Miracle-dz/UniFAR-FTUs huggingface dataset:
A Core Filamentation Response Network in Candida albicans Is Restricted to Eight Genes

Although morphological plasticity is a central virulence trait of Candida albicans, the number of filament-associated genes and the interplay of mechanisms regulating their expression remain unknown. By correlation-based network modeling of the transcriptional response to different defined external stimuli for morphogenesis we identified a set of eight genes with highly correlated expression patterns, forming a core filamentation response. This group of genes included ALS3, ECE1, HGT2, HWP1, IHD1 and RBT1 which are known or supposed to encode for cell- wall associated proteins as well as the Rac1 guanine nucleotide exchange factor encoding gene DCK1 and the unknown function open reading frame orf19.2457. The validity of network modeling was confirmed using a dataset of advanced complexity that describes the transcriptional response of C. albicans during epithelial invasion as well as comparing our results with other previously published transcriptome studies. Although the set of core filamentation response genes was quite small, several transcriptional regulators are involved in the control of their expression, depending on the environmental condition.
Frequency and technical standard of endodontic treatment in a Swedish population.

The purpose of this investigation was to study the frequency and technical standard of endodontic treatment in a Swedish population. The material consisted of full-mouth radio-graphic surveys from 200 patients treated by general practice dentists, and the radiographs were analyzed by two observers. Thirteen percent of the teeth had been endodontically treated. Periradicular radiolucencies were found in 5.2% of the teeth and 26.4% of the endodontically treated teeth had such periradicular radiolucencies. In nearly half of the root-filled teeth, the root filling ended more than 2 mm from the apex, and only 56.3% were judged to have a proper seal. It is concluded that the need for endodontic treatment is great and the technical standard of the root fillings is poor. This strongly indicates that there is a need for standardized endodontic treatment methods and for more specialists in endodontics in Sweden.
Algorithmic Approach for Improved Mixed-Integer Reformulations of Convex Generalized Disjunctive Programs

In this work, we propose an algorithmic approach to improve mixed-integer models that are originally formulated as convex generalized disjunctive programs (GDPs). The algorithm seeks to obtain an improved continuous relaxation of the mixed-integer linear and mixed-integer nonlinear programming (MILP/MINLP) model reformulation of the GDP while limiting the growth in the problem size. There are three main stages that form the basis of the algorithm. The first one is a presolve, consequence of the logic nature of GDP, which allows us to reduce the problem size, find good relaxation bounds, and identify properties that help us determine where to apply a basic step. The second stage is the iterative application of basic steps, selecting where to apply them and monitoring the improvement of the formulation. Finally, we use a hybrid reformulation of GDP that seeks to exploit both of the advantages attributed to the two common GDP-to-MILP/MINLP transformations, the Big-M, and the Hull reformulation. We illustrate.
Identification Optimized With Retrieval Mechanism

identifying the writer of a handwritten document has been an active research area over the last few years with applications in biometrics, forensics, smart meeting rooms and historical document analysis. In this paper, we present a new writer identification system based on a retrieval mechanism. Texture based edge-hinge and run-length features are used to characterize the writing style of an individual. The effectiveness of the proposed system is evaluated on a total of 1583 writing samples in Arabic, German, English, French, and Greek from two different databases. The experimental evaluations reveal that reducing the search space using a writer retrieval mechanism prior to identification improves the identification rates. Keywordsedge-hinge features; multi-script handwritten documents; run-length features; writer identification; writer retrieval.
Influence-Optimistic Local Values for Multiagent Planning - Extended Version

