Miracle-dz/UniFAR-FTUs huggingface dataset:
Change of Antibiotic Susceptibility Testing Guidelines from CLSI to EUCAST: Influence on Cumulative Hospital Antibiograms

Objective We studied whether the change in antibiotic susceptibility testing (AST) guidelines from CLSI to EUCAST influenced cumulative antibiograms in a tertiary care hospital in Switzerland. Methods Antibiotic susceptibilities of non-duplicate isolates collected within a one-year period before (period A) and after (period B) changing AST interpretation from CLSI 2009 to EUCAST 1.3 (2011) guidelines were analysed. In addition, period B isolates were reinterpreted according to the CLSI 2009, CLSI 2013 and EUCAST 3.1 (2013) guidelines. Results The majority of species/drug combinations showed no differences in susceptibility rates comparing periods A and B. However, in some gram-negative bacilli, decreased susceptibility rates were observed when comparing CLSI 2009 with EUCAST 1.3 within period B: Escherichia coli / cefepime, 95.8% (CLSI 2009) vs. 93.1% (EUCAST 1.3), P=0.005; Enterobacter cloacae / cefepime, 97.0 (CLSI 2009) vs. 90.5% (EUCAST 1.3), P=0.012; Pseudomonas aeruginosa / meropenem, 88.1% (CLSI 2009) vs. 78.3% (EUCAST 1.3), P=0.002. These differences were still evident when comparing susceptibility rates according to the CLSI 2013 guideline with EUCAST 3.1 guideline. For P. aeruginosa and imipenem, a trend towards a lower antibiotic susceptibility rate in ICUs compared to general wards turned into a significant difference after the change to EUCAST: 87.9% vs. 79.8%, P=0.08 (CLSI 2009) and 86.3% vs. 76.8%, P=0.048 (EUCAST 1.3). Conclusions The change of AST guidelines from CLSI to EUCAST led to a clinically relevant decrease of susceptibility rates in cumulative antibiograms for defined species/drug combinations, particularly in those with considerable differences in clinical susceptibility breakpoints between the two guidelines.
-Linked Glycosylation N Inhibition of Expression of NKG2D Ligands through 2-Deoxy d-Glucose Prevents Cell Surface

NKG2D ligand surface expression is important for immune recognition of stressed and neotransformed cells. In this study, we show that surface expression of MICA/B and other NKG2D ligands is dependent on N -linked glycosylation. The inhibitor of glycolysis and N -linked glycosylation, 2-deoxy- D -glucose (2DG), potently inhibited surface expression of MICA/B after histone deacetylase inhibitor treatment; the inhibition occurred posttranscriptionally without affecting MICA promoter activity. Transient overexpression of MICA surface expression was also inhibited by 2DG. 2DG blocks N -linked glycosylation of MICA/B by a reversible mechanism that can be alleviated by addition of D -mannose; this does not, however, affect the inhibition of glycolysis. Addition of D -mannose restored MICA/B surface expression after 2DG treatment. In addition, speciﬁc pharmacological or small interfering RNA-mediated targeting of glycolytic enzymes did not affect MICA/B surface expression, strongly suggesting that N -linked glycosylation, and not glycolysis, is essential for MICA/B surface expression. Corroborating this, tunicamycin, a selective inhibitor of N -linked glycosylation, abolished MICA/B surface expression without compromising activation of MICA promoter activity. NK cell-mediated killing assay and staining with a recombinant NKG2D–Fc fusion protein showed that all functional NKG2D ligands induced by histone deacetylase inhibitor treatment were abolished by 2DG treatment and fully reconstituted by further addition of D -mannose. Our data suggest that posttranslational N -linked glycosylation is strictly required for NKG2D ligand surface expression. Cancer and infection often result in aberrant glycosylation, R&D Systems) was added at a ﬁnal concentration of 2.5 m g/ml. After 4 h incubation, the cells were stained with propidium iodide and immediately analyzed by ﬂow cytometry. To measure cytolytic activity, we gated on DiO-positive cells and recorded the percentage of propidium iodide-positive cells. The NKG2D-speciﬁc cytolytic activity was found as the cytolytic activity of a given sample subtracted the cy- tolytic activity of an equivalent sample containing blocking NKG2D Ab.
The Pathological Export Boom and the Bazaar Effect: How to Solve the German Puzzle

