Miracle-dz/UniFAR-FTUs huggingface dataset:
Associative memory by collective regulation of non-coding RNA

The majority of mammalian genomic transcripts do not directly code for proteins and it is currently believed that most of these are not under evolutionary constraint. However given the abundance non-coding RNA (ncRNA) and its strong affinity for inter-RNA binding, these molecules have the potential to regulate proteins in a highly distributed way, similar to artificial neural networks. We explore this analogy by devising a simple architecture for a biochemical network that can function as an associative memory. We show that the steady state solution for this chemical network has the same structure as an associative memory neural network model. By allowing the choice of equilibrium constants between different ncRNA species, the concentration of unbound ncRNA can be made to follow any pattern and many patterns can be stored simultaneously. The model is studied numerically and within certain parameter regimes it functions as predicted. Even if the starting concentration pattern is quite different, it is shown to converge to the original pattern most of the time. The network is also robust to mutations in equilibrium constants. This calls into question the criteria for deciding if a sequence is under evolutionary constraint.
Gentamicin Rapidly Inhibits Mitochondrial Metabolism in High-Frequency Cochlear Outer Hair Cells

Aminoglycosides (AG), including gentamicin (GM), are the most frequently used antibiotics in the world and are proposed to cause irreversible cochlear damage and hearing loss (HL) in 1/4 of the patients receiving these life-saving drugs. Akin to the results of AG ototoxicity studies, high-frequency, basal turn outer hair cells (OHCs) preferentially succumb to multiple HL pathologies while inner hair cells (IHCs) are much more resilient. To determine if endogenous differences in IHC and OHC mitochondrial metabolism dictate differential sensitivities to AG-induced HL, IHC- and OHC-specific changes in mitochondrial reduced nicotinamide adenine dinucleotide (NADH) fluorescence during acute (1 h) GM treatment were compared. GM-mediated decreases in NADH fluorescence and succinate dehydrogenase activity were observed shortly after GM application. High-frequency basal turn OHCs were found to be metabolically biased to rapidly respond to alterations in their microenvironment including GM and elevated glucose exposures. These metabolic biases may predispose high-frequency OHCs to preferentially produce cell-damaging reactive oxygen species during traumatic challenge. Noise-induced and age-related HL pathologies share key characteristics with AG ototoxicity, including preferential OHC loss and reactive oxygen species production. Data from this report highlight the need to address the role of mitochondrial metabolism in regulating AG ototoxicity and the need to illuminate how fundamental differences in IHC and OHC metabolism may dictate differences in HC fate during multiple HL pathologies.
Low voltage low power neuron circuit design based on subthreshold FGMOS transistors and XOR implementation

In this work, design of low-voltage low-power analog artificial neural network (ANN) circuit blocks by using subthreshold floating-gate MOS (FGMOS) transistors and a neuron circuit is implemented. The circuit blocks, four-quadrant analog current multiplier and FGMOS based differential pair, have been designed and simulated in CADENCE environment with TSMC 0. 35µm process parameters. Using the proposed neuron circuits a neural network was realized. XOR problem was applied to test accuracy of the network and the results were concluded.
Moral preferences

