Miracle-dz/UniFAR-FTUs huggingface dataset:
Stitchprofiles.uio.no: analysis of partly melted DNA conformations using stitch profiles

In this study, we describe a web server that performs computations on DNA melting, thus predicting the localized separation of the two strands for sequences provided by the users. The output types are stitch profiles, melting curves, probability profiles, etc. Stitch profile diagrams visualize the ensemble of alternative conformations that DNA can adopt with different probabilities. For example, a stitch profile shows the possible loop openings in terms of their locations, sizes, probabilities and fluctuations at a given temperature. Sequences with lengths up to several tens or hundreds of kilobase pairs can be analysed. The tools are freely available at .
User-click modeling for understanding and predicting search-behavior

Recent advances in search users' click modeling consider both users' search queries and click/skip behavior on documents to infer the user's perceived relevance. Most of these models, including dynamic Bayesian networks (DBN) and user browsing models (UBM), use probabilistic models to understand user click behavior based on individual queries. The user behavior is more complex when her actions to satisfy her information needs form a search session, which may include multiple queries and subsequent click behaviors on various items on search result pages. Previous research is limited to treating each query within a search session in isolation, without paying attention to their dynamic interactions with other queries in a search session. Investigating this problem, we consider the sequence of queries and their clicks in a search session as a task and propose a task-centric click model~(TCM). TCM characterizes user behavior related to a task as a collective whole. Specifically, we identify and consider two new biases in TCM as the basis for user modeling. The first indicates that users tend to express their information needs incrementally in a task, and thus perform more clicks as their needs become clearer. The other illustrates that users tend to click fresh documents that are not included in the results of previous queries. Using these biases, TCM is more accurately able to capture user search behavior. Extensive experimental results demonstrate that by considering all the task information collectively, TCM can better interpret user click behavior and achieve significant improvements in terms of ranking metrics of NDCG and perplexity.
Fumigation with acetic acid vapor to control decay of stored apples

Introduction. Apples are potentially subject to blue mold decay caused by Penicil- lium expansum if stored at 1 °C for three or more months or if wounded during handling. Results from trials with apples contaminated with conidia of P. expansum and fumigated in small cham- bers with acetic acid (AA) vapor indicated that fruit could be sterilized to reduce decay without effect on fruit quality. The objective of this study was to determine if larger quantities of apples treated with AA vapor would have less decay after storage and/or wounding. It was also impor- tant to determine if fumigation would affect apple quality and aroma. Materials and methods. Apple cultivars were harvested at commercial maturity for use in AA fumigation trials. Apples arti- ficially or naturally contaminated with conidia of P. expansum were fumigated with AA vapor in a 1 m3 gas tight chamber at 10 °C for 1 h to 24 h or dipped in 450 μg thiabendazole 〈 L -1 solu- tion. Fruit fumigated in standard wooden or plastic apple boxes, or small wooden bins were either wounded and evaluated for decay after a week at 20 °C or stored at 1 °C for three or more months and evaluated for decay. Then apple quality was assessed. Results. Apples naturally contaminated with Penicillium spp. that had been stored at 1 °C in air storage and treated with AA vapour had 50% less decay than the control fruit. In another experiment, AA fumigation was as effective as thiabendazole in reducing decay. AA fumigation reduced decay of fruit coming out of storage for apples stored for 3 months, and a second AA fumigation reduced infection of wounds on these same apples. AA fumigation before storage did not affect apple quality or vinegar aroma. Discussion. AA fumigation showed great potential for reducing decay in stored apples. It could be used as an organic alternative to synthetic fungicides for control of blue mold decay.
Study on Electrochemical Insulin Sensing Utilizing a DNA Aptamer-Immobilized Gold Electrode

We investigated an insulin-sensing method by utilizing an insulin-binding aptamer IGA3, which forms an anti-parallel G-quadruplex with folded single strands. Spectroscopic observation indicates that some anti-parallel G-quadruplex bind hemin and show peroxidase activity. In this study, the peroxidase activity of IGA3 with hemin was confirmed by spectrophotometric measurements, i.e., the activity was three-times higher than hemin itself. IGA3 was then immobilized onto a gold electrode to determine its electrochemical activity. The peroxidase activity of the immobilized IGA3-hemin complex was determined by cyclic voltammetry, and a cathodic peak current of the electrode showed a dependence on the concentration of H2O2. The cathodic peak current of the IGA3-hemin complex decreased by binding it to insulin, and this decrease depended on the concentration of insulin.
Physiology of rat retinal pericytes: modulation of ion channel activity by serum‐derived molecules