Recent years have seen the development of a number of methods for multiagent planning under uncertainty that scale to tens or even hundreds of agents. However, most of these methods either make restrictive assumptions on the problem domain, or provide approximate solutions without any guarantees on quality. To allow for meaningful benchmarking through measurable quality guarantees on a very general class of problems, this paper introduces a family of influence-optimistic upper bounds for factored Dec-POMDPs. Intuitively, we derive bounds on very large multiagent planning problems by subdividing them in sub-problems, and at each of these sub-problems making optimistic assumptions with respect to the influence that will be exerted by the rest of the system. We numerically compare the different upper bounds and demonstrate how, for the first time ever, we can achieve a non-trivial guarantee that the heuristic solution of problems with hundreds of agents is close to optimal. Furthermore, we provide evidence that the upper bounds may improve the effectiveness of heuristic influence search, and discuss further potential applications to multiagent planning.
When in Doubt, Do it Both Ways: Brain Evidence of the Simultaneous Activation of Conflicting Motor Responses in a Spatial Stroop Task

Response competition is often considered an important contributor to the delayed reaction to stimuli for which physical and semantic information are in conflict (Stroop effect). Response competition implies that brain areas associated with correct and incorrect responses (e.g., left and right motor cortices) should be simultaneously activated in conflict conditions. However, there is at present little direct evidence of this phenomenon, in part because of the paucity of brain imaging techniques that can independently monitor the time course of activation of adjacent brain areas, such as the motor areas. In the present study, we show that the event-related optical signal (EROS) can provide these types of data. The results confirm the prediction that conflict trials elicit simultaneous activation of both motor cortices, whereas nonconflict trials elicit brain activity only in the contralateral motor cortex. These data support a parallel view of the human information processing system.
Diet patterns are associated with demographic factors and nutritional status in South Indian children

Abstract The burden of non‐communicable chronic disease (NCD) in India is increasing. Diet and body composition ‘track’ from childhood into adult life and contribute to the development of risk factors for NCD. Little is known about the diet patterns of Indian children. We aimed to identify diet patterns and study associations with body composition and socio‐demographic factors in the Mysore Parthenon Study cohort. We collected anthropometric and demographic data from children aged 9.5 years (n = 538). We also administered a food frequency questionnaire and measured fasting blood concentrations of folate and vitamin B12. Using principal component analysis, we identified two diet patterns. The ‘snack and fruit’ pattern was characterised by frequent intakes of snacks, fruit, sweetened drinks, rice and meat dishes and leavened breads. The ‘lacto‐vegetarian’ pattern was characterised by frequent intakes of finger millet, vegetarian rice dishes, yoghurt, vegetable dishes and infrequent meat consumption. Adherence to the ‘snack and fruit’ pattern was associated with season, being Muslim and urban dwelling. Adherence to the lacto‐vegetarian pattern was associated with being Hindu, rural dwelling and a lower maternal body mass index. The ‘snack and fruit’ pattern was negatively associated with the child's adiposity. The lacto‐vegetarian pattern was positively associated with blood folate concentration and negatively with vitamin B12 concentration. This study provides new information on correlates of diet patterns in Indian children and how diet relates to nutritional status. Follow‐up of these children will be important to determine the role of these differences in diet in the development of risk factors for NCD including body composition.
Efficacy and tolerability of racecadotril in the treatment of cholera in adults: a double blind, randomised, controlled clinical trial

Background: The enkephalins, endogenous opiate substances, act as neurotransmitters along the entire digestive tract where they elicit intestinal antisecretory activity without affecting intestinal transit time or motility. Racecadotril, through inhibition of enkephalinase, reinforces the physiological activity of endogenous enkephalins and, therefore, shows intestinal antisecretory activity. Aim: We conducted the study to determine the role of racecadotril as an adjunct to the standard treatment of cholera in adults. Methods: The study was a double blind, randomised, placebo controlled clinical trial involving 110 adult male cholera patients who received either racecadotril or placebo in addition to standard cholera treatment. The major outcome measures (stool output, oral rehydration solution (ORS) intake, requirements for unscheduled intravenous fluid infusion, and duration of diarrhoea) were compared between the groups. Results: Of 110 patients enrolled, 54 received racecadotril and 56 received placebo. Admission clinical characteristics were comparable between the groups. There was no significant difference in (mean (SD)) total stool output (racecadotril v placebo 315 (228) v 280 (156) g/kg), total ORS intake (390 (264) v 369 (240) ml/kg), or duration of diarrhoea (35 (15) v 32 (13) hours) between the groups. Clinical success, defined as resolution of diarrhoea within 72 hours of initiation of study intervention, was similar in both groups (racecadotril v placebo 96% v 89%). The number of patients receiving unscheduled intravenous infusions was not significantly different between the groups (racecadotril v placebo 22% v 14%). No drug related adverse effect was noted. Conclusion: The study demonstrated that racecadotril therapy, although found to be safe, does not provide additional benefit in the treatment of severe cholera in adults.
Histone H3 Lysine 4 Methylation Disrupts Binding of Nucleosome Remodeling and Deacetylase (NuRD) Repressor Complex*

