Miracle-dz/UniFAR-FTUs huggingface dataset:
Chemically mediated behavior of recruiting corals and fishes: A tipping point that may limit reef recovery

Corals and reef fish choose nice homes Young animals tend to disperse into new habitats. Can we use populations in protected areas to colonize nearby recovering or overused habitats? It seems that for corals and reef fish, the answer may be no. Dixson et al. show that dispersing juvenile corals and reef fish were overwhelmingly attracted to healthy reefs but were repelled by seaweeds that colonize degraded reefs (see the Perspective by Bruno). Thus, even species that appear passive in their choice of habitat may have stronger preferences than we thought. Science, this issue p. 892; see also p. 879 Juvenile corals and reef fish are attracted by chemical signals of healthy reefs, preventing settlement in degraded areas. [Also see Perspective by Bruno] Coral reefs are in global decline, converting from dominance by coral to dominance by seaweed. Once seaweeds become abundant, coral recovery is suppressed unless herbivores return to remove seaweeds, and corals then recruit. Variance in the recovery of fishes and corals is not well understood. We show that juveniles of both corals and fishes are repelled by chemical cues from fished, seaweed-dominated reefs but attracted to cues from coral-dominated areas where fishing is prohibited. Chemical cues of specific seaweeds from degraded reefs repulsed recruits, and cues from specific corals that are typical of healthy reefs attracted recruits. Juveniles were present at but behaviorally avoided recruiting to degraded reefs dominated by seaweeds. For recovery, degraded reefs may need to be managed to produce cues that attract, rather than repel, recruiting corals and fishes.
ALTERNATING MINIMAL ENERGY METHODS FOR LINEAR SYSTEMS IN HIGHER DIMENSIONS∗

We propose algorithms for the solution of high-dimensional symmetrical positive deﬁnite (SPD) linear systems with the matrix and the right-hand side given and the solution sought in a low-rank format. Similarly to density matrix renormalization group (DMRG) algorithms, our methods optimize the components of the tensor product format subsequently. To improve the convergence, we expand the search space by an inexact gradient direction. We prove the geometrical convergence and estimate the convergence rate of the proposed methods utilizing the analysis of the steepest descent algorithm. The complexity of the presented algorithms is linear in the mode size and dimension, and the demonstrated convergence is comparable to or even better than the one of the DMRG algorithm. In the numerical experiment we show that the proposed methods are also eﬃcient for non-SPD systems, for example, those arising from the chemical master equation describing the gene regulatory model at the mesoscopic scale.
Docetaxel and carboplatin combination chemotherapy as outpatient palliative therapy in carcinoma of unknown primary: A multicentre Hellenic Cooperative Oncology Group phase II study

Introduction. Taxane/platinum combinations exhibit synergistic cytotoxicity and activity against a broad range of solid tumours. We sought to optimise the regimen as a suitable outpatient palliative treatment for cancer of unknown primary (CUP). Patients and methods. Eligible CUP patients with adenocarcinoma or poorly differentiated carcinoma, performance status of 0-2, adequate organ function and assessable disease were treated with docetaxel 75 mg/m2 and carboplatin at an area under the concentration time-curve (AUC) of 5, both as 30-minute intravenous infusions, every three weeks. Patients with isolated axillary adenopathy, squamous cell cervical or inguinal adenopathy and PSA or germ-cell serum tumour markers were excluded. Results. Forty-seven patients entered the trial, 24 with predominantly nodal disease or non-mucinous peritoneal carcinomatosis (favourable risk) and 23 with visceral metastases (unfavourable risk). A median of 6 cycles of chemotherapy were administered, with relative dose intensities of both drugs >90%. Response rates were 32% (46% in favourable risk, 17% in unfavourable), comparable to the activity of paclitaxel/platinum regimes, though complete remissions were seen only in favourable risk patients. Granulocyte-colony stimulating factor support was used in a third of treatment cycles. Toxicity was mild and manageable, with grade 3–4 neutropenia in 26% of patients, febrile neutropenia in 7% and severe non-hematologic side-effects in less than 8% of patients. No toxic deaths or severe neurotoxicity were seen. Median time to progression (TTP) and overall survival (OS) were 5.5 and 16.2 months respectively. Survival was driven mainly by favourable-risk patients (22.6 months), as those with visceral metastases had a poor median survival of only 5.3 months. Good performance status and low-volume disease predicted for superior outcome, while docetaxel relative dose-intensity was a positive prognosticator only in favourable-risk patients. Conclusions. One-hour docetaxel/carboplatin is a convenient, safe and effective outpatient palliative treatment for CUP patients, providing meaningful survival prolongation only in favourable-risk patients. Insights in the molecular biology of CUP are needed for the development of targeted therapeutic manipulations of malignant resistance and progression.
A new approach to the control of autolevelling for drafting process: part 1: theoretical model based on the discrete-event simulation

