Miracle-dz/UniFAR-FTUs huggingface dataset:
Title Preclinical evaluation of a novel cyanine dye for tumorimaging with in vivo photoacoustic imaging

Photoacoustic imaging (PA imaging or PAI) has shown great promise in the detection and monitoring of cancer. Although nanocarrier-based contrast agents have been studied for use in PAI, small molecule contrast agents are required due to their ease of preparation, costeffectiveness, and low toxicity. Here, we evaluated the usefulness of a novel cyanine dye IC7-1-Bu as a PAI contrast agent without conjugated targeting moieties for in vivo tumor imaging in a mice model. Basic PA characteristics of IC7-1-Bu were compared with indocyanine green (ICG), a Food and Drug Administration approved dye, in an aqueous solution. We evaluated the tumor accumulation profile of IC7-1-Bu and ICG by in vivo fluorescence imaging. In vivo PAI was then performed with a photoacoustic tomography system 24 and 48 h after intravenous injection of IC7-1-Bu into tumor bearing mice. IC7-1-Bu showed about a 2.3-fold higher PA signal in aqueous solution compared with that of ICG. Unlike ICG, IC7-1-Bu showed high tumor fluorescence after intravenous injection. In vivo PAI provided a tumor to background PA signal ratio of approximately 2.5 after intravenous injection of IC7-1-Bu. These results indicate that IC7-1-Bu is a promising PAI contrast agent for cancer imaging without conjugation of targeting moieties. © 2014 Society of Photo-Optical Instrumentation Engineers (SPIE) [DOI: 10.1117/1.JBO. 19.9. 090501]
AUCpreD: proteome-level protein disorder prediction by AUC-maximized deep convolutional neural fields

MOTIVATION Protein intrinsically disordered regions (IDRs) play an important role in many biological processes. Two key properties of IDRs are (i) the occurrence is proteome-wide and (ii) the ratio of disordered residues is about 6%, which makes it challenging to accurately predict IDRs. Most IDR prediction methods use sequence profile to improve accuracy, which prevents its application to proteome-wide prediction since it is time-consuming to generate sequence profiles. On the other hand, the methods without using sequence profile fare much worse than using sequence profile. METHOD This article formulates IDR prediction as a sequence labeling problem and employs a new machine learning method called Deep Convolutional Neural Fields (DeepCNF) to solve it. DeepCNF is an integration of deep convolutional neural networks (DCNN) and conditional random fields (CRF); it can model not only complex sequence-structure relationship in a hierarchical manner, but also correlation among adjacent residues. To deal with highly imbalanced order/disorder ratio, instead of training DeepCNF by widely used maximum-likelihood, we develop a novel approach to train it by maximizing area under the ROC curve (AUC), which is an unbiased measure for class-imbalanced data. RESULTS Our experimental results show that our IDR prediction method AUCpreD outperforms existing popular disorder predictors. More importantly, AUCpreD works very well even without sequence profile, comparing favorably to or even outperforming many methods using sequence profile. Therefore, our method works for proteome-wide disorder prediction while yielding similar or better accuracy than the others. AVAILABILITY AND IMPLEMENTATION http://raptorx2.uchicago.edu/StructurePropertyPred/predict/ CONTACT wangsheng@uchicago.edu, jinboxu@gmail.com SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Compatible sequences and a slow Winkler percolation

Two infinite 0-1 sequences are called compatible when it is possible to cast out 0's from both in such a way that they become complementary to each other. Answering a question of Peter Winkler, we show that if the two 0-1-sequences are random i.i. d. and independent from each other, with probability p of 1's, then if p is sufficiently small they are compatible with positive probability. The question is equivalent to a certain dependent percolation with a power-law behavior: the probability that the origin is blocked at distance n but not closer decreases only polynomially fast and not, as usual, exponentially.
Efficacy of Bronchoscopic Thermal Vapor Ablation and Lobar Fissure Completeness in Patients with Heterogeneous Emphysema