Germany is the laggard of Europe, yet the country is world champion in merchandise exports. The paper tries to solve this theoretical and empirical puzzle by diagnosing a “pathological export boom” and a “bazaar effect”. Excessively high wages defended by unions and the welfare state against the forces of international low-wage competition destroy too big a fraction of the labour intensive sectors and drive too much capital and labour into the capital intensive export sectors, causing both unemployment and excessive value added in exports. Moreover, excessive wages induce too much outsourcing of upstream production activities which implies that export quantities grow too much in relation to value added contained in exports. Finally, excessive wages cause capital flight resulting in a too large current account surplus.
Semantic Embedding for Information Retrieval

Capturing semantics in a computable way is desirable for many applications, such as information retrieval, document clustering or classification, etc. Embedding words or documents in a vector space is a common first-step. Different types of embedding techniques have their own characteristics which makes it difficult to choose one for an application. In this paper, we compared a few off-the-shelf word and document embedding methods with our own Ariadne approach in different evaluation tests. We argue that one needs to take into account the specific requirements from the applications to decide which embedding method is more suitable. Also, in order to achieve better retrieval performance, it is worth investigating the combination of bibliometric measures with semantic embedding to improve ranking.
On iterative adjustment of responses for the reduction of bias in binary regression models

The adjustment of the binomial data by small constants is a common practice in statistical modelling, for avoiding sparseness issues and, historically, for improving the asymptotic properties of the estimators. However, there are two main disadvantages with such practice: i) there is not a universal constant adjustment that results estimators with optimal asymptotic properties for all possible modelling settings, and ii) the resultant estimators are not invariant to the representation of the binomial data. In the current work, we present a parameter-dependent adjustment scheme which is applicable to binomial-response generalized linear models with arbitrary link functions. The adjustment scheme results by the expressions for the bias-reducing adjusted score functions in Kosmidis & Firth (2008, Biometrika) and thus its use guarantees estimators with second-order bias. Based on an appropriate expression of the adjusted data, a procedure for obtaining the bias-reduced estimates is developed which relies on the iterative adjustment of the binomial responses and totals using existing maximum likelihood implementations. Furthermore, it is shown that the bias-reduced estimator, like the maximum likelihood estimator, is invariant to the representation of the binomial data. A complete enumeration study is used to demonstrate the superior statistical properties of the bias-reduced estimator to the maximum likelihood estimator.
Layered Graph Match with Graph Editing

Many vision tasks are posed as either graph partitioning (coloring) or graph matching (correspondence) problems. The former include segmentation and grouping, and the latter include wide baseline stereo, large motion, object tracking and recognition. In this paper, we present an integrated solution for both graph matching and graph partition using an effective sampling algorithm in a Bayesian framework. Given two images for matching, we extract two graphs using a primal sketch algorithm [4]. The graph nodes are linelets and primitives (junctions). Both graphs are automatically partitioned into an unknown number of K + 1 layers of subgraphs so that K pairs of subgraphs are matched and the remaining layer contains unmatched backgrounds. Each matched pair represent a "moving object" with a TPS (thin-plate-spline) transform to account for its deformations and a set of graph operators to edit the pair of subgraphs to achieve perfect structural match. The matching energy between two subgraphs includes geometric deformations, appearance dissimilarities, and the cost of graph editing operators. We demonstrate its application on two tasks: (i) large motion with occlusion, and (ii) automatic detection and recognition of common objects in a pair of images.
Key management for wireless ad hoc networks