Abstract This paper presents a new approach to control the autollevelling process to decrease the output unevenness. A discrete autolevelling model is set up based on the balance of the fiber distributions in the drafting zone. The relationship between the velocity of rollers and fiber distributions is pointed out in the light of the discrete autolevelling formula. This model can keep the number of fast-floating fiber constant to eliminate the input unevenness and improve the output quality of strands. By autolevelling the input forms of rectangular wave, sinusoidal wave and random wave, the advantages of this model are illustrated. It is shown that this discrete autolevelling model can decline the abrupt, dramatical or sequential input unevenness and lower the value of output CV more effectively.
Activation of p53 by Chemotherapeutic Agents Enhances Reovirus Oncolysis

Mammalian reovirus is a benign virus that possesses the natural ability to preferentially infect and kill cancer cells (reovirus oncolysis). Reovirus exploits aberrant Ras signalling in many human cancers to promote its own replication and spread. In vitro and in vivo studies using reovirus either singly or in combination with anti-cancer drugs have shown very encouraging results. Presently, a number of reovirus combination therapies are undergoing clinical trials for a variety of cancers. Previously we showed that accumulation of the tumor suppressor protein p53 by Nutlin-3a (a specific p53 stabilizer) enhanced reovirus-induced apoptosis, and resulted in significantly higher levels of reovirus dissemination. In this study, we examined the role of p53 in combination therapies involving reovirus and chemotherapeutic drugs. We showed that sub-lethal concentrations of traditional chemotherapy drugs actinomycin D or etoposide, but not doxorubicin, enhanced reovirus-induced apoptosis in a p53-dependent manner. Furthermore, NF-κB activation and expression of p53-target genes (p21 and bax) were important for the p53-dependent enhancement of cell death. Our results show that p53 status affects the efficacy of combination therapy involving reovirus. Choosing the right combination partner for reovirus and a low dosage of the drug may help to both enhance reovirus-induced cancer elimination and reduce drug toxicity.
A simulink hybrid heart model for quantitative verification of cardiac pacemakers

We develop a novel hybrid heart model in Simulink that is suitable for quantitative verification of implantable cardiac pacemakers. The heart model is formulated at the level of cardiac cells, can be adapted to patient data, and incorporates stochasticity. It is inspired by the timed and hybrid automata network models of Jiang et al and Ye et al, where probabilistic behaviour is not considered. In contrast to our earlier work, we work directly with action potential signals that the pacemaker sensor inputs from a specific cell, rather than ECG signals. We validate the model by demonstrating that its composition with a pacemaker model can be used to check safety properties by means of approximate probabilistic verification.
Role of VAMP3 and VAMP7 in the commitment of Yersinia pseudotuberculosis to LC3-associated pathways involving single- or double-membrane vacuoles