How do humans or machines make a decision? Whenever we make a decision, we consider our preferences over the possible options. Also, in a social context, collective decisions are made by aggregating the preferences of the individuals. AI systems that support individual and collective decision making have been studied for a long time, and several preference modelling and reasoning frameworks have been defined and exploited in order to provide rationality to the decision process and its result. However, little effort has been devoted to understand whether this decision process, or its result, is ethical or moral. Rationality does not imply morality. How can we embed morality into a decision process? And how do we ensure that the decision we make, as an individual or a collectivity of individuals, are moral? In other words, how do we pass from the individuals’ personal preferences to moral behaviour and decision making? When we pass from humans to AI systems, the task of modelling and embedding morality and ethical principles is even more vague and elusive. Are the existing ethical theories applicable also to AI systems? On one hand, things seem easier since we can narrow the scope of an AI system, so that the contextual information can help us in define the correct moral values it should work according to. However, it is not clear what moral values we should embed in the system, nor how to embed them. Should we code them in a set of rules, or should we let the system learn the values by observing us humans? Preferences and ethical theories are not that different in one respect: they both define priorities over actions. So, can we use existing preference formalisms to also model ethical theories? We discuss how to exploit and adapt current preference formalisms in order to model morality and ethics theories, as well as the dynamic integration of moral code into personal preferences. We also discuss the use of meta-preferences, since morality seems to need a way to judge preferences according to their morality level. It is imperative that we build intelligent systems which behave morally. To work and live with us, we need to trust such systems, and this requires that we are ”reasonably” sure that it behaves morally, according to values that are aligned to the
Two-way successively refined joint source-channel coding

Consider a source, {X/sub i/,Y/sub i/}/sub i=1//sup /spl infin//, producing independent copies of a pair of jointly distributed random variables (RVs). The {X/sub i/} part of the process is observed at some location, say A, and is supposed to be reproduced at a different location, say B, where the {Y/sub i/} part of the process is observed. Similarly, {Y/sub i/} should be reproduced at location A. The communication between the two locations is carried out across two memoryless channels in K iterative bi-directional rounds. In each round, the source components are reconstructed at the other locations based on the information exchanged in all previous rounds and the source component known at that location, and it is desired to find the amount of information that should be exchanged between the two locations in each round, so that the distortions incurred (in each round) will not exceed given thresholds. Our setting extends the results of Steinberg and Merhav as well as Kaspi, combining the notion of successive refinement with this of two-way interactive communication. We first derive a single-letter characterization of achievable rates for a pure source-coding problem with successive refinement. Then, for a joint source-channel coding setting, we prove a separation theorem, asserting that in the limit of long blocks, no optimality is lost by first applying lossy (two-way) successive-refinement source coding, regardless of the channels, and then applying good channel codes to each one of the resulting bitstreams, regardless of the source.
Situations, a General Framework for Studying Information Retrieval

This paper presents a framework for the theoretical comparison of information retrieval models based on how the models decide aboutness. The framework is based on concepts emerging from the eld of situation theory. So called infons and profons represent elementary information carriers which can be manipulated by union and fusion operators. These operators allow relationships between information carriers to be established. Sets of infons form so called situations which are used to model the information born by objects such as documents. An arbitrary information retrieval model can be mapped down into the framework. Special functions are de ned for this purpose depending on the model at hand. An important aspect is the inference mechanism which is mapped to inference between situations. Two examples are given based on the Boolean retrieval and coordination level matching models. The framework allows the comparison of retrieval models at an abstract level. Starting from an axiomatization of aboutness, retrieval models can be compared according to which axioms they are governed by. This approach is highlighted by the theoretical comparison of Boolean retrieval with coordinate level matching. This work was partly performed while employed at the Utrecht University.
Transmission Policies for Energy Harvesting Sensors with Time-Correlated Energy Supply

This paper considers a wireless sensor powered by an energy harvesting device, which reports data of varying importance to its receiver. Modeling the ambient energy supply by a two-state Markov chain ("GOOD" and "BAD"), assuming a finite battery capacity constraint, and associating data transmission with a given energy cost, we propose low-complexity transmission policies, that achieve near-optimal performance in terms of the average long-term importance of the reported data. In particular, we derive the performance of the Balanced Policy (BP), which adapts the transmission probability to the harvesting state, such that energy harvesting and consumption are balanced. Our analysis demonstrates that the performance of the BP largely depends on the power-to-depletion, defined as the power that a fully charged battery can supply on average over a BAD period. Numerical results show that the optimal BP achieves near-optimal performance and that a BP which avoids energy overflow further reduces the gap with respect to the globally optimal policy. A heuristic BP, based on the analysis of a system with a deterministic and periodic energy supply, is also proposed, and the parallels between the deterministic system and its stochastic counterpart are discussed.
Subjective neuronal coding of reward: temporal value discounting and risk

