Miracle-dz/UniFAR-FTUs huggingface dataset:
Stage susceptibility of Japanese medaka (Oryzias latipes) to selenomethionine and hypersaline developmental toxicity

Anthropogenic disturbance of seleniferous soils can lead to selenium contamination of waterways. Although selenium is an essential micronutrient, bioaccumulation and maternal transfer of proteinaceous selenomethionine (SeMet) can result in embryo toxicity. Furthermore, as the climate changes, the salinity of spawning grounds in water‐restrained estuaries is increasing. Although a small increase in salinity may not directly impact adult fish, it may alter the detoxification strategies of developing organisms. Previous research indicates that hypersalinity may potentiate SeMet embryo toxicity at an early developmental stage. However, embryonic development is a complex, spatiotemporal process with a constantly shifting cellular microenvironment. To generate thresholds and an adverse outcome pathway for the interactions between selenium and salinity, we sought to identify windows of susceptibility for lethality and deformities in the Japanese medaka (Oryzias latipes). Embryos were treated in freshwater or saltwater for 24 h with 0.5 µM, 5 µM, and 50 µM SeMet at 6 different developmental stages (9, 17, 25, 29, 34, and 38). Survival, hatch, deformities (total, type, and severity), and days to hatch were quantified. Selenium embryo tissue measurements were performed. Selenomethionine exposures of 5 µM and 50 µM significantly decreased survival and hatch at all stages. However, SeMet uptake was stage‐dependent and increased with stage. Stage 17 (early neurulation) was identified as the most susceptible stage for lethality and deformities. Selenomethionine in saltwater caused significantly greater toxicity than freshwater at stage 25 (early organogenesis), suggesting a role for liver and osmoregulatory organogenesis in toxicity. Environ Toxicol Chem 2016;35:1247–1256. © 2015 SETAC
Cerebral response to patient's own name in the vegetative and minimally conscious states

Background: A challenge in the management of severely brain-damaged patients with altered states of consciousness is the differential diagnosis between the vegetative state (VS) and the minimally conscious state (MCS), especially for the gray zone separating these clinical entities. Objective: To evaluate the differences in brain activation in response to presentation of the patient's own name spoken by a familiar voice (SON-FV) in patients with VS and MCS. Methods: By using fMRI, we prospectively studied residual cerebral activation to SON-FV in seven patients with VS and four with MCS. Behavioral evaluation was performed by means of standardized testing up to 3 months post-fMRI. Results: Two patients with VS failed to show any significant cerebral activation. Three patients with VS showed SON-FV induced activation within the primary auditory cortex. Finally, two patients with VS and all four patients with MCS not only showed activation in primary auditory cortex but also in hierarchically higher order associative temporal areas. These two patients with VS showing the most widespread activation subsequently showed clinical improvement to MCS observed 3 months after their fMRI scan. Conclusion: The cerebral responses to patient's own name spoken by a familiar voice as measured by fMRI might be a useful tool to preclinically distinguish minimally conscious state–like cognitive processing in some patients behaviorally classified as vegetative.
Immersive Environments and Virtual Reality: Systematic Review and Advances in Communication, Interaction and Simulation

Today, virtual reality and immersive environments are lines of research which can be applied to numerous scientific and educational domains. Immersive digital media needs new approaches regarding its interactive and immersive features, which means the design of new narratives and relationships with users. Additionally, ICT (information and communication theory) evolves through more immersive and interactive scenarios, it being necessary to design and conceive new forms of representing information and improving users’ interaction with immersive environments. Virtual reality and technologies associated with the virtuality continuum, such as immersive and digital environments, are emerging media. As a medium, this approach may help to build and represent ideas and concepts, as well as developing new languages. This review analyses the cutting-edge expressive, interactive and representative potential of immersive digital technologies. It also considers future possibilities regarding the evolution of these immersive technologies, such as virtual reality, in coming years, in order to apply them to diverse scientific, artistic or informational and educational domains. We conclude that virtual reality is an ensemble of technological innovations, but also a concept, and propose models to link it with the latest in other domains such as UX (user experience), interaction design. This concept can help researchers and developers to design new experiences and conceive new expressive models that can be applied to a wide range of scientific lines of research and educational dynamics.
The regulatory mechanism of a client kinase controlling its own release from Hsp90 chaperone machinery through phosphorylation