Yersinia pseudotuberculosis can replicate inside macrophages by hijacking autophagy and blocking autophagosome acidification. In bone marrow-derived macrophages, the bacteria are mainly observed inside double-membrane vacuoles positive for LC3, a hallmark of autophagy. Here, we address the question of the membrane traffic during internalization of Yersinia investigating the role of vesicle- associated membrane proteins (VAMPs). First, we show that as in epithelial cells, Yersinia pseudotuberculosis replicates mainly in nonacidic LC3-positive vacuoles. Second, in these cells, we unexpectedly found that VAMP3 localizes preferentially to Yersinia-containing vacuoles (YCVs) with single membranes using correlative light-electron microscopy. Third, we reveal the precise kinetics of VAMP3 and VAMP7 association with YCVs positive for LC3. Fourth, we show that VAMP7 knockdown alters LC3′s association with single-and multimembrane-YCVs. Finally, in uninfected epithelial cells stimulated for autophagy, VAMP3 overexpression and knockdown led respectively to a lower and higher number of double-membrane, LC3-positive vesicles. Hence, our results highlight the role that VAMPs play in selection of the pathways leading to generation of ultrastructurally different LC3 compartments and pave the way for determining the full set of docking and fusion proteins involved in Yersinia pseudotuberculosis’ intravesicular life cycle.
A method of defining learning processes

Currently many instructional Web sites just simply deliver course materials without integrating the role of teacher in guiding learners to use these materials to construct knowledge. Learners only passively receive the presented materials. Our research is to provide support services to actively assist learners to construct knowledge using the constructivist approach to learning. This paper focuses on providing services to assist learners to choose appropriate resources and methods, and guide them to align learning towards their study objectives. These services are implemented through electronic workspaces that manage the learning processes. A specification language will be presented to specify the learning processes in a way that constructivist learning can be supported and facilitated. The approach to managing the learning processes will be investigated. A learning environment that assists learners to use constructivist methods of learning to build new competences will be presented.
Computational Embodiment: Constructing Autonomous Software Systems

Computational embodiment is the computer implementation of principles of autonomy that allows software systems to exist in and interact with complex environments. We restrict our attention here to symbolic environments MUDs , as an initial step towards understanding and constructing ''interaction spaces'' in which humans and computer programs can interact on an equal footing. Our approach to constructing autonomous software systems is based on theoretical work on the organization of structures underlying language and movement in biological systems and on the structure of constructed complex systems mediated or integrated by software. We have developed an approach to integration called ''wrapping,'' which is a computationally reflective dynamic integration infrastructure. We regard integration infrastructure as an essential part of operating robust, flexible systems that exhibit appropriate behavior in the face of failures and uncertainties. The wrapping approach supports autonomy by supporting at least pr.
Modification of tribological tester t-01m allowing testing in conditions of lubrication

Researchers often want to develop their experiments in terms of wide range of testing conditions and results possible to acquire. One way to achieve this is to adapt existing testing equipment to new requirements. This paper proposes a method for extending the capabilities of the T-01M tester with a pressure lubrication system of a pin on disc contact, its construction and adjustments. Tribological tests carried out with the presence of a lubricant showed the correct functioning of the modified tester. We obtained several variables for the selected friction pair and friction parameters in the lubricated joint: friction force, friction coefficient, mass wear, friction work, wear intensity and specific wear. Verification tests confirmed suitability of the tester modification, adapting it to friction and wear tests in a lubricated contact. The expanded stand can be used (in the future) for tribological tests of lubricated frictional pairs to measure friction, wear, friction pairs temperature and to compare used lubricants.
Obstructive sleep apnea and adverse outcomes in surgical and nonsurgical patients on the wards.

