Miracle-dz/UniFAR-FTUs huggingface dataset:
Inter-regional ECoG correlations predicted by communication dynamics, geometry, and correlated gene expression

Electrocorticography (ECoG) provides direct measurements of synchronized postsynaptic potentials at the exposed cortical surface. Patterns of signal covariance across ECoG sensors have been associated with diverse cognitive functions and remain a critical marker of seizure onset, progression, and termination. Yet, a systems level understanding of these patterns (or networks) has remained elusive, in part due to variable electrode placement and sparse cortical coverage. Here, we address these challenges by constructing inter-regional ECoG networks from multi-subject recordings, demonstrate similarities between these networks and those constructed from blood-oxygen-level-dependent signal in functional magnetic resonance imaging, and predict network topology from anatomical connectivity, interregional distance, and correlated gene expression patterns. Our models accurately predict out-of-sample ECoG networks and perform well even when fit to data from individual subjects, suggesting shared organizing principles across persons. In addition, we identify a set of genes whose brain-wide co-expression is highly correlated with ECoG network organization. Using gene ontology analysis, we show that these same genes are enriched for membrane and ion channel maintenance and function, suggesting a molecular underpinning of ECoG connectivity. Our findings provide fundamental understanding of the factors that influence interregional ECoG networks, and open the possibility for predictive modeling of surgical outcomes in disease.
Polarimetric remote sensing of ocean waves

Polarimetric remote sensing provides information about imaged scenes which cannot be obtained from luminance and spectral measurements alone, such as surface orientation, surface roughness, and index of refraction. Exploiting the polarization state of light reflected off of the ocean surface will enable measurement of the two-dimensional slope field of the surface. From this measurement, the significant wave height of the waves can be calculated. This paper presents an initial investigation of remotely-sensed multi-spectral polarimetric time-series imagery collected over a deep-water buoy using Arete Associates' Airborne Remote Optical Spotlight System-MultiSpectral Polarimeter (AROSS-MSP). In addition to preliminary data analysis, we describe a model of the expected polarimetric signature of ocean waves as measured by a remote sensing electro-optical imager. Comparisons between the measured polarimetric data and the modeled polarization signature agree fairly well.
Aspergillus fumigatus flbB Encodes Two Basic Leucine Zipper Domain (bZIP) Proteins Required for Proper Asexual Development and Gliotoxin Production

ABSTRACT The opportunistic human pathogen Aspergillus fumigatus reproduces asexually by forming a massive number of mitospores called conidia. In this study, we characterize the upstream developmental regulator A. fumigatusflbB (AfuflbB). Northern blotting and cDNA analyses reveal that AfuflbB produces two transcripts predicted to encode two basic leucine zipper domain (bZIP) polypeptides, AfuFlbBβ (420 amino acids [aa]) and AfuFlbBα (390 aa). The deletion of AfuflbB results in delayed/reduced sporulation, precocious cell death, the lack of conidiophore development in liquid submerged culture, altered expression of AfubrlA and AfuabaA, and blocked production of gliotoxin. While introduction of the wild-type (WT) AfuflbB allele fully complemented these defects, disruption of the ATG start codon for either one of the AfuFlbB polypeptides leads to a partial complementation, indicating the need of both polypeptides for WT levels of asexual development and gliotoxin biogenesis. Consistent with this, Aspergillus nidulansflbB+ encoding one polypeptide (426 aa) partially complements the AfuflbB null mutation. The presence of 0.6 M KCl in liquid submerged culture suppresses the defects caused by the lack of one, but not both, of the AfuFlbB polypeptides, suggesting a genetic prerequisite for AfuFlbB in A. fumigatus development. Finally, Northern blot analyses reveal that both AfuflbB and AfuflbE are necessary for expression of AfuflbD, suggesting that FlbD functions downstream of FlbB/FlbE in aspergilli.
Requirement analysis for abstracting security in software defined network