Histone N-terminal tails are post-translationally modified in many ways. At lysine residues, histones can be either acetylated or methylated. Both modifications lead to the binding of specific proteins; bromodomain proteins, such as GCN5, bind acetyl lysines and the chromodomain protein, HP1, binds methyl lysine 9 of histone H3. Here we show that the previously characterized transcriptional repressor complex NuRD (nucleosomeremodeling and deacetylase) binds to the histone H3 N-terminal tail and that methylation at lysine 4, but not lysine 9, prevents binding. Given that lysine 4 methylation is found at sites of active transcription, these results suggest that a function of lysine 4 methylation is to disrupt the association of histones with a repressor complex.
The phycobilisomes: an early requisite for efficient photosynthesis in cyanobacteria

Cyanobacteria trap light energy by arrays of pigment molecules termed “phycobilisomes (PBSs)”, organized proximal to "reaction centers" at which chlorophyll perform the energy transduction steps with highest quantum efficiency. PBSs, composed of sequential assembly of various chromophorylated phycobiliproteins (PBPs), as well as nonchromophoric, basic and hydrophobic polypeptides called linkers. Atomic resolution structure of PBP is a heterodimer of two structurally related polypeptides but distinct specialised polypeptides- a and ß, made up of seven alpha-helices each which played a crucial step in evolution of PBPs. PBPs carry out various light dependent responses such as complementary chromatic adaptation. The aim of this review is to summarize and discuss the recent progress in this field and to highlight the new and the questions that remain unresolved.
Downscaling Cokriging for Super-Resolution Mapping of Continua in Remotely Sensed Images

The main aim of this paper is to show the implementation and application of downscaling cokriging for super-resolution image mapping. By super-resolution, we mean increasing the spatial resolution of satellite sensor images where the pixel size to be predicted is smaller than the pixel size of the empirical image with the finest spatial resolution. It is assumed that coregistered images with different spatial and spectral resolutions of the same scene are available. The main advantages of cokriging are that it takes into account the correlation and cross correlation of images, it accounts for the different supports (i.e., pixel sizes), it can explicitly take into account the point spread function of the sensor, and it has the property of prediction coherence. In addition, ancillary images (topographic maps, thematic maps, etc.) as well as sparse experimental data could be included in the process. The main problem is that super-resolution cokriging requires several covariances and cross covariances, some of which are not empirically accessible (i.e., from the pixel values of the images). In the adopted solution, the fundamental concept is that of covariances and cross-covariance models with point support. Once the set of point-support models is estimated using linear systems theory, any pixel-support covariance and cross covariance can be easily obtained by regularization. We show the performance of the method using Landsat Enhanced Thematic Mapper Plus images.
What Uncertainties Do We Need in Bayesian Deep Learning for Computer Vision?

