Miracle-dz/UniFAR-FTUs huggingface dataset:
Stillbirth and intrauterine fetal death: factors affecting determination of cause of death at autopsy

There have been several attempts to classify cause of death (CoD) in stillbirth; however, all such systems are subjective, allowing for observer bias and making comparisons between systems challenging. This study aimed to examine factors relating to determination of CoD using a large dataset from two specialist centers in which observer bias had been reduced by classifying findings objectively and assigning CoD based on predetermined criteria.
New developments and concepts related to biomarker application to vaccines

This minireview will provide a perspective on new developments and concepts related to biomarker applications for vaccines. In the context of preventive vaccines, biomarkers have the potential to predict adverse events in select subjects due to differences in genetic make‐up/underlying medical conditions or to predict effectiveness (good versus poor response). When expanding them to therapeutic vaccines, their utility in identification of patients most likely to respond favourably (or avoid potentially negative effects of treatment) becomes self‐explanatory. Despite the progress made so far on dissection of various pathways of biological significance in humans, there is still plenty to unravel about the mysteries related to the quantitative and qualitative aspects of the human host response. This review will provide a focused overview of new concepts and developments in the field of vaccine biomarkers including (i) vaccine‐dependent signatures predicting subject response and safety, (ii) predicting therapeutic vaccine efficacy in chronic diseases, (iii) exploring the genetic make‐up of the host that may modulate subject‐specific adverse events or affect the quality of immune responses, and (iv) the topic of volunteer stratification as a result of biomarker screening (e.g. for therapeutic vaccines but also potentially for preventive vaccines) or as a reflection of an effort to compare select groups (e.g. vaccinated subjects versus patients recovering from infection) to enable the discovery of clinically relevant biomarkers for preventive vaccines.
Hydrophobic folding units at protein‐protein interfaces: Implications to protein folding and to protein‐protein association

A hydrophobic folding unit cutting algorithm, originally developed for dissecting single‐chain proteins, has been applied to a dataset of dissimilar two‐chain protein‐protein interfaces. Rather than consider each individual chain separately, the two‐chain complex has been treated as a single chain. The two‐chain parsing results presented in this work show hydrophobicity to be a critical attribute of two‐state versus three‐state protein‐protein complexes. The hydrophobic folding units at the interfaces of two‐state complexes suggest that the cooperative nature of the two‐chain protein folding is the outcome of the hydrophobic effect, similar to its being the driving force in a single‐chain folding. In analogy to the protein‐folding process, the two‐chain, two‐state model complex may correspond to the formation of compact, hydrophobic nuclei. On the other hand, the three‐state model complex involves binding of already folded monomers, similar to the association of the hydrophobic folding units within a single chain. The similarity between folding entities in protein cores and in two‐state protein‐protein interfaces, despite the absence of some chain connectivities in the latter, indicates that chain linkage does not necessarily affect the native conformation. This further substantiates the notion that tertiary, non‐local interactions play a critical role in protein folding. These compact, hydrophobic, two‐chain folding units, derived from structurally dissimilar protein‐protein interfaces, provide a rich set of data useful in investigations of the role played by chain connectivity and by tertiary interactions in studies of binding and of folding. Since they are composed of non‐contiguous pieces of protein backbones, they may also aid in defining folding nuclei.
Scaling Reliably: Improving the Scalability of the Erlang Distributed Actor Platform

