Miracle-dz/UniFAR-FTUs huggingface dataset:
Transposon Insertion Reveals pRM, a Plasmid of Rickettsia monacensis

ABSTRACT Until the recent discovery of pRF in Rickettsia felis, the obligate intracellular bacteria of the genus Rickettsia (Rickettsiales: Rickettsiaceae) were thought not to possess plasmids. We describe pRM, a plasmid from Rickettsia monacensis, which was detected by pulsed-field gel electrophoresis and Southern blot analyses of DNA from two independent R. monacensis populations transformed by transposon-mediated insertion of coupled green fluorescent protein and chloramphenicol acetyltransferase marker genes into pRM. Two-dimensional electrophoresis showed that pRM was present in rickettsial cells as circular and linear isomers. The 23,486-nucleotide (31.8% G/C) pRM plasmid was cloned from the transformant populations by chloramphenicol marker rescue of restriction enzyme-digested transformant DNA fragments and PCR using primers derived from sequences of overlapping restriction fragments. The plasmid was sequenced. Based on BLAST searches of the GenBank database, pRM contained 23 predicted genes or pseudogenes and was remarkably similar to the larger pRF plasmid. Two of the 23 genes were unique to pRM and pRF among sequenced rickettsial genomes, and 4 of the genes shared by pRM and pRF were otherwise found only on chromosomes of R. felis or the ancestral group rickettsiae R. bellii and R. canadensis. We obtained pulsed-field gel electrophoresis and Southern blot evidence for a plasmid in R. amblyommii isolate WB-8-2 that contained genes conserved between pRM and pRF. The pRM plasmid may provide a basis for the development of a rickettsial transformation vector.
Distributed Energy Efficient Clouds Over Core Networks

In this paper, we introduce a framework for designing energy efficient cloud computing services over non-bypass IP/WDM core networks. We investigate network related factors including the centralization versus distribution of clouds and the impact of demand, content popularity and access frequency on the clouds placement, and cloud capability factors including the number of servers, switches and routers and amount of storage required in each cloud. We study the optimization of three cloud services: cloud content delivery, storage as a service (StaaS), and virtual machines (VMS) placement for processing applications. First, we develop a mixed integer linear programming (MILP) model to optimize cloud content delivery services. Our results indicate that replicating content into multiple clouds based on content popularity yields 43% total saving in power consumption compared to power un-aware centralized content delivery. Based on the model insights, we develop an energy efficient cloud content delivery heuristic, DEER-CD, with comparable power efficiency to the MILP results. Second, we extend the content delivery model to optimize StaaS applications. The results show that migrating content according to its access frequency yields up to 48% network power savings compared to serving content from a single central location. Third, we optimize the placement of VMs to minimize the total power consumption. Our results show that slicing the VMs into smaller VMs and placing them in proximity to their users saves 25% of the total power compared to a single virtualized cloud scenario. We also develop a heuristic for real time VM placement (DEER-VM) that achieves comparable power savings.
Mice lacking matrilin‐1 (cartilage matrix protein) have alterations in type II collagen fibrillogenesis and fibril organization

Matrilin‐1 (cartilage matrix protein) is a homotrimeric protein that forms collagen‐dependent and collagen‐independent fibrils in the extracelluar matrix of cartilage. In the growth plate of developing long bones, the gene for matrilin‐1 is transcribed exclusively by the chondrocytes of the zone of maturation which is situated between the zones of proliferation and hypertrophy. When associated with the cartilage collagen fibril, which consists of collagens type II, IX, and XI, matrilin‐1 displays a periodicity of 59.3 nm. Matrilin‐1 also interacts with the proteoglycan, aggrecan. Because of its association with the collagen fibril, we tested the hypothesis that matrilin‐1 may play a role in collagen fibril formation and cartilage matrix assembly by generating mice with targeted mutations in the matrilin‐1 gene. Ultrastructural studies of the cartilage of growth plates of matrilin‐1 null mice reveal an abnormal type II collagen fibrillogenesis and fibril organization in the matrix of the zone of maturation. These results represent the first report on the regulation of the heterotypic type II collagen fibril by a non‐collagenous protein. The abnormal fibrillogenesis had no obvious effects on skeletal development, on the organization of chondrocytes in the growth plate and on the deposition of aggrecan and the hypertrophic‐specific type X collagen in the cartilaginous matrix. Dev Dyn 1999;216:434–441. ©1999 Wiley‐Liss, Inc.
Risk Adjustment Systems in Health Insurance Markets in the US, Germany, Netherlands and Switzerland

