Miracle-dz/UniFAR-FTUs huggingface dataset:
Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2

Protein secretion systems are complex molecular machineries that translocate proteins through the outer membrane and sometimes through multiple other barriers. They have evolved by co-option of components from other envelope-associated cellular machineries, making them sometimes difficult to identify and discriminate. Here, we describe how to identify protein secretion systems in bacterial genomes using the MacSyFinder program. This flexible computational tool uses the knowledge gathered from experimental studies to identify homologous systems in genome data. It can be used with a set of pre-defined MacSyFinder models—”TXSScan”, to identify all major secretion systems of diderm bacteria (i.e., with inner and LPS-containing outer membranes) as well as evolutionarily related cell appendages (pili and flagella). For this, it identifies and clusters co-localized genes encoding proteins of secretion systems using sequence similarity search with Hidden Markov Model (HMM) protein profiles. Finally, it checks if the clusters’ genetic content and genomic organization satisfy the constraints of the model. TXSScan models can be altered in the command line or customized to search for variants of known secretion systems. Models can also be built from scratch to identify novel systems. In this chapter, we describe a complete pipeline of analysis, starting from i) the integration of information from a reference set of experimentally studied systems, ii) the identification of conserved proteins and the construction of their HMM protein profiles, iii) the definition and optimization of “macsy-models”, and iv) their use and online distribution as tools to search genomic data for secretion systems of interest. MacSyFinder is available here: https://github.com/gem-pasteur/macsyfinder, and MacSyFinder models here: https://github.com/macsy-models.
Skeletal Colonization by Breast Cancer Cells Is Stimulated by an Osteoblast and β2AR‐Dependent Neo‐Angiogenic Switch

The skeleton is a common site for breast cancer metastasis. Although significant progress has been made to manage osteolytic bone lesions, the mechanisms driving the early steps of the bone metastatic process are still not sufficiently understood to design efficacious strategies needed to inhibit this process and offer preventative therapeutic options. Progression and recurrence of breast cancer, as well as reduced survival of patients with breast cancer, are associated with chronic stress, a condition known to stimulate sympathetic nerve outflow. In this study, we show that stimulation of the beta 2‐adrenergic receptor (β2AR) by isoproterenol, used as a pharmacological surrogate of sympathetic nerve activation, led to increased blood vessel density and Vegf‐a expression in bone. It also raised levels of secreted Vegf‐a in osteoblast cultures, and accordingly, the conditioned media from isoproterenol‐treated osteoblast cultures promoted new vessel formation in two ex vivo models of angiogenesis. Blocking the interaction between Vegf‐a and its receptor, Vegfr2, blunted the increase in vessel density induced by isoproterenol. Genetic loss of the β2AR globally, or specifically in type 1 collagen‐expressing osteoblasts, diminished the increase in Vegf‐positive osteoblast number and bone vessel density induced by isoproterenol, and reduced the higher incidence of bone metastatic lesions induced by isoproterenol after intracardiac injection of an osteotropic variant of MDA‐MB‐231 breast cancer cells. Inhibition of the interaction between Vegf‐a and Vegfr2 with the blocking antibody mcr84 also prevented the increase in bone vascular density and bone metastasis triggered by isoproterenol. Together, these results indicate that stimulation of the β2AR in osteoblasts triggers a Vegf‐dependent neo‐angiogenic switch that promotes bone vascular density and the colonization of the bone microenvironment by metastatic breast cancer cells. © 2017 American Society for Bone and Mineral Research.
Reproductive performance of cows after fixed‐time artificial insemination with ovulation synchronisation and re‐synchrony in southern Australian dairy herds

