Miracle-dz/UniFAR-FTUs huggingface dataset:
Epidemiological methods in diarrhoea studies—an update

Background Diarrhoea remains a leading cause of morbidity and mortality but is difficult to measure in epidemiological studies. Challenges include the diagnosis based on self-reported symptoms, the logistical burden of intensive surveillance and the variability of diarrhoea in space, time and person. Methods We review current practices in sampling procedures to measure diarrhoea, and provide guidance for diarrhoea measurement across a range of study goals. Using 14 available data sets, we estimated typical design effects for clustering at household and village/neighbourhood level, and measured the impact of adjusting for baseline variables on the precision of intervention effect estimates. Results Incidence is the preferred outcome measure in aetiological studies, health services research and vaccine trials. Repeated prevalence measurements (longitudinal prevalence) are appropriate in high-mortality settings where malnutrition is common, although many repeat measures are rarely useful. Period prevalence is an inadequate outcome if an intervention affects illness duration. Adjusting point estimates for age or diarrhoea at baseline in randomized trials has little effect on the precision of estimates. Design effects in trials randomized at household level are usually <2 (range 1.0–3.2). Design effects for larger clusters (e.g. villages or neighbourhoods) vary greatly among different settings and study designs (range 0.1–25.8). Conclusions Using appropriate sampling strategies and outcome measures can improve the efficiency, validity and comparability of diarrhoea studies. Allocating large clusters in cluster randomized trials is compromized by unpredictable design effects and should be carried out only if the research question requires it.
California Hospitals Response to State and Federal Policies Related to Health Care–Associated Infections

In October 2008, the Centers for Medicare and Medicaid Services (CMS) denied payment for ten selected health care–associated infections (HAI). In January 2009, California enacted mandatory reporting of infection prevention processes and HAI rates. This longitudinal mixed-methods study examined the impact of federal and state policy changes on California hospitals. Data on structures, processes, and outcomes of care were collected pre- and post-policy changes. In-depth interviews with hospital personnel were performed after policy implementation. More than 200 hospitals participated with 25 personnel interviewed. We found significant increases in adoption of and adherence to evidence-based practices and decreased HAI rates (p < .05). Infection preventionists (IP) spent more time on surveillance and in their offices and less time on education and in other locations (p < .05). Qualitative data confirmed mandatory reporting had intended and unintended consequences and highlighted the importance of technology and organizational climate in preventing infections and the changing IPs’ role. This is especially relevant because the California Department of Public Health has since mandated hospitals to report data on 29 different for surgical site infections and a lawsuit has been filed to delay the implementation of these requirements.
Unsupervised Spike Detection and Sorting with Wavelets and Superparamagnetic Clustering

This study introduces a new method for detecting and sorting spikes from multiunit recordings. The method combines the wave let transform, which localizes distinctive spike features, with super paramagnetic clustering, which allows automatic classification of the data without assumptions such as low variance or gaussian distributions. Moreover, an improved method for setting amplitude thresholds for spike detection is proposed. We describe several criteria for implementation that render the algorithm unsupervised and fast. The algorithm is compared to other conventional methods using several simulated data sets whose characteristics closely resemble those of in vivo recordings. For these data sets, we found that the proposed algorithm outperformed conventional methods.
Comparative analysis of the structures of the outer membrane protein P1 genes from major clones of Haemophilus influenzae type b

P1 outer membrane proteins from Haemophilus influenzae type b are heterogeneous antigenically and with respect to apparent molecular weight in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. For determination of the molecular basis for the differences in the P1 proteins, the genes for the P1 proteins from strain 1613, representative of outer membrane protein subtype 3L, and strain 8358, representative of outer membrane protein subtype 6U, were cloned, sequenced, and compared with the previously reported gene for the P1 protein from strain MinnA, a strain with the outer membrane protein subtype 1H. These prototype strains are representatives of the three major clonal families of H. influenzae type b responsible for invasive disease in diverse areas of the world. The nucleotide sequences of the P1 genes from strains 1613 and 8358 were 94 and 90% identical to the MinnA sequence, respectively. The derived amino acid sequences were 91 and 86% identical, respectively. Heterogeneity between the MinnA and 1613 proteins was largely localized to two short variable regions; the protein from strain 8538 contained a third variable region not observed in the other P1 proteins. Thus, the outer membrane protein P1 genes are highly conserved; the variable regions may code for the previously demonstrated strain-specific antigenic determinants.
Internet-Facilitated Feedback Trading