A risk adjustment system is a necessary prerequisite for competition between health plans or sickness funds. It is only unnecessary in a national insurance plan or in a system with risk-related premiums. Risk adjustment primarily serves the purposes of preventing or, as far as possible, restricting risk selection between the sickness funds and enouraging them and the service providers to act along cost-effective lines (Van de Ven and Ellis 2000). Therefore, competition does not constitute a goal in itself, but an instrument for achieving efficient and effective health care provision based on the preferences of the insured. Competition between sickness funds is largely designed to spill-over to the benefits sector and to improve the provision of health benefits. Viewed from this perspective, risk adjustment possesses a merely instrumental character. Firstly, it constitutes a means of achieving competition and secondly, it impacts only indirectly the efficiency and effectiveness of health care provision. As a consequence, the reform of the risk adjustment system is not done “for its own sake”. In other words, the aim should not be find-ing the maximum degree of differentiation, but it is rather an “optimum” risk adjustment system that is intended.
Dual Polyhedra and Mirror Symmetry for Calabi-Yau Hypersurfaces in Toric Varieties

We consider families ${\cal F}(\Delta)$ consisting of complex $(n-1)$-dimensional projective algebraic compactifications of $\Delta$-regular affine hypersurfaces $Z_f$ defined by Laurent polynomials $f$ with a fixed $n$-dimensional Newton polyhedron $\Delta$ in $n$-dimensional algebraic torus ${\bf T} =({\bf C}^*)^n$. If the family ${\cal F}(\Delta)$ defined by a Newton polyhedron $\Delta$ consists of $(n-1)$-dimensional Calabi-Yau varieties, then the dual, or polar, polyhedron $\Delta^*$ in the dual space defines another family ${\cal F}(\Delta^*)$ of Calabi-Yau varieties, so that we obtain the remarkable duality between two {\em different families} of Calabi-Yau varieties. It is shown that the properties of this duality coincide with the properties of {\em Mirror Symmetry} discovered by physicists for Calabi-Yau $3$-folds. Our method allows to construct many new examples of Calabi-Yau $3$-folds and new candidats for their mirrors which were previously unknown for physicists. We conjecture that there exists an isomorphism between two conformal field theories corresponding to Calabi-Yau varieties from two families ${\cal F}(\Delta)$ and ${\cal F}(\Delta^*)$.
Perceived food and labor equity and school attendance among Ugandan children living in kin care

Emerging research suggests that biological relatedness contributes to differential treatment between children being raised by kin and the biological children in the caregiver's household. This potential concern may be elevated especially when household resources are stretched thin. In this study, 518 Ugandan youth and their caregivers were interviewed individually, examining the association between relatedness and perceived food and work equity, and school attendance. Household income, but not relatedness, was negatively associated with food inequity. However, relatedness was positively associated with perceived disparity in the distribution of work among children living in the household, and with children's school attendance. These findings support and challenge previous findings, raising further research questions and suggesting practice implications. Key Practitioner Message: ● Children in kinship care may be experiencing intrahousehold disparity in the amount of household work they are asked to perform; ● Disparity in school attendance between biological and kin children in the same household could have negative implications for the long-term wellbeing of children in kin care; ● Programs should be tailored to monitor this type of intrahousehold disparity in treatment.
Reordering pPhrase-based machine translation over chunks

The paper presents a new method for reordering in phrase based statistical machine translation (PBMT). Our method is based on previous chunk-level reordering methods for PBMT. First, we parse the source language sentence to a chunk tree, according to the method developed by [16]. Second, we apply a series of transformation rules which are learnt automatically from the parallel corpus to the chunk tree over chunk level. Finally, we integrate a global reordering model directly in a decoder as a graph of phrases, and solve the overlapping phrase and chunk problem. The experimental results with English-Vietnamese pairs show that our method outperforms the baseline PBMT in both accuracy and speed.
The Ties That Bind: Measuring the Strength of Consumers’ Emotional Attachments to Brands