Distributed actor languages are an effective means of constructing scalable reliable systems, and the Erlang programming language has a well-established and influential model. While Erlang model conceptually provides reliable scalability, it has some inherent scalability limits and these force developers to depart from the model at scale. This article establishes the scalability limits of Erlang systems, and reports the work to improve the language scalability. We systematically study the scalability limits of Erlang and address the issues at the virtual machine (VM), language, and tool levels. More specifically: (1) We have evolved the Erlang VM so that it can work effectively in large scale single-host multicore and NUMA architectures. We have made important architectural improvements to the Erlang/OTP. (2) We have designed and implemented Scalable Distributed (SD) Erlang libraries to address language-level scalability issues, and provided and validated a set of semantics for the new language constructs. (3) To make large Erlang systems easier to deploy, monitor, and debug we have developed and made open source releases of five complementary tools, some specific to SD Erlang. Throughout the article we use two case studies to investigate the capabilities of our new technologies and tools: a distributed hash table based Orbit calculation and Ant Colony Optimisation (ACO). Chaos Monkey experiments show that two versions of ACO survive random process failure and hence that SD Erlang preserves the Erlang reliability model. Even for programs with no global recovery data to maintain, SD Erlang partitions the network to reduce network traffic and hence improves performance of the Orbit and ACO benchmarks above 80 hosts. ACO measurements show that maintaining global recovery data dramatically limits scalability; however scalability is recovered by partitioning the recovery data.
Characterization of the AdoMet-Dependent Guanylyltransferase Activity That Is Associated with the N Terminus of Bamboo Mosaic Virus Replicase

ABSTRACT Bamboo mosaic virus (BaMV), a member of the potexvirus group, infects primarily members of the Bambusoideae. Open reading frame 1 (ORF1) of BaMV encodes a 155-kDa polypeptide that has long been postulated to be a replicase involved in the replication and formation of the cap structure at the 5′ end of the viral genome. To identify and characterize the enzymatic activities associated with the N-terminal domain of the BaMV ORF1 protein, the intact replicase and two C-terminally truncated proteins were expressed in Saccharomyces cerevisiae. All three versions of BaMV ORF1 proteins could be radiolabeled by [α-32P]GTP, which is a characteristic of guanylyltransferase activity. The presence ofS-adenosylmethionine (AdoMet) was essential for this enzymatic activity. Thin-layer chromatography analysis suggests that the radiolabeled moiety linked to the N-terminal domain of the BaMV ORF1 protein is m7GMP. The N-terminal domain also exhibited methyltransferase activity that catalyzes the transfer of the [3H]methyl group from AdoMet to GTP or guanylylimidodiphosphate. Therefore, during cap structure formation in BaMV, methylation of GTP may occur prior to transguanylation as for alphaviruses and brome mosaic virus. This study establishes the association of RNA capping activity with the N-terminal domain of the replicase of potexviruses and further supports the idea that the reaction sequence of RNA capping is conserved throughout the alphavirus-like superfamily of RNA viruses.
The emergence of KM Governance in a knowledge intensive research organisation

In this paper the KM governance configuration of a knowledge intensive research organisation is outlined, and the impact of this configuration on the organisational KM approach is discussed. Findings show the particular importance of the structure of the KM function, the communication and coordination processes that have been put in place, and the provision of leadership for the knowledge management approach. The paper concludes that the KM governance configuration describes a trade-off between creating synergies among the different support functions and integrating the knowledge management initiatives with the various business operations.
Outpatient Antibiotic Use in France between 2000 and 2010: after the Nationwide Campaign, It Is Time To Focus on the Elderly

ABSTRACT Antibiotic overconsumption is the main force driving the emergence of multidrug-resistant bacterial strains. To promote better antibiotic use in France, a nationwide campaign has been run every year from October to March since 2002. In 2007, it was shown that winter outpatient antibiotic consumption had decreased by 26.5% compared to the 2000-2002 baseline period. Here, we quantified outpatient antibiotic use between 2000 and 2010 as a follow-up analysis of the nationwide campaign. Reimbursed outpatient antibiotic prescriptions were extracted from computerized French National Health Insurance databases. Entire series and age group and antibiotic class analyses were computed. Time series analyses used autoregressive moving-average models with exogenous variables and intervention functions. Two periods were considered: October to March “campaign” periods and April to September “warm” periods. Compared to the precampaign (2000-2002) baseline period, the numbers of weekly antibiotic prescriptions per 1,000 inhabitants during campaign periods decreased until winter 2006 to 2007 (−30% [95% confidence interval {CI}, −36.3 to −23.8%]; P < 0.001) and then stabilized except for individuals >60 years of age, for whom prescriptions reached the precampaign level. During the warm periods from April to September, no significant differences were estimated compared to the baseline level for the entire series, but seniors had an increasing trend that became significant as of 2005, reaching +21% (95% CI, +12.9 to +29.6%) in 2009 (P < 0.0001). These results highlight the need for a better understanding of antibiotic use by the elderly, requiring research with targeted and tailored public health actions for this population.
Development and characterization of fiber-based systems for biomedical imaging