A key question in the neurobiology of reward relates to the nature of coding. Rewards are objects that are advantageous or necessary for the survival of individuals in a variety of environmental situations. Thus reward appears to depend on the individual and its environment. The question arises whether neuronal systems in humans and monkeys code reward in subjective terms, objective terms or both. The present review addresses this issue by dealing with two important reward processes, namely the individual discounting of reward value across temporal delays, and the processing of information about risky rewards that depends on individual risk attitudes. The subjective value of rewards decreases with the temporal distance to the reward. In experiments using neurophysiology and brain imaging, dopamine neurons and striatal systems discount reward value across temporal delays of a few seconds, despite unchanged objective reward value, suggesting subjective value coding. The subjective values of risky outcomes depend on the risk attitude of individual decision makers; these values decrease for risk‐avoiders and increase for risk‐seekers. The signal for risk and the signal for the value of risky reward covary with individual risk attitudes in regions of the human prefrontal cortex, suggesting subjective rather than objective coding of risk and risky value. These data demonstrate that important parameters of reward are coded in a subjective manner in key reward structures of the brain. However, these data do not rule out that other neurons or brain structures may code reward according to its objective value and risk.
Power aware network interface management for streaming multimedia

A significant fraction of the power in portable devices (handheld terminals, PDAs, laptops, etc.) is drawn by the wireless network interface card (NIC). We test the viability of a novel power management technique, based on the exploitation of the NIC off-mode while a client-controlled streaming multimedia application is in progress. The basic idea is to switch off the card while frames are being played back, until a low-threshold level is reached in the client buffer. In this paper, pessimistic assumptions are made on the timing and power overheads associated with recovering the card from off-mode, but nevertheless a power saving of about 25% is achieved over the average power consumption incurred by the standard IEEE 802.11 mechanism. We also provide design curves showing the minimum buffer size that makes our technique effective, as a function of the network bandwidth and of the card characteristics.
Rodent Animal Models for Surrogate Analysis of Cell Therapy in Acute Liver Failure

Without therapeutic intervention acute liver failure (ALF) is the consequence of a progredient destruction of the liver parenchyma due to metabolic exhaustion of the hepatocytes. Perivenous hepatocytes are responsible for the detoxification of noxious compounds via the cytochrome P450 enzyme system. Liver transplantation is the only remaining therapeutic option in the end-stage of the disease. Assuming that metabolic capacity could be provided by healthy hepatocytes and thus substitute for the genuine parenchymal cells hepatocyte transplantation since quite some time is considered to be an alternative to whole liver transplantation. While this hypothesis achieved proof-of-concept in animal trials clinical breakthrough is still awaiting success, the reasons of which are ongoing matter of debate. In recent times mesenchymal stem cells (MSC) came into focus as a transplantable cell source to treat ALF. Interestingly, as demonstrated in various rodent animal models their mode of action is rather based on trophic support of hepatocytes remaining in the damaged host parenchyma rather than substitution of tissue loss. Mechanistically, either direct or indirect paracrine effects from the transplanted cells acting pro-proliferative, anti-apoptotic, and anti-inflammatory seem to trigger the regenerative response of the residual healthy hepatocytes in the otherwise lethally injured liver parenchyma. Thus, allogeneic MSC may be the best choice for the treatment of ALF taking advantage of their short-term benefit to sustain the critical phase of the acute insult avoiding long-term immunosuppression.
A single chip FSK/ASK 900 MHz transceiver in a standard 0.25 um CMOS technology