Background: Bronchoscopic thermal vapor ablation (BTVA) ablates emphysematous tissue through a localized inflammatory response followed by contractive fibrosis and tissue shrinkage leading to lung volume reduction that should not be influenced by collateral ventilation. Objectives: To determine the correlation of clinical data from a trial of BTVA with fissure integrity visually assessed by computed tomography (CT). Methods: We conducted a single-arm study of patients with upper lobe-predominant emphysema (n = 44). Patients received BTVA either to the right upper lobe or left upper lobe, excluding the lingula. Primary efficacy outcomes were forced expiratory volume in 1 s (FEV1) and St. George’s Respiratory Questionnaire (SGRQ) at 6 months. Lobar volume reduction from CT was another efficacy outcome measurement. The fissure of the treated lobe was analyzed visually on preinterventional CT. Incompleteness of the small fissure, the upper half of the right large fissure and the whole left large fissure were estimated visually in 5% increments, and the relative amount of fissure incompleteness was calculated. Pearson correlation coefficients were calculated for the association between fissure incompleteness and change in efficacy outcomes (baseline to 6 months) of BTVA. Results: A total of 38 out of 44 patients (86%) had incompleteness in the relevant fissure. Calculated relevant fissure incompleteness was a mean of 13% of fissure integrity (range 0–63). Correlation coefficients for the association of incompleteness with outcomes were as follows: FEV1 = 0.17; lung volume reduction = –0.27; SGRQ score = –0.10; 6-min walk distance = 0.0; residual volume (RV) = –0.18, and RV/total lung capacity = –0.14. Conclusions: Lobar fissure integrity has no or minimal influence on BTVA-induced lung volume reduction and improvements in clinical outcomes.
TRIO: measuring asymmetric capacity with three minimum round-trip times

Measuring network path capacity is an important capability to many Internet applications. But despite over ten years of effort, the capacity measurement problem is far from being completely solved. This paper addresses the problem of measuring network paths of asymmetric capacity without requiring the remote node's control or overwhelming the bottleneck link. We first show through analysis and measurement that the current packet-dispersion methods, due to the packet size limitations, can only measure up to a certain degree of capacity asymmetry. Second, we propose TRIO that removes the limitation by using round-trip times (RTTs). TRIO cleverly exploits two types of probes to obtain three minimum RTTs to compute bothforward and reverse capacities, and another minimum RTT for measurement validation. We validate TRIO's accuracy and versatility on a testbed and the Internet, and develop a system to measure path capacity from the server or user side.
Glutamate receptor 5/6/7‐like and glutamate transporter‐1‐like immunoreactivity in the leech central nervous system

Previous physiological and pharmacological evidence has suggested a neurotransmitter role for the excitatory amino acid glutamate in the leech central nervous system (CNS). In the present study, we sought to localize glutamate receptor (GluR) subunits (GluR 5/6/7, GluR 2/3 and N‐methyl‐D‐aspartate receptor 1 [NMDAR 1]) and a glutamate transporter subtype [GLT‐1] within the leech CNS using mono‐ and polyclonal antibodies. In whole‐mounted tissue, small cells of the outer capsule and putative microglia labeled with both GluR 5/6/7 and GluR 2/3 but not NMDAR 1 subunit antisera. In general, GluR 5/6/7‐like immunofluorescence was both more intense and more widespread than GluR 2/3‐like immunolabeling. Cryostat‐sectioned tissue revealed extensive GluR 5/6/7‐like immunoreactivity throughout the neuropil as well as labeling within a few neuronal somata. GLT‐1‐like immunoreactivity localized to the inner capsule, which is the interface between neuronal somata and the neuropil and is deeply invested by processes of neuropil glia. These results complement previous physiological and pharmacological findings indicating that the leech CNS possesses the cellular machinery to respond to glutamate and to transport glutamate from extracellular spaces. Together, they provide further evidence for glutamate's role as a neurotransmitter within the leech CNS. J. Comp. Neurol. 405:334–344, 1999. © 1999 Wiley‐Liss, Inc.
A new approach to construct multicast trees in MPLS networks