Extant research suggests that consumers can become emotionally attached to consumption objects, including brands. However, a scale to measure the strength of consumers’ emotional attachments to brands has yet to be devised. We develop such a scale in Studies 1 and 2. Study 3 validates the scale's internal consistency and dimensional structure. Study 4 examines its convergent validity with respect to four behavioral indicators of attachments. Study 5 demonstrates discriminant validity, showing that the scale is differentiated from measures of satisfaction, involvement, and brand attitudes. That study also examines the scale's predictive validity, showing that it is positively associated with indicators of both commitment and investment. The limitations of the scale and the boundary conditions of its applicability are also discussed.
UTD-CRSS system for the NIST 2015 language recognition i-vector machine learning challenge

In this paper, we present the system developed by the Center for Robust Speech Systems (CRSS), University of Texas at Dallas, for the NIST 2015 language recognition i-vector machine learning challenge. Our system includes several subsystems, based on Linear Discriminant Analysis - Support Vector Machine (LDA-SVM) and deep neural network (DNN) approaches. An important feature of this challenge is the emphasis on out-of-set language detection. As a result, our system development focuses mainly on the evaluation and comparison of two different out-of-set language detection strategies: direct out-of-set detection and indirect out-of-set detection. These out-of-set detection strategies differ mainly on whether the unlabeled development data are used or not. The experimental results indicate that indirect out-of-set detection strategies used in our system could efficiently exploit the unlabeled development data, and therefore consistently outperform the direct out-of-set detection approach. Finally, by fusing four variants of indirect out-of-set detection based subsystems, our system achieves a relative performance gain of up to 45%, compared to the baseline cosine distance scoring (CDS) system provided by organizer.
Insusceptibility to disinfectants in bacteria from animals, food and humans—is there a link to antimicrobial resistance?

Enterococcus faecalis (n = 834) and Enterococcus faecium (n = 135) from blood and feces of hospitalized humans, from feces of outpatients and livestock and from food were screened for their susceptibility to a quaternary ammonium compound (didecyldimethylammoniumchloride, DDAC) and to 28 antibiotics by micro-/macrodilution. The maximum DDAC-MIC in our field study was 3.5 mg/l, but after adaptation in the laboratory, MIC values of 21.9 mg/l were observed. Strains for which DDAC had MICs > 1.4 mg/l (“non-wildtype,” in total: 46 of 969 isolates/4.7%) were most often found in milk and dairy products (14.6%), while their prevalence in livestock was generally low (0–4%). Of human isolates, 2.9–6.8% had a “non-wildtype” phenotype. An association between reduced susceptibility to DDAC, high-level-aminoglycoside resistance and aminopenicillin resistance was seen in E. faecium (p < 0.05). No indications for a common source of non-wildtype strains were found by RAPD-PCR; however, several non-wildtype E. faecalis shared the same variant of the emeA-gene. In addition, bacteria (n = 42) of different genera were isolated from formic acid based boot bath disinfectant (20 ml of 55% formic acid/l). The MICs of this disinfectant exceeded the wildtype MICs up to 20-fold (staphylococci), but were still one to three orders of magnitude below the used concentration of the disinfectant (i. e., 1.1% formic acid). In conclusion, the bacterial susceptibility to disinfectants still seems to be high. Thus, the proper use of disinfectants in livestock surroundings along with a good hygiene praxis should still be highly encouraged. Hints to a link between antibiotic resistance and reduced susceptibility for disinfectants—as seen for E. faecium—should be substantiated in further studies and might be an additional reason to confine the use of antibiotics.
Long-term response in episodic acidification to declining SO 4 2– deposition in two streams in Nova Scotia

