Miracle-dz/UniFAR-FTUs huggingface dataset:
Effectiveness of Palivizumab in High-risk Infants and Children

Background: Infants with premature birth ⩽35 weeks gestational age, chronic lung disease of prematurity and congenital heart disease are at an increased risk for lower respiratory tract infections and hospitalization from respiratory syncytial virus (RSV), which has been shown in randomized trials to be prevented by palivizumab. However, palivizumab effectiveness (PE) has not been studied in a large clinical setting. Methods: A multicenter study among high-risk US and Canadian children younger than 24 months hospitalized with lower respiratory tract infection and whose nasopharyngeal aspirates were tested for human metapneumovirus (HMPV) and RSV were the subjects of the trial. We conducted a test-negative case–control study in these subjects to determine PE. We used an inverse propensity score weighted (IPSW) multiple logistic regression model to adjust PE. Results: Palivizumab was used in 434 (51%) of 849 eligible children. RSV was identified in 403 (47%) children. The unadjusted PE was 43% [95% confidence interval (CI), 34%–51%)]. After IPSW adjustment, the adjusted PE was 58% (95% CI, 43%–69%). Palivizumab prevented intensive care unit admissions (PE, 62%; 95% CI, 35%–78%). PE for 29–35 weeks gestational age and ⩽6 months of chronologic age without chronic lung disease of prematurity or congenital heart disease was 74% (95% CI, 56%–85%). Conclusions: Using a test-negative case–control design with RSV molecular detection, palivizumab is shown to prevent RSV hospitalizations and intensive care unit admissions in high-risk infants.
PGG.Population: a database for understanding the genomic diversity and genetic ancestry of human populations

Abstract There are a growing number of studies focusing on delineating genetic variations that are associated with complex human traits and diseases due to recent advances in next-generation sequencing technologies. However, identifying and prioritizing disease-associated causal variants relies on understanding the distribution of genetic variations within and among populations. The PGG.Population database documents 7122 genomes representing 356 global populations from 107 countries and provides essential information for researchers to understand human genomic diversity and genetic ancestry. These data and information can facilitate the design of research studies and the interpretation of results of both evolutionary and medical studies involving human populations. The database is carefully maintained and constantly updated when new data are available. We included miscellaneous functions and a user-friendly graphical interface for visualization of genomic diversity, population relationships (genetic affinity), ancestral makeup, footprints of natural selection, and population history etc. Moreover, PGG.Population provides a useful feature for users to analyze data and visualize results in a dynamic style via online illustration. The long-term ambition of the PGG.Population, together with the joint efforts from other researchers who contribute their data to our database, is to create a comprehensive depository of geographic and ethnic variation of human genome, as well as a platform bringing influence on future practitioners of medicine and clinical investigators. PGG.Population is available at https://www.pggpopulation. org.
N 4-acyl-2′-deoxycytidine-5′-triphosphates for the enzymatic synthesis of modified DNA

Abstract A huge diversity of modified nucleobases is used as a tool for studying DNA and RNA. Due to practical reasons, the most suitable positions for modifications are C5 of pyrimidines and C7 of purines. Unfortunately, by using these two positions only, one cannot expand a repertoire of modified nucleotides to a maximum. Here, we demonstrate the synthesis and enzymatic incorporation of novel N4-acylated 2′-deoxycytidine nucleotides (dCAcyl). We find that a variety of family A and B DNA polymerases efficiently use dCAcylTPs as substrates. In addition to the formation of complementary CAcyl•G pair, a strong base-pairing between N4-acyl-cytosine and adenine takes place when Taq, Klenow fragment (exo–), Bsm and KOD XL DNA polymerases are used for the primer extension reactions. In contrast, a proofreading phi29 DNA polymerase successfully utilizes dCAcylTPs but is prone to form CAcyl•A base pair under the same conditions. Moreover, we show that terminal deoxynucleotidyl transferase is able to incorporate as many as several hundred N4-acylated-deoxycytidine nucleotides. These data reveal novel N4-acylated deoxycytidine nucleotides as beneficial substrates for the enzymatic synthesis of modified DNA, which can be further applied for specific labelling of DNA fragments, selection of aptamers or photoimmobilization.
Dynamization of the trapezoid method for planar point location in monotone subdivisions