Software Defined Network(SDN) decouples the control plane from the data plane. The aim of this decoupling in SDN helps to create an open programmable network. Programmability offers the capability to write custom network modules i.e. topology discovery, switching, routing, traffic monitoring, access control, etc. Building SDN applications in the primary controller(i.e. Pox, Opendaylight, etc.) configuration is tedious due to low-level programming. The programmability in SDN not only allows flexibility in network management but also introduce new security holes. Indeed the researchers have proposed several abstractions for network management, but we believe the similar abstractions for security is needed to realize the holistic view of SDN fully. In this paper, we review the existing programming model and available abstractions for SDN and show the need for a new security abstraction through an example. We determine that existing abstractions lack the expressiveness for security measures precisely. So there is a need for abstractions which can express the threat detection, mitigation or even prevention by analyzing huge number of logs and can classify them into groups based on their intent.
Effects of the P1 Plasmid Centromere on Expression of P1 Partition Genes

ABSTRACT The partition operon of P1 plasmid encodes two proteins, ParA and ParB, required for the faithful segregation of plasmid copies to daughter cells. The operon is followed by a centromere analog, parS, at which ParB binds. ParA, a weak ATPase, represses the par promoter most effectively in its ADP-bound form. ParB can recruit ParA to parS, stimulate its ATPase, and significantly stimulate the repression. We report here that parS also participates in the regulation of expression of the par genes. A single chromosomal parS was shown to augment repression of several copies of the par promoter by severalfold. The repression increase was sensitive to the levels of ParA and ParB and to their ratio. The increase may be attributable to a conformational change in ParA mediated by the parS-ParB complex, possibly acting catalytically. We also observed an in cis effect of parS which enhanced expression of parB, presumably due to a selective modulation of the mRNA level. Although ParB had been earlier found to spread into and silence genes flanking parS, silencing of the par operon by ParB spreading was not significant. Based upon analogies between partitioning and septum placement, we speculate that the regulatory switch controlled by the parS-ParB complex might be essential for partitioning itself.
Rabies Virus‐Inspired Silica‐Coated Gold Nanorods as a Photothermal Therapeutic Platform for Treating Brain Tumors

Rabies virus-inspired silica-coated gold nanorods are fabricated by mimicking size, shape, surface glycoprotein property and in vivo behavior of the rabies virus. These nanorods not only resemble the appearance of the actual rabies virus but also travel into the brain through the neuronal pathway bypassing the blood-brain barrier, and moreover respond to near-infrared laser (808 nm) irradiation, emit heat, and effectively suppress brain tumors.
Nup153 is an M9‐containing mobile nucleoporin with a novel Ran‐binding domain

We employed a phage display system to search for proteins that interact with transportin 1 (TRN1), the import receptor for shuttling hnRNP proteins with an M9 nuclear localization sequence (NLS), and identified a short region within the N‐terminus of the nucleoporin Nup153 which binds TRN1. Nup153 is located at the nucleoplasmic face of the nuclear pore complex (NPC), in the distal basket structure, and functions in mRNA export. We show that this Nup153 TRN1‐interacting region is an M9 NLS. We found that both import and export receptors interact with several regions of Nup153, in a RanGTP‐regulated fashion. RanGTP dissociates Nup153–import receptor complexes, but is required for Nup153–export receptor interactions. We also show that Nup153 is a RanGDP‐binding protein, and that the interaction is mediated by the zinc finger region of Nup153. This represents a novel Ran‐binding domain, which we term the zinc finger Ran‐binding motif. We provide evidence that Nup153 shuttles between the nuclear and cytoplasmic faces of the NPC. The presence of an M9 shuttling domain in Nup153, together with its ability to move within the NPC and to interact with export receptors, suggests that this nucleoporin is a mobile component of the pore which carries export cargos towards the cytoplasm.
Numerical response of a helminth community in the course of a multi-annual abundance cycle of the Water Vole (Arvicola terrestris)

