Miracle-dz/UniFAR-FTUs huggingface dataset:
Heteropathogenic virulence and phylogeny reveal phased pathogenic metamorphosis in Escherichia coli O2:H6

Extraintestinal pathogenic and intestinal pathogenic (diarrheagenic) Escherichia coli differ phylogenetically and by virulence profiles. Classic theory teaches simple linear descent in this species, where non‐pathogens acquire virulence traits and emerge as pathogens. However, diarrheagenic Shiga toxin‐producing E. coli (STEC) O2:H6 not only possess and express virulence factors associated with diarrheagenic and uropathogenic E. coli but also cause diarrhea and urinary tract infections. These organisms are phylogenetically positioned between members of an intestinal pathogenic group (STEC) and extraintestinal pathogenic E. coli. STEC O2:H6 is, therefore, a ‘heteropathogen,’ and the first such hybrid virulent E. coli identified. The phylogeny of these E. coli and the repertoire of virulence traits they possess compel consideration of an alternate view of pathogen emergence, whereby one pathogroup of E. coli undergoes phased metamorphosis into another. By understanding the evolutionary mechanisms of bacterial pathogens, rational strategies for counteracting their detrimental effects on humans can be developed.
Pain anticipation: An activation likelihood estimation meta‐analysis of brain imaging studies

The anticipation of pain has been investigated in a variety of brain imaging studies. Importantly, today there is no clear overall picture of the areas that are involved in different studies and the exact role of these regions in pain expectation remains especially unexploited. To address this issue, we used activation likelihood estimation meta‐analysis to analyze pain anticipation in several neuroimaging studies. A total of 19 functional magnetic resonance imaging were included in the analysis to search for the cortical areas involved in pain anticipation in human experimental models. During anticipation, activated foci were found in the dorsolateral prefrontal, midcingulate and anterior insula cortices, medial and inferior frontal gyri, inferior parietal lobule, middle and superior temporal gyrus, thalamus, and caudate. Deactivated foci were found in the anterior cingulate, superior frontal gyrus, parahippocampal gyrus and in the claustrum. The results of the meta‐analytic connectivity analysis provide an overall view of the brain responses triggered by the anticipation of a noxious stimulus. Such a highly distributed perceptual set of self‐regulation may prime brain regions to process information where emotion, action and perception as well as their related subcategories play a central role. Not only do these findings provide important information on the neural events when anticipating pain, but also they may give a perspective into nocebo responses, whereby negative expectations may lead to pain worsening. Hum Brain Mapp 36:1648–1661, 2015. © 2014 Wiley Periodicals, Inc.
Computing Reliability for Coreference Annotation

Coreference annotation is annotation of language corpora to indicate which expressions have been used to co-specify the same discourse entity. When annotations of the same data are collected from two or more coders, the reliability of the data may need to be quanti(cid:2)ed. Two obstacles have stood in the way of applying reliability metrics: incommensurate units across annotations, and lack of a convenient representation of the coding values. Given N coders and M coding units, reliability is computed from an N-by-M matrix that records the value assigned to unit M j by coder N k . The solution I present accommodates a wide range of coding choices for the annotator, while preserving the same units across codings. As a consequence, it permits a straightforward application of reliability measurement. In addition, in coreference annotation, disagreements can be complete or partial so I incorporate a distance metric to scale disagreements. This method has also been applied to a quite distinct coding task, namely semantic annotation of summaries.
Passive smoking and sudden infant death syndrome: review of the epidemiological evidence.