1 Pericytes, which are contractile cells located on the outer wall of microvessels, are thought to be particularly important in the retina where the ratio of these cells to vascular endothelial cells is the highest of any tissue. Retinal pericytes are of interest since they may regulate capillary blood flow and because their selective loss is an early event in diabetic retinopathy, which is a common sight‐threatening disorder associated with dysfunction of the blood‐retinal barrier. 2 Although a breakdown in the vascular endothelial barrier is a frequent pathophysiological event, knowledge of the effects of blood‐derived molecules on pericyte function is limited. Based on the premise that ion channels play a vital role in cellular function, we examined the effect of serum on the ionic currents of retinal pericytes. To do this, we used the perforated‐patch configuration of the patch‐clamp technique to monitor the whole‐cell currents of pericytes located on freshly isolated rat retinal microvessels. 3 Exposure to serum reversibly activated inward and outward currents in virtually all of the sampled retinal pericytes. Two types of sustained conductances were induced by serum. These were a calcium‐permeable non‐specific cation (NSC) current and a voltage‐dependent potassium current. In addition, exposure to serum increased the activity of chloride channels which caused transient depolarizing currents. 4 Associated with the activation of these conductances, the membrane potential showed a sustained decrease of 10 ± 2 mV from −56 mV to −46 mV and, also, transient depolarizations to near −30 mV. The serum‐induced depolarizations can activate the voltage‐gated calcium channels expressed by the retinal pericytes. 5 Calcium‐permeable NSC channels appear to play a critical role in the response of pericytes to serum‐derived molecules. Consistent with this, activation of the chloride and potassium channels was sensitive to SK&F 96365, which is a blocker of NSC channels. In addition, chloride and potassium channel activation was dependent on extracellular calcium. 6 The effects of serum on the activity of channels in retinal pericytes were qualitatively mimicked by insulin‐like growth factor‐1 (IGF‐1), which is a normal constituent of the blood. 7 There are significant differences in the effects of serum on retinal pericytes compared with vascular smooth muscle cells. Serum activated sustained conductances in retinal pericytes but not in the vascular smooth muscle cells. This suggests a fundamental difference in the mechanisms by which serum‐derived molecules affect these two types of cells. 8 We conclude that serum‐derived molecules, such as IGF‐1, can activate several types of ion channels in retinal pericytes. These changes in channel activity are likely to influence pericyte function at sites of a breakdown in the blood‐retinal barrier.
Benson Relaxation Technique in Reducing Pain Intensity in Women After Cesarean Section

Background: Post-cesarean section women experience pain due to operative trauma. Pain sensation can be reduced by pain management. Pharmacological and non-pharmacological treatments can be used. The Benson Relaxation Technique is a non-pharmacological way suitable to reduce pain, but there are limited studies on its post-cesarean section use. Objectives: This study aimed to determine the effect of Benson Relaxation Technique in reducing pain intensity in women after cesarean section. Patients and Methods: This was a quasi-experiment study with pre and post-test design. A prospective, not blind, randomized assign, two groups parallel study was conducted in Cibabat hospital Cimahi as intervention group (IG) and Sartika Asih hospital as control group (CG). Post cesarean section women with quota sampling who met the inclusion criteria were consecutively assigned to either experimental (n = 30) or control group (n = 30). Women in the experimental group received the Benson relaxation technique and those in the control group received regular care from the health workers. The outcome pain severity was measured by visual analogue scale. Those instruments were applied before and after intervention. Results: The mean of pain score before intervention at CG was 4.43 cm. It was decreased to 4.40 cm (1 min), 4.27 cm (12 h), 4.10 cm (24 h), 4.00 cm (36 h), 3.93 cm (48 h), 3.83 cm (60 h), 3.67 cm (72 h) and 3.51 cm (84 h). Meanwhile, the IG was 4.97 cm. It was decreased to 4.90 cm (1 min), 4.23 cm (12 h), 3.57 cm (24 h), 3.03 cm (36 h), 2.77 cm (48 h), 2.73 cm (60 h), 2.67 cm (72 h) and 2.63 cm (84 h). The study found a significant difference comparing pain intensity before and after the intervention in CG and IG (P = 0.001), but pain reduced in IG more than CG. Conclusions: The Benson relaxation could reduce pain intensity in women after cesarean section.
The Merchants, Not the Customers: Resisting the Alcohol and Tobacco Industries' Strategy to Blame Young People for Illegal Alcohol and Tobacco Sales