BACKGROUND Obstructive sleep apnea (OSA) has been associated with clinical deterioration in postoperative patients and patients hospitalized with pneumonia. Paradoxically, OSA has also been associated with decreased risk of inpatient mortality in these same populations. OBJECTIVES To investigate the association between OSA and in-hospital mortality in a large cohort of surgical and nonsurgical ward patients. DESIGN Observational cohort study. SETTING A 500-bed academic tertiary care hospital in the United States. PATIENTS A total of 93,676 ward admissions from 53,150 unique adult patients between November 1, 2008 and October 1, 2013. INTERVENTION None. MEASUREMENTS OSA diagnoses and comorbidities were identified by International Classification of Diseases, Ninth Revision, Clinical Modification codes. Logistic regression was used to control for patient characteristics, location prior to ward admission, and admission severity of illness. The primary outcome was in-hospital death. Secondary outcomes included rapid response team (RRT) activation, intensive care unit (ICU) transfer, intubation, and cardiac arrest on the wards. MAIN RESULTS OSA was identified in 5,625 (10.6%) patients. Patients with OSA were more likely to be older, male, and obese, and had higher rates of comorbidities. OSA patients had more frequent RRT activations (1.5% vs 1.1%) and ICU transfers (8% vs 7%) than controls (P < 0.001 for both comparisons), but a lower inpatient mortality rate (1.1% vs 1.4%, P < 0.05). OSA was associated with decreased adjusted odds for ICU transfer (odds ratio [OR]: 0.91 [0.84-0.99]), cardiac arrest (OR: 0.72 [0.55-0.95]), and in-hospital mortality (OR: 0.70 [0.58-0.85]). CONCLUSIONS After adjustment for important confounders, OSA was not associated with clinical deterioration on the wards and was associated with significantly decreased in-hospital mortality.
Molecular analysis of two FMRFamide‐encoding transcripts expressed during the development of the tropical abalone haliotis asinina

FMRFamide‐related peptides (FaRPs) are involved in numerous neural functions across the animal kingdom and serve as important models for understanding the evolution of neuropeptides. Gastropod molluscs have proved to be particularly useful foci for such studies, but the developmental expression of FaRPs and the evolution of specific transcripts for different peptides are unclear within the molluscs. Here we show that FaRPs are encoded by two transcripts that appear to be splice variants of a single gene in the abalone, Haliotis asinina, which represents the basal vetigastropods. Has‐FMRF1 comprises 1,438 nucleotides and encodes a precursor protein of 329 amino acids that can potentially produce two copies of FLRFamide, one copy each of TLAGDSFLRFamide, QFYRIamide, SDPDLDDVIRASLLAYSLDDSPNN, and SVATAPVEAKAVEAGNKDIE, and 13 copies of FMRFamide. The second 1,241‐nucleotide transcript, Has‐FMRF2, encodes a 206‐amino acid precursor protein with single copies of FLRFamide and FMRFamide along with such extended forms as NFGEPFLRFamide, FDSYEDKALRFamide, and NGWLHFamide, in addition to SDPGEDMLKSILLRGAPSNNGLQY and DTUDETTUNDNAHSRQ. Both transcripts are present early in life and are expressed in different but overlapping patterns within the developing larval nervous system. Mass spectrometry and immunocytochemistry demonstrate that FaRPs are cleaved from larger precursors and localize to the developing nervous system. Our results confirm previous evidence that FaRPs are expressed early and potentially play many roles during molluscan development and suggest that the last common ancestor to living gastropods used alternative splicing of an FMRFamide gene to generate a diversity of FaRPs in spatially restricted patterns in the nervous system. J. Comp. Neurol. 519:2043–2059, 2011. © 2011 Wiley‐Liss, Inc.
Hybrid neural networks for social emotion detection over short text

Short text is prevalent on the Web, but it brings challenges to content analysis methods for the lack of contextual information. Biterm topic model (BTM) is a variant of latent Dirichlet allocation, which effectively infers the latent topic distribution of short text by modeling the generation of biterms in the whole corpus. However, it needs fine-tuning from labels to reduce noise when applied to supervised learning. Motivated by the transfer learning approach, we propose the hybrid neural networks based on BTM and conventional neural networks, which first make the hidden layer of neural networks approximate the inference of BTM. Following this initial pre-training phase, we then use the simple back-propagation algorithm to fine-tune the topic distribution learned from BTM, so as to improve the performance of supervised learning. Our experiment on two diverse collections of short text validates the effectiveness of the proposed hybrid neural networks for social emotion detection.
Polymorphism in the serotonin transporter gene polymorphisms (5-HTTLPR) modifies the association between significant life events and depression in people with multiple sclerosis