This thesis focuses on the instrumentation aspect of biomedical imaging with the use of optical ber probes across three di erent disciplines. This includes the design and development of novel ber optic based techniques and instruments in elds of optical coherence tomography (OCT), bioremediation and optical mapping of cardiac action potentials. Although the mechanism behind the imaging techniques of uorescence and OCT are fundamentally di erent, the fact that both techniques permit the use of ber probes gives rise to the possibility of a combined uorescence-OCT probe. For example, the OCT and uorescence portions of the integrated system are optically distinct, except for the nal optics of the uorescence-OCT ber probe. Analog processing electronics for the subsystems can also be distinct, but for the purpose of synchronization and simultaneous data acquisition, both should be controlled by a central computer. Tumlinson and co-workers [140] have already demonstrated the development of such a system for simultaneous optical coherence tomography and laser-induced uorescence measurement. We begin by demonstrating the feasibility of using the novel source, supercontinuum, in an OCT system. Its capabilities and limitations are also discussed. A prototype allber OCT system was subsequently constructed to meet the design requirements of combined uorescence-OCT probes. Current bioremediation methods are hindered by the lack of reliable, non destructive, and in situ monitoring techniques. We investigate the feasibility of developing a novel spectroscopic technique that can monitor bacterial species in situ. A uorescence spectroscopy system that meets the design criteria is subsequently built.
Greater Trochanteric Pain Syndrome: A Review of Anatomy, Diagnosis and Treatment

Greater trochanteric pain syndrome (GTPS) is a term used to describe chronic pain overlying the lateral aspect of the hip. This regional pain syndrome, once described as trochanteric bursitis, often mimics pain generated from other sources, including, but not limited to myofascial pain, degenerative joint disease, and spinal pathology. The incidence of greater trochanteric pain is reported to be approximately 1.8 patients per 1000 per year with the prevalence being higher in women, and patients with coexisting low back pain, osteoarthritis, iliotibial band tenderness, and obesity. Symptoms of GTPS consist of persistent pain in the lateral hip radiating along the lateral aspect of the thigh to the knee and occasionally below the knee and/or buttock. Physical examination reveals point tenderness in the posterolateral area of the greater trochanter. Most cases of GTPS are self-limited with conservative measures, such as physical therapy, weight loss, nonsteroidal antiinflammatory drugs and behavior modification, providing resolution of symptoms. Other treatment modalities include bursa or lateral hip injections performed with corticosteroid and local anesthetic. More invasive surgical interventions have anecdotally been reported to provide pain relief when conservative treatment modalities fail.
Early lung cancer with lepidic pattern: adenocarcinoma in situ, minimally invasive adenocarcinoma, and lepidic predominant adenocarcinoma

Purpose of review This review gives a comprehensive overview on recent developments in the classification of neoplastic lung lesions with lepidic growth patterns, comprising the adenocarcinoma (ADC) precursor lesions atypical adenomatous hyperplasia (AAH), adenocarcinoma in situ (AIS), and minimally invasive adenocarcinoma (MIA) as well as lepidic predominant adenocarcinoma (LPA). Recent findings The concept of a continuum between the precursor lesions AAH and AIS to MIA and frankly invasive ADC is backed by a wealth of recent data showing a gradual decrease in overall survival from 100% for AAH, AIS, and MIA to moderately lower rates for LPA. Further, it has been shown that the morphologic categorization of these tumors can be done with reasonable reliability and that nonmucinous lepidic tumors show distinct molecular alterations with high rates of epidermal growth factor receptor mutations. Importantly, lepidic tumor growth is also mirrored by specific characteristics in computed tomography images, arguing for a combined assessment of histomorphology and imaging data for an optimized classification of lepidic neoplasms. Summary The validity and clinical importance of the novel concept of ADC precursor lesions and LPA have been confirmed by clinical, radiological, morphological, and molecular data. Thereby, it has evolved into a valuable tool to aid in clinical decision-making.
SELECTION AND STRAIN SPECIFICITY OF COMPATIBILITY BETWEEN SNAIL INTERMEDIATE HOSTS AND THEIR PARASITIC SCHISTOSOMES

