Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure-specific Nuclease Activity in Yeast Nucleotide Excision Repair Protein Rad2 (*)

Saccharomyces cerevisiae Rad2 protein functions in the incision step of the nucleotide excision repair of DNA damaged by ultraviolet light. Rad2 was previously shown to act endonucleolytically on circular single-stranded M13 DNA and also to have a 5′ 3′ exonuclease activity (Habraken, Y., Sung, P., Prakash, L., and Prakash, S.(1993) Nature 366, 365-368; Habraken, Y. , Sung, P., Prakash, L. , and Prakash, S. (1994) J. Biol. Chem. 269, 31342-31345). Using two different branched DNA structures, pseudo Y and flap, we have determined that Rad2 specifically cleaves the 5′-overhanging single strand in these DNAs. Rad2 nuclease is more active on the flap structure than on the pseudo Y structure. Rad2 also acts on a bubble structure that contains an unpaired region of 14 nucleotides, but with a lower efficiency than on the pseudo Y or flap structure. The incision points occur at and around the single strand-duplex junction in the three classes of DNA structures.
Bilateral subthalamic stimulation for Parkinson's disease by using three-dimensional stereotactic magnetic resonance imaging and electrophysiological guidance.

OBJECT Several methods are used for stereotactically guided implantation of electrodes into the subthalamic nucleus (STN) for continuous high-frequency stimulation in the treatment of Parkinson's disease (PD). The authors present a stereotactic magnetic resonance (MR) method relying on three-dimensional (3D) T1-weighted images for surgical planning and multiplanar T2-weighted images for direct visualization of the STN, coupled with electrophysiological recording and stimulation guidance. METHODS Twelve patients with advanced PD were enrolled in this study of bilateral STN implantation. Both STNs were visible as 3D ovoid biconvex hypointense structures located in the upper mesencephalon. The coordinates of the centers of the STNs were determined with reference to the patient's anterior commissure-posterior commissure line by using a new landmark, the anterior border of the red nucleus. Electrophysiological monitoring through five parallel tracks was performed simultaneously to define the functional target accurately. Microelectrode recording identified high-frequency, spontaneous, movement-related activity and tremor-related cells within the STNs. Acute STN macrostimulation improved contralateral rigidity and akinesia, suppressed tremor when present, and could induce dyskinesias. The central track, which was directed at the predetermined target by using MR imaging, was selected for implantation of 19 of 24 electrodes. No surgical complications were noted. CONCLUSIONS At evaluation 6 months after surgery, continuous STN stimulation was shown to have improved parkinsonian motor disability by 64% and 78% in the "off' and "on" medication states, respectively. Antiparkinsonian drug treatment was reduced by 70% in 10 patients and withdrawn in two patients. The severity of levodopa-induced dyskinesias was reduced by 83% and motor fluctuations by 88%. Continuous high-frequency stimulation of the STN applied through electrodes implanted with the aid of 3D MR imaging and electrophysiological guidance is a safe and effective therapy for patients suffering from severe, advanced levodopa-responsive PD.
Reduced complexity interleaved multi-carrier CDMA for indoor visible light communications

We propose a novel technique that we call reduced complexity interleaved multi-carrier CDMA (RC I-MC-CDMA) as an alternative to MC-CDMA for indoor VLC systems. It uses shorter CDMA codes and interleaved sub-bands to lower the overall complexity without a significant additional power penalty.
Modeling and analysis of speed controls in hydro-turbines for frequency performance

This paper presents a discussion of the principal control strategies for frequency control in hydro-turbines and their performance under nonlinearities. Practical considerations for the dynamic modeling of the control systems in hydro-turbines are introduced. Actuator dynamics and their importance in the control loop are analyzed. A study is also performed on an exemplifying small hydro system to show how the frequency response in the system behaves with the addition of nonlinearities in its controls.
HOW TO DISTINGUISH BETWEEN CLOUDY MINI-NEPTUNES AND WATER/VOLATILE-DOMINATED SUPER-EARTHS