Reducing access of alcohol and tobacco to young people constitutes a pressing public health policy agenda. Research has established that alcohol and tobacco are readily available to young people and that early use of these products increases both short term and long term health problems. Research also shows that the most effective way to reduce underage access is to implement merchant compliance programs as part of a comprehensive prevention strategy. Successful merchant compliance programs involve the use of young people who attempt to purchase alcohol or tobacco from merchants. These attempted purchases should be conducted on a routine basis and should result in increasingly severe fines and civil penalties against merchants who violate the law.This article reviews the research outlined above and documents the industries' efforts to redirect public policy to blame the young person rather than the merchant for the problem of youth access to alcohol and tobacco. The industry is using several tactics to reach this goal. The article concludes with a nine point proposal for reducing youth access, outlining the key elements of a merchant compliance program, and presenting other essential components of a community-based, comprehensive strategy.
A Putative ABC Transporter, HatABCDE, Is among Molecular Determinants of Pyomelanin Production in Pseudomonas aeruginosa

ABSTRACT Pyomelanin overproduction is a common phenotype among Pseudomonas aeruginosa isolates recovered from cystic fibrosis and urinary tract infections. Its prevalence suggests that it contributes to the persistence of the producing microbial community, yet little is known about the mechanisms of its production. Using transposon mutagenesis, we identified factors that contribute to melanogenesis in a clinical isolate of P. aeruginosa. In addition to two enzymes already known to be involved in its biosynthesis (homogentisate dioxygenase and hydroxyphenylpyruvate dioxygenase), we identified 26 genes that encode regulatory, metabolic, transport, and hypothetical proteins that contribute to the production of homogentisic acid (HGA), the monomeric precursor of pyomelanin. One of these, PA14_57880, was independently identified four times and is predicted to encode the ATP-binding cassette of an ABC transporter homologous to proteins in Pseudomonas putida responsible for the extrusion of organic solvents from the cytosol. Quantification of HGA production by P. aeruginosa PA14 strains missing the predicted subcomponents of this transporter confirmed its role in HGA production: mutants unable to produce the ATP-binding cassette (PA14_57880) or the permease (PA14_57870) produced substantially less extracellular HGA after growth for 20 h than the parental strain. In these mutants, concurrent accumulation of intracellular HGA was observed. In addition, quantitative real-time PCR revealed that intracellular accumulation of HGA elicits upregulation of these transport genes. Based on their involvement in h omogentisic a cid t ransport, we rename the genes of this operon hatABCDE.
Study of home-monitored night blood pressure and its correlation with left ventricular hypertrophy in treatment-naive hypertensive patients.

INTRODUCTION 24-hour ambulatory blood pressure (BP) monitoring is a well-validated tool that can reveal the patient's nocturnal dipping pattern. However, to the best of our knowledge, the role of home BP monitoring in identifying nocturnal dipping has not been studied. METHODS We evaluated the nocturnal BP of 30 treatment-naive subjects using a home BP monitoring device. BP measurements were taken once during the daytime and once at night (three hours after sleep) by a blinded observer. Readings were correlated with left ventricular mass index. RESULTS Night BP measurements were significantly lower in subjects without left ventricular hypertrophy (LVH) as compared to those with LVH, while the daytime readings were not significantly different between the two. The mean dips in nocturnal systolic and diastolic BP were 1.92% ± 6.89% and -0.55% ± 14.31%, respectively, in subjects with LVH. The corresponding values were 12.96% ± 6.16% and 11.36% ± 11.90% in those without LVH. The correlation between left ventricular mass index and night BP readings was statistically significant (systolic r = 0.66, p < 0.001; diastolic r = 0.496, p < 0.005). CONCLUSION Nocturnal BP measurement using a home BP monitoring device may be a reliable and cost-effective method for detecting early signs of end-organ involvement such as LVH in hypertensives, especially in a resource-limited setting.
Using millions of emoji occurrences to learn any-domain representations for detecting sentiment, emotion and sarcasm