The ease of Internet trading has lured relatively inexperienced investors into the financial markets. We study the impact of the influx of these uninformed traders in a dynamic setting. Our results show that these strategic uninformed online traders who adopt feedback strategies do not outperform noise traders and feedback trading does not affect market volatility. An insider's equilibrium strategy and expected profit remain the same as if the feedback traders were noise traders. On the individual level, feedback traders earn higher risk-adjusted expected profits than noise traders. The presence of feedback trading in the market changes market depth, but the speed at which information gets incorporated into prices is constant.
Lexical availability and grammatical encoding scope during spoken sentence production

Three sentence production experiments investigate the relationship between lexical and structural processing scope. Speakers generated sentences with varying phrase structures in response to visual displays (e.g., The dog and the hat move above the fork and the tree/The dog moves above the hat and the fork and the tree). On half of the trials, one of the pictures in the arrays was previewed. Filler sentences varied preview position and sentence structure from trial to trial. When speakers could not anticipate the position of the previewed picture in the upcoming sentence (Experiment 1), preview benefit for pictures corresponding to the second noun to be produced was limited to pictures that fell within the sentence-initial phrase. When the linear position of the previewed picture was predictable, preview benefits were observed for the second noun to be produced, irrespective of phrase position (Experiment 2). However, no preview benefits were observed for the third noun to be produced (Experiment 3). In contrast, significant effects of initial phrase structure were observed in all experiments, with latencies increasing with initial phrase length. The results are consistent with speakers operating a phrasal scope for structural planning within which the scope of lexical access can vary.
OpenFABMAP: An open source toolbox for appearance-based loop closure detection

Appearance-based loop closure techniques, which leverage the high information content of visual images and can be used independently of pose, are now widely used in robotic applications. The current state-of-the-art in the field is Fast Appearance-Based Mapping (FAB-MAP) having been demonstrated in several seminal robotic mapping experiments. In this paper, we describe OpenFABMAP, a fully open source implementation of the original FAB-MAP algorithm. Beyond the benefits of full user access to the source code, OpenFABMAP provides a number of configurable options including rapid codebook training and interest point feature tuning. We demonstrate the performance of OpenFABMAP on a number of published datasets and demonstrate the advantages of quick algorithm customisation. We present results from OpenFABMAP's application in a highly varied range of robotics research scenarios.
High Genetic Diversity Detected in Olives beyond the Boundaries of the Mediterranean Sea

Background Olive trees (Olea europaea subsp. europaea var. europaea) naturally grow in areas spanning the Mediterranean basin and towards the East, including the Middle East. In the Iranian plateau, the presence of olives has been documented since very ancient times, though the early history of the crop in this area is shrouded in uncertainty. Methods The varieties presently cultivated in Iran and trees of an unknown cultivation status, surviving under extreme climate and soil conditions, were sampled from different provinces and compared with a set of Mediterranean cultivars. All samples were analyzed using SSR and chloroplast markers to establish the relationships between Iranian olives and Mediterranean varieties, to shed light on the origins of Iranian olives and to verify their contribution to the development of the current global olive variation. Results Iranian cultivars and ecotypes, when analyzed using SSR markers, clustered separately from Mediterranean cultivars and showed a high number of private alleles, on the contrary, they shared the same single chlorotype with the most widespread varieties cultivated in the Mediterranean. Conclusion We hypothesized that Iranian and Mediterranean olive trees may have had a common origin from a unique center in the Near East region, possibly including the western Iranian area. The present pattern of variation may have derived from different environmental conditions, distinct levels and selection criteria, and divergent breeding opportunities found by Mediterranean and Iranian olives.These unexpected findings emphasize the importance of studying the Iranian olive germplasm as a promising but endangered source of variation.
Effect of Antioxidants on the Outcome of Therapy in Paraquat-intoxicated Patients

Purpose: The present study was conducted to determine the effect of vitamins C and E administration on the outcome of therapy in patients with paraquat intoxication admitted in the Poisoning Emergency Department (PED) of Noor Teaching General Hospital, Isfahan, Iran. Methods: We studied retrospectively medical records of 186 patients admitted to the PED in two different study periods: 157 patients were evaluated from 1985 to 2001 (first study period) in which patients received conventional treatment protocol consisting of fluid replacement, oral absorbents, haemodialysis, etc, Also, 29 other patients were assessed from 2001 to 2005 (second study period) in which vitamins C and E had been administered to the patients, in addition to the conventional protocol. The patients' mortality rate after the first study period was compared to that of the second one, with regard to the impact of the additional therapeutic intervention (use of antioxidant vitamins). Results: Most of the patients (40.5 %) had ingested more than 20 mL of 20 % paraquat solution and were admitted to the hospital during the first 4 h after exposure. Paraquat poisoning was more common in men (76.6 %), young adults in the age group 19 - 34 (47 %) and during summer (43.3 %). Mean (± SE) length of hospital stay was 62.6 ± 15.6 h. Overall mortality rates were 31 and 55.2 % in the first and second periods, respectively. Conclusion : Although the addition of antioxidants (vitamins C and E) to the conventional therapy did not reduce the mortality rate, other dependent variables including different doses of antioxidants may be considered for future studies.
Roles of M cells in infection and mucosal vaccines