OBJECTIVE To describe reproductive performance of lactating dairy cows after fixed-time artificial insemination (FTAI) with ovulation synchronisation and re-synchrony in Australian dairy herds, and to compare reproductive outcomes with those of conventional mating programs. METHODS The study was conducted in two seasonally calving dairy herds in which lactating dairy cows (n = 675) were enrolled into three treatment groups: group 1, oestrus detection and AI for 34 days followed by a natural service period; group 2, FTAI on day 1 followed by re-synchrony of all cows prior to ultrasound pregnancy diagnosis at day 31 and FTAI of cows diagnosed not pregnant at day 34, then a natural service period; group 3, FTAI on day 1 followed by oestrus detection and AI for 34 days, then a natural service period. First-service conception rate (FSCR), 6-week in-calf (6WIC) rate and proportions pregnant at the end of mating were compared using logistic regression with farm fitted as a fixed effect. Times from mating start date to conception were described using survival analysis with Kaplan-Meier failure functions. RESULTS FSCRs (45.3%, 49.1% and 45.6% for groups 1, 2 and 3, respectively) and proportions pregnant at the end of mating (77.6%, 76.0% and 76.8% for groups 1, 2 and 3, respectively) were similar for all groups. The 6WIC rate in group 2 was similar to that in group 3 (70.4% vs. 67.2%; P = 0.486), but tended to be higher than in group 1 (70.4% vs. 62.0%, P = 0.066). The median days to pregnancy for cows that conceived was 1 day in groups 2 and 3 and 10 days in group 1. CONCLUSION Mating plans that use FTAI with ovulation synchronisation and re-synchrony during the AI period can achieve comparable reproductive performance to conventional mating programs in seasonally calving dairy herds.
Effect of Composition and Thermo-Mechanical Processing on Microstructure Development in Ni-30Fe-Nb-C Model Alloys

The unavoidable phase transformation upon cooling makes a direct observation of austenite microstructure impossible. One of the methods to investigate the high temperature condition of austenite is to use a model alloy, which would not transform to martensite on quenching. In the present work the recrystallisation and grain growth of austenite during thermo-mechanical processing (TMP) were studied for three Ni-30Fe-Nb-C alloys containing 0.33, 0.85 and 1.42 wt% Nb. The austenite microstructures were characterised using optical and scanning electron microscopy, and energy dispersive X-ray spectroscopy. The austenite recrystallisation kinetics was investigated with respect to the precipitate distribution variations. A relative strength of the grain boundary pinning effect from solute Nb and precipitated particles is discussed.
A dual-exposure in-pixel charge subtraction CTIA CMOS image sensor for centroid measurement in star trackers

In this work, we present a CMOS image sensor for star centroid measurement in star trackers. The analysis of the star tracker system shows that long integration will cause "tail effect" in the star image. It significantly reduces the signal magnitude, which in turn increases the centroiding errors. In order to capture limited photons generated from dim stars within shortened integration time, we propose a new capacitive transimpedance amplifier (CTIA) pixel architecture with a small integration capacitor. On the other hand, bright stars can easily saturate the pixels, which can also induce significant measurement errors. To avoid pixel saturation, the pixel is able to perform in-pixel charge subtraction based on photocurrent thresholding. In order to validate the pixel design, we have fabricated a test chip consisting of a 4×4 pixel array using Global Foundry 65 nm mixed signal CMOS process.
Data set for the reporting of intrahepatic cholangiocarcinoma, perihilar cholangiocarcinoma and hepatocellular carcinoma: recommendations from the International Collaboration on Cancer Reporting (ICCR)