BACKGROUND: This paper provides a systematic, quantitative review of the epidemiological evidence relating parental smoking and sudden infant death. METHODS: Thirty two relevant publications were identified after consideration of 692 articles selected by electronic search of the Embase and Medline databases using keywords and Mesh headings relevant to passive smoking in children. Eleven further articles were identified from reviews and by talking to authors. The search was completed in April 1997 and identified 39 studies. RESULTS: The unadjusted pooled odds ratio for prenatal maternal smoking was 2.77 (95% CI 2.45 to 3.13). After adjustment for a variety of confounders the pooled odds ratio was reduced to 2.08 (95% CI 1.83 to 2.38) and was similar in cohort and case-control studies. Four studies reported on maternal postnatal smoking after controlling for prenatal maternal smoking (pooled odds ratio 1.94 (95% CI 1.55 to 2.43)). Of three studies reporting on the risk of paternal smoking where the mother was a non-smoker, two found significant effects while one found no effect. Dose-response relationships with both prenatal and postnatal maternal smoking were present in most studies which provided data. CONCLUSIONS: Maternal smoking doubles the risk of sudden infant death syndrome. The relationship is almost certainly causal. There is good evidence that postnatal exposure to environmental tobacco smoke from both mother and father are important. Because prenatal smoking is almost invariably associated with postnatal smoking, the role of prenatal smoking per se will be difficult to resolve using epidemiological studies.
Social Media Use of Older Adults: A Mini-Review

Background: Maintaining social relationships has been defined as a core element of aging well. With a considerable amount of older adults living alone, social media provides the possibility to engage in meaningful social contact, e.g. by joining online social networks and online discussion forums. Objective: The review encompasses current knowledge of prerequisites in social media use of older adults such as functional capacity, information and communications technology-related knowledge, and favorable attitudes towards social media. Then, the potential of social media use for clinical practice and possible negative consequences are outlined. Method: Literature on social media use from a gerontological perspective was reviewed in July and August 2012. Results: Online communities are suitable for providing and receiving social support when confronted with a difficult life situation, regardless of geographical location or time. From a practitioner's perspective, social media can be used to advance health-related knowledge such as information on prevention, diagnosis, and treatment of specific conditions and disorders. Further positive consequences have been shown to be overcoming loneliness, relieving stress, and raising feelings of control and self-efficacy. Possible negative consequences could be misuse of personal data as well as the distribution and uncritical adoption of potentially harmful information via online communities. Discussion: The potential of social media in clinical practice is reflected in a wide range of intervention possibilities for older adults. However, with the rise of social media, new threats emerge for older adults as well.
Monocytes Are Major Players in the Prognosis and Risk of Infection After Acute Stroke

Background and Purpose— Monocytes participate in adaptive and innate immune responses. Monocyte numbers increase in patients with stroke associated infection (SAI) or severe stroke. Whether changes in monocytes are related to specific effects, or simply mark brain damage, remains unsettled. Methods— We used flow cytometry in 45 consecutive strokes and 12 healthy controls to assess the time course of monocytes, their phenotype, and the production of cytokines after stimulation. Cortisol, TNF-α, IFN-γ, and IL-10 were measured in serum and metanephrine in plasma. The effects of humoral and cellular parameters on the risk of SAI and poor outcome were tested in multivariate analyses adjusted for confounders (NIHSS score, age, and tube feeding). Results— Surface expression of human leukocyte antigen-DR, Toll-like receptor-2, and production of TNF-α in monocytes were independently associated with stroke. Distinct immune mechanisms were related with functional outcome and the risk of SAI; the signature of SAI included an increase of cortisol, metanephrine, and IL-10 in serum, and reduced production of TNF-α in monocytes; poor outcome was associated with increased expression of Toll-like receptor-4 in monocytes (OR, 9.61; 95% CI, 1.27–72.47). SAI did not predict poor outcome (OR, 5.63; 95% CI, 0.45–70.42; P=0.18). Conclusions— In human stroke, poor outcome is associated to innate responses mediated by Toll-like receptor-4 in monocytes. SAI may result from the immunosuppressive and antiinflammatory effects of corticoids, catecholamines, IL-10, and deactivated monocytes. Early treated SAI does not contribute significantly to additional brain damage. These findings encourage the exploration of strategies aimed to inhibit Toll-like receptor-4 signaling in acute stroke.
On the use and misuse of Bayesian filters

Since the groundbreaking work of the Kalman filter in the 1960s, considerable effort has been devoted to discrete time filters for dynamic state estimation, especially including a variety of suboptimal implementations of the Bayesian filter. The essence of the Bayesian filter is to make the (sub)optimum fusion of the observation information in time sequence based on the hidden Markov model of the state process. While admitting the success of filters in many cases, this study investigates the cases when they in fact loose to the deterministic observation-only (O2) inference that infers the estimate by using the observation information only without modeling the state dynamics. Special attention has been paid to quantitatively analyzing when and why the Bayesian filter will underperform the O2 inference from the information fusion perspective. Classic state space models have shown that the O2 inference can perform better (in terms of both accuracy and computing speed) than filters in certain cases. Therefore attention is desired for the use of a filter when the model is not guaranteed to be accurate and much approximation is used.
Pointer analysis: haven't we solved this problem yet?