Key management is a fundamental security service to nable secure wireless ad hoc networks (WAHN). To date existing key management so lutions based on either public key infrastructures (PKI) or key pre-distribution s cheme (KPS) exhibit limitations for WAHNs. We firstly develop the Hybrid Key Management Infrastructure (HKMI) for WAHNs composed of moderate-resource devices. The HKMI com ple ents PKI with trust and cooperation protocols to construct an performance e fficient security solution. We secondly develop the Deterministic Pairwise Key Pre-Distribution Scheme (DPKPS) for large-scale dynamic WAHNs composed of l ow-resource devices. The DPKPS applies a combinatorial design for the pre-di stribution of multiple bivariate polynomial shares to WAHN nodes. Future work comprises further improving the resilie ncy of the DPKPS, completing a key management infrastructure on the basis of the D PKPS, the design of DPKPS-based access control mechanisms, and the integration of t he HKMI with the DPKPS in a unified key management architecture.
The dynamic placement of virtual network functions

This paper addresses the problem of managing highly dynamic network and service environments, where virtual nodes and virtual links are created and destroyed depending on traffic volumes, service requests, or high-level goals such as reduction in energy consumption. This problem will be one of the main technical challenges to be faced in the evolution towards Future Networks (FN). Emerging paradigms such as Software Defined Networks (SDN) and Network Function Virtualization (NfV) are concrete steps towards infrastructures where network functions and services will be executed as applications in ensembles of virtual machines (VMs) hosted in pervasive standard hardware resources located across a network. The paper argues that in order to manage these virtual infrastructures there is a need to introduce high-level systems orchestration. The paper describes an architecture based on an orchestrater that ensures the automatic placement of the virtual nodes and the allocation of network services on them, supported by a monitoring system that collects and reports on the behaviour of the resources. The orchestrater manages the creation and removal of the virtual nodes, as well as configuring, monitoring, running and stopping software on them. As a proof of these concepts, a distributed orchestrater prototype has been designed, implemented and tested with the results of different placement algorithms presented.
CCR5Δ32 Polymorphism Associated with a Slower Rate Disease Progression in a Cohort of RR-MS Sicilian Patients

Multiple sclerosis (MS) disease is carried through inflammatory and degenerative stages. Based on clinical feaures, it can be subdivided into three groups: relapsing-remitting MS, secondary progressive MS, and primary progressive MS. Multiple sclerosis has a multifactorial etiology with an interplay of genetic predisposition, environmental factors, and autoimmune inflammatory mechanism in which play a key role CC-chemokines and its receptors. In this paper, we studied the frequency of CCR5 gene Δ32 allele in a cohort of Sicilian RR-MS patients comparing with general Sicilian population. Also, we evaluate the association between this commonly polymorphism and disability development and age of disease onset in the same cohort. Our results show that presence of CCR5Δ32 is significantly associated with expanded disability status scale score (EDSS) but not with age of disease onset.
Transmit/receive MIMO antenna subset selection

The paper discusses antenna subset selection in MIMO wireless systems. The subsets of transmit and receive antennas are selected so as to maximise the channel capacity. First of all, we establish the relationship between the multiplexing gain and the diversity gain achievable with adaptive antenna subset selection. Second, we indicate a selection rule that allows a full diversity advantage to be achieved with a reduced computational effort, by decoupling the combined transmit/receive selection into the separate selection of transmit/receive subsets. Finally, we study the performance of practical systems with antenna selection in the context of high throughput MIMO-OFDM WLAN.
Factors determining UK album success

This article uses a recently compiled dataset on the UK album sales to determine which factors contribute to best-selling album sales success. We control for factors including length of time since release, nationality of artist, artist type and album type, testing the increasing returns to information hypothesis. Information on general public online review scores for the albums in the dataset allows for a strong test of the accuracy of online reviews in predicting music sales, as online reviews are a relatively recent phenomenon, while the release of many of the albums predates the widespread use of Internet.
2XMM J083026+524133: the most X-ray luminous cluster at redshift 1

