Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining evidence using p-values: application to sequence homology searches

MOTIVATION To illustrate an intuitive and statistically valid method for combining independent sources of evidence that yields a p-value for the complete evidence, and to apply it to the problem of detecting simultaneous matches to multiple patterns in sequence homology searches. RESULTS In sequence analysis, two or more (approximately) independent measures of the membership of a sequence (or sequence region) in some class are often available. We would like to estimate the likelihood of the sequence being a member of the class in view of all the available evidence. An example is estimating the significance of the observed match of a macromolecular sequence (DNA or protein) to a set of patterns (motifs) that characterize a biological sequence family. An intuitive way to do this is to express each piece of evidence as a p-value, and then use the product of these p-values as the measure of membership in the family. We derive a formula and algorithm (QFAST) for calculating the statistical distribution of the product of n independent p-values. We demonstrate that sorting sequences by this p-value effectively combines the information present in multiple motifs, leading to highly accurate and sensitive sequence homology searches.
The Impact of Sanctions and Neo-Liberalism on Women’s Organising in Iran

As in the case of many contemporary movements, Iranian women’s activism is connected into local, international and transnational politics. However, Iranian women’s views of transnational solidarity and perceptions of foreign support for women’s rights in Iran are complicated by the experience of Western foreign policy of the last three decades. This is perceived to have claimed to support women’s rights and liberalism against what is often described as a “conservative theocratic state” but has, in some ways, made it more difficult for women to organise “on the ground” and strengthened the hand of conservative forces both materially and ideologically. Two facets of Western foreign policy towards Iran will be discussed and analysed in relation to their impact on women; firstly, this article will investigate the impact of sanctions and the international isolation of the country since 1979 on women’s organisations. Secondly, it will analyse neo-liberalism and the changing nature of the Iranian state, as well as political elites. Utilising interviews with Iranian women activists conducted in 2009, in addition to April 2015, the article will discuss views of transnational solidarity and the diverse political strategies utilised by women activists and organisations in Iran today.
Synthesis of silver nanoparticles by using tea leaf extract from Camellia Sinensis

The development of the biological synthesis of nanoparticles using microorganisms or plant extracts plays an important role in the field of nanotechnology as it is environmentally friendly and does not involve any harmful chemicals. In this study, the synthesis of silver nanoparticles using the leaves extract of Chinese tea from Camellia sinensis is reported. The synthesized nanoparticles were characterized using UV-vis spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM), and Fourier transform infrared (FTIR) spectroscopy. The XRD analysis shows that the synthesized silver nanoparticles are of face-centered cubic structure. Well-dispersed silver nanoparticles with an approximate size of 4 nm were observed in the TEM image. The application of the green synthesized nanoparticles can be used in many fields such as cosmetics, foods, and medicine.
Keyphrase Extraction for N-best Reranking in Multi-Sentence Compression

Multi-Sentence Compression (MSC) is the task of generating a short single sentence summary from a cluster of related sentences. This paper presents an N-best reranking method based on keyphrase extraction. Compression candidates generated by a word graph-based MSC approach are reranked according to the number and relevance of keyphrases they contain. Both manual and automatic evaluations were performed using a dataset made of clusters of newswire sentences. Results show that the proposed method significantly improves the informativity of the generated compressions.
A Contrast-Sensitive Visible Watermarking Scheme

The authors use a visible watermarking algorithm for digital rights management that computes composite coefficients using global and local characteristics of the host and watermark images. They also use a contrast-sensitive function and block classification in the discrete wavelet transform domain for a better visual effect. The original and watermark images are divided into different blocks and classified based on visual masking. Experiments indicate that this approach provides a better visual effect than other schemes.
Strategies for sound internet measurement

Conducting an Internet measurement study in a sound fashion can be much more difficult than it might first appear. We present a number of strategies drawn from experiences for avoiding or overcoming some of the pitfalls. In particular, we discuss dealing with errors and inaccuracies; the importance of associating <i>meta-data</i> with measurements; the technique of calibrating measurements by examining outliers and testing for consistencies; difficulties that arise with large-scale measurements; the utility of developing a discipline for reliably reproducing analysis results; and issues with making datasets publicly available. We conclude with thoughts on the sorts of tools and community practices that can assist researchers with conducting sound measurement studies.
Processus réfléchis en finance et probabilité numérique : régularités et approximation d'EDSR réfléchies et options américaines en présence de coûts de transaction