During the past twenty-one years, over seventy-five papers and nine Ph.D. theses have been published on pointer analysis. Given the tomes of work on this topic one may wonder, “Haven'trdquo; we solved this problem yet? '' With input from many researchers in the field, this paper describes issues related to pointer analysis and remaining open problems.
Efficient Multiplicative Updates for Support Vector Machines

The dual formulation of the support vector machine (SVM) objective function is an instance of a nonnegative quadratic programming problem. We reformulate the SVM objective function as a matrix factorization problem which establishes a connection with the regularized nonnegative matrix factorization (NMF) problem. This allows us to derive a novel multiplicative algorithm for solving hard and soft margin SVM. The algorithm follows as a natural extension of the updates for NMF and semi-NMF. No additional parameter setting, such as choosing learning rate, is required. Exploiting the connection between SVM and NMF formulation, we show how NMF algorithms can be applied to the SVM problem. Multiplicative updates that we derive for SVM problem also represent novel updates for semi-NMF. Further this unified view yields algorithmic insights in both directions: we demonstrate that the Kernel Adatron algorithm for solving SVMs can be adapted to NMF problems. Experiments demonstrate rapid convergence to good classifiers. We analyze the rates of asymptotic convergence of the updates and establish tight bounds. We test them on several datasets using various kernels and report equivalent classification performance to that of a standard SVM.
Mathematical Models for Controlling Wetted Soil Masses Forming under the Practice of Water Added Corn seeding

As one China specific practice, the practice of water added seeding is simple, convenient and cheap to adopt and its most important strength is that it is suitable for developing countries to adopt it. In order to increase penetration depth and reduce evaporation of irrigation water with the conventional practice of water added seeding, get rid of white pollution caused by plastic film mulching, and determine the appropriate parameters of wetted soil masses for effective irrigation use efficiency in light of soil conditions and droughts, especially downward depth and horizontal distances of irrigation water infiltration into soil, the authors successfully developed the practice of water added seeding integrating soil clod formation by loosening. Upon the adoption of the practice in soil tillage, soil clods ranging within 10~20mm in size will form and brace against each another to create porous spaces among them , so that irrigation water quickly moved down through porous spaces upon the action of gravity. And in the meantime, when they meet irrigation water, the clods will quickly break up, thereby not affecting seed germination and seedling emergence of corn. The study established the mathematical models for wetted soil masses occurring with the practice of water added seeding and then verified them by experimentation. Where the soil loosening techniques, holing methods, soil water content, horizontal distance and downward depth of added water infiltration required after water adding were obtained, the appropriate added water rate per seeding hole and loosened soil depth could be calculated by adopting the proposed mathematical model. As a result, the study made it feasible to simply and effectively manage the parameters of irrigation water wetted soil spaces, thereby helpful to realize the two targets of drought fighting and water saving that the conventional practice of water added seeding intended to realize. Keywords-water added seeding; soil loosening; controlling wetted soil mass; mathematical model
The impact of process parameters on mechanical properties of parts fabricated in PLA with an open-source 3-D printer

Purpose – This study aims to quantify the ultimate tensile strength and the nominal strain at break (ɛf) of printed parts made from polylactic acid (PLA) with a Replicating Rapid prototyper (Rep-Rap) 3D printer, by varying three important process parameters: layer thickness, infill orientation and the number of shell perimeters. Little information is currently available about mechanical properties of parts printed using open-source, low-cost 3D printers. Design/methodology/approach – A computer-aided design model of a tensile test specimen was created, conforming to the ASTM:D638. Experiments were designed, based on a central composite design. A set of 60 specimens, obtained from combinations of selected parameters, was printed on a Rep-Rap Prusa I3 in PLA. Testing was performed using a JJ Instruments – T5002-type tensile testing machine and the load was measured using a load cell of 1,100 N. Findings – This study investigated the main impact of each process parameter on mechanical properties and the effe.
Ammonia Assimilation by Saccharomyces cerevisiae