One of the most profound questions about the newly discovered class of low-density super-Earths is whether these exoplanets are predominately H2-dominated mini-Neptunes or volatile-rich worlds with gas envelopes dominated by H2O, CO2, CO, CH4, or N2. Transit observations of the super-Earth GJ 1214b rule out cloud-free H2-dominated scenarios, but are not able to determine whether the lack of deep spectral features is due to high-altitude clouds or the presence of a high mean molecular mass atmosphere. Here, we demonstrate that one can unambiguously distinguish between cloudy mini-Neptunes and volatile-dominated worlds based on wing steepness and relative depths of absorption features in moderate-resolution near-infrared transmission spectra (R ∼ 100). In a numerical retrieval study, we show for GJ 1214b that an unambiguous distinction between a cloudy H2-dominated atmosphere and cloud-free H2O atmosphere will be possible if the uncertainties in the spectral transit depth measurements can be reduced by a factor of ∼3 compared to the published Hubble Space Telescope Wide-Field Camera 3 and Very Large Telescope transit observations by Berta et al. and Bean et al. We argue that the required precision for the distinction may be achievable with currently available instrumentation by stacking 10–15 repeated transit observations. We provide a scaling law that scales our quantitative results to other transiting super-Earths and Neptunes such as HD 97658b, 55 Cnc e, GJ 3470b and GJ 436b. The analysis in this work is performed using an improved version of our Bayesian atmospheric retrieval framework. The new framework not only constrains the gas composition and cloud/haze parameters, but also determines our confidence in having detected molecules and cloud/haze species through Bayesian model comparison. Using the Bayesian tool, we demonstrate quantitatively that the subtle transit depth variation in the Berta et al. data is not sufficient to claim the detection of water absorption.
Time , Place and Environment : Can Conceptual Modelling improve Context-Aware Recommendation ?

Recommendation refers to the automatic process of discovering and suggesting new but relevant items to users, according to the preferences inferred from their previous activity. But, not only the items or their content are related to the user preferences but also the context in which the user have consumed the items. In this regard, the so-called context-aware recommenders refer to the systems integrating such contextual information in the recommendation process. However, sometimes it is not clear what context information is the best in order to improve the recommendation process or how it should be included. In this sense, we present a novel approach for context-aware recommendation based on a conceptual modelling for the user-item-context matrix. The modelling is conducted by means of the application of Formal Concept Analysis (FCA) to infer and organize the user preferences derived from their previous contextualized activity. We have experimented with different ways to integrate the contextual information by splitting it in the different dimensions that it addresses (e.g. location, time, company.). To that end, we have proposed different recommendation algorithms (content-based, collaborative filtering and hybrid recommenders) and also different ways to manage the user’s ratings. The obtained results prove the suitability of FCA for context-aware recommendation, outperforming other state-of-the-art proposals.
Neutral Sphingomyelinase-2 Mediates Growth Arrest by Retinoic Acid through Modulation of Ribosomal S6 Kinase*

All-trans-retinoic acid (ATRA) induces growth arrest of many cell types. Previous studies have reported that ATRA can modulate cellular sphingolipids, but the role of sphingolipids in the ATRA response is not clear. Using MCF-7 cells as a model system, we show that ATRA stimulates an increase in ceramide levels followed by G0/G1 growth arrest. Notably, induction of nSMase2 was the primary effect of ATRA on the sphingolipid network and was both time- and dose-dependent. Importantly, pretreatment with nSMase2 siRNA significantly inhibited ATRA effects on ceramide levels and growth arrest. In contrast, nSMase2 overexpression was sufficient to increase ceramide levels and induce G0/G1 growth arrest of asynchronous MCF-7 cells. Surprisingly, neither ATRA stimulation nor nSMase2 overexpression had significant effects on classical cell cycle regulators such as p21/WAF1 or retinoblastoma. In contrast, ATRA suppressed phosphorylation of ribosomal S6 kinase (S6K) and its downstream targets S6 and eIF4B. Importantly, these effects were significantly inhibited by nSMase2 siRNA. Reciprocally, nSMase2 overexpression was sufficient to suppress S6K phosphorylation and signaling. Notably, neither ATRA effects nor nSMase2 effects on S6K phosphorylation required the ceramide-activated protein phosphatase PP2A, previously identified as important for S6K regulation. Finally, nSMase2 overexpression was sufficient to decrease translation as measured by methionine incorporation and analysis of polyribosome profiles. Taken together, these results implicate nSMase2 as a major component of ATRA-induced growth arrest of MCF-7 cells and identify S6K as a novel downstream target of nSMase2.
Genetic Algorithm Approach for Solving the Falkner – Skan Equation T

