Miracle-dz/UniFAR-FTUs huggingface dataset:
Comparative study of sequence-dependent hybridization kinetics in solution and on microspheres

Hybridization kinetics of DNA sequences with known secondary structures and random sequences designed with similar melting temperatures were studied in solution and when one strand was bound to 5 μm silica microspheres. The rates of hybridization followed second-order kinetics and were measured spectrophotometrically in solution and fluorometrically in the solid phase. In solution, the rate constants for the model sequences varied by almost two orders of magnitude, with a decrease in the rate constant with increasing amounts of secondary structure in the target sequence. The random sequences also showed over an order of magnitude difference in the rate constant. In contrast, the hybridization experiments in the solid phase with the same model sequences showed almost no change in the rate constant. Solid phase rate constants were approximately three orders of magnitude lower compared with the solution phase constants for sequences with little or no single-stranded structure. Sequences with a known secondary structure yielded solution phase rate constants as low as 3 × 103 M−1 s−1 with solid phase rate constants for the same sequences measured at 2.5 × 102 M−1 s−1. The results from these experiments indicate that (i) solid phase hybridization occurs three orders of magnitude slower than solution phase, (ii) trends observed in structure-dependent kinetics of solution phase hybridization may not be applicable to solid phase hybridization and (iii) model probes with known secondary structure decrease reaction rates; however, even random sequences with no known internal single-stranded structure can yield a broad range of reaction rates.
Capacity evaluation of MIMO systems by Monte-Carlo methods

In order to form the theoretical information foundation of multiple input and multiple output channel techniques and its applications, the analysis and simulations of the capacity of MIMO based on Monte-Carlo are presented in this paper. We can get a conclusion that with a circularly symmetric Gaussian transmit vector, the extremely high capacity of the Rayleigh fading MIMO channel can be achieved.
The E3 ubiquitin ligase NEDD4 induces endocytosis and lysosomal sorting of connexin 43 to promote loss of gap junctions

ABSTRACT Intercellular communication via gap junctions has an important role in controlling cell growth and in maintaining tissue homeostasis. Connexin 43 (Cx43; also known as GJA1) is the most abundantly expressed gap junction channel protein in humans and acts as a tumor suppressor in multiple tissue types. Cx43 is often dysregulated at the post-translational level during cancer development, resulting in loss of gap junctions. However, the molecular basis underlying the aberrant regulation of Cx43 in cancer cells has remained elusive. Here, we demonstrate that the oncogenic E3 ubiquitin ligase NEDD4 regulates the Cx43 protein level in HeLa cells, both under basal conditions and in response to protein kinase C activation. Furthermore, overexpression of NEDD4, but not a catalytically inactive form of NEDD4, was found to result in nearly complete loss of gap junctions and increased lysosomal degradation of Cx43 in both HeLa and C33A cervical carcinoma cells. Collectively, the data provide new insights into the molecular basis underlying the regulation of gap junction size and represent the first evidence that an oncogenic E3 ubiquitin ligase promotes loss of gap junctions and Cx43 degradation in human carcinoma cells. Highlighted Article: The proto-oncogenic E3 ubiquitin ligase NEDD4 induces ubiquitylation and lysosomal degradation of connexin 43, a protein that is often dysregulated during cancer development, resulting in loss of gap junctions in human carcinoma cells.
Functional Information Stored in the Conserved Structural RNA Domains of Flavivirus Genomes

The genus Flavivirus comprises a large number of small, positive-sense single-stranded, RNA viruses able to replicate in the cytoplasm of certain arthropod and/or vertebrate host cells. The genus, which has some 70 member species, includes a number of emerging and re-emerging pathogens responsible for outbreaks of human disease around the world, such as the West Nile, dengue, Zika, yellow fever, Japanese encephalitis, St. Louis encephalitis, and tick-borne encephalitis viruses. Like other RNA viruses, flaviviruses have a compact RNA genome that efficiently stores all the information required for the completion of the infectious cycle. The efficiency of this storage system is attributable to supracoding elements, i.e., discrete, structural units with essential functions. This information storage system overlaps and complements the protein coding sequence and is highly conserved across the genus. It therefore offers interesting potential targets for novel therapeutic strategies. This review summarizes our knowledge of the features of flavivirus genome functional RNA domains. It also provides a brief overview of the main achievements reported in the design of antiviral nucleic acid-based drugs targeting functional genomic RNA elements.
Prognostic Factors for Outcome in Patients With Aneurysmal Subarachnoid Hemorrhage