Trends in anthropogenically driven episodic acidification associated with extended winter snow melt/rain episodes between 1983 and 1998 were investigated for two streams in Nova Scotia, Canada. The anthropogenic contribution to Acid Neutralization Capacity (ANC) was analysed using the Boreal Dilution Model (Bishop et al. , 2000) modified by applying a sea-salt correction to all input hydrochemistry. The anthropogenic contribution to episodic ANC decline was statistically significant and strongly correlated with the decline in acid deposition, which decreased by approximately 50% during the period of record. Sensitivity analysis demonstrated that the BDM can be applied to surface waters with sea-salt contributions although the correction increases model uncertainty. Results of this study demonstrate the effectiveness of reduced emissions in North America in the last decades in decreasing the severity of episodic acidification in the Atlantic region of Canada. Keywords: episodic acidification, acidification recovery, Nova Scotia, snowmelt, winter
HLA-DPB1*0402 Protects Against Type 1A Diabetes Autoimmunity in the Highest Risk DR3-DQB1*0201/DR4-DQB1*0302 DAISY Population

OBJECTIVE— A major goal in genetic studies of type 1A diabetes is prediction of anti-islet autoimmunity and subsequent diabetes in the general population, as >85% of patients do not have a first-degree relative with type 1A diabetes. Given prior association studies, we hypothesized that the strongest candidates for enhancing diabetes risk among DR3-DQB1*0201/DR4-DQB1*0302 individuals would be alleles of DP and DRB1*04 subtypes and, in particular, the absence of reportedly protective alleles DPB1*0402 and/or DRB1*0403. RESEARCH DESIGN AND METHODS— We genotyped 457 DR3-DQB1*0201/DR4-DQB1*0302 Diabetes Autoimmunity Study of the Young (DAISY) children (358 general population and 99 siblings/offspring of type 1 diabetic patients) at the DPB1, DQB1, and DRB1 loci using linear arrays of immobilized sequence-specific oligonucleotides, with direct sequencing to differentiate DRB1*04 subtypes. RESULTS— By survival curve analysis of DAISY children, the risk of persistently expressing anti-islet autoantibodies is ∼55% for relatives (children with a parent or sibling with type 1 diabetes) in the absence of these two protective alleles vs. 0% (P = 0.02) with either protective allele, and the risk is 20 vs. 2% (P = 0.004) for general population children. Even when the population analyzed is limited to DR3-DQB1*0201/DR4-DQB1*0302 children with DRB1*0401 (the most common DRB1*04 subtype), DPB1*0402 influences development of anti-islet autoantibodies. CONCLUSIONS— The ability to identify a major group of general population newborns with a 20% risk of anti-islet autoimmunity should enhance both studies of the environmental determinants of type 1A diabetes and the design of trials for the primary prevention of anti-islet autoimmunity.
Role of (cid:2) B in the Expression of Staphylococcus aureus Cell Wall Adhesins ClfA and FnbA and Contribution to Infectivity in a Rat Model of Experimental Endocarditis

Isogenic Staphylococcus aureus strains with different capacities to produce (cid:1) B activity were analyzed for their ability to attach to ﬁbrinogen- or ﬁbronectin-coated surfaces or platelet-ﬁbrin clots and to cause endocarditis in rats. In comparison to the (cid:1) B -deﬁcient strain, BB255, which harbors an rsbU mutation, both rsbU complemented and (cid:1) B -overproducing derivatives exhibited at least ﬁve times greater attachment to ﬁbrinogen-and ﬁbronectin-coated surfaces and showed increased adherence to platelet-ﬁbrin clots. No differences in adherence were seen between BB255 and a (cid:2) rsbUVWsigB isogen. Northern blotting analyses revealed that transcription of clfA , encoding ﬁbrinogen-binding protein clumping factor A, and fnbA , encoding ﬁbronectin-binding protein A, were positively inﬂuenced by (cid:1) B . (cid:1) B overproduction resulted in a statistically signiﬁcant increase in positive spleen cultures and enhanced bacterial densities in both the aortic vegetations and spleens at 16 h postinoculation. In contrast, at 72 h postinoculation, tissues infected with the (cid:1) B overproducer had lower bacterial densities than did those infected with BB255. These results suggest that although (cid:1) B appears to increase the adhesion of S. aureus to various host cell-matrix proteins in vitro, it has limited effect on pathogenesis in the rat endocarditis model. (cid:1) B appears to have a transient enhancing effect on bacterial density in the early stages of infection that is lost during progression.
Local Multipliers