This paper presents a low power consumption single chip FSK/ASK transceiver for half-duplex low datarate communication in the 868-870 MHz band. The IC was processed in a standard 0.25 um CMOS technology, offers a very high level of integration and needs only few external components. The transmit/receive RF front end contains a high efficiency power amplifier, a low noise amplifier (LNA), a double balanced RF mixer and an I/Q mixer for down conversion to an intermediate frequency (IF) of 289 MHz and further to zero IF. The transmit/receive frequency synthesis of 868/1157 MHz is done by a fully integrated switchable frequency range voltage controlled oscillator (VCO), a phase locked loop synthesizer (PLL) and a tunable crystal oscillator used as reference frequency generator as well as FSK modulator. A bandwidth configurable I/Q channel select filter, an I/Q limiter with RSSI generation used also for AM demodulation, a FSK demodulator, a bandwidth configurable data filter and a dataslicer are implemented for further zero IF and baseband analog signal processing. The transceiver can be configured by a 2/3-wire bus interface. Low-drop voltage regulators are implemented to allow supply voltages up to 3.6 V because the maximum allowed voltages for the standard MOS transistors are 2.8 V. The overall current consumption of the transceiver in the receive and transmit mode is 11 mA and 20 mA, respectively. Additionally, a standby mode and idle mode is realized to increase battery lifetime.
Why Tell Children: A Synthesis of the Global Literature on Reasons for Disclosing or Not Disclosing an HIV Diagnosis to Children 12 and under

While the psychological and health benefits of knowing one’s HIV diagnosis have been documented for adults and adolescents, practice is still in development for younger children. Moderating conditions for whether or not to tell a child he/she has HIV vary by region and local context. They include accessibility of treatment, consideration of HIV as a stigmatizing condition, prevalence of HIV, and an accompanying presumption that any illness is HIV-related, parent or caregiver concerns about child reactions, child’s worsening health, assumptions about childhood and child readiness to know a diagnosis, and lack of policies such as those that would prevent bullying of affected children in schools. In this systematic review of the global literature, we summarize the reasons caregivers give for telling or not telling children 12 and under their HIV diagnosis. We also include articles in which children reflect on their desires for being told. While a broad number of reasons are given for telling a child – e.g., to aid in prevention, adaptation to illness (e.g., primarily to promote treatment adherence), understanding social reactions, and maintaining the child–adult relationship – a narrower range of reasons, often related to immediate child or caregiver well-being or discomfort, are given for not telling. Recommendations are made to improve the context for disclosure by providing supports before, during, and after disclosure and to advance the research agenda by broadening samples and refining approaches.
Rank-order filter design with a sampled-analog multiple-winners-take-all core

We propose a sampled-analog rank-order filter (ROF) architecture of complexity O(n/sup 2/). It yields a very compact structure because the devices used are essentially of minimum geometry. Its sole active building block being the simple CMOS inverter, the circuit exhibits an excellent low-voltage compatibility. Furthermore, it can support a rail-to-rail common-mode input range. It is inherently fast due to fully parallel signal processing and speed is expected to increase with technological scaling at the same rate as purely digital circuitry. Finally, it supports full programmability of the rank by means of an analog reference voltage. The ROF is based on a pair of multiple-winners-take-all (mWTA) circuits and a set of AND gates. The paper includes a description of the architecture and a detailed analysis of the mWTA. Most relevant design issues are addressed and experimental results obtained from a fabricated ROF are presented.
Severe Acute Respiratory Syndrome Coronavirus nsp1 Suppresses Host Gene Expression, Including That of Type I Interferon, in Infected Cells

