Miracle-dz/UniFAR-FTUs huggingface dataset:
Sequential Information Maximization: When is Greedy Near-optimal?

Optimal information gathering is a central challenge in machine learning and science in general. A common objective that quantifies the usefulness of observations is Shannon’s mutual information, defined w.r. t. a probabilistic model. Greedily selecting observations that maximize the mutual information is the method of choice in numerous applications, ranging from Bayesian experimental design to automated diagnosis, to active learning in Bayesian models. Despite its importance and widespread use in applications, little is known about the theoretical properties of sequential information maximization, in particular under noisy observations. In this paper, we analyze the widely used greedy policy for this task, and identify problem instances where it provides provably near-maximal utility, even in the challenging setting of persistent noise. Our results depend on a natural separability condition associated with a channel injecting noise into the observations. We also identify examples where this separability parameter is necessary in the bound: if it is too small, then the greedy policy fails to select informative tests.
The Adenovirus Genome Contributes to the Structural Stability of the Virion

Adenovirus (Ad) vectors are currently the most commonly used platform for therapeutic gene delivery in human gene therapy clinical trials. Although these vectors are effective, many researchers seek to further improve the safety and efficacy of Ad-based vectors through detailed characterization of basic Ad biology relevant to its function as a vector system. Most Ad vectors are deleted of key, or all, viral protein coding sequences, which functions to not only prevent virus replication but also increase the cloning capacity of the vector for foreign DNA. However, radical modifications to the genome size significantly decreases virion stability, suggesting that the virus genome plays a role in maintaining the physical stability of the Ad virion. Indeed, a similar relationship between genome size and virion stability has been noted for many viruses. This review discusses the impact of the genome size on Ad virion stability and emphasizes the need to consider this aspect of virus biology in Ad-based vector design.
Numerical issues in plasticitymodels for granular flows

Friction plays a fundamental role in the Mechanics of granular materials. Two problems are considered: (i) heap formation, (ii) granular flow. Both problems admit closely related mathematical models. In each case, analytical and numerical difficulties are discussed. Efficient and reliable numerical methods are proposed and implemented. The results are illustrated by several computational experiments.
Learning Dynamics of Reaching

When one moves one’s hand from one point to another, the brain guides the arm by relying on neural structures that estimate the physical dynamics of the task. For example, if one is about to lift a bottle of milk that appears full rather than empty, the brain takes into account the subtle changes in the dynamics of the task and this is reflected in the altered motor commands. The neural structures that compute the task’s dynamics are “internal models” that transform the desired motion into motor commands. Internal models are learned with practice and are a fundamental part of voluntary motor control. What do internal models compute, and which neural structures perform that computation? We approach these problems by considering a task where physical dynamics of reaching movements are altered by force fields that act on the hand. Experiments by a number of laboratories on this paradigm suggest that internal models are sensorimotor transformations that map a desired sensory state
Definability on a random 3-CNF formula

We consider the question of certifying unsatisfiability of random 3-CNF formulas. At which densities can we hope for a simple sufficient condition for unsatisfiability that holds almost surely? We study this question from the point of view of definability theory. The main result is that first-order logic cannot express any sufficient condition that holds almost surely on random 3-CNF formulas with n/sup 2-/spl alpha// clauses, for any irrational positive number /spl alpha/. In contrast, it can when the number of clauses is n/sup 2+/spl alpha//, for any positive /spl alpha/. As an intermediate step, our proof exploits the planted distribution for 3-CNF formulas in a new technical way. Moreover, the proof requires us to extend the methods of Shelah and Spencer for proving the zero-one law for sparse random graphs to arbitrary relational languages.
Mutation in EGFP Domain of LDL Receptor-Related Protein 6 Impairs Cellular LDL Clearance