Optimal patient management benefits from comprehensive and accurate pathology reports that contribute to cancer staging and prognostication. Proforma reports are used in many countries, but these vary in their structure and implementation. The International Collaboration on Cancer Reporting (ICCR) is an alliance formed by the Royal College of Pathologists of Australasia, the Royal College of Pathologists of the United Kingdom, the College of American Pathologists, the Canadian Partnership Against Cancer the European Society of Pathology and the American Society of Clinical Pathology (ASCP), with the aim of developing an evidence‐based reporting data set for each cancer site. It is argued that this should reduce the global burden of cancer data set development and reduplication of effort by different international institutions that commission, publish and maintain standardised cancer reporting data sets. The resultant standardisation of cancer reporting will benefit not only those countries directly involved in the collaboration but also others not in a position to develop their own data sets. We describe the development of a cancer data set by the ICCR expert panel for the reporting of the main malignant liver tumours: intrahepatic cholangiocarcinoma, perihilar cholangiocarcinoma and hepatocellular carcinoma and present the ‘required’ and ‘recommended’ elements to be included in the report with an explanatory commentary. This data set incorporates definitions and classifications in the most recent World Health Organisation (WHO) publication on hepatic malignancies (4th edition) and the recently published tumour–node–metastasis (TNM)8 staging system. Widespread adoption and implementation of this data set will enable consistent and accurate data collection, comparison of epidemiological and pathological parameters between different populations, facilitate research and ultimately result in better patient outcomes.
Performance and physiological analysis of 500 km non-stop cycling: a case study

ABSTRACT Ultra-endurance sports have gained popularity over the last years. In this case, a well-trained cyclist completed 503.5 km non-stop (33.3 km.h−1). Speed and power output were reduced during the trial, being the reduction of power attributable to changes in pedal velocity rather than pedal forces. Heart rate (HR) showed an initial cardiovascular drift and progressively decreased independently of power. A decreased HR variability, a marked inflammatory response, signs of muscle damage and alterations of the haematological profile were observed after the trial. These adverse physiological effects were still present 24–48 h after exercise. A reduction in handgrip maximal voluntary contraction was observed immediately after the trial and 24 h later despite these muscles being minimally active during exercise. These findings show the high levels of stress to which the organism is subjected during ultra-endurance exercise even in the case of a trained cyclist.
Influence of Granule Character on Strength and Weibull Modulus of Sintered Alumina

Alumina specimens were prepared by compacting well-characterized spray-dried alumina granules of excellent deformability, followed by sintering. The strength and Weibull modulus were measured and microstructure was evaluated for specimens prepared from granules with different density and morphology. Compacts of spheroidal granules with lower density and lower granule strength sintered to 98% relative density and had fewer microstructural defects than compacts prepared from spheroidal or hollow granules of higher density. Flexural strength of sintered material was found to depend on initial granule size but not density or morphology of the granules. Weibull moduli of 18–20 were independent of particular granule characteristics.
What do farmers' weed control decisions imply about glyphosate resistance? Evidence from surveys of US corn fields.

BACKGROUND The first case of glyphosate-resistant weeds in the United States was documented in 1998, 2 years after the commercialization of genetically engineered herbicide-resistant (HR) corn and soybeans. Currently, over 15 glyphosate-resistant weed species affect US crop production areas. These weeds have the potential to reduce yields, increase costs, and lower farm profitability. The objective of our study is to develop a behavioral model of farmers' weed management decisions and use it to analyze weed resistance to glyphosate in US corn farms. RESULTS On average, we find that weed control increased US corn yields by 3700 kg ha-1 (worth approximately $US 255 ha-1 ) in 2005 and 3500 kg ha-1 (worth approximately $US 575 ha-1 ) in 2010. If glyphosate resistant weeds were absent, glyphosate killed approximately 99% of weeds, on average, when applied at the label rate in HR production systems. Average control was dramatically lower in states where glyphosate resistance was widespread. CONCLUSION We find that glyphosate resistance had a significant impact on weed control costs and corn yields of US farmers in 2005 and 2010. Published 2017. This article is a U.S. Government work and is in the public domain in the USA.
Byzantine Stochastic Gradient Descent

This paper studies the problem of distributed stochastic optimization in an adversarial setting where, out of the $m$ machines which allegedly compute stochastic gradients every iteration, an $\alpha$-fraction are Byzantine, and can behave arbitrarily and adversarially. Our main result is a variant of stochastic gradient descent (SGD) which finds $\varepsilon$-approximate minimizers of convex functions in $T = \tilde{O}\big( \frac{1}{\varepsilon^2 m} + \frac{\alpha^2}{\varepsilon^2} \big)$ iterations. In contrast, traditional mini-batch SGD needs $T = O\big( \frac{1}{\varepsilon^2 m} \big)$ iterations, but cannot tolerate Byzantine failures. Further, we provide a lower bound showing that, up to logarithmic factors, our algorithm is information-theoretically optimal both in terms of sampling complexity and time complexity.
Effect of space allowance and cage size on laying hens housed in furnished cages, Part I: Performance and well-being

