Miracle-dz/UniFAR-FTUs huggingface dataset:
A Stacked Graphical Model for Associating Sub-Images with Sub-Captions

There is extensive interest in mining data from full text. We have built a system called SLIF (for Subcellular Location Image Finder), which extracts information on one particular aspect of biology from a combination of text and images in journal articles. Associating the information from the text and image requires matching sub-figures with the sentences in the text. We introduce a stacked graphical model, a meta-learning scheme to augment a base learner by expanding features based on related instances, to match the labels of sub-figures with labels of sentences. The experimental results show a significant improvement in the matching accuracy of the stacked graphical model (81.3%) as compared with a relational dependency network (70.8%) or the current algorithm in SLIF (64.3%).
AP‐1 and AP‐3 Mediate Sorting of Melanosomal and Lysosomal Membrane Proteins into Distinct Post‐Golgi Trafficking Pathways

The adaptor complexes AP‐1 and AP‐3 are localized to endosomes and/or the trans Golgi network (TGN). Because of limitations in analysing intracellular adaptor function directly, their site of function is a matter of ongoing uncertainty. To overcome this problem and to analyse adaptor sorting at the TGN, we reconstituted vesicle formation from Golgi/TGN‐enriched membranes in a novel in vitro budding assay. Melanocytes were metabolically labelled followed by a 19°C temperature block to accumulate newly synthesized proteins in Golgi membranes, which were then enriched by subcellular fractionation and used as donor membranes for vesicle formation in vitro. The incorporation of the melanosomal proteins tyrosinase and tyrosinase‐related protein 1 (TRP‐1) as well as Lamp‐1 and 46 kDa mannose‐6‐phosphate receptor (MPR46) into Golgi/TGN‐derived vesicles was temperature, nucleotide, cytosol, ADP ribosylation factor 1 and adaptor dependent. We show that sorting of TRP‐1 and MPR46 was AP‐1 dependent, while budding of tyrosinase and Lamp‐1 required AP‐3. Depletion of clathrin inhibited sorting of all four cargo proteins, suggesting that AP‐1 and AP‐3 are involved in the formation of distinct types of clathrin‐coated vesicles, each of which is characterized by the incorporation of specific cargo membrane proteins.
A 4-kV/2-A/5-kHz Compact Modulator for Nitrogen Plasma Ion Implantation

To treat stainless-steel surfaces by nitrogen plasma implantation, a solid-state compact modulator was devised, in which a 8.0-muF capacitor discharges through a forward converter composed of a low-blocking-voltage insulated-gate-bipolar-transistor switch (1.0 kV) and three step-up pulse transformers, rather than employing hard-tube devices such as in conventional plasma ion implantation pulsers, which are expensive and cumbersome. For this, a modulator was built to produce pulses with amplitudes of the order of 4 kV, duration of about 5.0 mus, and rise time of ~1.0 mus with maximum current/frequencies capabilities of 2.0 A and 5 kHz, respectively
Resolution enhancement and sampling with wavelets and footprints

In this paper, we consider classes of not bandlimited signals, namely, streams of Diracs and piecewise polynomial signals, and show that these signals can be sampled and perfectly reconstructed using wavelets as sampling kernel. Due to the multiresolution structure of the wavelet transform, these new sampling theorems naturally lead to the development of a new resolution enhancement algorithm based on wavelet footprints. Preliminary results show that this algorithm is also very resilient to noise.
Analysis of Synchronizer, Data Loss and Occurrence of Metastability

The many applications consist of multiple clock domains. There is data transfer between these clock domain systems. Due to different frequencies between sender and receiver there is data loss. Synchronizer is used for data synchronization. Synchronizer is having non-zero probability of failure in Globally Asynchronous Locally synchronous System on Chip. Synchronizer plays very crucial role in determining the reliability of system. The synchronizer is having parameters. These parameters associated with synchronizer are clock, data rate and timing window (setup and hold time). But in practice the synchronizer suffers from metastability as data changes in timing window due to which synchronizer failure occurs. As the metastability occurs we cannot predict the correct level of output. Metastability states are common in digital circuits, and synchronizers are must to protect their fatal effects. Originally, they were required when reading an asynchronous input. Now, with multiple clock domains on the same chip, synchronizers are required when on-chip data crosses the clock domain boundaries. The proposed architecture is modeled with verilog and simulated with Xilinx ISE design suit 13.1 and Quartus II 10.1. Analog behavior is studied by using Tanner 13.1. The probability of failure is analyzed and simulated. It has been found that it is affected by clock rate.
Efficacy of Hedgehog Pathway Inhibitors in Basal Cell Carcinoma