It is believed that the stability and activity of client proteins are passively regulated by the Hsp90 (heat-shock protein 90) chaperone machinery, which is known to be modulated by its intrinsic ATPase activity, co-chaperones and post-translational modifications. However, it is unclear whether client proteins themselves participate in regulation of the chaperoning process. The present study is the first example to show that a client kinase directly regulates Hsp90 activity, which is a novel level of regulation for the Hsp90 chaperone machinery. First, we prove that PKCγ (protein kinase Cγ) is a client protein of Hsp90α, and, that by interacting with PKCγ, Hsp90α prevents PKCγ degradation and facilitates its cytosol-to-membrane translocation and activation. A threonine residue set, Thr115/Thr425/Thr603, of Hsp90α is specifically phosphorylated by PKCγ, and, more interestingly, this threonine residue set serves as a ‘phosphorylation switch’ for Hsp90α binding or release of PKCγ. Moreover, phosphorylation of Hsp90α by PKCγ decreases the binding affinity of Hsp90α towards ATP and co-chaperones such as Cdc37 (cell-division cycle 37), thereby decreasing its chaperone activity. Further investigation demonstrated that the reciprocal regulation of Hsp90α and PKCγ plays a critical role in cancer cells, and that simultaneous inhibition of PKCγ and Hsp90α synergistically prevents cell migration and promotes apoptosis in cancer cells.
Effects of medium composition on the morphology and function of rat hepatocytes cultured as spheroids and monolayers

SummaryPrimary hepatocytes cultured as monolayers or as spheroids were studied to compare the effects of four different culture media (Williams' E, Chee's, Sigma Hepatocyte, and HepatoZYME medium). Rat hepatocytes were cultured as conventional monolayers for 3 d or as spheroids for 2 wk. For spheroid formation a method was employed that combined the use of a nonadherent substratum with rotation of cultures. Hepatocyte integrity and morphology were assessed by light and electron microscopy and by reduced glutathione content. Hepatocyte function was measured by albumin secretion and 7-ethoxycoumarin metabolism. Chee's medium was found to be optimal for maintenance of hepatocyte viability and function in monolayers, but it failed to support spheroid formation. For spheroid formation and for the maintenance of spheroid morphology and function, Sigma HM was found to be optimal. These results demonstrate that the medium requirements of hepatocytes differ markedly depending on the culture model employed. Spheroid culture allowed better preservation of morphology and function of hepatocytes compared with conventional monolayer culture. Hepatocytes in spheroids formed bile canaliculi, and expressed an actin distribution resembling that found in hepatocytes in vivo. Albumin secretion was maintained at the same level as that found during the first d in primary culture, and 7-ethoxycoumarin metabolism was maintained over 2 wk in culture at approximately 30% of the levels found in freshly isolated hepatocytes. The improved morphology and function of hepatocyte cultures as spheroids may provide a more appropriate in vitro model for certain applications where the maintenance of liver-specific functions in long-term culture is crucial.
On-the-fly layout generation for PTL macrocells

Pass transistor logic (PTL) has been recently proposed as an alternative to standard MOS for aggressive circuit design. Even though PTL has been successful in a few hand-crafted designs, its acceptance into mainstream digital design critically depends on the availability of tools for logic and physical synthesis and optimization. The automatic synthesis of pass transistor circuits starting from BDDs has been intensively studied in the past with promising results, but back-end tools for PTL cell generation are still missing. We describe an automatic layout generator that has been designed for seamless integration in a library-free PTL design flow. The generator exploits the distinctive characteristics of pass transistor networks produced by synthesis to achieve quality of results comparable with state-of-the art commercial cell generation tools in a function of the execution time.
Manifold learning using robust Graph Laplacian for interactive image search