Mutation in the EGFP domain of LDL receptor-related protein 6 (LRP6R611C) is associated with hypercholesterolemia and early-onset atherosclerosis, but the mechanism by which it causes disease is not known. Cholesterol uptake was examined in cells from LRP6+/− mice and LRP6R611C mutation carriers. Splenic B cells of LRP6+/− mice have significantly lower LRP6 expression and low-density lipoprotein (LDL) uptake than those of the wild-type littermates. Although similar levels of total LRP6 were found in lymphoblastoid cells (LCLs) of LRP6R611C mutation carriers and those of the unaffected family member, LDL uptake was significantly lower in the mutant cells. Mutant and wild-type receptors show similar affinities for apolipoprotein B at neutral pH. LRP6 colocalized with LDL and was coimmunoprecipitated with NPC1 (Niemann–Pick disease type C1), an endocytic regulator of LDL trafficking. However, the cellular localization of LRP6 in the mutant cells shifted from cell surface to late endosomes/lysosomes. Plasma membrane expression levels of LRP6R611C was lower compared to wild-type receptor and declined to a greater extent in LDL-rich medium. Further examinations revealed lower efficacy of apolipoprotein B dissociation from LRP6R611C compared to wild-type receptor at an acidic pH. These studies identify LRP6 as a receptor for LDL endocytosis and imply that R611C mutation results in reduced LRP6 membrane expression and decreased LDL clearance. Based on our findings, we conclude that the increased affinity of the mutant receptor for LDL in acidic pH leads to their impaired dissociation in late endosomes, which compromises their recycling to the plasma membrane.
Comment on “Cigarette Smoke-Induced Pulmonary Inflammation Is TLR4/MyD88 and IL-1R1/MyD88 Signaling Dependent”

I n their article, Doz et al. (1) investigate the role of TLR4/ MyD88 and IL-1R1/MyD88 signaling in cigarette smoke (CS)-induced pulmonary inflammation to unravel mechanisms involved in the development of chronic obstructive pulmonary disease (COPD). In an acute CS exposure model of 3 days, they demonstrate a reduced CS-induced influx of neutrophils in bronchoalveolar lavage (BAL) fluid in TLR4 / , MyD88 / , and IL-R1 / mice compared with C57BL/6 controls, as well as reduced IL-1, IL-6, and KC levels and reduced matrix metalloproteinase-9 activity in BAL. In contrast, TLR4 / (C57BL/6J, C57BL/10ScNJ, or C3H/HeJ background) and MyD88 / animals appear to develop spontaneous age-related emphysema, which is not associated with an inflammatory response in BAL or lung tissue (2). We demonstrated (3) that subacute CS exposure for 5 wk in TLR4-defective animals (C3H/HeJ) results in a reduced pulmonary accumulation of neutrophils, lymphocytes, and dendritic cells in BAL as well as lower levels of MCP-1 and TNFcompared with wild-type (C3H/HeOuJ) animals. However, after chronic cigarette smoke exposure for 26 wk TLR4 became of less importance, with only minor differences in pulmonary inflammation between the two strains, similar MCP-1 and TNFlevels in BAL, and similar matrix metalloproteinase-12 expression in the lung. These studies highlight the complexity of the pathogenic mechanisms in COPD and emphysema, because CS-induced pulmonary inflammation is TLR4-dependent in (sub) acute experiments (1) whereas it is TLR4-independent in chronic experiments (3). In conclusion, these papers underscore the importance of both acute and chronic models in unraveling the pathogenesis of COPD.
Conjunctiva-Sparing Posterior Ptosis Surgery: A Novel Approach

Purpose: Müller’s muscle conjunctiva resection is a well-established means of correcting blepharoptosis. The primary objective of this prospective study was to determine if modifying Müller’s muscle conjunctiva resection by sparing the conjunctiva would accomplish successful repair while allowing patients to retain their conjunctiva. The potential advantages of preserving conjunctiva are significant and include: conservation of an anatomically normal tissue, retention of goblet cells, reduction of suture-related complications such as corneal irritation or abrasion as the conjunctiva covers the suture during postoperative healing, and preservation of conjunctiva for potential future surgical procedures critical to ocular health. Methods: This is a prospective study enrolling patients with mild to moderate ptosis. Results: The procedure has been performed in 18 patients and 30 eyelids. Follow up at 1 week revealed normal healing with expected postoperative edema and ecchymosis. Notably, all patients were free of any corneal abrasion or irritation. Follow up at 1 month and a minimum of 3 months (average 5.7 months) revealed that all patients had satisfactory correction of their blepharoptosis with Margin Reflex Distance 1 (MRD1) improvement to within 1 mm of the anticipated goal, preserved eyelid margin contour, and good symmetry (average 0.26 mm difference in MRD1 between the sides). Conclusion: These results show an effective correction of blepharoptosis with a favorable cosmetic outcome and low postoperative complication rate; all while preserving the conjunctiva.
Clinical Application of Pharmacogenomics