ABSTRACT The severe acute respiratory syndrome coronavirus (SARS-CoV) nsp1 protein has unique biological functions that have not been described in the viral proteins of any RNA viruses; expressed SARS-CoV nsp1 protein has been found to suppress host gene expression by promoting host mRNA degradation and inhibiting translation. We generated an nsp1 mutant (nsp1-mt) that neither promoted host mRNA degradation nor suppressed host protein synthesis in expressing cells. Both a SARS-CoV mutant virus, encoding the nsp1-mt protein (SARS-CoV-mt), and a wild-type virus (SARS-CoV-WT) replicated efficiently and exhibited similar one-step growth kinetics in susceptible cells. Both viruses accumulated similar amounts of virus-specific mRNAs and nsp1 protein in infected cells, whereas the amounts of endogenous host mRNAs were clearly higher in SARS-CoV-mt-infected cells than in SARS-CoV-WT-infected cells, in both the presence and absence of actinomycin D. Further, SARS-CoV-WT replication strongly inhibited host protein synthesis, whereas host protein synthesis inhibition in SARS-CoV-mt-infected cells was not as efficient as in SARS-CoV-WT-infected cells. These data revealed that nsp1 indeed promoted host mRNA degradation and contributed to host protein translation inhibition in infected cells. Notably, SARS-CoV-mt infection, but not SARS-CoV-WT infection, induced high levels of beta interferon (IFN) mRNA accumulation and high titers of type I IFN production. These data demonstrated that SARS-CoV nsp1 suppressed host innate immune functions, including type I IFN expression, in infected cells and suggested that SARS-CoV nsp1 most probably plays a critical role in SARS-CoV virulence.
Scheduling network requests with transmission window

We consider the problem of bulk data transfers and bandwidth sharing in the context of grid infrastructures. Grid computing empowers high-performance computing in a large-scale distributed environment. Network bandwidth, which makes the expensive computational and storage resources work in concert, plays an active role on performance. Due to specific traffic patterns, network topology and application scenarios, bandwidth sharing encounters new challenges. From this perspective, this research report looks at bulk transfers among computing and storage elements. Referred to as short-lived, transfer requests with transmission window and volume are scheduled in the network. By manipulating the transmission window, the request accept rate and network resource utilization are to be optimized. The formulated optimization problem is proven NP-complete. Associated with proposed heuristics, simulations are carried out to study each bandwidth sharing strategy and its application scenarios. A tuning factor, that allows adaptation of performance objective, is introduced to adjust network infrastructure and workload.
Inhibition of hemangiogenesis and lymphangiogenesis after normal-risk corneal transplantation by neutralizing VEGF promotes graft survival.

PURPOSE To evaluate the occurrence and time course of hem- and lymphangiogenesis after normal-risk corneal transplantation in the mouse model and to test whether pharmacologic strategies inhibiting both processes improve long-term graft survival. METHODS Normal-risk allogeneic (C57BL/6 to BALB/c) and syngeneic (BALB/c to BALB/c) corneal transplantations were performed and occurrence and time course of hem- and lymphangiogenesis after keratoplasty was observed, by using double immunofluorescence of corneal flatmounts (with CD31 as a panendothelial and LYVE-1 as a lymphatic vascular endothelium-specific marker). A molecular trap designed to eliminate VEGF-A (VEGF Trap(R1R2); 12.5 mg/kg) was tested for its ability to inhibit both processes after keratoplasty and to promote long-term graft survival (intraperitoneal injections on the day of surgery and 3, 7, and 14 days later). RESULTS No blood or lymph vessels were detectable immediately after normal-risk transplantation in either donor or host cornea, but hem- and lymphangiogenesis were clearly visible at day 3 after transplantation. Both vessel types reached donor tissue at 1 week after allografting and similarly after syngeneic grafting. Early postoperative trapping of VEGF-A significantly reduced both hem- and lymphangiogenesis and significantly improved long-term graft survival (78% vs. 40%; P < 0.05). CONCLUSIONS There is concurrent, VEGF-A-dependent hem- and lymphangiogenesis after normal-risk keratoplasty within the preoperatively avascular recipient bed. Inhibition of hem- and lymphangiogenesis (afferent and efferent arm of an immune response) after normal-risk corneal transplantation improves long-term graft survival, establishing early postoperative hem- and lymphangiogenesis as novel risk factors for graft rejection even in low-risk eyes.