Cette these se compose de deux parties independantes qui portent sur l'application des probabilites au champ de la finance. La premiere partie etudie la regularite des solutions de certains types d'equations differentielles stochastiques retrogrades (EDSR) et reflechies, ainsi que des schemas d'approximation numerique de ces solutions. En finance, l'application principale est le calcul du prix et de la couverture d'options americaines et d'options de jeu, mais nos travaux ne se limitent pas a ce cadre. La methode systematique proposee est fondee sur l'etude d'equations qui ne sont reflechies que sur une grille de temps discrete. En finance, ces equations s'interpretent comme des options bermudeennes. Dans un cadre general de domaines convexes multidimensionnels pouvant, sous certaines conditions, evoluer aleatoirement, nous obtenons des resultats de convergence et de regularite pour ces equations a reflexions discretes que nous etendons aux EDSR reflechies de maniere continue. La seconde partie porte sur un probleme theorique de finance mathematique. Nous y traitons de la valorisation d'options americaines dans le cadre des modeles de marche avec couts de transaction proportionnels, a la fois pour le temps discret et pour le temps continu. Nous obtenons un theoreme de sur-replication pour ces actifs contingents dans le cadre tres general de processus optionnels ladlag.
Upregulations of Glucocorticoid-Induced Leucine Zipper by Hypoxia and Glucocorticoid Inhibit Proinflammatory Cytokines under Hypoxic Conditions in Macrophages

Hypoxia and inflammation often develop concurrently in numerous diseases, and the influence of hypoxia on natural evolution of inflammatory responses is widely accepted. Glucocorticoid-induced leucine zipper (GILZ) is thought to be an important mediator of anti-inflammatory and immune-suppressive actions of glucocorticoid (GC). However, whether GILZ is involved in hypoxic response is still unclear. In this study, we investigated the effects of hypoxic exposure and/or the administration of dexamethasone (Dex), a synthetic GC on GILZ expression both in vitro and in vivo, and further explored the relationship between GILZ and proinflammatory cytokines IL-1β, IL-6, and TNF-α under normoxic and hypoxic conditions. We found that hypoxia not only remarkably upregulated the expression of GILZ, but also significantly enhanced Dex-induced expression of GILZ in macrophages and the spleen of rats. ERK activity is found involved in the upregulation of GILZ induced by hypoxia. Inhibiting the expression of GILZ in RAW264.7 cells using specific GILZ small interfering RNA led to a significant increase in mRNA production and protein secretion of IL-1β and IL-6 in hypoxia and abrogated the inhibitory effect of Dex on expression of IL-1β and IL-6 in hypoxia. We also found that adrenal hormones played pivotal roles in upregulation of GILZ expression in vivo. Altogether, data presented in this study suggest that GILZ has an important role not only in adjusting adaptive responses to hypoxia by negatively regulating the activation of macrophages and the expression of proinflammatory cytokines, but also in mediating the anti-inflammatory action of GC under hypoxic conditions.
Absorption, distribution, metabolism and excretion of the novel SARM GTx-024 [(S)-N-(4-cyano-3-(trifluoromethyl)phenyl)-3-(4-cyanophenoxy)-2-hydroxy-2-methylpropanamide] in rats