Interactive image search or relevance feedback is the process which helps a user refining his query and finding difficult target categories. This consists in partially labeling a very small fraction of an image database and iteratively refining a decision rule using both the labeled and unlabeled data. Training of this decision rule is referred to as transductive learning. Our work is an original approach for relevance feedback based on Graph Laplacian. We introduce a new Graph Laplacian which makes it possible to robustly learn the embedding, of the manifold enclosing the dataset, via a diffusion map. Our approach is three-folds: it allows us (i) to integrate all the unlabeled images in the decision process (ii) to robustly capture the topology of the image set and (iii) to perform the search process inside the manifold. Relevance feedback experiments were conducted on simple databases including Olivetti and Swedish as well as challenging and large scale databases including Corel. Comparisons show clear and consistent gain, of our graph Laplacian method, with respect to state-of-the art relevance feedback approaches.
Quorum-Based Asynchronous Power-Saving Protocols for IEEE 802.11 Ad Hoc Networks

This paper investigates the power mode management problem for an IEEE 802.11-based mobile ad hoc network (MANET) that allows mobile hosts to tune to the power-saving (PS) mode. There are two major issues that need to be addressed in this problem: (a) wakeup prediction and (b) neighbor discovery. The former is to deliver buffered packets to a PS host at the right time when its radio is turned on. The latter is to monitor the environment change under a mobile environment. One costly, and not scalable, solution is to time-synchronize all hosts. Another possibility is to design asynchronous protocols as proposed by Tseng et al. in [25]. In this paper, we adopt the latter approach and correlate this problem to the quorum system concept. We identify a rotation closure property for quorum systems. It is shown that any quorum system that satisfies this property can be translated to an asynchronous power-saving protocol for MANETs. Thus, the result bridges the classical quorum system design problem in the area of distributed systems to the power mode management problem in the area of mobile ad hoc networks. We derive a lower bound for quorum sizes for any quorum system that satisfies the rotation closure property. We identify a group of quorum systems that are optimal or near optimal in terms of quorum sizes, which can be translated to efficient asynchronous power-saving protocols. We also propose a new e-torus quorum system, which can be translated to an adaptive protocol that allows designers to trade hosts' neighbor sensibility for power efficiency. Simulation experiments are conducted to evaluate and compare the proposed protocols.
Voting, the Symmetric Group, and Representation Theory

We show how voting may be viewed naturally from an algebraic perspective by viewing voting profiles as elements of certain well-studied $\mathbb{Q}S_n$-modules. By using only a handful of simple combinatorial objects (e.g., tabloids) and some basic ideas from representation theory (e.g., Schur's Lemma), this allows us to recast and extend some well-known results in the field of voting theory.
Adenosine Receptor Regulation of Coronary Blood Flow in Ossabaw Miniature Swine