We present a fully dynamic data structure for point location in a monotone subdivision, based on the trapezoid method. The operations supported are insertion and deletion of vertices and edges, and horizontal translation of vertices. Let n be the current number of vertices of the subdivision. Point location queries take O(log n) time, while updates take O (log2 n) time (amortized for vertex insertion/deletion and worst-case for the other updates). The space requirement is O(n log n). This is the first fully dynamic point location data structure for monotone subdivisions that achieves optimal query time.
Low complexity affine MMSE detector for iterative detection-decoding MIMO OFDM systems

Iterative turbo processing between detection and decoding shows near-capacity performance on a multiple-antenna system. Combining iterative processing with optimum front-end detection is particularly challenging because the front-end maximum a posteriori (MAP) algorithm has a computational complexity that is exponential. Sub-optimum detector such as the soft interference cancellation linear minimum mean square error (SIC-LMMSE) detector with near front-end MAP performance has been proposed in the literature. The asymptotic computational complexity of SIC-LMMSE is O(n<sub>t</sub> <sup>2</sup>n<sub>r</sub> + n<sub>t</sub>n<sub>r</sub> <sup>3</sup> + n<sub>t</sub>M<sub>c</sub>2<sup>Mc</sup>) per detection-decoding cycle where n<sub>t</sub> is number of transmit antenna, nr is number of receive antenna, and Mc is modulation size. A lower complexity detector is the hard interference cancellation LMMSE (HIC-LMMSE) detector. HIC-LMMSE has asymptotic complexity of O(n<sub>t</sub> <sup>2</sup>n<sub>r</sub> + n<sub>t</sub>M<sub>c</sub>2<sup>Mc</sup>) but suffers extra performance degradation. In this paper, two front-end detection algorithms are introduced that not only achieve asymptotic computational complexity of O(n<sub>t</sub> <sup>2</sup>n<sub>r</sub> + n<sub>t</sub>n<sub>r</sub> <sup>2</sup> [Gamma (beta) + 1] + n<sub>t</sub>M<sub>c</sub>2<sup>Mc</sup>) where Gamma(beta) is a function with discrete output {-1, 2, 3, . ,n<sub>t</sub>} and O(n<sub>t</sub>M<sub>c</sub>2<sup>Mc</sup>) respectively. Simulation results demonstrate that the proposed low complexity detection algorithms offer exactly same performance as their full complexity counterpart in an iterative receiver while being computational more efficient.
A Well-Kept Treasure at Depth: Precious Red Coral Rediscovered in Atlantic Deep Coral Gardens (SW Portugal) after 300 Years

Background The highly valuable red coral Corallium rubrum is listed in several Mediterranean Conventions for species protection and management since the 1980s. Yet, the lack of data about its Atlantic distribution has hindered its protection there. This culminated in the recent discovery of poaching activities harvesting tens of kg of coral per day from deep rocky reefs off SW Portugal. Red coral was irregularly exploited in Portugal between the 1200s and 1700s, until the fishery collapsed. Its occurrence has not been reported for the last 300 years. Results Here we provide the first description of an Atlantic red coral assemblage, recently rediscovered dwelling at 60–100 m depth in southern Portugal. We report a very slow growth rate (0.23 mm year-1), comparable to Mediterranean specimens. In comparison with most of the Mediterranean reports, the population reaches much larger sizes, estimated to be over one century old, and has a more complex coral branch architecture that promotes a rich assemblage of associated species, with boreal and Mediterranean affinities. Atlantic red coral is genetically distinct, yet mitochondrial analyses suggest that red corals from the Atlantic may have introgressed the Mediterranean ones after migration via the Algeria current. Our underwater surveys, using advanced mixed-gas diving, retrieved lost fishing gear in all coral sites. Besides illegal harvesting, the use and loss of fishing gears, particularly nets, by local fisheries are likely sources of direct impacts on these benthic assemblages. Conclusions We extended the knowledge on the distribution of C. rubrum in the Atlantic, discovered its genetic distinctiveness, and reveal a rich deep-dwelling fauna associated to these coral assemblages. These findings support a barrier role of the Atlantic-Mediterranean transition zone, but reveal also hints of connectivity along its southern margin. The results highlight the genetic and demographic uniqueness of red coral populations from SW Iberia. However, we also report threats to these vulnerable populations by direct and indirect fishing activities and argue that its protection from any mechanically destructive activities is urgent as a precautionary approach. This study advances our understanding of phylogeographic barriers and range edge genetic diversity, and serves as a baseline against which to monitor future human and environmental disturbances to Atlantic C. rubrum.
Compositional Shape Analysis by Means of Bi-Abduction