The purpose of this review is to discuss the clinical application of pharmacogenomics for select drug therapies (eg, proton pump inhibitors [PPIs], codeine, and carbamazepine) and to highlight limitations and challenges that preclude implementation of pharmacogenomics into clinical practice. Genetic polymorphisms of cytochrome P450 (CYP) enzymes and the presence of the human leukocyte antigen (HLA)-B*1502 allele influence drug disposition and/or response. A portion of PPI pharmacokinetic and pharmacodynamic variability can be explained by CYP2C19 genotype. However, conflicting evidence exists related to Helicobacter pylori cure rates based on CYP2C19 genotype. For codeine, adverse drug reactions in neonates through breast-feeding from CYP2D6 ultra-rapid metabolizers have been reported. However, there is lack of conclusive evidence regarding the overall influence of CYP2D6 polymorphisms on codeine efficacy and toxicity. Although CYP2C19 and CYP2D6 genotyping tests are available, clinical utility remains low. The presence of the HLA-B*1502 allele is associated with carbamazepine-induced Stevens-Johnson syndrome (SJS) and/or toxic epidermal necrolysis (TEN). Pharmacogenomic testing is required prior to initiating carbamazepine in high-risk patients. Lack of sufficient resources, provider knowledge, and ethical, legal, and social issues are several limitations and challenges to implementing pharmacogenomic testing in clinical practice.
Multiple-Line Inference of Selection on Quantitative Traits

Trait differences between species may be attributable to natural selection. However, quantifying the strength of evidence for selection acting on a particular trait is a difficult task. Here we develop a population genetics test for selection acting on a quantitative trait that is based on multiple-line crosses. We show that using multiple lines increases both the power and the scope of selection inferences. First, a test based on three or more lines detects selection with strongly increased statistical significance, and we show explicitly how the sensitivity of the test depends on the number of lines. Second, a multiple-line test can distinguish between different lineage-specific selection scenarios. Our analytical results are complemented by extensive numerical simulations. We then apply the multiple-line test to QTL data on floral character traits in plant species of the Mimulus genus and on photoperiodic traits in different maize strains, where we find a signature of lineage-specific selection not seen in two-line tests.
Water Price Prediction for Increasing Market Efficiency Using Random Forest Regression: A Case Study in the Western United States

The existence of water markets establishes water prices, promoting trading of water from low- to high-valued uses. However, market participants can face uncertainty when asking and offering prices because water rights are heterogeneous, resulting in inefficiency of the market. This paper proposes three random forest regression models (RFR) to predict water price in the western United States: a full variable set model and two reduced ones with optimal numbers of variables using a backward variable elimination (BVE) approach. Transactions of 12 semiarid states, from 1987 to 2009, and a dataset containing various predictors, were assembled. Multiple replications of k-fold cross-validation were applied to assess the model performance and their generalizability was tested on unused data. The importance of price influencing factors was then analyzed based on two plausible variable importance rankings. Results show that the RFR models have good predictive power for water price. They outperform a baseline model without leading to overfitting. Also, the higher degree of accuracy of the reduced models is insignificant, reflecting the robustness of RFR to including lower informative variables. This study suggests that, due to its ability to automatically learn from and make predictions on data, RFR-based models can aid water market participants in making more efficient decisions.
Importance of Interface Agent Characteristics from End-User Perspective