Adenosine clearly regulates coronary blood flow (CBF); however, contributions of specific adenosine receptor (AR) subtypes (A1, A2A, A2B, A3) to CBF in swine have not been determined. ARs generally decrease (A1, A3) or increase (A2A, A2B) cyclic adenosine monophosphate, a major mediator of vasodilation. We hypothesized that A1 antagonism potentiates coronary vasodilation and coronary stent deployment in dyslipidemic Ossabaw swine elicits impaired vasodilation to adenosine that is associated with increased A1/A2A expression. The left main coronary artery was accessed with a guiding catheter allowing intracoronary infusions. After placement of a flow wire into the left circumflex coronary artery the responses to bolus infusions of adenosine were obtained. Steady-state infusion of AR-specific agents was achieved by using a small catheter fed over the flow wire in control pigs. CBF was increased by the A2-nonselective agonist 2-phenylaminoadenosine (CV1808) in a dose-dependent manner. Baseline CBF was increased by the highly A1-selective antagonist 8-cyclopentyl-1,3-dipropylxanthine (DPCPX), but not changed by other AR-specific agents. The nonselective A2 antagonist 3,7-dimethyl-1-propargylxanthine and A2A-selective antagonist 4-(2-[7-amino-2-(2-furyl)[1,2,4]triazolo[2,3-a][1,3,5]triazin-5-ylamino]ethyl)phenol (ZM241385) abolished adenosine-induced CBF, whereas A2B and A3 antagonism had no effect. Dyslipidemia and stenting decreased adenosine-induced CBF ∼70%, whereas A1, A2A, and A2B mRNA were up-regulated in dyslipidemic versus control >5-fold and there was no change in the ratio of A1/A2A protein in microvessels distal to the stent. In control Ossabaw swine A1 antagonism by DPCPX positively regulated basal CBF. Impaired adenosine-induced CBF after stenting in dyslipidemia is most likely caused by the altered balance between A1 and A2A signaling, not receptor expression.
Functional Outcome of Ischemic and Hemorrhagic Stroke Patients After Inpatient Rehabilitation: A Matched Comparison

Background and Purpose— The goal of this study was to assess the specific influence of stroke etiology on rehabilitation results. Methods— This was a case-control study of 270 inpatients with sequelae of first stroke who were enrolled in homogeneous subgroups and matched for stroke severity, basal disability, age (within 1 year), sex, and onset admission interval (within 3 days) who were different only in terms of stroke origin, infarction versus hemorrhage. We compared the groups’ length of stay, efficiency and effectiveness of treatment, and percentage of low and high responder patients. Odds ratios of dropouts and of low and high therapeutic response were also quantified. Results— Compared with ischemic patients, hemorrhagic patients had significantly higher Canadian Neurological Scale and Rivermead Mobility Index scores at discharge; higher effectiveness and efficiency on the Canadian Neurological Scale, Barthel Index, and Rivermead Mobility Index; and a higher percentage of high responders on the Barthel Index. Hemorrhagic patients showed a probability of a high therapeutic response on the Barthel Index that was ≈2.5 times greater than that of ischemic patients (odds ratio, 2.48; 95% confidence interval, 1.19 to 5.20; accuracy on prediction, 87.06%). Conclusions— The results of this study provide further evidence of better functional prognosis in stroke survivors with hemorrhagic stroke.
Information Theory and Network Coding

This book contains a thorough discussion of the classical topics in information theory together with the first comprehensive treatment of network coding, a subject first emerged under information theory in the mid 1990's that has now diffused into coding theory, computer networks, wireless communications, complexity theory, cryptography, graph theory, etc. With a large number of examples, illustrations, and original problems, this book is excellent as a textbook or reference book for a senior or graduate level course on the subject, as well as a reference for researchers in related fields.
Increased Production of CXCL16 in Experimental and Clinical Heart Failure: A Possible Role in Extracellular Matrix Remodeling

Background—Inflammation has been implicated in the pathogenesis of heart failure (HF), but knowledge about the production and role of inflammatory actors remains incomplete. On the basis of its role in vascular inflammation, vascular proliferation, and matrix degradation, we hypothesized a role for the chemokine CXCL16 in the pathogenesis of myocardial remodeling and development of HF. Methods and Results—Our main findings were (1) patients with chronic HF (n=188) had increased plasma levels of CXCL16, which correlated with disease severity. (2) Left ventricular tissue from patients with end-stage HF (n=8) showed enhanced CXCL16 levels compared with nonfailing left ventricular (n=6) as assessed by Western blotting. (3) In mice with postmyocardial infarction HF, expression of CXCL16, as assessed by real-time RT-PCR, was increased in the infarcted and the noninfarcted areas of left ventricular 3 and 7 days after coronary ligation, indicating early onset of CXCL16 production. Furthermore, mice exposed to aortic banding had enhanced CXCL16 expression in left ventricular, indicating that CXCL16 expression is not related to ischemia alone. (4) In vitro, CXCL16 promoted proliferation and impaired collagen synthesis in myocardial fibroblasts, and in cardiomyocytes and myocardial fibroblasts, CXCL16 increased matrix metalloproteinase activity, primarily reflecting increased matrix metalloproteinase-2 levels. (5) By using specific inhibitors, we showed that the effect of CXCL16 on fibroblasts involved activation of Jun N-terminal kinase. Conclusion—We show enhanced myocardial CXCL16 expression in experimental and clinical HF. The effect of CXCL16 on cardiomyocytes and fibroblasts suggests a role for CXCL16 in matrix remodeling and ultimately in the development of HF.
Severity of coronary artery calcification by electron beam computed tomography predicts silent myocardial ischemia.