Basal cell carcinoma (BCC) is the most commonly diagnosed cancer. While most BCCs are amenable to surgery, some tumors can reach a more advanced stage or metastasize, and become ineligible for surgical resection or radiotherapy. Abnormal activation of the Hedgehog (Hh) pathway is a key driver in BCC pathophysiology. Consequently, inhibitors of the Hh pathway have been developed. Molecules that inhibit the receptor protein Smoothened (SMO) are the most advanced in clinical development. Vismodegib is the first-in-class SMO inhibitor and has been approved in a number of countries for the treatment of metastatic or locally advanced BCC. Several molecules have demonstrated antitumoral activity, but treatment may be limited in duration by a number of side effects, and it is not yet established whether these agents are truly curative or whether continued treatment will be required. Resistance to SMO inhibition has been reported in the clinic for which incidence and mechanisms must be elucidated to inform future therapeutic strategies. Intermittent dosing regimens to improve tolerability, as well as neoadjuvant use of Hh pathway inhibitors, are currently under investigation. Here, we review the most recent outcomes obtained with Hh inhibitors under clinical investigation in BCC. Mol Cancer Ther; 14(3); 633–41. ©2015 AACR.
5-HT Receptor Regulation of Neurotransmitter Release

Serotoninergic neurons in the central nervous system impinge on many other neurons and modulate their neurotransmitter release. This review focuses on 1) the function of presynaptic 5-hydroxytryptamine (5-HT) heteroreceptors on axon terminals of central cholinergic, dopaminergic, noradrenergic, or GABAergic neurons and 2) the role of GABAergic interneurons expressing 5-HT heteroreceptors in the regulation of acetylcholine, dopamine, or noradrenaline release. In vitro studies on slices or synaptosomes and in vivo microdialysis experiments have shown that 5-HT1A, 5-HT1B, 5-HT2A, 5-HT2C, 5-HT3, and/or 5-HT4 heteroreceptors mediate this modulation. 5-HT1B receptors on neocortical cholinergic, striatal dopaminergic, or hippocampal GABAergic axon terminals are examples for release-inhibiting 5-HT heteroreceptors; 5-HT3 receptors on hippocampal GABAergic or 5-HT4 receptors on hippocampal cholinergic axon terminals are examples for release-facilitating 5-HT heteroreceptors. GABA released from GABAergic interneurons upon activation of facilitatory 5-HT receptors, e.g., 5-HT2A or 5-HT3 receptors, mediates inhibition of the release of other neurotransmitters such as prefrontal neocortical dopamine or neocortical acetylcholine release, respectively. Conversely, attenuated GABA release in response to activation of inhibitory 5-HT heteroreceptors, e.g., 5-HT1A or 5-HT1B receptors on GABAergic interneurons is involved in paradoxical facilitation of hippocampal acetylcholine and striatal dopamine release, respectively. Such 5-HT heteroreceptors are considered potential targets for appropriate 5-HT receptor ligands which, by enhancing the release of a relevant neurotransmitter, can compensate for its hypothesized deficiency in distinct brain areas. Examples for such deficiencies are the impaired release of hippocampal or neocortical acetylcholine, striatal dopamine, and hippocampal or neocortical noradrenaline in disorders such as Alzheimer's disease, Parkinson's disease, and major depression, respectively.
Exploit Programming From Buffer Overflows to “Weird Machines” and Theory of Computation