Background and Purpose— The purpose of this study was to describe prognostic factors for outcome in a large series of patients undergoing neurosurgical clipping of aneurysms after subarachnoid hemorrhage (SAH). Methods— Data were analyzed from 3567 patients with aneurysmal SAH enrolled in 4 randomized clinical trials between 1991 and 1997. The primary outcome measure was the Glasgow outcome scale 3 months after SAH. Multivariable logistic regression with backwards selection and Cox proportional hazards regression models were derived to define independent predictors of unfavorable outcome. Results— In multivariable analysis, unfavorable outcome was associated with increasing age, worsening neurological grade, ruptured posterior circulation aneurysm, larger aneurysm size, more SAH on admission computed tomography, intracerebral hematoma or intraventricular hemorrhage, elevated systolic blood pressure on admission, and previous diagnosis of hypertension, myocardial infarction, liver disease, or SAH. Variables present during hospitalization associated with poor outcome were temperature >38°C 8 days after SAH, use of anticonvulsants, symptomatic vasospasm, and cerebral infarction. Use of prophylactic or therapeutic hypervolemia or prophylactic-induced hypertension were associated with a lower risk of unfavorable outcome. Time from admission to surgery was significant in some models. Factors that contributed most to variation in outcome, in descending order of importance, were cerebral infarction, neurological grade, age, temperature on day 8, intraventricular hemorrhage, vasospasm, SAH, intracerebral hematoma, and history of hypertension. Conclusions— Although most prognostic factors for outcome after SAH are present on admission and are not modifiable, a substantial contribution to outcome is made by factors developing after admission and which may be more easily influenced by treatment.
Truncated decompositions and filtering methods with Reflective/Anti-Reflective boundary conditions: a comparison

The paper analyzes and compares some spectral filtering methods as truncated singular/eigen-value decompositions and Tikhonov/Re-blurring regularizations in the case of the recently proposed Reflective [M.K. Ng, R.H. Chan, and W.C. Tang, A fast algorithm for deblurring models with Neumann boundary conditions, SIAM J. Sci. Comput. , 21 (1999), no. 3, pp.851-866] and Anti-Reflective [S. Serra Capizzano, A note on anti-reflective boundary conditions and fast deblurring models, SIAM J. Sci. Comput. , 25-3 (2003), pp. 1307-1325] boundary conditions. We give numerical evidence to the fact that spectral decompositions (SDs) provide a good image restoration quality and this is true in particular for the Anti-Reflective SD, despite the loss of orthogonality in the associated transform. The related computational cost is comparable with previously known spectral decompositions, and results substantially lower than the singular value decomposition. The model extension to the cross-channel blurring phenomenon of color images is also considered and the related spectral filtering methods are suitably adapted.
Instance Search Based on Parallel Approximate Searches