NLP tasks are often limited by scarcity of manually annotated data. In social media sentiment analysis and related tasks, researchers have therefore used binarized emoticons and specific hashtags as forms of distant supervision. Our paper shows that by extending the distant supervision to a more diverse set of noisy labels, the models can learn richer representations. Through emoji prediction on a dataset of 1246 million tweets containing one of 64 common emojis we obtain state-of-the-art performance on 8 benchmark datasets within emotion, sentiment and sarcasm detection using a single pretrained model. Our analyses confirm that the diversity of our emotional labels yield a performance improvement over previous distant supervision approaches.
Outcome of patients with hepatocellular carcinoma listed for liver transplantation within the Eurotransplant allocation system

Although hepatocellular carcinoma (HCC) has become a recognized indication for liver transplantation, the rules governing priority and access to the waiting list are not well defined. Patient‐ and tumor‐related variables were evaluated in 226 patients listed primarily for HCC in Belgium, a region where the allocation system is patient‐driven, priority being given to sicker patients, based on the Child‐Turcotte‐Pugh (CTP) score. Intention‐to‐treat and posttransplantation survival rates at 4 years were 56.5 and 66%, respectively, and overall HCC recurrence rate was 10%. The most significant predictors of failure to receive a transplant in due time were baseline CTP score equal to or above 9 (relative risk [RR] 4.1; confidence interval [CI]: 1.7–9.9) and α fetoprotein above 100 ng/mL (RR 3.0; CI: 1.2–7.1). Independent predictors of posttransplantation mortality were age equal to or above 50 years (RR 2.5; CI: 1.0–3.7) and United Network for Organ Sharing pathological tumor nodule metastasis above the Milan criteria (RR 2.1; CI: 1.0–5.9). Predictors of recurrence (10%) were α fetoprotein above 100 ng/mL (RR 3.2; CI:1.1–10) and vascular involvement of the tumor on the explant (RR 3.6; CI: 1.1–11.3). Assessing the value of the pretransplantation staging by imaging compared to explant pathology revealed 34% accuracy, absence of carcinoma in 8.3%, overstaging in 36.2%, and understaging in 10.4%. Allocation rules for HCC should consider not only tumor characteristics but also the degree of liver impairment. Patients older than 50 years with a stage above the Milan criteria at transplantation have a poorer prognosis after transplantation. Liver Transpl 14:526–533, 2008. © 2008 AASLD.
Diversity of Beta-Propeller Phytase Genes in the Intestinal Contents of Grass Carp Provides Insight into the Release of Major Phosphorus from Phytate in Nature

ABSTRACT Phytate is the most abundant organic phosphorus compound in nature, and microbial mineralization of phytate by phytase is a key process for phosphorus recycling in the biosphere. In the present study, beta-propeller phytase (BPP) gene fragments were readily amplified from the intestinal contents of grass carp (Ctenopharyngodon idellus) directly or from phytate-degrading isolates from the same source, confirming the widespread occurrence of BPP in aquatic communities. The amounts of sequences collected using these two methods differed (88 distinct genes versus 10 isolates), but the sequences showed the same general topology based on phylogenetic analysis. All of the sequences fell in five clusters and were distinct from those of Anabaena, Gloeobacter, Streptomyces, Flavobacterium, Prosthecochloris, and Desulfuromonas, which have never been found in the grass carp intestine. Analysis of the microbial diversity by denaturing gradient gel electrophoresis demonstrated that unculturable bacteria were dominant bacteria in the grass carp intestine and thus the predominant phytate-degrading organisms. The predominant cultured species corresponding to the phytate-degrading isolates, Pseudomonas, Bacillus and Shewanella species, might be the main source of known BPPs. A phytase from Brevundimonas was first obtained from cultured species. Combining our results with Lim et al.'s inference that phytate-mineralizing bacteria are widely distributed and highly diverse in nature (B. L. Lim, P. Yeung, C. Cheng, and J. E. Hill, ISME J. 1:321-330, 2007), we concluded that BPP is the major phytate-degrading enzyme in nature, that most of this enzyme might originate from unculturable bacteria, and that the distribution of BPP may be related to the type of niche. To our knowledge, this is the first study to experimentally estimate BPP diversity in situ.
Alcohol abuse and dependence criteria as predictors of a chronic course of alcohol use disorders in the general population.