Hacker-driven exploitation research has developed into a discipline of its own, concerned with practical exploration of how unexpected computational properties arise in actual multi-layered, multi-component computing systems, and of what these systems could and could not compute as a result. The staple of this research is describing unexpected (and unexpectedly powerful) computational models inside targeted systems, which turn a part of the target into a so-called “weird machine” programmable by the attacker via crafted inputs (a.k.a. “exploits”). Exploits came to be understood and written as programs for these “weird machines” and served as constructive proofs that a computation considered impossible could actually be performed by the targeted environment.
On the sum-rate capacity of the phase fading z-interference channel with a relay in the weak interference regime

We study the sum-rate capacity of the Z-interference channel with a relay (Z-ICR) in the weak interference regime, when the channel coefficients are subject to phase fading. This fading model represents many practical communication systems in which phase noise is a major concern, such as OFDM communications and line-of-sight microwave communications. We consider the case in which the relay receives transmissions from only one of the two transmitters, but the transmission of the relay is received at both destinations. We present conditions on the channel coefficients under which the sum-rate capacity of the phase fading Z-ICR is achieved by treating interference as noise at each receiver, and derive the corresponding sum-rate capacity. Our results show the benefits of relaying in the presence of interference when interference is weak and relay power is finite.
Greedy Face Routing with Face ID Support in Wireless Networks

Geographic face routing provides an attractive way for packet delivery in wireless networks due to its high reliability and low overhead. A good face routing protocol should provide guaranteed packet delivery and efficient routing paths. In this paper, we present a new face routing method named GFRIS that has both features by actively probing each face for the face size and the unique face identification sequence -face ID. Face switch occurs only if the outgoing edge intersects with the local minimum-destination line at a progressing location and the edge is shared between two different faces. To avoid the huge performance penalty when selecting an inefficient face traversal direction on a large face, GFRIS uses the face size to trigger the bounded face traversal procedure as proposed earlier in GOAFR+. Simulation results show that, by using face ID to assist face switch and adaptively applying the normal and bounded face traversal rules according to the face size, GFRIS achieves lower path stretch factor compared to GFG, GPSR, GFG2 and GOAFR+. The worst case performance of GFRIS is even better than that of GOAFR+ in critical node densities from 4 to 7.
Transcription through the roadblocks: the role of RNA polymerase cooperation

During transcription, cellular RNA polymerases (RNAP) have to deal with numerous potential roadblocks imposed by various DNA binding proteins. Many such proteins partially or completely interrupt a single round of RNA chain elongation in vitro. Here we demonstrate that Escherichia coli RNAP can effectively read through the site‐specific DNA‐binding proteins in vitro and in vivo if more than one RNAP molecule is allowed to initiate from the same promoter. The anti‐roadblock activity of the trailing RNAP does not require transcript cleavage activity but relies on forward translocation of roadblocked complexes. These results support a cooperation model of transcription whereby RNAP molecules behave as ‘partners’ helping one another to traverse intrinsic and extrinsic obstacles.
On trust models and trust evaluation metrics for ad hoc networks

Within the realm of network security, we interpret the concept of trust as a relation among entities that participate in various protocols. Trust relations are based on evidence created by the previous interactions of entities within a protocol. In this work, we are focusing on the evaluation of trust evidence in ad hoc networks. Because of the dynamic nature of ad hoc networks, trust evidence may be uncertain and incomplete. Also, no preestablished infrastructure can be assumed. The evaluation process is modeled as a path problem on a directed graph, where nodes represent entities, and edges represent trust relations. We give intuitive requirements and discuss design issues for any trust evaluation algorithm. Using the theory of semirings, we show how two nodes can establish an indirect trust relation without previous direct interaction. We show that our semiring framework is flexible enough to express other trust models, most notably PGP's Web of Trust. Our scheme is shown to be robust in the presence of attackers.
A Fully Automated Offline Handwriting Recognition System Incorporating Rule Based Neural Network Validated Segmentation And Hybrid Neural Network Classifier