In this paper, we present a new approach to construct multicast trees in MPLS networks. This approach utilizes MPLS LSP between multicast tree branching node routers in order to reduce forwarding states and enhance scalability. In our approach only routers that are acting as multicast tree branching node for a group need to keep the forwarding state for that group. All other non-branching node routers simply forward data packets over traffic engineered unicast routes using MPLS LSP. We can deduce that our approach can be largely deployed because it uses for multicast traffic the same unicast MPLS forwarding scheme. In this paper we briefly discuss MPLS, the multicast scalability problem, merging the two technologies, related works and different techniques for forwarding state reduction. We evaluate the approach and present some related issues to conclude finally that it is feasible and promising.
The co-production of knowledge about water resources: framing, uncertainty and climate change

In addressing the challenge for institutions to respond to climate change, we focus on how different actors frame global climate related water problems in different ways. We take "frame" to mean a sensemaking device that creates meaning by selecting certain issue elements and arranging them in a meaningful way. Through framing, actors relate to a problem situation in a specific way, and this evolves with changes in the physical, social and interactional context. Multiple frames create a specific kind of uncertainty, called ambiguity, which complicates decision-making and is not easily resolved. Here we link frames to knowledge, by considering frames as connected to "ways of knowing" about a specific situation, which can be related to but are different from interests or ideologies. Both framing and knowing can be understood as emergent relations between actors and social and natural systems. "Configurations" arise because actors not only develop frames in interactions but also often lean towards actors with similar ways of knowing. When actors become closely included in configurations they run the risk of only confirming their own frames and of not being open to actors with different ways of knowing. Relying on examples from different areas of the world, we observe the ways in which multiple frames about climate issues, like equity, ecological sustainability or economic development challenge each other and are often not in balance. Forging collaborative links between multiple frames or ways of knowing is a relatively unexplored but essential process for reaching more socially and technically robust solutions.
A preliminary report of nursing in the three‐stair‐position to prevent apnoea of prematurity

Recurrent apnoea associated with hypoxaemia and brady-cardia is the most common monitor alarm situation inneonatal intensive care units. Previous studies have demon-stratedthatapnoeaeventsareassociatedwithacutechangesin cerebral perfusion and blood volume and may induceor aggravate pre-existing cerebral injuries (1). Therefore,apnoea should be prevented effectively. Interventions toreduce apnoea resulting in hypoxaemia and bradycardia in-clude continuous positive airway pressure (CPAP) (2) andmethylxanthines (3). Nursing in the prone, rather than inthe supine position has its proponents (4,5) as well as itsopponents (6,7). Jenni OG et al. 1997 showed in their study that nursingin the head elevated tilt position (HETP) placing the infantsprone reduces apnoea episodes significantly (8). In HETP the infant is placed on its underlay, which istilted until the infant is in an inclined position of 15
Road recognition for a tracked vehicle

The well known road detection and tracking algorithm (RDT), developed at the Universitat der Bundeswehy Muchen (UBM), has been adapted for following unpaved paths and contour lines. The vision system consists of a color CCD-camera mounted on UBM's high bandwidth pan-tilt head, dubbed TACC. The monochrome and color signals from the camera are processed in parallel. This vision system is used for lateral control of the Primus-C experimental vehicle Digitized Wiesel 2, an air-transportable tracked tank. Image processing simultaneously exploits the results from edge-based feature extraction and area-based segmentation. Feature matching is facilitated by exploiting the photometric homogeneity along contours. A flexible algorithm for active viewing direction control was implemented. The two axis camera carrier (TACC) is controlled by fixating on a point moving on the ceterline of the road segment. A semi-autonomous initialization mode is integrated using image points on the contour to be followed, specific by an operator. Autonomous driving speeds up to 50km/h on unpaved roads was demonstrated publicly in June 1999.
A Bio-inspired Neural Sensory-Motor Coordination Scheme for Robot Reaching and Preshaping