This article reports on an empirical investigation of user perceptions of the importance of several characteristics of interface agents. Interface agents are software entities that are incorporated into various computer applications, including electronic mail systems. As evidenced by the growing body of empirical studies and the increasing number of interface agent-based applications on the software market, there is a strong need for the development of this technology. According to a meta-review of agent-related literature by Dehn and van Mulken (2000), there are several characteristics of interface agents that require special attention from agent developers. However, prior to this study, the importance of these characteristics from the end-user perspective remained unclear. In order to identify the significance of these characteristics, a group of actual users of an e-mail interface agent was surveyed. The results indicate that information accuracy and the degree of the usefulness of an agent are the most salient factors, followed by user comfortability with an agent, the extent of user enjoyment, and visual attractiveness of an agent. The implications of the findings for both theory and practice are discussed.
Decreasing Effects of Iron Toxicosis on Selenium and Glutathione Peroxidase Activity

Heart failure due to chronic iron overload is a leading cause of cardiovascular mortality in the second and third decades of life worldwide, but its mechanism is not known. Deficiencies of selenium have been shown to result in damage to the myocardium and to the development of various cardiomyopathies. In the current investigation, the dose-dependent effects of chronic iron toxicosis on heart tissue concentrations of selenium and the protective antioxidant enzyme glutathione peroxidase (GPx) were investigated in a murine model of iron-overload cardiomyopathy (n = 20). Significant dose-dependent decreases in heart tissue selenium concentrations (r =-0.95, p <0.001) and selenium-dependent GPx activity (r =-0.93, p <0.001) were observed in chronically iron-loaded mice in comparison with placebo controls. These results suggest that dietary supplementation with selenium may be beneficial in the clinical management of disorders of iron metabolism.
Monitoring of some pesticides residues in raw milk in Alexandria province, Egypt

Pesticides are used worldwide to increase the production but many persistent residues of pesticides cause problems in environment contamination and human health. Therefore, the present study was conducted to monitor the concentrations of some organochlorines pesticides (OC), organophosphorus (OP) pesticide and synthetic pyrethroids using Gas chromatography in raw milk samples collected from different three districts at Alexandria province, Egypt. The obtained results revealed that some of organochlorines pesticides DDT, Dieldrin, Endrin and Lindane were monitored respectively at percent of 10,10, 2.5, and 5% in district A; 6.66, 6.66, 3.33 and 0% in district B and 10, 3.33, 3.33 and 6.66 % in district C. Concerning organophosphorus pesticides including (malathion and Chlorpyrifos) were detected at percent 5 and 2.5% in district A; 6.66 and 3.33 % in district B and district C were detect in 3.33 and 3.33% of examined raw milk samples. Cyhalothrin and Deltamethrin synthetic pyrethroids were detected in district A, B and C at percent 5 and 7.5%; 3.33 and 6.66%; 3.33 and 3.33%, respectively in examined positive raw milk samples. This study illustrated the risks of pesticides residues exposure that threaten consumer health. Thus, monitoring survey of pesticide residues in milk is necessary to safeguard consumer health.
Mapping the global geographic potential of Zika virus spread

The Americas are presently experiencing the most serious known outbreak of Zika virus (ZIKV). Here, we present a novel set of analyses using environmental characteristics, vector mosquito distributions, and socioeconomic risk factors to develop the first map to detail global ZIKV transmission risk in multiple dimensions based on ecological niche models. Our model predictions were tested against independent evaluation data sets, and all models had predictive ability significantly better than random expectations. The study addresses urgent knowledge gaps regarding (1) the potential geographic scope of the current ZIKV epidemic, (2) the global potential for spread of ZIKV, and (3) drivers of ZIKV transmission. Our analysis of potential drivers of ZIKV distributions globally identified areas vulnerable in terms of some drivers, but not for others. The results of these analyses can guide regional education and preparedness efforts, such that medical personnel will be better prepared for diagnosis of potential ZIKV cases as they appear.
Gadolinium-enhanced magnetic resonance angiography, digital subtraction angiography and duplex of the iliac arteries compared with intra-arterial pressure gradient measurements.