In this paper we propose a fully automated offline handwriting recognition system that incorporates rule based segmentation, contour based feature extraction, neural network validation, a hybrid neural network classifier and a hamming neural network lexicon. The work is based on our earlier promising results in this area using heuristic segmentation and contour based feature extraction. The segmentation is done using many heuristic based set of rules in an iterative manner and finally followed by a neural network validation system. The extraction of feature is performed using both contour and structure based feature extraction algorithm. The classification is performed by a hybrid neural network that incorporates a hybrid combination of evolutionary algorithm and matrix based solution method. Finally a hamming neural network is used as a lexicon. A benchmark dataset from CEDAR has been used for training and testing.
Medical case retrieval

The proposed PhD project addresses the problem of finding descriptions of diseases or patients' health records that are relevant for a given description of patient's symptoms, also known as medical case retrieval (MCR). Designing an automatic multimodal MCR system applicable to general medical data sets still presents an open research problem, as indicated by the ImageCLEF 2013 MCR challenge, where the best submitted runs achieved only moderate retrieval performance and used purely textual techniques. This project therefore aims at designing a multimodal MCR model that is capable of achieving a substantially better retrieval performance on the ImageCLEF data set than state-of-the-art techniques. Moreover, the potential of further improvement by leveraging relevance feedback of medical expert users for long-term learning will be investigated.
Bradykinin-activated transmembrane signals are coupled via No or Ni to production of inositol 1,4,5-trisphosphate, a second messenger in NG108-15 neuroblastoma-glioma hybrid cells.

The addition of bradykinin to NG108-15 cells results in a transient hyperpolarization followed by prolonged cell depolarization. Injection of inositol 1,4,5-trisphosphate or Ca2+ into the cytoplasm of NG108-15 cells also elicits cell hyperpolarization followed by depolarization. Tetraethylammonium ions inhibit the hyperpolarizing response of cells to bradykinin or inositol 1,4,5-trisphosphate. Thus, the hyperpolarizing phase of the cell response may be due to inositol 1,4,5-trisphosphate-dependent release of stored Ca2+ into the cytoplasm, which activates Ca2+-dependent K+ channels. The depolarizing phase of the cell response to bradykinin is due largely to inhibition of M channels, thereby decreasing the rate of K+ efflux from cells and, to a lesser extent, to activation of Ca2+-dependent ion channels and Ca2+ channels. In contrast, injection of inositol 1,4,5-trisphosphate or Ca2+ into the cytosol did not alter M channel activity. Incubation of NG108-15 cells with pertussis toxin inhibits bradykinin-dependent cell hyperpolarization and depolarization. Bradykinin stimulates low Km GTPase activity and inhibits adenylate cyclase in NG108-15 membrane preparations but not in membranes prepared from cells treated with pertussis toxin. Reconstitution of NG108-15 membranes from cells treated with pertussis toxin with nanomolar concentrations of a mixture of highly purified No and Ni [guanine nucleotide-binding proteins that have no known function (No) or inhibit adenylate cyclase (Ni)] restores bradykinin-dependent activation of GTPase and inhibition of adenylate cyclase. These results show that [bradykinin . receptor] complexes interact with No or Ni and suggest that No and/or Ni mediate the transduction of signals from bradykinin receptors to phospholipase C and adenylate cyclase.
Experimental model of small deep infarcts involving the hypothalamus in rats: changes in body temperature and postural reflex.