Every time a local economy generates a new job by attracting a new business, additional jobs might also be created, mainly through increased demand for local goods and services. This positive effect on employment is partially offset by general equilibrium effects induced by changes in local wages and prices of local services. In this paper, I estimate the long-term employment multiplier at the local level. Specifically, I quantify the long-term change in the number of jobs in a city’s tradable and nontradable sectors generated by an exogenous increase in the number of jobs in the tradable sector, allowing for the endogenous reallocation of factors and adjustment of prices. I find that for each additional job in manufacturing in a given city, 1.6 jobs are created in the nontradable sector in the same city. As the number of workers and the equilibrium wage increase in a city, the demand for local goods and services increases. This effect is significantly larger for skilled jobs, because they command higher earnings. Adding one additional skilled job in the tradable sector generates 2.5 jobs in local goods and services. The corresponding figure for unskilled jobs is one. The multiplier also varies across industries. Industry-specific multipliers indicate that high tech industries have the largest multiplier. A simple framework suggests that the local multiplier for the tradable sector should be smaller than the one for the nontradable sector, and possibly even negative. This is because the increase in labor costs generated by the initial labor demand shock hurts local producers of tradables. This negative effect may be in part offset by agglomeration externalities, if they exist, and an increase in the demand for intermediate inputs, if supply chains are localized. Empirically, I find that adding one additional job in one part of the tradable sector has no significant effect on employment in other parts of the tradable sector. Local Multipliers
Early Proliferation Does Not Prevent the Loss of Oligodendrocyte Progenitor Cells during the Chronic Phase of Secondary Degeneration in a CNS White Matter Tract

Partial injury to the central nervous system (CNS) is exacerbated by additional loss of neurons and glia via toxic events known as secondary degeneration. Using partial transection of the rat optic nerve (ON) as a model, we have previously shown that myelin decompaction persists during secondary degeneration. Failure to repair myelin abnormalities during secondary degeneration may be attributed to insufficient OPC proliferation and/or differentiation to compensate for loss of oligodendrocyte lineage cells (oligodendroglia). Following partial ON transection, we found that sub-populations of oligodendroglia and other olig2+ glia were differentially influenced by injury. A high proportion of NG2+/olig2–, NG2+/olig2+ and CC1−/olig2+ cells proliferated (Ki67+) at 3 days, prior to the onset of death (TUNEL+) at 7 days, suggesting injury-related cues triggered proliferation rather than early loss of oligodendroglia. Despite this, a high proportion (20%) of the NG2+/olig2+ OPCs were TUNEL+ at 3 months, and numbers remained chronically lower, indicating that proliferation of these cells was insufficient to maintain population numbers. There was significant death of NG2+/olig2– and NG2−/olig2+ cells at 7 days, however population densities remained stable, suggesting proliferation was sufficient to sustain cell numbers. Relatively few TUNEL+/CC1+ cells were detected at 7 days, and no change in density indicated that mature CC1+ oligodendrocytes were resistant to secondary degeneration in vivo. Mature CC1+/olig2– oligodendrocyte density increased at 3 days, reflecting early oligogenesis, while the appearance of shortened myelin internodes at 3 months suggested remyelination. Taken together, chronic OPC decreases may contribute to the persistent myelin abnormalities and functional loss seen in ON during secondary degeneration.
Word Length Effects in a Contextual Model of Verbal Perception

Retrieved-context models have played a crucial role in the understanding of serialposition effects in free recall. In this paper, a simple model in that class is proposed and tested against the case of word-length experiments. In recent years, standard interpretations of the word-length effect have been undermined by a series of experimental results, culminating with data that display an inversion of the effect for mixed lists. The model discussed in this paper predicts the experimental behavior as an effect of the different level of localization of short and long words in semantic space. Events corresponding to the recognition of a nonlocal word have a clustering property in phase space, which facilitates associative retrieval. The standard word-length effect arises directly from this property, and the inverse effect from its breakdown. The theory predicts that the contiguity effect should be stronger for shorter words. Several other predictions are listed, and experiments are proposed to further test the model. Finally, a possible interpretation of the results is discussed.