The mucosal immune system plays a crucial part in the control of infection. Exposure of humans and animals to potential pathogens generally occurs through mucosal surfaces, thus, strategies that target the mucosa seem rational and efficient vaccination measures. Vaccination through the mucosal immune system can induce effective systemic immune responses simultaneously with mucosal immunity compared with parenteral vaccination. M cells are capable of transporting luminal antigens to the underlying lymphoid tissues and can be exploited by pathogens as an entry portal to invade the host. Therefore, targeting M-cell-specific molecules might enhance antigen entry, initiate the immune response, and induce protection against mucosal pathogens. Here, we outline our understanding of the distribution and function of M cells, and summarize the advances in mucosal vaccine strategies that target M cells.
Systematic identification of cell size regulators in budding yeast

Cell size is determined by a complex interplay between growth and division, involving multiple cellular pathways. To identify systematically processes affecting size control in G1 in budding yeast, we imaged and analyzed the cell cycle of millions of individual cells representing 591 mutants implicated in size control. Quantitative metric distinguished mutants affecting the mechanism of size control from the majority of mutants that have a perturbed size due to indirect effects modulating cell growth. Overall, we identified 17 negative and dozens positive size control regulators, with the negative regulators forming a small network centered on elements of mitotic exit network. Some elements of the translation machinery affected size control with a notable distinction between the deletions of parts of small and large ribosomal subunit: parts of small ribosomal subunit tended to regulate size control, while parts of the large subunit affected cell growth. Analysis of small cells revealed additional size control mechanism that functions in G2/M, complementing the primary size control in G1. Our study provides new insights about size control mechanisms in budding yeast.
Empowered to change: evidence from a qualitative exploration of a user-informed psycho-educational programme for people with type 1 diabetes

Objectives: To evaluate the impact of a user-informed psycho-educational programme for people with type 1 diabetes. Methods: Qualitative data derived from repeated interviews and diaries enabled an appraisal of participants' unique, individual experiences. Results: Thematic analysis elicited a number of themes from each type of data (interview and diaries) which bore similarities in their representation of a process whereby change was desired, solutions were found to bring about that change, and then the process was planned or embarked upon. Discussion: The acquisition of trustworthy information and a repertoire of coping skills accompanied by regular contact with other people with type 1 diabetes meant that participants achieved an increased sense of control in their lives and were empowered to change.
Apple tasting and nearly one-sided learning

In the standard on-line model the learning algorithm tries to minimize the total number of mistakes made in a series of trials. On each trial the learner sees an instance, either accepts or rejects that instance, and then is told the appropriate response. The authors define a natural variant of this model ('apple tasting') where the learner gets feedback only when the instance is accepted. They use two transformations to relate the apple tasting model to an enhanced standard model where false acceptances are counted separately from false rejections. They present a strategy for trading between false acceptances and false rejections in the standard model. From one perspective this strategy is exactly optimal, including constants. They apply the results to obtain a good general purpose apple tasting algorithm as well as nearly optimal apple tasting algorithms for a variety of standard classes, such as conjunctions and disjunctions of n boolean variables. They also present and analyze a simpler transformation useful when the instances are drawn at random rather than selected by an adversary. <<ETX>>
Leber hereditary optic neuropathy

Leber hereditary optic neuropathy (LHON) is a mitochondrial genetic disease that preferentially causes blindness in young adult males, affecting about 1 in 25 000 of the British population. It is characterised by bilateral subacute loss of central vision owing to focal degeneration of the retinal ganglion cell layer and optic nerve. Over 95% of LHON cases are primarily the result of one of three mitochondrial DNA (mtDNA) point mutations, G3460A, G11778A, and T14484C, which all involve genes encoding complex I subunits of the respiratory chain. An intriguing feature of LHON is that only ∼50% of males and ∼10% of females who harbour a pathogenic mtDNA mutation actually develop the optic neuropathy. This marked incomplete penetrance and gender bias imply that additional mitochondrial and/or nuclear genetic factors must be modulating the phenotypic expression of LHON. It is also likely that environmental factors contribute to the onset of visual failure. However, these secondary precipitating factors remain poorly defined at present. In this review, we describe the natural history of this optic nerve disorder and highlight issues relating to clinical diagnosis, management, and genetic counselling. We also discuss the findings of recently published studies and the light they shed on the complex aetiology and pathophysiology of LHON.
Noradrenaline and neuropeptide Y contribute to initial, but not sustained, vasodilatation in response to local skin warming in humans