In Saccharomyces cerevisiae , ammonia can be incorporated into the amino group of glutamate, the source of 80% of cellular nitrogen, by two pathways: the reductive amination of 2-ketoglutarate, catalyzed by glutamate dehydrogenase, in which NADPH serves as the source of electrons, or by the ATP-
PCSK9: A Key Modulator of Cardiovascular Health

Since the discovery of proprotein convertase subtilisin kexin 9 (PCSK9) in 2003, this PC has attracted a lot of attention from the scientific community and pharmaceutical companies. Secreted into the plasma by the liver, the proteinase K–like serine protease PCSK9 binds the low-density lipoprotein (LDL) receptor at the surface of hepatocytes, thereby preventing its recycling and enhancing its degradation in endosomes/lysosomes, resulting in reduced LDL-cholesterol clearance. Surprisingly, in a nonenzymatic fashion, PCSK9 enhances the intracellular degradation of all its target proteins. Rare gain-of-function PCSK9 variants lead to higher levels of LDL-cholesterol and increased risk of cardiovascular disease; more common loss-of-function PCSK9 variants are associated with reductions in both LDL-cholesterol and risk of cardiovascular disease. It took 9 years to elaborate powerful new PCSK9-based therapeutic approaches to reduce circulating levels of LDL-cholesterol. Presently, PCSK9 monoclonal antibodies that inhibit its function on the LDL receptor are evaluated in phase III clinical trials. This review will address the biochemical, genetic, and clinical aspects associated with PCSK9’s biology and pathophysiology in cells, rodent and human, with emphasis on the clinical benefits of silencing the expression/activity of PCSK9 as a new modality in the treatment of hypercholesterolemia and associated pathologies.
Efficacy and safety of ixekizumab treatment for Japanese patients with moderate to severe plaque psoriasis, erythrodermic psoriasis and generalized pustular psoriasis: Results from a 52‐week, open‐label, phase 3 study (UNCOVER‐J)

Psoriasis, a chronic, immune‐mediated skin disease characterized by red, scaly plaques, affects approximately 0.3% of the population in Japan. The aim of this open‐label study was to evaluate the long‐term efficacy and safety of ixekizumab, a humanized, anti‐interleukin‐17A monoclonal antibody, in Japanese patients with plaque psoriasis (n = 78, including 11 psoriatic arthritis), erythrodermic psoriasis (n = 8) and generalized pustular psoriasis (n = 5). Ixekizumab was administrated s.c. at baseline (week 0, 160 mg), from weeks 2 to 12 (80 mg every 2 weeks), and from weeks 16 to 52 (80 mg every 4 weeks). At week 52, 92.3% of patients with plaque psoriasis achieved Psoriasis Area and Severity Index (PASI) 75, 80.8% achieved PASI 90, 48.7% achieved PASI 100, and 52.6% had remission of plaques (by static Physician Global Assessment, sPGA [0]). Difficult to treat areas of psoriasis (nail or scalp) also responded to ixekizumab. All patients with psoriatic arthritis who were assessed (5/5) achieved an American College of Rheumatology 20 response. Most patients with erythrodermic psoriasis or generalized pustular psoriasis responded to ixekizumab and the clinical outcome was maintained over 52 weeks (75% and 60% of patients achieved sPGA [0, 1] at week 52, respectively). Mostly mild or moderate treatment‐emergent adverse events were reported by 79 of 91 patients; the most common were nasopharyngitis, eczema, seborrheic dermatitis, urticaria and injection site reactions. In conclusion, 52‐week ixekizumab treatment was efficacious and well tolerated in Japanese patients with plaque psoriasis. Efficacy was also observed in patients with erythrodermic psoriasis, generalized pustular psoriasis and psoriatic arthritis.
Implementation of Measurement System Analysis System (MSA): In the Piston Ring Company "Case Study"