ABSTRACT There are few published data on the effects of housing laying hens at different densities in large furnished cages (FC; a.k.a. enriched colony cages). The objective of this study was to determine the effects of housing laying hens at 2 space allowances (SA) in 2 sizes of FC on measures of production and well‐being. At 18 wk of age, 1,218 LSL‐Lite hens were housed in cages furnished with a curtained nesting area, perches, and scratch mat, and stocked at either 520 cm2 (Low) or 748 cm2 (High) total floor space. This resulted in 4 group sizes: 40 vs. 28 birds in smaller FC (SFC) and 80 vs. 55 in larger FC (LFC). Data were collected from 20 to 72 wks of age. There was no effect of cage size (P = 0.21) or SA (P = 0.37) on hen day egg production, egg weight (PSize = 0.90; PSA = 0.73), or eggshell deformation (PSize = 0.14; PSA = 0.053), but feed disappearance was higher in SFC than LFC (P = 0.005). Mortality to 72 wk was not affected by cage size (P = 0.78) or SA (P = 0.55). BW (P = 0.006) and BW CV (P = 0.008) increased with age but were not affected by treatment. Feather cleanliness was poorer in FC with low SA vs. high (P < 0.0001) and small vs. large FC (P < 0.0001). Feather condition was poorer in low SA (P = 0.048) and the best in small cages with high SA (P = 0.006), but deteriorated in all treatments over time (P < 0.0001). Treatments did not affect the breaking strengths of femur, tibia, or humerus, proportions of birds suffering keel deformations, or foot health scores. Overall, the SA studied in the 2 cage sizes in this trial had few effects on production parameters. However, stocking birds at the lower space allowance resulted in some measures of poorer external condition in both sizes of FC, which indicates that the welfare of hens housed at the lower space allowance may be compromised according to some welfare assessment criteria.
Recent Progress in Retrieving Air Temperature Profiles and Air-Sea Temperature Differences from Infrared and Microwave Scanning Radiometer Data

A system of two scanning radiometers has been developed by National Oceanic and Atmospheric Administration (NOAA) Environmental Technology Laboratory (ETL) and deployed on the NOAA Ron H. Brown (RHB) Research Vessel (RV) during the Nauru99 cruise in the Tropical Western Pacific, in June/July 1999. Measurements were taken in a vertically scanning mode, sounding radiation intensity at different elevation angles. In a full scanning cycle, we sequentially measured natural emission intensity from the atmosphere (upward looking) and from the ocean (downward looking). Relative measurement of the air and sea skin temperatures is the key of the robustness of this technique. At the same time, this technique can recover boundary layer air temperature profiles and air-sea temperature differences, providing a relatively simple, yet powerful tool for marine boundary layer study. In this work, we first compare radiometric data collected during the experiment with simulations obtained by atmospheric and ocean Radiative Transfer Models (RTM). Then we use upand down-looking measurements to retrieve air temperature profiles and air-sea temperature differences, respectively. Finally, we determine the achieved retrieval accuracy and we compare radiometric estimates with in situ measurements, discussing similarities and discrepancies.
Structure of stratlingite and effect of hydration methodology on microstructure