Many theoretical models of host‐parasite coevolution assume that variation in host resistance to parasite infection is, at least partially, genetically determined and specific to the strain of infecting parasite. However, very few experimental studies have been conducted to test this assumption in animal‐parasite systems. Biomphalaria glabrata snails serve as the intermediate hosts of Schistosoma mansoni. Although some snails are resistant to infection, there is no evidence of fixation of resistance in field populations. Two possible explanations for this are high fitness costs associated with resistance and a dynamic coevolution between parasite and host, perhaps involving matching alleles or gene‐for‐gene interactions. Two strains of B. glabrata were artificially selected for either resistance or susceptibility to each of two strains of S. mansoni parasite for three generations. Third‐generation snails were then were exposed to either the parasite strain to which they had been selected or to a different parasite strain. In both host strains, resistance and susceptibility (compatibility) were found to be heritable. Moreover, compatibility to one parasite strain was not associated with compatibility to another strain, implying no genetic trade‐off. Our results are discussed in terms of potential mechanisms of resistance in this host‐parasite system and their implications to general coevolutionary theory.
Analysis of variables associated with surgery versus observation in patients with pancreatic cystic lesions referred for endoscopic ultrasound.

BACKGROUND AND STUDY AIM Endoscopic ultrasound (EUS) with fine-needle aspiration (FNA) for cyst fluid analysis (CFA) is often requested for pancreatic cystic lesions, to determine whether to operate or to observe. If this decision is not influenced by the EUS findings, the procedure may be unjustifiable. We aimed to determine whether EUS-CFA results predict surgery or observation in patients with pancreatic cysts referred for EUS. PATIENTS AND METHODS Consecutive patients referred to a quaternary pancreaticobiliary center for EUS evaluation of pancreatic cysts were eligible. Clinical data, computed tomography (CT) results, EUS findings, and CFA results were reviewed retrospectively. Statistical analysis was performed to determine variables associated with surgery versus observation. RESULTS Over 33 months, data on 194 consecutive patients referred for EUS for evaluation of pancreatic cysts were analyzed. Of these, 136 (70 %) patients had EUS-FNA. After the initial workup (including EUS with/without CFA), 35 (18 %) underwent surgery. Predictors of surgery were: younger age (< 65 years) (P = 0.0027), malignant appearance at EUS (P = 0.02), and history of EUS-FNA (P = 0.012). Cyst fluid appearance, and carcinoembryonic antigen (CEA), carbohydrate antigen 19–9 (CA 19–9), and amylase levels were not significant determinants of surgery. In 14/50 (28 %) of cases where EUS-CFA clearly suggested benign serous lesions, surgery was still performed and in 9/11 (82 %) of cases with malignant EUS-CFA findings, surgery was not done. CONCLUSIONS In patients with pancreatic cysts referred for EUS, age and EUS appearance independently predict surgery. The “perceived need for EUS-CFA” also predicts surgery, but not the EUS-CFA results. The clinical value of EUS-CFA requires further study.
Reliable Computation in Noisy Backgrounds Using Real-Time Neuromorphic Hardware

Spike-time based coding of neural information, in contrast to rate coding, requires that neurons reliably and precisely fire spikes in response to repeated identical inputs, despite a high degree of noise from stochastic synaptic firing and extraneous background inputs. We investigated the degree of reliability and precision achievable in various noisy background conditions using real-time neuromorphic VLSI hardware which models integrate-and-fire spiking neurons and dynamic synapses. To do so, we varied two properties of the inputs to a single neuron, synaptic weight and synchrony magnitude (number of synchronously firing pre-synaptic neurons). Thanks to the realtime response properties of the VLSI system we could carry out extensive exploration of the parameter space, and measure the neurons firing rate and reliability in real-time. Reliability of output spiking was primarily influenced by the amount of synchronicity of synaptic input, rather than the synaptic weight of those synapses. These results highlight possible regimes in which real-time neuromorphic systems might be better able to reliably compute with spikes despite noisy input.
Intelligent detection of impulse noise using multilayer neural network with multi-valued neurons