SUMMARY The impact of parasitism on population dynamics is determined in part by the numerical responses of parasites during population fluctuations of their hosts. Vole populations fluctuate in multi-annual cycles allowing such responses to be studied over successive phases of population growth, abundance and decline. We investigate how a helminth community (5 nematode and 7 cestode species) evolved over a full 6-year Water Vole (Arvicola terrestris) population cycle. Brillouin and individual parasite species richness (IPSR) indices were used to measure the numerical response of the parasite community. We report a correlation between levels of parasite intensity and vole population cycle phases. Both indices were consistently higher during pre-decline and decline phases for male and female voles alike. The numerical response of the parasite community suggests that populations may be regulated by parasitism and that studies of this mechanism should allow both for the cyclic or non-cyclic character of the host populations and for the response of the broadest possible set of the local parasite community.
Timely-efficient and reliable topologies for 3-D sensor networks

Recently, sensor network technology has brought the attention of many researchers due to its scalability and efficiency. However, to improve its efficiency level, several design challenging factors should be taken into account. Among these challenges, we focus on the underlying topology of sensor networks in three-dimensional environments and extend a new set of graphs referred to as the Derived Sphere (DSα) graphs from their 2-D version [1][30]. We show that DSα graphs are locally constructed, connected, and have the rotation-ability property. Achieving the connectivity and the rotation-ability properties imply strong reliability for these graphs. Moreover, we show that the new set of graphs has a bounded Euclidean (or length) when 0 < α ≤ 1. Furthermore, via simulations, we confirm and validate these properties. In addition, we demonstrate that DSα graphs outperform 3-D Half Space Proximal (HSP ) and 3-D Gabriel Graph (GG) graphs in terms of network and Euclidean dilations. This, in turn, increases the speed for message delivery. Therefore, the DSα graphs are considered timely-efficient graphs.
A controller design framework for telerobotic systems

A framework for designing a telerobotic system controller is presented. This controller is designed so the dynamic behaviors of the master robot and the slave robot are functions of each other. These functions, which the designer chooses based upon the application, are described, and a control architecture is proposed to achieve these functions. To guarantee that the specified functions and proposed architecture govern the system behavior, H/sub infinity / control theory and model reduction techniques are used. Several experiments were conducted to verify the theoretical derivations. This control method is unique, because it does not require any transfer of either position or velocity information between the master robot and the slave robot; it only requires the transfer of forces. Although this property leads to a wider communication bandwidth between the master and slave robots, the entire system may still suffer from a positional error buildup between the master robot and slave robot. >
Use of lipid-lowering medicinal herbs during pregnancy: A systematic review on safety and dosage

BACKGROUND Hyperlipidemia is one of the important diseases in pregnancy that causes fetal abnormalities during pregnancy and after the birth. Unfortunately, the usual anti-fat drugs are associated with high morbidity in fetus and due to people's inclination towards taking herbs, it is required to identify side effects of medicinal herbs in pregnancy. The aim of this study was to present hypolipidemic herbs that would not any complications for mother and fetus. METHODS In this review article, the major electronic databases such as EBSCO, Central Register of Controlled Trials (CENTRAL), China Network Knowledge Infrastructure (CNKI), Cochrane, Google scholar, MEDLINE, SciVerse, Scopus, and Web of Science were searched using the key words “herbal” and “hyperlipidemia”, “herbal” and “pregnancy” matched by MeSH from their respective inceptions till September, 2016. Total of 1723 publications (145 review articles, 855 original research articles, and 723 abstracts) about the effect of herbals on hyperlipidemia and 682 publications (200 abstracts, 423 original research articles, and 59 review articles) about the effect of herbals in pregnancy were retrieved. At the end, a list of medicinal plants effective on hyperlipidemia alongside their effects on pregnancy was developed. Finally, the plants effective on hyperlipidemia and safe during pregnancy were determined and their dosage, complications, mechanism of action, and side effects were reported. RESULTS A total of 110 effective herbs on hyperlipidemia were identified and complications of 95 plants in pregnancy were studied. At last, among the 55 selected plants effective on hyperlipidemia and examined for pregnancy, we reported 12 herbs with their dosage and special considerations that can be used to treat hyperlipidemia during pregnancy. CONCLUSION Some medicinal plants can be used to treat hyperlipidemia during pregnancy without any significant side effects both on mother or fetus.
Empathetic healthcare services based on u-pillbox system