Stratlingite, Ca4Al2(OH)12[AlSi(OH)8]2·2H2O, is an AFm phase which appears as a hydration product of aluminium-rich cements. These binders may be calcium aluminate cements, calcium sulfoaluminate cements and also belite calcium sulfo-aluminate (BCSA) cements. The structure of stratlingite is known from single-crystal studies of tiny minerals but their bulk formation, crystal structure and microstructure of powders is poorly understood. This paper reports on the synthesis of stratlingite and a complete structural and microstructural characterisation by synchrotron X-ray powder diffraction, nuclear magnetic resonance, scanning electron microscopy and thermal analyses. The structural and microstructural models have important implications for a correct quantitative phase analysis of stratlingite in cement pastes (for instance, in pastes of BCSA cements). The microstructure of stratlingite formed in cement pastes is highly dependent on the hydration conditions. In BCSA pastes, the (003) line position of stratl.
Serologic Evidence of Ebolavirus Infection in a Population With No History of Outbreaks in the Democratic Republic of the Congo

Background Previous studies suggest that cases of Ebola virus disease (EVD) may go unreported because they are asymptomatic or unrecognized, but evidence is limited by study designs and sample size. Methods A large population-based survey was conducted (n = 3415) to assess animal exposures and behaviors associated with Ebolavirus antibody prevalence in rural Kasai Oriental province of the Democratic Republic of Congo (DRC). Fourteen villages were randomly selected and all healthy individuals ≥1 year of age were eligible. Results Overall, 11% of subjects tested positive for Zaire Ebolavirus (EBOV) immunoglobulin G antibodies. Odds of seropositivity were higher for study participants older than 15 years of age and for males. Those residing in Kole (closer to the outbreak site) tested positive at a rate 1.6× higher than Lomela, with seropositivity peaking at a site located between Kole and Lomela. Multivariate analyses of behaviors and animal exposures showed that visits to the forest or hunting and exposure to rodents or duikers predicted a higher likelihood of EBOV seropositivity. Conclusions These results provide serologic evidence of Ebolavirus exposure in a population residing in non-EBOV outbreak locations in the DRC and define statistically significant activities and animal exposures that associate with EBOV seropositivity.
Comparison of Three Surgical Approaches for Thoracic Spinal Tuberculosis in Adult: Minimum 5-Year Follow Up

Study Design. Retrospective study. Objective. To assess the minimum 5-year follow up outcomes of the surgical management of adults with thoracic tuberculosis by comparing posterior only (PO), anterior only (AO), and combined posterior and anterior (AP) surgical approaches. Summary of Background Data. Surgeons use multiple methods to treat spinal tuberculosis, including an anterior, posterior, and combined anterior and posterior approach. However, there are a few reports comparing the mid- and long-term outcomes of these surgical methods. Methods. The medical records for 184 patients treated for thoracic tuberculosis between January 2003 and November 2010 were retrospectively reviewed. Among them, 62 patients were treated with a single-stage posterior debridement and interbody fusion with instrumentation (Group A), 65 patients with posterior instrumentation, anterior debridement, and bone graft in a single or two-stage procedure (Group B), and 57 patients with anterior debridement and strut grafting with instrumentation (Group C). Operative time, blood loss, Visual Analog Scale for pain, complications, recovery of neurological function, Cobb angle, correction rate, and loss angle were compared among all groups. Results. Groups A, B, and C were followed for 72.7 ± 3.8 months, 74.3 ± 4.2 months, and 73.6 ± 4.5 months, respectively. The operative time, blood loss, and rate of complications for Group A were significantly less than Groups B and C (P < 0.05). The correction rate and loss angle were superior in Groups A and B compared with C, whereas the Visual Analog Scale for pain and fusion time showed no statistically significant difference among the groups (P > 0.05). Conclusion. For patients with thoracic tuberculosis, use of the AO approach should be limited. Although the AP approach produced satisfactory outcomes, it remains more traumatic. Therefore, the PO approach is recommended, not only because it achieves good results, but because it has reduced complications, operative time, and blood loss. Level of Evidence: 3
Modular programming of recurrences: a comparison of two approaches

We present two methods for expressing computations based on recurrence relations and discuss their relative merits. One method, the structural blanks approach, is built on top of traditional programming languages like Fortran or Pascal. It aims at program reuse and bases a certain architecture of software packages. The other method, the constructive recursive approach, is based on recursive relations over graphs.