Aims. In the distant universe X-ray luminous clusters of galaxies are rare objects. Large area surveys are therefore needed to probe the high luminosity end of the cluster population at redshifts z > 1. Methods. We correlated extended X-ray sources from the second XMM-Newton source catalogue (2XMM) with the SDSS in order to identify new clusters of galaxies. Distant cluster candidates in empty SDSS fields were imaged in the r -a ndz-bands with the Large Binocular Telescope. We extracted the X-ray spectra of the cluster candidates and fitted thermal plasma models to the data. Results. We determined the redshift 0.99 ± 0.03 for 2XMM J083026.2+524133 from its X-ray spectrum. With a bolometric luminosity of 1.8 × 10 45 erg s −1 this is the most X-ray luminous cluster at redshifts z ≥ 1. We measured a gas temperature of 8.2 ± 0. 9k eV and estimate a cluster mass M500 = 5.6 × 10 14 M� . The optical imaging revealed a rich cluster of galaxies.
Human Amnion-Derived Mesenchymal Stem Cells Protect Human Bone Marrow Mesenchymal Stem Cells against Oxidative Stress-Mediated Dysfunction via ERK1/2 MAPK Signaling

Epidemiological evidence suggests that bone is especially sensitive to oxidative stress, causing bone loss in the elderly. Previous studies indicated that human amnion-derived mesenchymal stem cells (HAMSCs), obtained from human amniotic membranes, exerted osteoprotective effects in vivo. However, the potential of HAMSCs as seed cells against oxidative stress-mediated dysfunction is unknown. In this study, we systemically investigated their antioxidative and osteogenic effects in vitro. Here, we demonstrated that HAMSCs signi cantly promoted the proliferation and osteoblastic differentiation of H2O2-induced human bone marrow mesenchymal stem cells (HBMSCs), and down-regulated the reactive oxygen species (ROS) level. Further, our results suggest that activation of the ERK1/2 MAPK signal transduction pathway is essential for both HAMSCs-mediated osteogenic and protective effects against oxidative stress-induced dysfunction in HBMSCs. U0126, a highly selective inhibitor of extracellular ERK1/2 MAPK signaling, significantly suppressed the antioxidative and osteogenic effects in HAMSCs. In conclusion, by modulating HBMSCs, HAMSCs show a strong potential in treating oxidative stress- mediated bone deficiency.
FloSIS: A Highly Scalable Network Flow Capture System for Fast Retrieval and Storage Efficiency

Network packet capture performs essential functions in network management such as attack analysis, network troubleshooting, and performance debugging. As the network edge bandwidth exceeds 10 Gbps, the demand for scalable packet capture and retrieval is rapidly increasing. However, existing software-based packet capture systems neither provide high performance nor support flow-level indexing for fast query response. This would either prevent important packets from being stored or make it too slow to retrieve relevant flows. In this paper, we present FloSIS, a highly scalable, software-based flow storing and indexing system. Flo-SIS is characterized as the following three aspects. First, it exercises full parallelism in multiple CPU cores and disks at all stages of packet processing. Second, it constructs two-stage flow-level indexes, which helps minimize expensive disk access for user queries. It also stores the packets in the same flow at a contiguous disk location, which maximizes disk read throughput. Third, we optimize storage usage by flow-level content deduplication at real time. Our evaluation shows that FloSIS on a dual octa-core CPU machine with 24 HDDs achieves 30 Gbps of zero-drop performance with real traffic, consuming only 0.25% of the space for indexing.
Social network capital, economic mobility and poverty traps