On the basis of advanced network and sensor technology, u-healthcare (ubiquitous healthcare) systems, which reshape the traditional healthcare systems and enhance e-healthcare (electronic healthcare) systems with awareness of a patient's situation, are the promising healthcare service provision systems. The empathetic personalized u-pillbox system is a heuristic example of u-health care systems that emphasizes humanistic healthcare service provision to the elderly. This paper briefly describes a u-pillbox system, which takes into consideration the characteristics of users, demonstrates a home server based system design, and shows the simulation of how the u-pillbox provides humanistic medication dispensing services. Finally it is addressed that how the system can be extended for potential widely applications such as further healthcare services to elderly users, their family members or other concerned parties.
Cell cycle regulation of cyclin A gene expression by the cyclic AMP-responsive transcription factors CREB and CREM

Cyclin A is a pivotal regulatory protein which, in mammalian cells, is involved in the S phase of the cell cycle. Transcription of the human cyclin A gene is cell cycle regulated. We have investigated the role of the cyclic AMP (cAMP)-dependent signalling pathway in this cell cycle-dependent control. In human diploid fibroblasts (Hs 27), induction of cyclin A gene expression at G1/S is stimulated by 8-bromo-cAMP and suppressed by the protein kinase A inhibitor H89, which was found to delay S phase entry. Transfection experiments showed that the cyclin A promoter is inducible by activation of the adenylyl cyclase signalling pathway. Stimulation is mediated predominantly via a cAMP response element (CRE) located at positions -80 to -73 with respect to the transcription initiation site and is able to bind CRE-binding proteins and CRE modulators. Moreover, activation by phosphorylation of the activators CRE-binding proteins and CRE modulator tau and levels of the inducible cAMP early repressor are cell cycle regulated, which is consistent with the pattern of cyclin A inducibility by cAMP during the cell cycle. These results suggest that the CRE is, at least partly, implicated in stimulation of cyclin A transcription at G1/S.
Neonatal outcome in obstetric cholestasis patients at Ayub Teaching Hospital Abbottabad.

BACKGROUND Obstetric cholestasis is a liver disease specific to pregnancy characterised by pruritus affecting the whole body but particularly the palms and soles and abnormal liver function tests. Objective of this cross sectional study was to evaluate obstetric cholestasis as a potential risk factor for adverse neonatal outcome. The study was conducted at Department of Obstetrics and Gynaecology, Unit 'B', Ayub Teaching Hospital, Abbottabad from April 1, 2007 to March 31, 2008. METHODS All patients presenting with obstetric cholestasis irrespective of their age and parity were included in the study. Patients presenting with other causes of pruritus during pregnancy like Hepatitis (A, B, C), eczema, pruritus gravidarum and herpes gestationes were excluded from the study. Patients with liver involvement due to pre-eclampsia were also excluded. Baseline investigations, liver chemistries, viral screening, liver autoimmune screen, liver and obstetrical ultrasound were all done before the diagnosis was confirmed. Patients were treated symptomatically. Neonatal outcome was calculated in terms of increased incidence of passage of meconium, preterm delivery and foetal distress requiring delivery by Caesarean-Section. RESULTS Thirty patients were selected. Babies of 10 patients did well after delivery, 8 required NICU care within first 24 hours of birth and rest were delivered with low APGAR score. Two babies were delivered stillborn. CONCLUSION Pruritus is quite common in pregnancy with obstetric cholestasis being one of them and earlier detection of the disease allows better identification of foetuses at risk.
Parallel Secretion of Pancreatic Phospholipase A2, Phospholipase A1, Lipase, and Colipase in Children with Exocrine Pancreatic Dysfunction