The accurate and efficient treatment of mutable data structures is one of the outstanding problem areas in automatic program verification and analysis. Shape analysis is a form of program analysis that attempts to infer descriptions of the data structures in a program, and to prove that these structures are not misused or corrupted. It is one of the more challenging and expensive forms of program analysis, due to the complexity of aliasing and the need to look arbitrarily deeply into the program heap. This article describes a method of boosting shape analyses by defining a compositional method, where each procedure is analyzed independently of its callers. The analysis algorithm uses a restricted fragment of separation logic, and assigns a collection of Hoare triples to each procedure; the triples provide an over-approximation of data structure usage. Our method brings the usual benefits of compositionality---increased potential to scale, ability to deal with incomplete programs, graceful way to deal with imprecision---to shape analysis, for the first time. The analysis rests on a generalized form of abduction (inference of explanatory hypotheses), which we call bi-abduction. Bi-abduction displays abduction as a kind of inverse to the frame problem: it jointly infers anti-frames (missing portions of state) and frames (portions of state not touched by an operation), and is the basis of a new analysis algorithm. We have implemented our analysis and we report case studies on smaller programs to evaluate the quality of discovered specifications, and larger code bases (e.g., sendmail, an imap server, a Linux distribution) to illustrate the level of automation and scalability that we obtain from our compositional method. This article makes number of specific technical contributions on proof procedures and analysis algorithms, but in a sense its more important contribution is holistic: the explanation and demonstration of how a massive increase in automation is possible using abductive inference.
Efficiency Optimization of a 100-W, 500 000-rpm Permanent-Magnet Machine Including Air Friction Losses

This paper proposes a method for the efficiency optimization of ultra-high-speed permanent-magnet machines. Analytical methods are applied for the modeling of the machine that is equipped with a diametrically magnetized rotor and a slotless stator. The outer dimensions of the machine are design constraints, and the internal dimensioning is optimized for minimum losses. The air friction losses are taken into account in addition to the usual iron losses, copper losses, and eddy current losses. Laminated silicon iron or laminated amorphous iron is used as the stator core material. The results show that air friction losses influence the optimum design considerably, leading to a small rotor diameter at high speeds. The loss minimization and the amorphous iron core make it possible to reduce the calculated losses by 63% as compared to a machine design not considering air friction losses. The resulting efficiency is 95% for a 100-W, 500 000-rpm machine excluding bearing losses.
STUDIES ON THE MECHANISM OF THE SHWARTZMAN PHENOMENON

The cutaneous, ophthalmic, and systemic reactions of normal rabbits to Gram-negative bacterial endotoxins have been compared with the classical reactions of bacterial hypersensitivity, and in each case certain similarities have been found. It has also been shown that the Shwartzman phenomenon can be reproduced with tuberculin, in BCG-vaccinated rabbits, and with suspensions or extracts of heat-killed Group A streptococci in rabbits previously sensitized to these bacteria. These considerations suggest the hypothesis that the biologic activity of endotoxins may be based on the existence in "normal" animals of delayed or tuberculin-type hypersensitivity to these materials.
Determination of operating policies for a barge transportation system through simulation and optimization modeling

This paper presents a simulation model of a barge transportation system for petroleum delivery within an inland waterway. The simulation is employed as an evaluation model within a decision support system which also includes a criterion model, represented as a decision maker’s utility function, and an optimization procedure which employs scatter search. Variance reduction techniques are also employed in order to improve the accuracy of the estimates of the performance measures associated with the system. The main purpose of the system is to determine values for important inventory policy variables.
Zinc Finger Targeter (ZiFiT): an engineered zinc finger/target site design tool