ORAND is a Chilean company focused on developing applied research in Computer Science. This paper describes the participation of the PRISMA-ORAND team for the Instance Search task (INS) at TRECVID 2012. Currently, the most common technique used to address the Instance Search problem is the codebook approach or some extension of it. In our participation we preferred a different approach which consisted in retrieving k nearest neighbors (k-NN) for each query descriptor on the full set of descriptors instead of computing a codebook. In order to efficiently solve the k-NN searches in large datasets we perform several parallel approximate searches using the open source project P-VCD and the Amazon Elastic Compute Cloud (EC2) service. We submitted four Runs to TRECVID 2012 INS task, namely: prisma-two180px, prisma-four90px, prisma-two90px, and prisma-one180px. In general, these Runs achieve satisfactory performance as their MAP are higher than the median of all the Runs in most of the topics. Additionally, we tested a fifth Run prisma-two280px by increasing both number of descriptors and search accuracy. This last Run demanded higher computational power to solve the k-NN searches but it highly improved the effectiveness compared with initial four Runs. The performance achieved by the presented approach shows some promising results. It presents an alternative to codebook approaches that can achieve satisfactory results in the Instance Search problem. The parallelization and approximation enable to solve k-NN searches in large datasets achieving high effectiveness. However, more research is needed in order to determine the potential performance that can be reached by k-NN searches compared to codebook approaches.
PLAT: An Automated Fault and Behavioural Anomaly Detection Tool for PLC Controlled Manufacturing Systems

Operational faults and behavioural anomalies associated with PLC control processes take place often in a manufacturing system. Real time identification of these operational faults and behavioural anomalies is necessary in the manufacturing industry. In this paper, we present an automated tool, called PLC Log-Data Analysis Tool (PLAT) that can detect them by using log-data records of the PLC signals. PLAT automatically creates a nominal model of the PLC control process and employs a novel hash table based indexing and searching scheme to satisfy those purposes. Our experiments show that PLAT is significantly fast, provides real time identification of operational faults and behavioural anomalies, and can execute within a small memory footprint. In addition, PLAT can easily handle a large manufacturing system with a reasonable computing configuration and can be installed in parallel to the data logging system to identify operational faults and behavioural anomalies effectively.
Molecular Basis for Hematopoietic/Mesenchymal Interaction during Initiation of Peyer's Patch Organogenesis

Mice deficient in lymphotoxin β receptor (LTβR) or interleukin 7 receptor α (IL-7Rα) lack Peyer's patches (PPs). Deficiency in CXC chemokine receptor 5 (CXCR5) also severely affects the development of PPs. A molecular network involving these three signaling pathways has been implicated in PP organogenesis, but it remains unclear how they are connected during this process. We have shown that PP organogenesis is initiated at sites containing IL-7Rα+ lymphoid cells and vascular cell adhesion molecule (VCAM)-1/intercellular adhesion molecule (ICAM)-1 expressing nonlymphoid elements. Here we characterize these lymphoid and nonlymphoid components in terms of chemokine signals. The lymphoid population expresses CXCR5 and has a strong chemotactic response to B lymphocyte chemoattractant (BLC). Importantly, chemokines produced by VCAM-1+ICAM-1+ nonlymphoid cells mediate the recruitment of lymphoid cells. Furthermore, we show that these VCAM-1+ICAM-1+ cells are mesenchymal cells that are activated by lymphoid cells through the LTβR to express adhesion molecules and chemokines. Thus, promotion of PP development relies on mutual interaction between mesenchymal and lymphoid cells.
Molecular epidemiologic research on the effects of environmental pollutants on the fetus.