In this paper, we solve the impulse noise detection problem using an intelligent approach. We use a multilayer neural network based on multi-valued neurons (MLMVN) as an intelligent impulse noise detector. MLMVN was already used for point spread function identification and intelligent edge enhancement. So it is very attractive to apply it for solving another image processing problem. The main result, which is presented in the paper, is the proven ability of MLMVN to detect impulse noise on different images after a learning session with the data taken just from a single noisy image. Hence MLMVN can be used as a robust impulse detector. It is especially efficient for salt and pepper noise detection and outperforms all competitive techniques. It also shows comparable results in detection of random impulse noise. Moreover, for random impulse noise detection, MLMVN with the output neuron with a periodic activation function is used for the first time.
Mechanism of Proton Permeation through Chloroplast Lipid Membranes

Electrical measurements were carried out to investigate the contribution of chloroplast lipids to the passive proton permeability of both the thylakoid and inner-envelope membranes. Permeability coefficient and conductance to protons were measured for solvent-free bilayers made from monogalactosyldiglyceride:digalactosyldiglycerid:sulfoquinovosyldiglyceride :phosphatidylglycer ol (2:1:0.5:0.5, w/w) in the presence of a pH gradient of 7.4/8.1. The permeability coefficient for protons in glycolipids was 5.5 [plus or minus] 1.1 x 10–4 cm s-1 (n = 14). To determine whether this high H+ permeability could be explained by the presence of lipid contaminants such as weak acids, we investigated the effects of (a) bovine serum albumin, which can remove some amphiphilic molecules such as free fatty acids, (b) 6-ketocholestanol, which increases the membrane dipole potential, (c) oleic acid, and (d) chlorodecane, which increases the dielectric constant of the lipid bilayer. Our results show that free fatty acids are inefficient protonophores, as compared with carbonylcyanide-m-chlorphenylhydrazone, and that the hypothesis of a weak acid mechanism is not valid with glycolipid bilayers. In the presence of deuterium oxide the H+ conductance was reduced significantly, indicating that proton transport through the glycolipid matrix could occur directly by a hydrogen bond process. The passive transport of H+ through the glycolipid matrix is discussed with regard to the activity of the thylakoid ATP synthase and the inner-envelope H+-ATPase.
Biological reduction of graphene oxide using plant leaf extracts

Two‐dimensional graphene has attracted significant attention due to its unique mechanical, electrical, thermal, and optical properties. Most commonly employed methods to chemically reduce graphene oxide to graphene use hydrazine or its derivatives as the reducing agent. However, they are highly hazardous and explosive. Various phytochemicals obtained from different natural sources such as leaves and peels of a plant are used as reducing agents in the preparation of different gold, silver, copper, and platinum nanoparticles. In this study, seven plant leaf extracts (Cherry, Magnolia, Platanus, Persimmon, Pine, Maple, and Ginkgo) were compared for their abilities to reduce graphene oxide. The optimized reaction conditions for the reduction of graphene oxide were determined as follows. Type of plant: Cherry (Prunus serrulata), reaction time: 12 h, composition of the reaction mixture: 16.7% v/v of plant leaf extract in total suspension, and temperature: 95°C. The degree of reduction caused by Cherry leaf extract was analyzed by elemental analysis and X‐ray photoelectron spectroscopy. The reduction of graphene oxide was also confirmed by ultraviolet‐visible spectroscopy, Fourier transform‐infrared spectroscopy, Raman spectroscopy, X‐ray diffraction, transmission electron microscopy, and thermogravimetric analysis. © 2013 American Institute of Chemical Engineers Biotechnol. Prog. , 30:463–469, 2014