A novel method based on Genetic Algorithm to solve the boundary value problems (BVPs) of the Falkner–Skan equation over a semi-infinite interval has been presented. In our approach, we use the free boundary formulation to truncate the semi-infinite interval into a finite one. Then we use the shooting method based on Genetic Algorithm to transform the BVP into initial value problems (IVPs). Genetic Algorithm is used to calculate shooting angle. The initial value problems arisen during shooting are computed by Runge-Kutta Fehlberg method. The numerical solutions obtained by the present method are in agreement with those obtained by previous authors. Keywords—Boundary Layer Flow, Falkner–Skan equation, Genetic Algorithm, Shooting method.
Effects of Animation on Attentional Resources of Online Consumers

Websites commonly use animation to capture the attentional resources of online consumers. While prior research has focused on the effects of animation on animated banner ads, limited research has examined the effects of animation on other items on the same webpage. Drawing from psychological theories that the amount of an individual’s attentional resources may vary under different conditions, this study focuses on the effects of animation on how individuals allocate attentional resources to both the animated item and the remaining non-animated items. We conducted an eye-tracking experiment to follow online consumers’ visual attention while they performed two types of online shopping tasks: browsing and searching tasks. The results showed that a product item that used animation led to increased visual attention to all items on a webpage, which suggests that the amount of attentional resources increases when a webpage includes animation. Meanwhile, animation influenced how individuals allocate their attentional resources such that it increased visual attention on the animated item at the expense of attention on non-animated items on the same webpage. In addition, the type of shopping task moderated animation’s effect on how individuals allocate their attentional resources. Specifically, animation’s effect on attracting attentional resources to the animated item was stronger when online consumers browsed than when they searched for a specific target item. We discuss the theoretical and practical implications of our findings.
Particle Swarm in Binary CSPs with Dynamic Variable Ordering

Summary The variable ordering of constraint satisfaction problems affect the performance of search algorithms in CSPs. Dynamic Variable Ordering (DVO) has more advantage in improving the performance of search algorithms than static variable ordering. It is a newly developed method recent years that using particle swarm algorithm to solve binary constraint satisfaction problems, which is a global stochastic optimized algorithm making use of swarm to search the whole solution space, and each particle represents a candidate solution of the problem. The algorithm discovers a solution satisfying condition specified of the solution space by acting each other among these particles. We add the dynamic variable ordering to the particle swarm algorithm in constraint satisfaction problems by improving the evaluation function of the particle swarm algorithm, which enhances the searching efficiency of particle swarm algorithm in CSPs and finds the solution of CSPs faster. Kinds of random constraint satisfaction problem experiments indicated that our efforts were effective.
Alcoholism Treatment and Potential Health Care Cost Saving

In 1979, MEDICAL CARE published a supplement1 that summarized and evaluated existing research on changes in health care patterns associated with mental health, alcoholism, and drug abuse treatment. This paper, limited to alcoholism treatment, reviews research that has been completed since the 1979 supplement. Considerations of appropriate research methods are discussed, recent studies that have employed a variety of research approaches are reviewed and evaluated, overall findings are summarized, implications and conclusions that can be drawn about offset are discussed, and recommendations for future research are made. These studies have fewer methodologic limitations and utilize larger study groups and longer follow-up periods than did earlier studies. They confirm earlier findings that general health care utilization and costs drop after initiation of alcoholism treatment;
Dendritic cells in cancer immunotherapy

DC initiate and regulate T‐cell immunity and are thus the key to optimization of all types of vaccines. Insights into DC biology offer many opportunities to enhance immunogenicity. In this Viewpoint, I discuss some recent developments and findings that are of immediate relevance for the clinical development of cancer vaccines. In addition, I emphasize my personal view that we should explore the potential of adoptively transferred DC (i.e. DC vaccination) as cancer vaccines by performing two‐armed trials that address critical variables and by delivering antigens via mRNA‐transfected DC.
Synergistic Effect of Keratinocyte Transplantation and Epidermal Growth Factor Delivery on Epidermal Regeneration