Evidence shows that fetuses and infants are more affected than adults by a variety of environmental toxicants because of differential exposure, physiologic immaturity, and a longer lifetime over which disease initiated in early life can develop. In this article we review data on the effects of in utero exposure to common environmental contaminants, including polycyclic aromatic hydrocarbons (PAH), particulate matter and environmental tobacco smoke (ETS). We then summarize results from our molecular epidemiologic study to assess risks from in utero exposures to ambient air pollution and ETS. This research study, conducted in Poland, used biomarkers to measure the internal and bioeffective dose of toxicants and individual susceptibility factors. The study included 160 mothers and 160 newborns. Ambient air pollution was significantly associated (p= 0.05) with the amount of PAH bound to DNA (PAH-DNA adducts) in both maternal and infant cord white blood cells (WBC). Newborns with elevated PAH-DNA adducts (greater than the median) had significantly decreased birth weight (p= 0.05), birth length (p= 0.02), and head circumference (p= 0.0005) compared to the newborns with lower adducts (n= 135). Maternal and infant cotinine levels were increased by active and passive cigarette smoke exposure of the mother (p= 0.01). An inverse correlation was seen between newborn plasma cotinine (nanograms per milliliter) and birth weight (p= 0.0001) and length (p= 0.003). Adducts were elevated in placental tissue and WBC of newborns who were heterozygous or homozygous for the cytochrome P4501A1 MspI restriction fragment length polymorphism (RFLP) compared to newborns without the RFLP. Levels of PAH-DNA and cotinine were higher in newborns than mothers. These results document that there is significant transplacental transfer of PAH and ETS constituents from mother to fetus; that PAH-DNA adduct levels in maternal and newborn WBC were increased with environmental exposure to PAH from ambient pollution; and that the fetus is more sensitive to genetic damage than the mother. The study also provided the first molecular evidence that transplacental PAH exposure to the fetus is compromising fetal development. If confirmed, these findings could have significant public health implications since a number of studies have found that reduction of head circumference at birth correlates with lower intelligence quotient as well as poorer cognitive functioning and school performance in childhood. ImagesFigure 1Figure 2
The efficacy of ampicillin and Lactobacillus casei rhamnosus in the active management of preterm premature rupture of membranes remote from term

Background We aimed to investigate the treatment efficacy of ampicillin prophylaxis accompanied by Lactobacillus casei rhamnosus over the latency period following preterm premature rupture of membranes (PPROM). Methods Records of 40 patients who presented with PPROM between 230/7–316/7 weeks were analyzed retrospectively. Patients were divided into two groups: group 1 (n=20), treated with ampicillin; and group 2 (n=20), treated with ampicillin plus L. casei rhamnosus. Clinical and laboratory parameters were compared. Delta (Δ) values of each laboratory parameter were calculated by subtracting the value at delivery from the values at admission to the clinic. Results Gestational weeks at delivery (28.1±0.3 weeks versus 31.5±0.4 weeks), latency periods (12.3±1.5 days versus 41.4±4.4 days), 5-minute APGAR scores (6.8±0.1 versus 7.8±0.1), and birth weights (1,320±98 g versus 1,947±128 g) were significantly higher in group 2. White blood cell (WBC) (12,820±353/mm3 versus 11,107±298/mm3), and neutrophil counts (10.7±0.5×103/L versus 8.2±0.5×103/L) were significantly lower in group 2 at delivery. The ΔWBC (2,295±74/mm3 versus −798±−406/mm3), ΔC-reactive protein (5±0.04 mg/L versus 1.6±0.2 mg/L), and Δneutrophil (3±0.2×103/L versus 0.2±−0.1×103/L) were significantly lower in group 2. Conclusion It seems that addition of L. casei rhamnosus to ampicillin prolongs the latency period in patients with PPROM remote from term.
Management and optimization for nonvolatile memory-based hybrid scratchpad memory on multicore embedded processors

The recent emergence of various Non-Volatile Memories (NVMs), with many attractive characteristics such as low leakage power and high-density, provides us with a new way of addressing the memory power consumption problem. In this article, we target embedded CMPs, and propose a novel Hybrid Scratch Pad Memory (HSPM) architecture which consists of SRAM and NVM to take advantage of the ultra-low leakage power, high density of NVM, and fast access of SRAM. A novel data allocation algorithm as well as an algorithm to determine the NVM/SRAM ratio for the novel HSPM architecture are proposed. The experimental results show that the data allocation algorithm can reduce the memory access time by 33.51% and the dynamic energy consumption by 16.81% on average for the HSPM architecture when compared with a greedy algorithm. The NVM/SRAM size determination algorithm can further reduce the memory access time by 14.7% and energy consumption by 20.1% on average.
Learning distributed caching strategies in small cell networks