Zinc Finger Targeter (ZiFiT) is a simple and intuitive web-based tool that facilitates the design of zinc finger proteins (ZFPs) that can bind to specific DNA sequences. The current version of ZiFiT is based on a widely employed method of ZFP design, the ‘modular assembly’ approach, in which pre-existing individual zinc fingers are linked together to recognize desired target DNA sequences. Several research groups have described experimentally characterized zinc finger modules that bind many of the 64 possible DNA triplets. ZiFiT leverages the combined capabilities of three of the largest and best characterized module archives by enabling users to select fingers from any of these sets. ZiFiT searches a query DNA sequence for target sites for which a ZFP can be designed using modules available in one or more of the three archives. In addition, ZiFiT output facilitates identification of specific zinc finger modules that are publicly available from the Zinc Finger Consortium. ZiFiT is freely available at http://bindr.gdcb. iastate.edu/ZiFiT/.
Mouse Genome Database (MGD)-2018: knowledgebase for the laboratory mouse

Abstract The Mouse Genome Database (MGD; http://www.informatics.jax.org) is the key community mouse database which supports basic, translational and computational research by providing integrated data on the genetics, genomics, and biology of the laboratory mouse. MGD serves as the source for biological reference data sets related to mouse genes, gene functions, phenotypes and disease models with an increasing emphasis on the association of these data to human biology and disease. We report here on recent enhancements to this resource, including improved access to mouse disease model and human phenotype data and enhanced relationships of mouse models to human disease.
Linear Arrays of Nuclear Envelope Proteins Harness Retrograde Actin Flow for Nuclear Movement

Line Up for Movement The nuclei of animal cells can move to specific locations and help to polarize migrating and differentiating cells. Luxton et al. (p. 956; see the Perspective by Starr) found that linear arrays of nuclear membrane proteins assembled on, and moved with, actin cables toward the rear of the cell during nuclear movement in polarizing fibroblasts. Interfering with the components of these linear arrays prevented nuclear movement and centrosome reorientation. Thus, nuclear membrane proteins assemble into actin-dependent arrays during force transduction. An actin-dependent mechanism is involved in moving nuclei so that they are properly positioned for cell migration. Nuclei move to specific locations to polarize migrating and differentiating cells. Many nuclear movements are microtubule-dependent. However, nuclear movement to reorient the centrosome in migrating fibroblasts occurs through an unknown actin-dependent mechanism. We found that linear arrays of outer (nesprin2G) and inner (SUN2) nuclear membrane proteins assembled on and moved with retrogradely moving dorsal actin cables during nuclear movement in polarizing fibroblasts. Inhibition of nesprin2G, SUN2, or actin prevented nuclear movement and centrosome reorientation. The coupling of actin cables to the nuclear membrane for nuclear movement via specific membrane proteins indicates that, like plasma membrane integrins, nuclear membrane proteins assemble into actin-dependent arrays for force transduction.
A probabilistic language based on sampling functions

As probabilistic computations play an increasing role in solving various problems, researchers have designed probabilistic languages which treat probability distributions as primitive datatypes. Most probabilistic languages, however, focus only on discrete distributions and have limited expressive power. This article presents a probabilistic language, called λ○, whose expressive power is beyond discrete distributions. Rich expressiveness of λ○ is due to its use of sampling functions, that is, mappings from the unit interval (0.0,1.0] to probability domains, in specifying probability distributions. As such, λ○ enables programmers to formally express and reason about sampling methods developed in simulation theory. The use of λ○ is demonstrated with three applications in robotics: robot localization, people tracking, and robotic mapping. All experiments have been carried out with real robots.
Transmission of chimeric HIV by mating in conventional mice: prevention by pre-exposure antiretroviral therapy and reduced susceptibility during estrus

