception increased during the study (from 68.5% to 88.1%). Conclusion: Although identified as at risk of nonadherence, few patients in this naturalistic study discontinued their prescribed antipsychotic medication during the study. The discrepancy between the physicians’ perception of their patient’s medication adherence and the patients’ self-perceived adherence highlights the need to better understand the underlying reasons for this phenomenon.
Synthesis of tetanus toxin fragment C in insect cells by use of a baculovirus expression system

The baculovirus expression vector p36C was used to express in cells of the insect Spodoptera frugiperda fragment C of tetanus toxin under the control of the strong polyhedrin promoter. Fragment C was expressed intracellularly at a high level and was soluble, allowing it to be purified by affinity chromatography with monoclonal antibody TT08. Purified fragment C from baculovirus was used to immunize mice and was shown to successfully prevent the symptoms of tetanus following a toxin challenge. The ganglioside-binding properties of baculovirus-derived fragment C were compared with those of intact tetanus toxin and native fragment C and were found to be dissimilar.
Sustained Currents Through ASIC3 Ion Channels at the Modest pH Changes That Occur During Myocardial Ischemia

Acid-sensing ion channel 3 (ASIC3) is highly expressed on sensory neurons that innervate heart and skeletal muscle and, therefore, is proposed to detect lactic acidosis and to transduce angina and muscle ischemic pain. A difficulty with this idea is that ASIC3 rapidly desensitizes. How can a desensitizing ion channel mediate a persisting sensation such as angina? Here, we show that rat ASIC3 produces a sustained current within the limited range of extracellular pH (7.3 to 6.7) that occurs during cardiac and skeletal muscle ischemia; experiments use patch clamp on transfected cell lines and on fluorescently tagged sensory neurons that innervate rat heart. No such sustained current occurs with ASIC1a (either as homomers or 1a/3 heteromers), whereas ASIC2a/3 heteromers give much larger currents than ASIC3 homomers. The sustained current persists even over tens of minutes because it is caused by a region of pH where there is overlap between inactivation and activation of the channel. Lactate, an anaerobic metabolite, allows the current to activate at slightly more basic pH. Surprisingly, amiloride, which blocks ASICs when they are activated at lower pH, increases ASIC3 current evoked at pH 7.0. Cardiac sensory neurons exhibit a small, perfectly sustained current when pH changes from 7.4 to 7.0. At least some of this current is carried by ASICs because the current is increased by both Zn2+, an ASIC modulator, and amiloride. We suggest that this sustained mode is the most relevant form of ASIC3 gating for triggering angina and other ischemic pain.
Measuring performance of processor instructions and operating system services in soft processor based systems

A flexible execution time benchmarking hardware setup for performance measurements at processor instruction and operating system level is presented, and the issues of methodology of measuring execution times inside operating systems running on modern processors is discussed. The benchmarking setup was implemented and the measurements were carried out in a system powered by a NIOS II soft processor and running the Micrium μC/OS-II operating system. Slight modifications to both the processor (adding custom instructions) and the operating system (adding alternative implementation of some system services) have been made. The goal of that study (published earlier) was to characterize quantitatively the performance changes made in interest of accelerating the execution of some operating system services. Because of the architectural solutions in both the hardware and the system software, special care was devoted towards providing clean measurement conditions. The basic building stone of the measurement setup is a hardware module connected to the processor in a way which minimizes the interference with the hardware operation. The control of the module is realized in instruction set architecture level and in operating system level, with the possibility of future extensions.