There are two major types of uncertainty one can model. Aleatoric uncertainty captures noise inherent in the observations. On the other hand, epistemic uncertainty accounts for uncertainty in the model - uncertainty which can be explained away given enough data. Traditionally it has been difficult to model epistemic uncertainty in computer vision, but with new Bayesian deep learning tools this is now possible. We study the benefits of modeling epistemic vs. aleatoric uncertainty in Bayesian deep learning models for vision tasks. For this we present a Bayesian deep learning framework combining input-dependent aleatoric uncertainty together with epistemic uncertainty. We study models under the framework with per-pixel semantic segmentation and depth regression tasks. Further, our explicit uncertainty formulation leads to new loss functions for these tasks, which can be interpreted as learned attenuation. This makes the loss more robust to noisy data, also giving new state-of-the-art results on segmentation and depth regression benchmarks.
Contemporary Galois theory and its classical problems

In this survey we outline the milestones of several classical problems in Galois theory: Noether’s problem, the inverse problem and the embedding problem. We demonstrate the connection between these problems in the bigger context of the invariant theory of finite groups. We also point out several new results of the author and his collaborators regarding Noether’s problem and the embedding problem.
Gastroenterologist Specialist Care and Care Provided by Generalists—An Evaluation of Effectiveness and Efficiency

OBJECTIVE:In this era of cost containment, gastroenterologists must demonstrate that they provide effective and efficient care. The aim of this study was to evaluate the process and outcomes of care provided by gastroenterologists and generalist physicians (internists, family physicians, general surgeons) for GI conditions.METHODS:We conducted a systematic literature review using a MEDLINE search of English language articles (January 1980 to September 1998). A total of 2157 articles were identified; 10 met inclusion criteria for systematic review. In addition, there were nine articles that described the results of physician surveys, and examined the process of care among gastroenterologists and generalist physicians.RESULTS:Care provided by gastroenterologists for GI bleeding and diverticulitis resulted in significantly shorter length of hospital stay. Gastroenterologists diagnosed celiac disease more accurately than generalists, and more adequately diagnosed colorectal cancer and prescribed antimicrobials for peptic ulcer disease. There was no difference between gastroenterologists and generalists in terms of colonoscopy procedure time, and family physicians detected a greater number of cancers. Furthermore, there was no difference in the outcomes of gastroesophageal reflux disease therapy in patients seen by gastroenterologists, versus those educated by nurses. The survey articles suggested that gastroenterologists were more likely to test and treat for Helicobacter pylori in patients with peptic ulcer disease, and were more likely recommended for medical versus surgical therapy. Gastroenterologists had a lower threshold for ordering ERCP before cholecystectomy than surgeons, but had similar responses regarding indications for surgery in inflammatory bowel disease. Finally, primary care physicians were less likely to associate symptoms of profuse watery diarrhea with cryptosporidium infection compared with gastroenterologists and infectious disease specialists.CONCLUSIONS:We reached the following conclusions: 1) The results suggest that gastroenterologists deliver effective and efficient care for GI bleeding and diverticulitis and provide more effective diagnosis in certain disorders. 2) Studies are limited by retrospective design, small sample size, and lack of control groups. 3) To fully evaluate care by gastroenterologists, prospective comparisons with greater attention to methodology are needed.
Speed-Dependent Treadmill Training in Ambulatory Hemiparetic Stroke Patients: A Randomized Controlled Trial

Background and Purpose— A new gait training strategy for patients with stroke seeks to increase walking speed through treadmill training. This study compares the effects of structured speed-dependent treadmill training (STT) (with the use of an interval paradigm to increase the treadmill speed stepwise according to principles of sport physiology) with limited progressive treadmill training (LTT) and conventional gait training (CGT) on clinical outcome measures for patients with hemiparesis. Methods— Sixty ambulatory poststroke patients were each randomly selected to receive 1 of the 3 different gait therapies: 20 subjects were treated with STT, 20 subjects were trained to walk on a treadmill with a 20% increase of belt speed over the treatment period (LTT), and 20 subjects were treated with CGT. Treatment outcomes were assessed on the basis of overground walking speed, cadence, stride length, and Functional Ambulation Category scores. Results— After a 4-week training period, the STT group scored significantly higher than the LTT and CGT groups for overground walking speed (STT versus LTT, P <0.001; STT versus CGT, P <0.001), cadence (STT versus LTT, P =0.007; STT versus CGT, P <0.001), stride length (STT versus LTT, P <0.001; STT versus CGT, P <0.001), and Functional Ambulation Category scores (STT versus LTT, P =0.007; STT versus CGT, P <0.001). Conclusions— Structured STT in poststroke patients resulted in better walking abilities than LTT or CGT. This gait training strategy provides a dynamic and integrative approach for the treatment of gait dysfunction after stroke.
Treatment with paracetamol in infants