PURPOSE to compare gadolinium-enhanced magnetic resonance angiography (Gd-MRA), digital subtraction angiography (DSA) and duplex of the iliac arteries with intra-arterial pressure gradient measurement as the reference method. MATERIALS AND METHODS Gd-MRA, DSA and duplex examinations of the iliac arteries were performed in 30 patients (60 arteries) with lower-limb arterial occlusive disease. In 29 arteries, pressure measurements were made (n=25) or the artery was found to be occluded on catheterisation (n=4). An aortofemoral peak systolic pressure gradient of 20 mmHg or more was regarded as haemodynamically significant. Stenoses with a diameter reduction of 50% or more on MRA or DSA, or an increase in peak systolic velocity greater than 150% (duplex) were considered significant. MRA examinations were evaluated by means of maximum intensity projections (MRA-MIP) and using source images and curved multiplanar reconstruction (MRA-MPR). RESULTS the sensitivity (specificity) for a significant iliac artery stenosis were 81% (75%) for MRA-MIP, 76% (75%) for MRA-MPR, 86% (88%) for DSA, and 72% (88%) for duplex. CONCLUSION with intra-arterial pressure measurements as the reference method, similar results were achieved with Gd-MRA, DSA and duplex concerning the detection of haemodynamically significant iliac artery stenoses. The use of source images and multiplanar reconstructions resulted in higher accuracy for the detection of occlusions.
Evaluation of risk factors for vancomycin‐resistant Enterococcus bacteremia among previously colonized hematopoietic stem cell transplant patients

Hematopoietic stem cell transplantation (HSCT) recipients colonized with vancomycin‐resistant Enterococcus (VRE) may have an increased risk of developing VRE bacteremia. Identification of risk factors for the development of subsequent VRE bacteremia among colonized HSCT recipients is necessary to predict which patients may benefit the most from receiving anti‐VRE antibiotic therapy as part of an initial antimicrobial regimen when gram‐positive bacteremia is suspected.
Splenic lymphoma with villous lymphocytes should be included in the differential diagnosis of massive splenomegaly.

AIM To distinguish between patients with reactive lymphocytosis and those with malignant lymphoid proliferations, with particular reference to hyper-reactive malarial splenomegaly and splenic lymphoma with villous lymphocytes. PATIENTS Forty-four patients, residents of the Ashanti region of Ghana that is hyperendemic for Plasmodium falciparum malaria, were studied. All patients had splenomegaly greater than 10 cm. They were given proguanil 100 mg/day for a minimum of 6 months. Lymphocyte surface phenotypes were studied on the peripheral blood smears, immunoglobulin gene rearrangement by the Southern blot technique, serum IgM concentration using the Nor-Partigen-IgM kit, and serum paraprotein concentration by electrophoresis. RESULTS Based on the response to proguanil, the patients were categorized into good respondents, partial respondents, and non respondents. Peripheral blood lymphocytes exceeded 30% in 19, and villous lymphocytes were less than 30% in 25 patients. CONCLUSION Splenic lymphoma with villous lymphocytes may be difficult to differentiate from the African variant of chronic lymphocytic leukemia which is associated with splenomegaly and from hyperreactive malarial splenomegaly with lymphocytosis. In West Africa, a peripheral blood lymphocyte count greater than 10 x 109/L, with more than 30% of villous lymphocytes and failure of splenic regression with anti-malarial therapy suggest a diagnosis of splenic lymphoma with villous lymphocytes.
THE ETIOLOGIC PATTERNS IN MICROCEPHALY WITH MENTAL RETARDATION

Microcephaly with mental retardation forms a distinct subgroup among mentally retarded individuals. The paucity of studies on the etiology of this condition in India made the investigators to study this population. It HTO aimed to study the demographic and clinical characteristics, and the etiologic pattern in children with microcepltaly and mental retardation The sample consisted of 82 children who were examined by detailed clinical assessment and a battery of investigations. A definite etiology could be found in 56% of children which have been grouped into prenatal embryonic, prenatal maternal/environmental, and birth and neonatal causes. Non-genetic causes were the most common. The prenatal etiology constituted nearly twice that of birth and neonatal causes. Majority of the etiologic factors were preventable. The role of socio-environmental factors has been discussed As a group, the neurological disorders were found to be the most commonly associated medical condition. Malnutrition, specially of severe degree, was significantly associated with this group compared to the general population. The study findings indicate that there is a significant place for prevention.