Both keratinocyte transplantation and epidermal growth factor (EGF) delivery stimulate epidermal regeneration. In this study, we hypothesized that the combined therapy of keratinocyte transplantation and EGF delivery accelerates epidermal regeneration compared to the single therapy of either keratinocyte transplantation or EGF delivery. To test this hypothesis, we utilized fibrin matrix as a keratinocyte/EGF delivery vehicle for epidermal regeneration. Full-thickness wounds were created on the dorsum of athymic mice, and human keratinocytes and EGF in fibrin matrix were sprayed onto the wounds to regenerate epidermal layers (group 1). As controls, human keratinocytes in fibrin matrix (group 2), EGF in fibrin matrix (group 3), or fibrin matrix alone (group 4) was sprayed onto the wounds. Spraying keratinocytes suspended in fibrin matrix did not affect the keratinocyte viability, as the cell viabilities before and after spraying were not different. EGF was released from fibrin matrix for 3 days. The wounds were analyzed with histology and immunohistochemistry at 1 and 3 weeks after treatments. Compared with the control groups, initial wound closure rate was highest in group 1. Histological analyses indicated that group 1 exhibited faster and better epidermal regeneration than the other groups. Immunohistochemical analyses showed that regenerated epithelium in groups 1 and 2 stained positively for human involucrin at 3 weeks, whereas the tissue sections of the groups 3 and 4 stained negatively. Human laminin was detected at the dermal–epidermal junction of the regenerated tissues in groups 1 and 2 at 3 weeks and was not detected in groups 3 and 4. The epidermal thickness of the regenerated tissues in group 1 was significantly thicker than that of the other groups at all time points. These results suggest that the combined therapy of keratinocyte transplantation and EGF delivery is more efficacious for epidermal regeneration than each separate therapy alone.
Zoonotic Disease Pathogens in Fish Used for Pedicure

“Doctor” fish might not be such good doctors after all. These fish are used for the increasingly popular spa treatment called fish pedicures. During these sessions, spa patrons immerse their feet in water, allowing the live fish to feed on dead skin, mainly for cosmetic reasons. However, examinations of doctor fish destined for these spas found that they can carry harmful bacteria. Thus, although reports of human infection after fish pedicures are few, there may be some risks. Spa patrons who have underlying medical conditions (such as diabetes, immunosuppression, or even simple breaks in the skin) are already discouraged from taking such treatments. However, spas that offer fish pedicures should also consider using only disease-free fish reared in controlled facilities under high standards of husbandry and welfare.
Selenoorganic compound, ebselen, inhibits nitric oxide and tumor necrosis factor‐α production by the modulation of Jun‐N‐terminal kinase and the NF‐κb signaling pathway in rat Kupffer cells

In response to the bacterial endotoxin, LPS, Kupffer cells are induced to express NO and TNF‐α. These compounds are involved in hepatic inflammation/injury, especially that associated with endotoxic shock. In this study, we demonstrate that ebselen (2‐phenyl‐1,2‐benzisoselenazol‐3[2H]one), a selenoorganic compound, blocks LPS‐induced NO and TNF‐α production by cultured rat liver Kupffer cells. LPS can activate both the NF‐κB signaling pathway and MAPK signal transduction pathways such as JNK and p38 MAPK. We find that ebselen inhibits LPS‐induced NF‐κB nuclear translocalization, and also suppresses the LPS‐induced phosphorylation of JNK, but not the phosphorylation of p38 MAPK. This inhibition of signal transduction leads to a decrease in the transcription of TNF‐α and the inducible isoform of NO. Furthermore, ebselen inhibits LPS‐induced COX‐2 expression, which is responsible for proinflammatory prostaglandin production, without affecting constitutive COX‐1 expression. These data suggest the mechanism by which ebselen acts as an antiinflammatory agent, and also suggest that ebselen may be potent in preventing hepatic injury such as endotoxic shock, in which Kupffer cell activation has been implicated. J. Cell. Biochem. 78:595–606, 2000. © 2000 Wiley‐Liss, Inc.
Topographical Organization of the Facial Motor Nucleus in Florida Manatees (Trichechus manatus latirostris)