Background: Paracetamol (N‐acetyl‐p‐amino‐phenol) or acetaminophen has become the most widely used analgesic and antipyretic in children. However, there is a wide discrepancy between the extent to which paracetamol is used and the limited available pharmacological data in small infants. The purpose of this article is to present a review of the current literature regarding the use of paracetamol in neonates and infants with a particular emphasis on pharmacological issues.
Random Walk on WordNet to Measure Lexical Semantic Relatedness

The need to determine semantic relatedness or its inverse, semantic distance, between two lexically expressed concepts is a problem that pervades much of natural language processing such as document summarization, information extraction and retrieval, word sense disambiguation and the automatic correction of word errors in text. Standard ways of measuring similarity between two words on a thesaurus, such as WordNet, are usually based on the path between those words in the thesaurus graph. By contrast, Hughes and Ramage (2007) proposed a Markov chain model of lexical semantic relatedness based on WordNet, which uses a random walk over nodes and edges derived from WordNet link and corpus statistics to compute a word-specific stationary distribution. Based on this model, we propose to apply α-divergence to score the semantic relatedness of a word pair. In our experiments, the resulting relatedness measure with α = . 9 outperforms the existing measures on certain classes of distributions, that is correlated with human similarity judgements by rank ordering at ρ = . 937. keywords: Random Walk, WordNet, Semantic Relatedness Measure, Similarity Measure, α-divergence, Markov Chain, PageRank
Evaluation of a Telemedicine-Based Service for the Follow-Up and Monitoring of Patients Treated With Oral Anticoagulant Therapy

The authors have designed and developed a telemedicine-based service for the follow-up and monitoring of patients on oral anticoagulant therapy (OAT) that consists of two phases; the first involving self-testing and the second involving guided self-management. To evaluate the first phase of the protocol, a project was conducted with 108 patients, with a mean age of 72.7 years and a mean treatment time at the start of the study of 55.2 months, divided into two groups: telemedicine and control (conventional procedure). The degree of anticoagulation control was similar in the two groups: individual in-range international normalized ratios (59.2% vs 61.1%; p = 0.55) and individual time within target range (65.7% vs 66.4%; p = 0.85) showed no significant differences. The incidence of adverse events--death (5.5% vs 5.5%; p = 1.0), major hemorrhagic complications (0% vs 1.8%; p = 1.0), minor hemorrhagic complications (7.4% vs 3.7%; p = 0.67), and thromboembolism (1.8% vs 3.7%; p = 1.0)--was also similar, with no significant differences. Acceptability of the change, measured in terms of quality of life (SF-12 and Sawicki questionnaires) and anxiety (state-trait anxiety inventory questionnaire) at the beginning and end of the study period was higher in the telemedicine group, with statistically significant improvements in mental component summary (3.6 vs -6.2; p = 0.02), dissatisfaction (-0.8 vs 0.2; p = 0.001), stress (-0.3 vs 0.05; p = 0.03), limitations (-0.2 vs 0.3; p = 0.005), social problems (-0.1 vs 0.3; p = 0.03), and state anxiety (-2.5 vs 2.3; p = 0.04). Parameters related to costs, such as the mean number per patient of office visits due to OAT (1.7 vs 13.8; p < 0.001) and other office visits (10.1 vs 11.5; p = 0.028), were also more favorable in the telemedicine group, as were additional parameters that enabled an exhaustive evaluation of the service. The positive results obtained indicate that the second phase of the trial can be initiated.