Abstract 1. GTx-024, a novel selective androgen receptor modulator, is currently being investigated as an oral treatment for muscle wasting disorders associated with cancer and other chronic conditions. 2. Absorption of GTx-024 was rapid and complete, with high oral bioavailability. A wide tissue distribution of [14C]GTx-024 derived radioactivity was observed. [14C]GTx-024-derived radioactivity had a moderate plasma clearance (117.7 and 74.5 mL/h/kg) and mean elimination half-life of 0.6 h and 16.4 h in male and female rats, respectively. 3. Fecal excretion was the predominant route of elimination, with ∼70% of total radioactivity recovered in feces and 21–25% in urine within 48 h. Feces of intact rats contained primarily unchanged [14C]GTx-024 (49.3–64.6%). Metabolites were identified in urine and feces resulting from oxidation of the cyanophenol ring (M8, 17.6%), hydrolysis and/or further conjugation of the amide moiety (M3, 8–12%) and the cyanophenol ring (M4, 1.3–1.5%), and glucuronidation of [14C]GTx-024 at the tertiary alcohol (M6, 3.5–3.7%). There was no quantifiable metabolite in plasma. 4. In summary, in the rat GTx-024 is completely absorbed, widely distributed, biotransformed through several metabolic pathways, and eliminated in feces primarily as an unchanged drug.
Performance Evaluation of Material Decomposition With Rapid-Kilovoltage-Switching Dual-Energy CT and Implications for Assessing Bone Mineral Density.

OBJECTIVE The purpose of this article is to quantitatively investigate the accuracy and performance of dual-energy CT (DECT) material density images and to calculate the areal bone mineral density (aBMD) for comparison with dual-energy x-ray absorptiometry (DEXA). MATERIALS AND METHODS A rapid-kilovoltage-switching DECT scanner was used to create material density images of various two-material phantoms of known concentrations under different experimental conditions. They were subsequently also scanned by single-energy CT and DEXA. The total uncertainty and accuracy of the DECT concentration measurements was quantified by the root-mean-square (RMS) error, and linear regression was performed to evaluate measurement changes under varying scanning conditions. Alterations to accuracy with concentric (anthropomorphic) phantom geometry were explored. The sensitivity of DECT and DEXA to changes in material density was evaluated. Correlations between DEXA and DECT-derived aBMD values were assessed. RESULTS The RMS error of DECT concentration measurements in air ranged from 9% to 244% depending on the materials. Concentration measurements made off-isocenter or with a different DECT protocol were slightly lower (≈ 5%), whereas measurement in scattering conditions resulted in a reduction of 8-27%. In concentric phantoms, higher-attenuating material in the outer chamber increased measured values of the inner material for all methods. DECT was more sensitive than DEXA to changes in BMD at 2 mg/mL K2HPO4. Measurements of aBMD using DECT and DEXA were highly correlated (R(2) = 0.98). CONCLUSION DECT material density images were linear in response but prone to poor accuracy and biases. DECT-based aBMD could be used to monitor relative change in bone density.
Protective effect of heme oxygenase induction in ischemic acute renal failure

Objective: To examine the role of heme oxygenase‐1 (HO‐1) induction in the recovery of renal function in rats with ischemic acute renal failure. Design: Randomized, masked, controlled animal study. Setting: University‐based animal research facility. Subjects: Sprague‐Dawley male rats, weighing 200‐250 g. Interventions: Anesthetized rats were subjected to bilateral flank incisions, and the right kidney was removed. Renal ischemia was performed by left renal microvascular clamping, followed by reflow of the blood. Measurements and Main Results: Ischemia of the kidney in the uninephrectomized rat significantly induced HO‐1 messenger RNA, protein, and enzyme activity, reaching a maximum at 6 hrs, which was mediated in part through an increase in microsomal heme concentration. Heat shock protein 70 was induced extremely rapidly, reaching a maximum at 1 hr, suggesting that HO‐1 and heat shock protein 70 gene expression are regulated separately. Inhibition of HO activity by tin mesoporphyrin, which resulted in an increase in microsomal heme concentration, significantly exacerbated renal function, as judged by the sustained increase in serum creatinine concentration and extensive tubular epithelial cell injuries. In contrast, animals that did not receive tin mesoporphyrin showed normal creatinine concentration and microsomal heme concentration 24 hrs after reperfusion, as well as restoration of abnormal renal histology. Conclusion: These findings indicate that the expression of HO‐1 in the ischemic kidney may be critical in the recovery of renal cell function in this animal model. These findings also suggest that HO‐1 induction may play an important role in conferring protection on renal cells from oxidative damage caused by heme.
A Multilaboratory Toxicological Assessment of a Panel of 10 Engineered Nanomaterials to Human Health—ENPRA Project—The Highlights, Limitations, and Current and Future Challenges