BACKGROUND AND PURPOSE Intraluminal middle cerebral artery (MCA) occlusion in rats has been reported to cause hyperthermia assumed to be caused by hypothalamic damage. To clarify the effects of hypothalamic ischemia on body temperature and to obtain a model simulating lacunar infarction, we attempted to produce small infarcts in deep structures (including the hypothalamus). METHODS A surgical suture was advanced to occlude the origin of the hypothalamic (HTA) and/or anterior choroidal arteries (AChA) without compromise of the anterior or middle cerebral artery origins. After treatment, rectal temperature and postural reflex were examined repeatedly for 3 days under nonanesthetic conditions. The AChA and HTA and their link with small deep infarction were then confirmed by TTC, hematoxylin and eosin, and TUNEL stains and by microsurgical dissection after colored silicone perfusion into the cerebral arteries. RESULTS Advancement of the suture near to but not occluding the MCA origin (0.5 to 1.9 mm proximal) produced small, deep, nonneocortical strokes in 25 of 36 animals without producing MCA ischemic changes. These infarctions mainly affected the hypothalamus in 13 animals (HTA area: infarct volume 6+/-1 mm(3)) and involved both the internal capsule and hypothalamus in 12 animals (HTA+AChA area infarct volume 48+/-10 mm(3)). Rats with HTA infarction alone exhibited persistent hyperthermia for 72 hours; some also had transient mild postural abnormality. The AChA+HTA infarct group showed a transient elevation of body temperature for 24 hours and definitive postural abnormality. In the remaining 11 animals, the suture was inadvertently advanced across the MCA origin, producing a large infarct that affected both the neocortex (MCA territory) and nonneocortical structures (volume 381+/-30 mm(3), n=11). The MCA infarct group displayed a transient hyperthermia and severe postural abnormality. CONCLUSIONS When properly positioned, the intraluminal suture method permits selective AChA and/or HTA obstruction without inducing MCA territory ischemia. This model confirms that selective hypothalamic infarction produces significant and sustained temperature regulation abnormalities. The model also may be useful in investigating the pathophysiology of small, deep, end-vessel infarction.
Intermolecular Ordering in Organic Semiconductor Layers and its Correlation to Electronic Properties

This thesis examines the influence of the morphology of organic semiconductors on their electronic properties using analytical transmission electron microscopy (TEM). For the first time, the dielectric properties of organic materials are derived from electron energy loss spectroscopy. A correlation between electron diffraction and current transient measurements of the solution processed polymer poly(3-hexylthiophene) indicates that the semicrystalline structure of the polymer leads to anisotropic charge transport. The study further investigates the structural properties of co-evaporated small molecule blends of fluorinated zincphtalocyanine (F4ZnPc) and fullerene (C60) on different substrates. Energy filtered TEM reveales strong fullerene agglomeration for all substrates considered here, which is shown to be facilitated by an elevated substrate temperature (100°C). These agglomerates are still largely amorphous if the blend is grown on a pristine F4ZnPc layer as required for non-inverted solar cells. However, on an underlying C60-layer, as is typically used for inverted devices, a pronounced order of the fullerene is observed. Device characterization indicates that the highly pure and crystalline C60 domains improve free charge carrier generation and solar cell efficiency. This thesis therefore provides a novel explanation why record efficiencies in small molecule solar cells are only achieved in inverted devices.
Non‐invasive markers for the prediction of fibrosis in chronic hepatitis C infection

Liver fibrosis occurs as a result of chronic liver injury and is the hallmark of chronic liver disease. The final stage of progressive liver fibrosis is cirrhosis, which is implicated in portal hypertension, end‐stage liver disease and hepatocellular carcinoma. Liver biopsy has historically been the gold standard test for the assessment of liver fibrosis for liver diseases such as viral hepatitis, autoimmune hepatitis and primary biliary cirrhosis. Improved serological tests have enhanced the diagnosis of these conditions and reduced the need for liver biopsy. Liver biopsy is unpopular among patients and clinicians. It is associated with morbidity and mortality, and in addition is subject to sampling error, inter‐ and intra‐observer variability. There is therefore a need for non‐invasive markers of liver fibrosis that are accurate, reliable, cheap and easy to use. The aim of this review is to examine the different non‐invasive methods that can be used to estimate the severity of fibrosis. The methods evaluated include clinical examination, routine laboratory investigations, imaging tests, specialized tests of liver function and finally serum extra‐cellular matrix markers of fibrosis. The review mainly focuses on fibrogenesis in the context of chronic hepatitis C infection.
VISUALIZING PASSENGER FLOW IN RAILWAY STATION USING LASER SCANNERS

Our goal in this study is to examine the feasibility for analyzing and visualizing passenger flows using laser scanners in a railway station. A network of laser scanners is located on different places and scan pedestrian's feet at a horizontal plane about 16 cm above the ground. Motion trajectories are extracted from the laser points on moving feet. They are analyzed to find the pattern of passenger flows and its change with time. Through three experiments in railway stations, we concluded that the proposed method is efficient in examining user behaviour even in the crowded stations.