We present a sensory-motor coordination scheme for a robot hand-arm-head system that provides the robot with the capability to reach for and to grasp an object, while pre-shaping the fingers to the required grasp configuration. A model for sensory-motor coordination derived from studies in humans inspired the development of the scheme. A special feature of this model is the prediction of the tactile image perceived after grasping. The proposed scheme is based on a neuro-fuzzy module that, after a learning phase, starting from visual data, calculates the position and orientation of the hand for grasping, selects the best-suited hand configuration, and predicts the tactile feedback after grasping. The implementation of the scheme on a humanoid robot allowed experimental validation of its effectiveness in robotics and provided perspectives on applications of sensory predictions in robot motor control
WinkTalk: a demonstration of a multimodal speech synthesis platform linking facial expressions to expressive synthetic voices

This paper describes a demonstration of the WinkTalk system, which is a speech synthesis platform using expressive synthetic voices. With the help of a webcamera and facial expression analysis, the system allows the user to control the expressive features of the synthetic speech for a particular utterance with their facial expressions. Based on a personalised mapping between three expressive synthetic voices and the users facial expressions, the system selects a voice that matches their face at the moment of sending a message. The WinkTalk system is an early research prototype that aims to demonstrate that facial expressions can be used as a more intuitive control over expressive speech synthesis than manual selection of voice types, thereby contributing to an improved communication experience for users of speech generating devices.
Assessment Criteria Indicative of Deception (ACID): Replication and Gender Differences

Assessment Criteria Indicative of deception (ACID) is a statement analysis technique that combines careful interviewing designed to facilitate the detection of deception with empirically-derived content criteria related to both the phenomenal and objective nature of deception. The current study of ACID had three goals. The first goal was to replicate ACID with a population of incarcerated witnesses. The second goal was to study the extension of this procedure by adding coherence and the type-token ratio for dependent measures. The third goal was to investigate the possibility of gender differences in verbal interpersonal deception. In meeting the first and second goals, this study demonstrated honest statements were longer and more detailed than deceptive statements, and that honest statements specifically had more words and more unique details added as a result of the recall enhancement effect of the interview. Honest statements were more coherent and had lower type-token ratios. In meeting the third goal, this study demonstrated that women's statements were more coherent and contained more words than male statements. Deceptive females gave less detail, fewer word, and had higher type-token ratios than deceptive men. Honest women gave more words and more detail than honest men. Importantly, coherence is very dependent upon gender, so that an honest man is more likely to tell an incoherent story than is a deceptive woman. Using gender-specific norms significantly increased the classification accuracy of a discriminant function analysis. Overall, 74 of 83 participants were accurately classified as honest or deceptive using the dependent measures. Future research is necessary to firmly establish the presence and cause of gender differences in verbal deception.
Sleep duration and cognitive performance in adolescence. The AVENA study

1.Department of Medical Physiology, School of Medicine, University of Granada, Granada, Spain 2.Unit for Preventive Nutrition, Department of Biosciences and Nutrition at NOVUM, Karolinska Institutet, Huddinge, Sweden 3.Department of Basic Psychology, School of Psychology, University of Malaga, Malaga, Spain 4.Department of Physical Education and Sport, School of Physical Activity and Sport Sciences, University of Granada, Granada, Spain 5.Department of Nutrition and Food Science, University of the Basque Country, Vitoria, Spain 6.Immunonutrition Research Group, Department of Metabolism and Nutrition, Instituto del Frio, Institute of Food Science, Technology and Nutrition (ICTAN), Spanish National Research Council (CSIC), Madrid, Spain 7.Department of Pediatrics, University of Cantabria, Santander, Spain 8.E.U. Health sciences, University of Zaragoza, Zaragoza, Spain
Characterization and comparison of four serine- and arginine-rich (SR) protein kinases.