ABSTRACT ENPRA was one of the earlier multidisciplinary European Commission FP7-funded projects aiming to evaluate the risks associated with nanomaterial (NM) exposure on human health across pulmonary, cardiovascular, hepatic, renal, and developmental systems. The outputs from this project have formed the basis of this review. A retrospective interpretation of the findings across a wide range of in vitro and in vivo studies was performed to identify the main highlights from the project. In particular, focus was placed on informing what advances were made in the hazard assessment of NM, as well as offering some suggestions on the future of “nanotoxicology research” based on these observations, shortcomings, and lessons learned from the project. A number of issues related to the hazard assessment of NM are discussed in detail and include use of appropriate NM for nanotoxicology investigations; characterization and dispersion of NM; use of appropriate doses for all related investigations; need for the correct choice of experimental models for risk assessment purposes; and full understanding of the test systems and correct interpretation of data generated from in vitro and in vivo systems. It is hoped that this review may assist in providing information in the implementation of guidelines, model systems, validation of assessment methodology, and integrated testing approaches for risk assessment of NM. It is vital to learn from ongoing and/or completed studies to avoid unnecessary duplication and offer suggestions that might improve different aspects of experimental design.
Foreign body injuries in children: a review

SUMMARY The aim of this paper was to overview existing knowledge on foreign body (FB) injuries in children, with particular focus on FB types and anatomical locations, clinical presentation and complications. FB injuries represent a severe public health problem in childhood. The fact that the highest prevalence of FB injuries is reported for children between 0 and 3 years of age depends primarily on the fact that they explore objects using their mouth and are also not able to distinguish edible objects from non-edible ones. Types of FB causing injuries depend on the symptoms related to FB ingestion/inhalation/insertion (providing an early diagnosis of FB injuries) and complications related to the FB characteristics (type, shape, dimensions). The analysis of the Susy Safe database showed that in 10,564 cases, in which the object type was available, 74% of objects were inorganic and were mostly represented by pearls and balls, followed by coins. The main concerning about FB injuries is the fact that they may be asymptomatic or that symptoms may be non-specific. Consequently, the FB injury can be misinterpreted as a gastrointestinal or respiratory infection. The absence of specific symptoms indicating the occurrence of FB injury can lead to delays in diagnosis, thereby increasing the risk of complications. Symptoms seem to mostly depend on the anatomical location. Many ingested FBs pass naturally through the gastrointestinal tract without complications or damage. However, severe complications can occur depending on the characteristics of the FB, its anatomical location, the child's age and delays in diagnosis.
Vector broadcast channels: Optimality of threshold feedback policies

Beamforming techniques utilizing only partial channel state information (CSI) has gained popularity over other communication strategies requiring perfect CSI thanks to their lower feedback requirements. The amount of feedback in beamforming based communication systems can be further reduced through selective feedback techniques in which only the users with channels good enough are allowed to feed back by means of a decentralized feedback policy. In this paper, we prove that thresholding at the receiver is the rate-wise optimal decentralized feedback policy for feedback limited systems with prescribed feedback constraints. This result is highly adaptable due to its distribution independent nature, provides an analytical justification for the use of threshold feedback policies in practical systems, and reinforces previous work analyzing threshold feedback policies as a selective feedback technique without proving its optimality. It is robust to selfish unilateral deviations. Finally, it reduces the search for rate-wise optimal feedback policies subject to feedback constraints from function spaces to a finite dimensional Euclidean space.
An enhanced handover oscillation control algorithm in LTE Self-Optimizing networks

In this paper we propose a new horizontal handover oscillation control algorithm for Long Term Evolution (LTE) Self-Optimizing based Networks (SON). Based on a pre-established policy, this algorithm automatically adjusts the Hysteresis and Time-To-Trigger (TTT) based on Ping-Pong Handover Performance Indicator (HPI). Additionally, the User Equipment (UE) type of traffic and speed is taken into account for a more accurate handover decision. Results show clear improvements when compared with other proposals, namely the fixed parameter scenario.
Comparison of modified Kessler tendon suture at different levels in the human flexor digitorum profundus tendon and porcine flexors and porcine extensors: an experimental biomechanical study