What is the central question of this study? Previous work has produced the counterintuitive finding that the vasoconstrictor neurotransmitters noradrenaline and neuropeptide Y are involved in vasodilatation. We aimed to discover whether sympathetic neurotransmitters are required for the sustained vasodilatation in response to local skin warming, as has been previously suggested, and to determine whether noradrenaline and neuropeptide Y are ‘mediating’ the sustained vasodilator response directly or acting to ‘prime’ (or kick‐start) it. What is the main finding and its importance? We have found that noradrenaline and neuropeptide Y are required at the initiation of vasodilatation in response to local skin warming, if a complete vasodilator response is to be achieved; however, they are not required once vasodilatation has begun.
Calcium Handling Abnormalities in Atrial Fibrillation as a Target for Innovative Therapeutics

Atrial electrical and structural alterations (remodeling) have emerged as key elements in the development of the atrial fibrillation (AF) substrate. Evidence points to abnormalities in intracellular Ca2+ (calcium) handling as crucial links in AF-initiating focal activity and in perpetuation by rapidly firing foci and reentry. This review focuses on the molecular basis of altered Ca2+ handling in AF, with the goal of providing new insights into molecular effective antiarrhythmic therapy.
Genome Rearrangements, Deletions, and Amplifications in the Natural Population of Bartonella henselae

ABSTRACT Cats are the natural host for Bartonella henselae, an opportunistic human pathogen and the agent of cat scratch disease. Here, we have analyzed the natural variation in gene content and genome structure of 38 Bartonella henselae strains isolated from cats and humans by comparative genome hybridizations to microarrays and probe hybridizations to pulsed-field gel electrophoresis (PFGE) blots. The variation in gene content was modest and confined to the prophage and the genomic islands, whereas the PFGE analyses indicated extensive rearrangements across the terminus of replication with breakpoints in areas of the genomic islands. We observed no difference in gene content or structure between feline and human strains. Rather, the results suggest multiple sources of human infection from feline B. henselae strains of diverse genotypes. Additionally, the microarray hybridizations revealed DNA amplification in some strains in the so-called chromosome II-like region. The amplified segments were centered at a position corresponding to a putative phage replication initiation site and increased in size with the duration of cultivation. We hypothesize that the variable gene pool in the B. henselae population plays an important role in the establishment of long-term persistent infection in the natural host by promoting antigenic variation and escape from the host immune response.
Interference Reduction in Multi-Cell Massive MIMO Systems II: Downlink Analysis for a Finite Number of Antennas

Sharing global channel information at base stations (BSs) is commonly assumed for downlink multi-cell precoding. In the context of massive multi-input multi-output (MIMO) systems where each BS is equipped with a large number of antennas, sharing instant fading channel coefficients consumes a large amount of resource. To consider practically implementable methods, we study in this paper interference reduction based on precoding using the large-scale fading coefficients that depend on the path-loss model and are independent of a specific antenna. We focus on the downlink multi-cell precoding designs when each BS is equipped with a practically finite number of antennas. In this operation regime, pilot contamination is not the dominant source of interference, and mitigation of all types of interference is required. This paper uses an optimization approach to design precoding methods for equal qualities of service (QoS) to all users in the network, i.e.,maximizing the minimum signal-to-interference-plus-noise ratios (SINRs) among all users. The formulated optimization is proved to be quasi-convex, and can be solved optimally. We also propose low-complexity suboptimal algorithms through uplink and downlink duality. Simulation results show that the proposed precoding methods improve 5% outage rate for more than 10 3 times, compared to other known interference mitigation techniques.
Carbonaceous materials modified catalysts for simultaneous SO2/NOx removal from flue gas: A review

ABSTRACT Globally, considerable effort and resources are being channeled toward controlling the rising threat from pollution and other related impacts from man-made activities, which have detrimental effects on human health and the environment. The presence of some associated gases such as nitrogen oxides and sulfur oxides in the flue gas interfering with the carbon capture processes are responsible for acid rain and ground-layer ozone formation. The wet flue gas desulfurization and the selective catalytic reduction technologies are associated with high investment, production of secondary pollution, poor catalyst durability, and high temperature requirements. In response to these limitations, the development of a hybrid environmental catalyst, especially using activated carbon, carbon-coated monolith, and metal oxides, is desirable. For a catalyst to be competitive, it must be cost-effective with enhanced sorption capacity, regenerability, and be safe for disposal. Some of the recent methods for dispersing the metal oxides on the supports and the simultaneous removal of sulfur oxides and nitrogen oxides were enumerated in this review and the possible ways for improvement have been presented.