Phosphorylated serine- and arginine-rich (SR) proteins are components of the spliceosomal complex, and have been implicated in the control of alternative splicing. Kinases that regulate the phosphorylation and possibly the intranuclear distribution of SR proteins may therefore contribute to changes in choice of splice site. We have cloned three mouse cDNAs with high sequence identity to the family of LAMMER kinases (i.e. kinases carrying the conserved signature EHLAMMERILG in the catalytic domain). A comparison of their amino acid sequences revealed two related subfamilies with high evolutionary conservation. We have compared the expression patterns of these proteins in mouse tissues and transformed cell lines with that of a previously cloned family member (mCLK1/STY), and detected various transcripts for each gene. This underlines previous findings of alternative splicing of mclk1/STY. Our results suggest that the proportions of products for each gene are regulated independently. We further demonstrate that all variants encode autophosphorylating proteins that can phosphorylate several biochemically purified SR proteins in vitro, leading to hyperphosphorylation of at least one SR protein in vivo. The observed tissue distributions and substrate specificities suggest that these kinases may all be constituents of a network of regulatory mechanisms that enable SR proteins to control RNA splicing.
Microbiological assessment of the implant-abutment interface in different connections: cross-sectional study after 5 years of functional loading.

OBJECTIVE To evaluate the bacterial microflora present inside the implant connection and in the peri-implant sulcus fluid of healthy implants, and to analyze the relationships between these harboring sites for four different implant systems after at least 5 years of functional loading. MATERIALS AND METHODS A cross-sectional study was performed involving 40 patients treated with metal-ceramic cemented bridges supported by at least two healthy implants functionally loaded for 5 years. Four different implant-abutment connections were studied: external hexagon (control group), double internal hexagon (test group 1), internal hexagon with external collar (test group 2), and conical connection (test group 3). Samples for microbiological analysis were obtained from three types of sites: peri-implant sulci, connections' inside and abutments surface and, as control, gingival sulci of neighboring teeth. Quantitative real-time PCR was carried out for Total Bacterial Count and for 10 microorganisms: Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Tannerella forsythensis, Treponema denticola, Prevotella intermedia, Peptostreptococcus micros, Fusobacterium nucleatum, Campylobacter rectus, Eikenella corrodens, and Candida albicans. The response variables were percentage of positive sites and absolute bacterial load. The relations of the response variables with the type of connection and of sampling site were assessed using generalized estimating equations. RESULTS Regarding the analysis of positivity to bacteria in the peri-implant sulcus no significant differences were observed. Analyzing the connection's inside, none of the connection designs had the capacity to prevent microbiological leakage through the implant/abutment microgap. Test group 3 presented the lowest mean values for red complex bacteria and control group the highest, although differences were non-significant. Statistical significance was only reached for Treponema denticola in the bacterial load analysis inside the connection. Test groups 1 and 2 yielded lower values for orange complex bacteria but only for Peptostreptococos micros the differences resulted significant. Test groups 2 and 3 had significantly lower total bacterial counts in the peri-implant sulcus and inside the connection. CONCLUSIONS Outcomes suggested that all the analyzed connections resulted contaminated after 5 years of functional loading. However, the connection design might influence bacterial activity levels qualitatively and quantitatively, especially inside the implant connection.
The Laforin–Malin Complex, Involved in Lafora Disease, Promotes the Incorporation of K63-linked Ubiquitin Chains into AMP-activated Protein Kinase β Subunits

A functional laforin–malin complex promotes the ubiquitination of AMP-activated protein kinase (AMPK), a sensor of cellular energy status. The laforin–malin complex promotes the formation of K63-linked ubiquitin chains, which are not involved in proteasome degradation but could regulate the subcellular localization of substrate proteins.