Caching has emerged as a vital tool in modern communication systems for reducing peak data rates by allowing popular files to be pre-fetched and stored locally at end users' devices. With the shift in paradigm from homogeneous cellular networks to the heterogeneous ones, the concept of data offloading to small cell base stations (sBS) has garnered significant attention. Caching at these small cell base stations has recently been proposed, where popular files are pre-fetched and stored locally in order to avoid bottlenecks in the limited capacity backhaul connection link to the core network. In this paper, we study distributed caching strategies in such a heterogeneous small cell wireless network from a reinforcement learning perspective. Using state of the art results, it can be shown that the optimal joint cache content placement in the sBSs turns out to be a NP-hard problem even when the sBS's are aware of the popularity profile of the files that are to be cached. To address this problem, we propose a coded caching framework, where the sBSs learn the popularity profile of the files (based on their demand history) via a combinatorial multi-armed bandit framework. The sBSs then pre-fetch segments of the Fountain-encoded versions of the popular files at regular intervals to serve users' requests. We show that the proposed coded caching framework can be modeled as a linear program that takes into account the network connectivity and thereby jointly designs the caching strategies. Numerical results are presented to show the benefits of the joint coded caching technique over naive decentralized cache placement strategies.
Perceptual Learning Reduces Crowding in Amblyopia and in the Normal Periphery

Amblyopia is a developmental visual disorder of cortical origin, characterized by crowding and poor acuity in central vision of the affected eye. Crowding refers to the adverse effects of surrounding items on object identification, common only in normal peripheral but not central vision. We trained a group of adult human amblyopes on a crowded letter identification task to assess whether the crowding problem can be ameliorated. Letter size was fixed well above the acuity limit, and letter spacing was varied to obtain spacing thresholds for central target identification. Normally sighted observers practiced the same task in their lower peripheral visual field. Independent measures of acuity were taken in flanked and unflanked conditions before and after training to measure crowding ratios at three fixed letter separations. Practice improved the letter spacing thresholds of both groups on the training task, and crowding ratios were reduced after posttest. The reductions in crowding in amblyopes were associated with improvements in standard measures of visual acuity. Thus, perceptual learning reduced the deleterious effects of crowding in amblyopia and in the normal periphery. The results support the effectiveness of plasticity-based approaches for improving vision in adult amblyopes and suggest experience-dependent effects on the cortical substrates of crowding.
Slide to X: unlocking the potential of smartphone unlocking

Unlock gestures are performed by billions of users across the world multiple times a day. Beyond preventing accidental input on mobile devices, they currently serve little to no other purpose. In this paper, we explore how replacing the regular unlock screen with one that asks the user to perform a simple, optional task, can benefit a wealth of application domains, including data collection, personal-health metrics collection, and human intelligence tasks. We evaluate this concept, which we refer to as Slide to X. Further, we show that people are willing to perform microtasks presented through this interface and continue to do so throughout the day while they visit different locations as part of their daily routines. We then discuss how to implement this concept and demonstrate three applications.
From prediction error to psychosis: ketamine as a pharmacological model of delusions

Recent cognitive neuropsychiatric models of psychosis emphasize the role of attentional disturbances and inappropriate incentive learning in the development of deLusions. These models highlight a pre-psychotic period in which the patient experiences perceptual and attentional disruptions. Irrelevant details and numerous associations between stimuli, thoughts and percepts are imbued with inappropriate significance and the attempt to rationalize and account for these bizarre experiences results in the formation of delusions. The present paper discusses delusion formation in terms of basic associative learning processes. Such processes are driven by prediction error signaLs. Prediction error refers to mismatches between an organism's expectation in a given environment and what actually happens and it is signalled by both dopaminergic and glutamatergic mechanisms. Disruption of these neurobiological systems may underie delusion formation. We review similarities between acute psychosis and the psychotic state induced by the NMDA receptor antagonist drug ketamine, which impacts upon both dopaminergic and glutamatergic function. We conclude by suggesting that ketamine may provide an appropriate model to investigate the formative stages of symptom evolution in schizophrenia, and thereby provide a window into the earliest and otherwise inaccessible aspects of the disease process.