AIMS To investigate whether DSM-IV abuse and dependence criteria and the ICD-10 criterion for craving differentially predict a chronic course of alcohol use disorders (AUD) in the general population. METHODS Data were derived from the Netherlands Mental Health Survey and Incidence Study, a large representative sample of the general Dutch population with a baseline and a 1- and 3-year follow-up assessment. In the present study, a cohort of subjects with a DSM-IV AUD diagnosis at baseline was followed (n = 382). Diagnostic criteria of AUD according to DSM-IV and ICD-10 were assessed using the Composite International Diagnostic Interview (CIDI). RESULTS In our cohort of subjects with an AUD diagnosis at baseline, the presence of all dependence criteria, except tolerance, significantly increased the risk for dependence at 1 and 3 years follow-up. Abuse criteria displayed much lower and often non-significant risks for dependence at follow-up, with the exception of the criterion 'legal problems'. The ICD-10 criterion 'craving' had the highest relative risk (RR) of all criteria for dependence at 1 year (RR = 12.4, 95% CI = 5.5-27.8) and 3 years follow-up (RR = 12.9, 95% CI = 4.4-37.7). CONCLUSION With the exception of tolerance, all DSM-IV dependence criteria are useful in predicting the course of AUD in the general population.
Comparative Analysis of the Complete Genome Sequence of the California MSW Strain of Myxoma Virus Reveals Potential Host Adaptations

ABSTRACT Myxomatosis is a rapidly lethal disease of European rabbits that is caused by myxoma virus (MYXV). The introduction of a South American strain of MYXV into the European rabbit population of Australia is the classic case of host-pathogen coevolution following cross-species transmission. The most virulent strains of MYXV for European rabbits are the Californian viruses, found in the Pacific states of the United States and the Baja Peninsula, Mexico. The natural host of Californian MYXV is the brush rabbit, Sylvilagus bachmani. We determined the complete sequence of the MSW strain of Californian MYXV and performed a comparative analysis with other MYXV genomes. The MSW genome is larger than that of the South American Lausanne (type) strain of MYXV due to an expansion of the terminal inverted repeats (TIRs) of the genome, with duplication of the M156R, M154L, M153R, M152R, and M151R genes and part of the M150R gene from the right-hand (RH) end of the genome at the left-hand (LH) TIR. Despite the extreme virulence of MSW, no novel genes were identified; five genes were disrupted by multiple indels or mutations to the ATG start codon, including two genes, M008.1L/R and M152R, with major virulence functions in European rabbits, and a sixth gene, M000.5L/R, was absent. The loss of these gene functions suggests that S. bachmani is a relatively recent host for MYXV and that duplication of virulence genes in the TIRs, gene loss, or sequence variation in other genes can compensate for the loss of M008.1L/R and M152R in infections of European rabbits.
Saliency Changes Appearance

Numerous studies have suggested that the deployment of attention is linked to saliency. In contrast, very little is known about how salient objects are perceived. To probe the perception of salient elements, observers compared two horizontally aligned stimuli in an array of eight elements. One of them was salient because of its orientation or direction of motion. We observed that the perceived luminance contrast or color saturation of the salient element increased: the salient stimulus looked even more salient. We explored the possibility that changes in appearance were caused by attention. We chose an event-related potential indexing attentional selection, the N2pc, to answer this question. The absence of an N2pc to the salient object provides preliminary evidence against involuntary attentional capture by the salient element. We suggest that signals from a master saliency map flow back into individual feature maps. These signals boost the perceived feature contrast of salient objects, even on perceptual dimensions different from the one that initially defined saliency.