This paper explores the role social network capital might play in facilitating poor agents’ escape from poverty traps. We model and simulate endogenous link formation among households heterogeneously endowed with both traditional and social network capital who make investment and technology choices over time in the absence of financial markets and faced with multiple production technologies featuring different fixed costs and returns. We show that social network capital can either complement or substitute for productive assets in facilitating some poor households’ escape from poverty. However, the voluntary nature of costly link formation also creates exclusionary mechanisms that impede some poor households’ use of social network capital. Through numerical simulation, we show that the ameliorative potential of social networks therefore depends fundamentally on the broader socio-economic wealth distribution in the economy, which determines the feasibility of social interactions and the net intertemporal benefits resulting from endogenous network formation. In some settings, targeted public transfers to the poor can crowd-in private resources by inducing new social links that the poor can exploit to escape from poverty.
Isolation and phylogenetic analysis of hemagglutinin gene of H9N2 influenza viruses from chickens in South China from 2012 to 2013

As part of our ongoing influenza surveillance program in South China, 19 field strains of H9N2 subtype avian influenza viruses (AIVs) were isolated from dead or diseased chicken flocks in Guangdong province, South China, between 2012 and 2013. Hemagglutinin (HA) genes of these strains were sequenced and analyzed and phylogenic analysis showed that 12 of the 19 isolates belonged to the lineage h9.4. 2.5, while the other seven belonged to h9.4. 2.6. Specifically, we found that all of the viruses isolated in 2013 belonged to lineage h9.4. 2.5. The lineage h9.4. 2.5 viruses contained a PSRSSR↓GLF motif at HA cleavage site, while the lineage h9.4. 2.6 viruses contained a PARSSR↓GLF at the same position. Most of the isolates in lineage h9.4. 2.5 lost one potential glycosylation site at residues 200-202, and had an additional one at residues 295-297 in HA1. Notably, 19 isolates had an amino acid exchange (Q226L) in the receptor binding site, which indicated that the viruses had potential affinity of binding to human like receptor. The present study shows the importance of continuing surveillance of new H9N2 strains to better prepare for the next epidemic or pandemic outbreak of H9N2 AIV infections in chicken flocks.
ENVIRONMENTAL CONDITIONS AFFECT THE MAGNITUDE OF INBREEDING DEPRESSION IN SURVIVAL OF DARWIN'S FINCHES

Abstract Understanding the fitness consequences of inbreeding (inbreeding depression) is of importance to evolutionary and conservation biology. There is ample evidence for inbreeding depression in captivity, and data from wild populations are accumulating. However, we still lack a good quantitative understanding of inbreeding depression and what influences its magnitude in natural populations. Specifically, the relationship between the magnitude of inbreeding depression and environmental severity is unclear. We quantified inbreeding depression in survival and reproduction in populations of cactus finches (Geospiza scandens) and medium ground finches (Geospiza fortis) living on Isla Daphne Major in the Galápagos Archipelago. Our analyses showed that inbreeding strongly reduced the recruitment probability (probability of breeding given that an adult is alive) in both species. Additionally, in G. scandens, first-year survival of an offspring with f = 0.25 was reduced by 21% and adults with f = 0.25 experienced a 45% reduction in their annual probability of survival. The magnitude of inbreeding depression in both adult and juvenile survival of this species was strongly modified by two environmental conditions, food availability and number of competitors. In juveniles, inbreeding depression was only present in years with low food availability, and in adults inbreeding depression was five times more severe in years with low food availability and large population sizes. The combination of relatively severe inbreeding depression in survival and the reduced recruitment probability led to the fact that very few inbred G. scandens ever succeeded in breeding. Other than recruitment probability, no other trait showed evidence of inbreeding depression in G. fortis, probably for two reasons: a relatively high rate of extrapair paternity (20%), which may lead to an underestimate of the apparent inbreeding depression, and low sample sizes of highly inbred G. fortis, which leads to low statistical power. Using data from juvenile survival, we estimated the number of lethal equivalents carried by G. scandens, G. fortis, and another congener, G. magnirostris. These results suggest that substantial inbreeding depression can exist in insular populations of birds, and that the magnitude of the inbreeding depression is a function of environmental conditions.
Ab Initio Methods for Electron Correlation in Molecules

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