Florida manatees (Trichechus manatus latirostris) possess modified vibrissae that are used in conjunction with specialized perioral musculature to manipulate vegetation for ingestion, and aid in the tactile exploration of their environment. Therefore it is expected that manatees possess a large facial motor nucleus that exhibits a complex organization relative to other taxa. The topographical organization of the facial motor nucleus of five adult Florida manatees was analyzed using neuroanatomical methods. Cresyl violet and hematoxylin staining were used to localize the rostrocaudal extent of the facial motor nucleus as well as the organization and location of subdivisions within this nucleus. Differences in size, length, and organization of the facial motor nucleus among mammals correspond to the functional importance of the superficial facial muscles, including perioral musculature involved in the movement of mystacial vibrissae. The facial motor nucleus of Florida manatees was divided into seven subnuclei. The mean rostrocaudal length, width, and height of the entire Florida manatee facial motor nucleus was 6.6 mm (SD 8 0.51; range: 6.2–7.5 mm), 4.7 mm (SD 8 0.65; range: 4.0–5.6 mm), and 3.9 mm (SD 8 0.26; range: 3.5–4.2 mm), respectively. It is speculated that manatees could possess direct descending corticomotorneuron projections to the facial motornucleus. This conjecture is based on recent data for rodents, similiarities in the rodent and sirenian muscular-vibrissal complex, and the analogous nature of the sirenian cortical Rindenkerne system with the rodent barrel system.
Energy-efficient and high-throughput FPGA-based accelerator for Convolutional Neural Networks

Convolutional Neural Networks (CNN) is widely applied in modern machine learning and pattern recognition area. Not only performance, more and more attention is paid on energy efficient and scalable devices like FPGA as a better solution than CPU and GPU. In this paper, we propose methods to optimize CNN by fixed-point quantization, activation function approximation, loops and tasks pipelining and parallelization, memory reorganization, and implement an energy-efficient and high-throughput FPGA-based CNN accelerator for LeNet-5 based on Zynq-7000 platform. The accelerator can run at 166MHz and achieve a low error rate of 0.99%, the same as software implementations, and has 37% higher throughput and 93.7% less energy dissipation than a GPU implementation.
Expression of SIALYL‐Lex antigen defined by MAb AM‐3 is an independent prognostic marker in colorectal carcinoma patients

Expression of mucin‐bound sialyl‐Lex antigen during the progression of colorectal carcinoma and its potential prognostic value were analysed in sections of tumours from 182 patients with a documented follow‐up by immunohistochemistry using the monoclonal antibody (MAb) AM‐3. Two groups of colonic carcinomas with weak (n = 79) and strong (n = 103) sialyl‐Lex expression were discerned. The percentage of strongly expressing tumours increased with the progression of the disease (UICC stage I = 10%, stage II = 46%, stage III = 63%, stage IV = 68%, p < 0.0001). Seventy‐four percent of patients with carcinomas exhibiting a strong sialyl‐Lex expression but only 34% of patients with weak sialyl‐Lex expression died of the disease (p = 0.0026). In multivariate analysis, strong sialyl‐Lex expression increased the relative risk of cancer‐related death 3.8‐fold (95% CI = 1.8–7.9, p = 0.00034). The separate analyses of patients in UICC stage II (n = 56), III (n =5 9) and IV (n = 57) revealed that strong sialyl‐Lex expression was associated with a reduction of the 5‐year overall survival rate in UICC stage II (84% vs. 54%, p = 0.0013) and in stage III patients (86% vs. 35%, p = 0.0008) after curative resection but was not relevant in patients with distant metastases. In conclusion, the strong expression of sialyl‐Lex antigen defined by the MAb AM‐3 in colorectal carcinomas is an independent unfavourable prognostic factor after curative resection in stage II and III patients. The predictive power of the sialyl‐Lex expression may be helpful to define subgroups of patients at high risk for whom preventive adjuvant therapy can be selectively applied before the occurrence of detectable metastases. Int. J. Cancer 88:281–286, 2000. © 2000 Wiley‐Liss, Inc.