Background: In the general population, variation in the serotonin-transporter-linked polymorphic region (5-HTTLPR) has been shown to modify the association between stressful events and depression/anxiety. This has not been examined in people with multiple sclerosis (MS). Objective: We examined the interaction between significant life events (SLE), 5-HTTLPR and depression/anxiety. Methods: A population-based longitudinal cohort of 198 people with MS was followed biannually for 2.5 years. Depression and anxiety symptoms were measured at each review using the Hospital Anxiety and Depression Scale (HADS). SLEs were assessed using a questionnaire based on the Social Readjustment Rating Scale. Results: We found an interaction between SLE load in the previous 12 months and functional variation in the 5-HTTLPR allele type in predicting depression, with the association between SLE load and depression being stronger for those with S/S allele type (β = 0.21 (95% confidence interval (CI): 0.09–0.33) per 10-unit increase) and S/L (β = 0.14 (95% CI: 0.05–0.24)) compared to L/L allele type (β = 0.04 (95% CI: −0.05 to 0.24); pinteraction < 0.001). No convincing evidence of an interaction was found with anxiety. Conclusion: We found that the association between SLE load and MS depression severity was stronger among those with one or two copies of the short allele of the 5-HTTLPR. The identification of a gene–environment interaction between SLEs and depression in a population where depression is partly disease-driven is novel.
NovaSearch at ImageCLEFmed 2016 Subfigure Classification Task

This paper describes the NovaSearch team participation in the ImageCLEF 2016 Medical Task in the subfigure classification subtask. Deep learning techniques have proved to be very effective in automatic representation learning and classification tasks with general data. More specifically, convolutional neural networks (CNNs) have surpassed humanlevel performance in the ImageNET classification task, making them a promising model for the task of medical modality classification. We assess how each model behave when dealing with medical images, by developing three different models, with different depths and components, and analyse the impact of these factors in the performance. One of the key ingredients for the effectiveness of CNNs (and deep learning in general) is the use of large amounts of data for training. This subtask scenario is completely different, due to the small size of the dataset, implying a significant risk of overfitting. We apply state-of-the-art techniques developed to reduce overfitting in these networks to our models and evaluate their effectiveness. Our best model achieves 65.31% accuracy on the test set using only the training data provided.
Dynamics of tilt-based browsing on mobile devices

A tilt-controlled photo browsing method for small mobile devices is presented. The implementation uses continuous inputs from an accelerometer, and a multimodal (visual, audio and vibrotactile) display coupled with the states of this model. The model is based on a simple physical model, with its characteristics shaped to enhance usability. We show how the dynamics of the physical model can be shaped to make the handling qualities of the mobile device fit the browsing task. We implemented the proposed algorithm on Samsung MITs PDA with tri-axis accelerometer and a vibrotactile motor. The experiment used seven novice users browsing from 100 photos. We compare a tilt-based interaction method with a button-based browser and an iPod wheel. We discuss the usability performance and contrast this with subjective experience from the users. The iPod wheel has significantly poorer performance than button pushing or tilt interaction, despite its commercial popularity.
"In A Good Way Weird": Exploring Positive Experiences with Technology-Mediated Pornography

Despite HCI's interest in topics around sexuality, pornography has remained underexplored. Specifically, the user experience (UX) of technology-mediated pornography has received little attention, even though it has been argued that it may contribute to a better understanding of pleasure and enjoyability of interactive systems. We surveyed 187 participants about a positive experience involving technology-mediated pornography. Autonomy and competence, as well as sexual arousal and desire emerged as the most characteristic dimensions of positive experiences with pornographic content. However, preliminary qualitative analysis suggests that many participants also experienced mixed feelings due to technology. Overall, our findings provide first insights into the complexity of the user experience of technology-mediated pornography.