The cosecretion of pancreatic lipase and colipase are important in normal fat digestion. As adsorption of phosphatidylcholine to the lipid substrate interferes with lipase activity, hydrolysis to lysophosphatidylcholine with subsequent desorption is also essential for fat digestion. There are some data regarding the secretion of pancreatic phospholipases in normal adults but none in children or patients with pancreatic disease. In the present study, we aimed a) to develop an accurate fast assay method to measure phospholipase A2 and b) to determine the secretion rate of pancreatic phospholipase A2 and whether it is cosecreted with lipase and colipase in children with exocrine pancreatic dysfunction. Nine male patients aged 0.5 to 16 y (seven with cystic fibrosis, two with malabsorption) underwent pancreatic stimulation tests. Their colipase and lipase secretion rates were measured by titrimetric methods and phospholipase A2 and A1 by phosphorus magnetic resonance spectroscopy (31P NMR). It was found that the phospholipases, colipase, and lipase were absent in the two patients with pancreatic insufficiency. In patients with normal absorption, there were marked inter-and intrasubject variations of lipase, colipase, and phospholipase secretion rates that were consistent with the degree of exocrine pancreatic dysfunction. However, in the three 20-min stimulation periods of the pancreatic function test, pancreatic phospholipase is cosecreted with lipase and colipase, and average colipase and phospholipase A2 secretion rates follow a similar or parallel pattern. These findings are consistent with the important role of pancreatic phospholipases in intestinal phospholipid hydrolysis leading to the desorption of phospholipids from the lipid substrate and enhancing lipid hydrolysis and phospholipid absorption.
Retinaldehyde dehydrogenase 2 (RALDH2)- independent patterns of retinoic acid synthesis in the mouse embryo

Knockout of the murine retinoic acid (RA)-synthesizing enzyme retinaldehyde dehydrogenase 2 (RALDH2) gene leads to early morphogenetic defects and embryonic lethality. Using a RA-responsive reporter transgene, we have looked for RA-generating activities in Raldh2-null mouse embryos and investigated whether these activities could be ascribed to the other known RALDH enzymes (RALDH1 and RALDH3). To this end, the early defects of Raldh2−/− embryos were rescued through maternal dietary RA supplementation under conditions that do not interfere with the activity of the reporter transgene in WT embryos. We show that RALDH2 is responsible for most of the patterns of reporter transgene activity in the spinal cord and trunk mesodermal derivatives. However, reporter transgene activity was selectively detected in Raldh2−/− embryos within the mesonephric area that expresses RALDH3 and in medial-ventral cells of the spinal cord and posterior hindbrain, up to the level of the fifth rhombomere. The craniofacial patterns of RA-reporter activity were unaltered in Raldh2−/− mutants. Although these patterns correlated with the presence of Raldh1 and/or Raldh3 transcripts in eye, nasal, and inner ear epithelia, no such correlation was found within forebrain neuroepithelium. These data suggest the existence of additional RA-generating activities in the differentiating forebrain, hindbrain, and spinal cord, which, along with RALDH1 and RALDH3, may account for the development of Raldh2−/− mutants once these have been rescued for early lethality.
Inhibition of Cell Proliferation, Vascular Endothelial Growth Factor and Tumor Growth by Albendazole

Vascular endothelial growth factor (VEGF) is the key molecule mediating tumor growth and malignant ascites formation. We recently reported that, in an end stage OVCAR-3 xenograft model, albendazole (ABZ) suppresses ascites formation, but not tumor growth. Hence, in the present study, we assessed the effect of ABZ on in vitro OVCAR-3 cell proliferation plus in vivo tumor growth, however, initiating ABZ treatment at mid stage (3 weeks post cell inoculation) rather than end stage disease. Here, ABZ treatment led to potent inhibition of cell proliferation, VEGF suppression, complete inhibition of ascites formation and most strikingly arrest of tumor growth.