In this survey, case study program is evaluated to improve one the Iran khodro company suppliers . And we tried to implement measurement analysis system that is one of the requirements of the automotive companies, leads to powerful increase in product quality and reducing the cost of duplication and external/internal failure and price. In this paper we used a methodology called; MSA along with APQP and designing the test in the form of three inspectors in the final control on one of important characteristics to measure (the AXIAL WIDTH of ring piston), with measurement, instruments capability(variable aspect),and inspector capability (attribute aspect). The MSA action strongly influences the company s general business performance as revealed by the final analysis in the article. In conclusion, the results concerning the first test (GR&R or capability of measuring instrument) was accepted by implementing the required corrective action, And the results for attribute test (inspector capability) and their ability were identified to detect the correct piece, and the inspectors were achieved in organizing arrangements.
Relevance of the eosinophil blood count in bancroftian filariasis as a screening tool for the treatment

Abstract Backgroud: Lymphatic filariasis constitutes a major public health issue in French Polynesia. Diagnosis has been revolutionized with the availability of circulating filarial antigen (CFA) tests which are easy to perform but are costly. Filariasis is responsible for acquired eosinophilia and eosinophil blood count (EBC) is commonly used as a screening tool. Methods: We retrospectively analysed all the results of EBCs and CFA tests performed in our laboratory over a 2-year period. We calculated the prevalence of antigenemia for nine different eosinophil cutoffs. We calculated the number of patients detected by CFA testing and the number of estimated CFA-positive patients according to their EBC. Results: Over a 2-year period, we detected 7503 eosinophilic patients. For an EBC above 500/mm3, the prevalence of positive CFA was 25·78% and the estimated number of positive CFA patients was 1934. During the same period, as CFA determination is not routinely performed, only 141 patients were detected and treated. Conclusion: Our current strategy against lymphatic filariasis which combines annual mass drug administration, systematic treatment of antigenemic and microfilaraemic patients, and vector control; failed to reach the target of 1% prevalence. Unfortunately, mainly for economical reasons, the antigenemia cannot be determined for all patients. In complement to existing strategy, we propose an additional action based on the treatment of eosinophilic patients in order to reduce the filariasis prevalence in our country.
Confidence Based Dual Reinforcement Q-Routing: An adaptive online network routing algorithm

This paper describes and evaluates the Confidence-based Dual Reinforcement Q-Routing algorithm (CDRQ-Routing) for adaptive packet routing in communication networks. CDRQ-Routing is based on the Q-learning framework of Q-Routing. The main contribution of this work is the increased quantity and improved quality of exploration in CDRQ-Routing, which lead to faster adaptation and better routing policies learned as compared to Q-Routing, the state-of-the-art adaptive Bellman-Ford Routing, and the non-adaptive shortest path routing. Experiments over several network topologies have shown that at different loads, CDRQ-Routing learns superior policies significantly faster than Q-Routing. Moreover, CDRQ-Routing learns policies that sustain higher load levels than Q-Routing. Analysis shows that overhead due to exploration is insignificant as eqmpared to the improvements in CDRQ-Routing.
Safely Interruptible Agents

Reinforcement learning agents interacting with a complex environment like the real world are unlikely to behave optimally all the time. If such an agent is operating in real-time under human supervision, now and then it may be necessary for a human operator to press the big red button to prevent the agent from continuing a harmful sequence of actions—harmful either for the agent or for the environment—and lead the agent into a safer situation. However, if the learning agent expects to receive rewards from this sequence, it may learn in the long run to avoid such interruptions, for example by disabling the red button— which is an undesirable outcome. This paper explores a way to make sure a learning agent will not learn to prevent (or seek! ) being interrupted by the environment or a human operator. We provide a formal definition of safe interruptibility and exploit the off-policy learning property to prove that either some agents are already safely interruptible, like Q-learning, or can easily be made so, like Sarsa. We show that even ideal, uncomputable reinforcement learning agents for (deterministic) general computable environments can be made safely interruptible.