BACKGROUND Detection of subclinical coronary artery disease (CAD) before the development of life-threatening cardiac complications has great potential clinical relevance. Electron beam computed tomography (EBCT) is currently the only noninvasive test that can detect CAD in all stages of its development and thus has the potential to be an excellent screening technique for identifying asymptomatic subjects with underlying myocardial ischemia. METHODS AND RESULTS Over 2.5 years, we prospectively studied 3895 generally asymptomatic subjects with EBCT, 411 of whom had stress myocardial perfusion tomography (SPECT) within a close (median, 17 days) time period. SPECT and exercise treadmill results were compared with the coronary artery calcium score (CACS) as assessed by EBCT. The total CACS identified a population at high risk for having myocardial ischemia by SPECT although only a minority of subjects (22%) with an abnormal EBCT had an abnormal SPECT. No subject with CACS <10 had an abnormal SPECT compared with 2.6% of those with scores from 11 to 100, 11.3% of those with scores from 101 to 399, and 46% of those with scores >/=400 (P<0.0001). CACS predicted an abnormal SPECT regardless of subject age or sex. CONCLUSIONS CACS identifies a high-risk group of asymptomatic subjects who have clinically important silent myocardial ischemia. Our results support the role of EBCT as the initial screening tool for identifying individuals at various stages of CAD development for whom therapeutic decision making may differ considerably.
The Climate Change Vulnerability and Risk Management Matrix for the Coastal Zone of The Gambia

Global Climate Change is one of the dire challenges facing the international community today. Coastal zones are vulnerable to its impacts. An effective approach with long-term prospects in addressing climate change impacts is it’s mainstreaming into development agenda of sectoral policies. A comprehensive risk and vulnerability assessment is a pre-requisite to ensure that the right adaptive response is taken for effective integration into developmental plans. The objective of this study is to evaluate and prioritize risks, vulnerability and adaptation issues of current and anticipated impacts of climate change on the coastal zone of The Gambia. The study will also give a methodological contribution for assessing risks, vulnerability and adaptation from the sub-national to local levels. The relevance of this study will be to create a link between the sub-national and local levels in order to facilitate the integration and mainstreaming of climate change into sectoral and local policies for more climate-resilient communities. This will aid in the promotion of strategic investment of constrained developmental resources to actualize successfully dynamic coping strategies, elude ‘maladaptation’ and less compelling responsive measures. A purposive expert sampling technique was used in selecting respondents for the study. The findings of the study reveal that by the end of the 21st century, the climatic variables likely to have the highest impact on the coastal zone of The Gambia are ‘increased flood severity’ and ‘increased temperature’. The coastal zone of The Gambia showed a high vulnerability to these climate change variables. The suggested adaptive response in addressing the impacts of increased flood intensity in the study area includes; improving regulations for restricting agriculture and livestock grazing activities to improve land cover; strengthening of early-warning systems, among others. The suggested adaptive response in addressing the increase in temperature includes: increase crop diversification and rotation to reduce total crop failure; switching to drought-tolerant crop and animal species, among others.