SUMMARY Heterosexual transmission accounts for the majority of new human immunodeficiency virus (HIV) cases worldwide. The current approach to investigate HIV heterosexual transmission in animals involves application of virus stock to the vaginal surface, a method that does not reproduce the physiological conditions of vaginal intercourse that influence the rate of transmission. We have previously described efficient infection of conventional mice using EcoHIV/NL4-3 and EcoHIV/NDK, chimeric HIV molecular clones constructed to express all HIV structural and regulatory genes except envelope, which is replaced by a rodent-tropic envelope gene. Here we investigated whether EcoHIV/NDK-infected male mice transmit virus to females during coitus, and the sensitivity of this transmission to HIV pre-exposure prophylaxis and the estrus state. Our general approach was to allow mating between EcoHIV/NDK-infected male mice and uninfected females for 1–7 nights. At 1–6 weeks after mating, mice were euthanized and virus burdens were measured by quantitative PCR (qPCR) amplification of HIV RNA or DNA in peritoneal macrophages, inguinal lymph node cells, spleen cells or vas deferens, or by ELISA for antibodies to HIV Gag. We found that 70–100% of female mice mated to EcoHIV/NDK-infected males acquired infection. Pericoital treatment of females with either 2′,3′-dideoxcytidine (ddC) or tenofovir largely prevented their EcoHIV/NDK infection by mating (P<0.05 and P<0.003, respectively). In males, T cells were dispensable for virus transmission. The rate of EcoHIV/NDK sexual transmission to females in estrus declined sharply (P=0.003) but their infection by injection was unaffected, indicating that the local environment in the female reproductive tract influences susceptibility to HIV. We conclude that this system of EcoHIV/NDK transmission during mouse mating reproduces key features of heterosexual transmission of HIV in humans and can be used to investigate its biology and control.
Draft Genome Sequence of Euryhalocaulis caribicus Strain JL2009T, a New Member of the Family Hyphomonadaceae Isolated from the Caribbean Sea

ABSTRACT Euryhalocaulis caribicus strain JL2009T is a novel genus and species of the family Hyphomonadaceae and was first isolated from surface water in the Caribbean Sea. Here, we report the first draft genome from this genus. Its genome contains genes encoding proteins that are involved in organic acid metabolism and probable low-affinity inorganic phosphate transporters, which suggests its competence in oligotrophic oceans.
Association of Empirically Derived Dietary Patterns with Cardiovascular Risk Factors: A Comparison of PCA and RRR Methods

Introduction Principal component analysis is used to determine dietary behaviors of a population whereas reduced rank regression is used to construct disease-related dietary patterns. This study aimed to compare both types of DP and theirs associations with cardiovascular risk factors (CVRF). Materiel and Methods Data were derived from the cross sectional NESCAV (Nutrition, Environment and Cardiovascular Health) study, aiming to describe the cardiovascular health of the Greater region’s population (Grand duchy of Luxembourg, Wallonia (Belgium), Lorraine (France)). 2298 individuals were included for this study and dietary intake was assessed using a 134-item food frequency questionnaire. Results We found that CVRF-related patterns also reflect eating behaviours of the population. Comparing concordant food groups between both dietary pattern methods, a diet high in fruits, oleaginous and dried fruits, vegetables, olive oil, fats rich in omega 6 and tea and low in fried foods, lean and fatty meat, processed meat, ready meal, soft drink and beer was associated with lower prevalence of CVRF. In the opposite, a pattern characterized by high intakes of fried foods, meat, offal, beer, wine and aperitifs and spirits, and low intakes of cereals, sugar and sweets and soft drinks was associated with higher prevalence of CVRF. Conclusion In sum, we found that a “Prudent” and “Animal protein and alcohol” patterns were both associated with CVRF and behaviourally meaningful. Moreover, the relationships of those dietary patterns with lifestyle characteristics support the theory that food choices are part of a larger pattern of healthy lifestyle.
Design and Application of Coal Blending Control System Based on HOLLiAS-LK Large-Scale PLC

To make full use of coal combustion heat energy, and for the purposes of energy savings and pollutant reductions, more than two different coal needs to optimize the preparation of coal. This article describes design and application of coal blending control system based on OLLiAS-LK large-scale PLC. It has realized the functions of automatic start and stop, interlock control, material level adjustment, speed control and others in the production process, improved the speed of the blending, realized the automation of the blending process, and reached the effects of the accurate ratio and homogeneous optimization.