This study compared the biomechanical behaviour of repairs in the human flexor digitorum profundus tendon in zones I, II and III with repairs of different segments of the porcine flexor tendon of the second digit and the extensor digiti quarti proprius tendon, in order to assess the validity of porcine tendons as models for human flexor tendon repairs. These porcine tendons were selected after comparing their size with the human flexor digitorum profundus tendon. The tendon repairs were done in three segments of each porcine tendon and repairs in the human tendons were done in zones I,II and III. Ten tendons in each group yielded a total of 90 specimens. A modified Kessler repair was done with 3-0 coated braided polyester suture and subjected to uniaxial tensile testing. In human flexor tendons, the ultimate force was higher in zones I and II than in zone III. The porcine flexor digitorum profundus tendon from the second digit and the proximal segment of the extensor digiti quarti proprius tendon behaved similarly to the human flexor tendon in zone III and can be considered as surrogates for the human flexor tendon.
Neonatal vitamin A supplementation for prevention of mortality and morbidity in infancy: systematic review of randomised controlled trials

Objective To evaluate the effect of neonatal vitamin A supplementation on infant mortality, morbidity and early adverse effects. Design Systematic review, meta-analysis, and meta-regression of randomised controlled trials. Data sources Electronic databases and hand search of reviews; abstracts and proceedings of conferences. Review methods Randomised or quasi-randomised or cluster randomised, placebo controlled trials evaluating the effect of prophylactic, neonatal (<1 month) supplementation with synthetic vitamin A on mortality or morbidity within infancy (<1 year), and early adverse effects (≤7 days). Results The six included trials were from developing countries. There was no convincing evidence of a reduced risk of mortality during infancy (relative risk 0.92, 95% confidence interval 0.75 to 1.12, P=0.393 random effect; I2=54.1%) or of an increase in early adverse effects including bulging fontanelle (1.16, 0.81 to 1.65, P=0.418; I2=65.3%). No variable emerged as a significant predictor of mortality, but data for important risk groups (high maternal night blindness prevalence and low birth weights) were restricted. Limited data (from one to four trials) did not indicate a reduced risk of mortality during the neonatal period (0.90, 0.75 to 1.08, P=0.270; I2=0%), cause specific mortality, common morbidities (diarrhoea and others), and admission to hospital. There was, however, evidence of an increased risk of acute respiratory infection and a reduced risk of clinic visits. Conclusions There is no convincing evidence of a reduced risk of mortality and possibly morbidity or of increased early adverse effects after neonatal supplementation with vitamin A. There is thus no justification for initiating such supplementation as a public health intervention in developing countries for reducing infant mortality and morbidity.
Evolution of management of major hepatic trauma: identification of patterns of injury.

Nonoperative management of hemodynamically stable patients following blunt hepatic trauma identified by computed tomography (CT) has been reported in up to 20% of patients presenting with hepatic injury, predominantly low grade. We reviewed 128 consecutive adult patients sustaining blunt hepatic trauma with the hypothesis that severe hepatic injuries (grades III to V) could be safely managed nonoperatively and to determine anatomic pattern and severity of hepatic injuries. Sixty-two of the 128 patients (47%) went directly for laparotomy, based on physical findings or positive peritoneal lavage. Sixty-six patients were hemodynamically stable and underwent abdominal CT scanning; 70% (46 of 66) were successfully managed nonoperatively. Fifty-one percent of grade III and IV injuries were treated nonoperatively. However, the majority of patients with grade V injuries were unstable, and 92% required laparotomy. Twenty-six of 46 patients treated nonoperatively (56%) had injury to the posterior segment of the right lobe of the liver or a "split liver. " In retrospect, only 33% of patients with hepatic injury required laparotomy for therapy of the liver injury. Hemodynamic stability and anatomic pattern of injury on presentation were important factors in successful nonoperative management of hepatic injury.