Inference of breed structure in farm animals: Empirical comparison between snp and microsatellite performance

Knowledge of population structure is essential to improve the management and conservation of farm animal genetic resources. Microsatellites, which have long been popular for this type of analysis, are more and more neglected in favor of whole-genome single nucleotide polymorphism (SNP) chips that are now available for the main farmed animal species. In this study, we compared genetic patterns derived from microsatellites to that inferred by SNPs, considering three pairs of datasets of sheep and cattle. Population genetic differentiation analyses (Fixation index, FST ), as well as STRUCTURE analyses showed a very strong consistency between the two types of markers. Microsatellites gave pictures that were largely concordant with SNPs, although less accurate. The best concordance was found in the most complex dataset, which included 17 French sheep breeds (with a Pearson correlation coefficient of 0.95 considering the 136 values of pairwise FST, obtained with both types of markers). The use of microsatellites reduces the cost and the related analyses do not require specific computer equipment (i.e., information technology (IT) infrastructure able to provide adequate computing and storage capacity). Therefore, this tool may still be a very appropriate solution to evaluate, in a first stage, the general state of livestock at national scales. At a time when local breeds are disappearing at an alarming rate, it is urgent to improve our knowledge of them, in particular by promoting tools accessible to the greatest number

A combination of methods needed to assess the actual use of provisioning ecosystem services

Failure to recognize that potential provisioning ecosystem services are not necessarily collected and used by people may have important consequences for management of land and resources. Accounting for people's actual use of ecosystem services in decision making processes requires a robust methodological approach that goes beyond mapping the presence of ecosystem services. But no such universally accepted method exists, and there are several shortcomings of existing methods such as the application of land use/cover as a proxy for provisioning ecosystem service availability and surveys based on respondents' recall to assess people's collection of e.g. wild food. By combining four complementary methods and applying these to the shifting cultivation systems of Laos, we show how people’s actual use of ecosystem services from agricultural fields differs from ecosystem service availability. Our study is the first in Southeast Asia to combine plot monitoring, collection diaries, repeat interviews, and participant observation. By applying these multiple methods borrowed from anthropology and botany among other research domains, the study illustrates that no single method is sufficient on its own. It is of key importance for scientists to adopt methods that can account for both availability of various services and actual use of those services

The liquid-vapor interface of an ionic fluid

We investigate the liquid-vapor interface of the restricted primitive model (RPM) for an ionic fluid using a density-functional approximation based on correlation functions of the homogeneous fluid as obtained from the mean-spherical approximation (MSA). In the limit of a homogeneous fluid our approach yields the well-known MSA (energy) equation of state. The ionic interfacial density profiles, which for the RPM are identical for both species, have a shape similar to those of simple atomic fluids in that the decay towards the bulk values is more rapid on the vapor side than on the liquid side. This is the opposite asymmetry of the decay to that found in earlier calculations for the RPM based on a square-gradient theory. The width of the interface is, for a wide range of temperatures, approximately four times the second moment correlation length of the liquid phase. We discuss the magnitude and temperature dependence of the surface tension, and argue that for temperatures near the triple point the ratio of the dimensionless surface tension and critical temperature is much smaller for the RPM than for simple atomic fluids.Comment: 6 postscript figures, submitted to Phys. Rev.

Robotic Versus Open Hepatic Arterial Infusion Pump Placement for Unresectable Intrahepatic Cholangiocarcinoma

Background: Hepatic arterial infusion pump (HAIP) chemotherapy is an effective treatment for patients with unresectable intrahepatic cholangiocarcinoma (iCCA). HAIP chemotherapy requires a catheter inserted in the gastroduodenal artery and a subcutaneous pump. The catheter can be placed using an open or robotic approach. Objective: This study aimed to compare perioperative outcomes of robotic versus open HAIP placement in patients with unresectable iCCA. Methods: We analyzed patients with unresectable iCCA included in the PUMP-II trial from January 2020 to September 2022 undergoing robotic or open HAIP placement at Amsterdam UMC, Erasmus MC, and UMC Utrecht. The primary outcome was time to functional recovery (TTFR). Results: In total, 22 robotic and 28 open HAIP placements were performed. The median TTFR was 2 days after robotic placement versus 5 days after open HAIP placement (p &lt; 0.001). One patient (4.5%) in the robotic group underwent a conversion to open because of a large bulky tumor leaning on the hilum immobilizing the liver. Postoperative complications were similar—36% (8/22) after robotic placement versus 39% (11/28) after open placement (p = 1.000). The median length of hospital stay was shorter in the robotic group—3 versus 5 days (p &lt; 0.001). All 22 robotic patients initiated HAIP chemotherapy post-surgery, i.e. 93% (26/28) in the open group (p = 0.497). The median time to start HAIP chemotherapy was 14 versus 18 days (p = 0.153). Conclusion: Robotic HAIP placement in patients with unresectable iCCA is a safe and effective procedure and is associated with a significantly shorter TTFR and hospital stay than open HAIP placement.</p

Robotic Versus Open Hepatic Arterial Infusion Pump Placement for Unresectable Intrahepatic Cholangiocarcinoma

Background: Hepatic arterial infusion pump (HAIP) chemotherapy is an effective treatment for patients with unresectable intrahepatic cholangiocarcinoma (iCCA). HAIP chemotherapy requires a catheter inserted in the gastroduodenal artery and a subcutaneous pump. The catheter can be placed using an open or robotic approach. Objective: This study aimed to compare perioperative outcomes of robotic versus open HAIP placement in patients with unresectable iCCA. Methods: We analyzed patients with unresectable iCCA included in the PUMP-II trial from January 2020 to September 2022 undergoing robotic or open HAIP placement at Amsterdam UMC, Erasmus MC, and UMC Utrecht. The primary outcome was time to functional recovery (TTFR). Results: In total, 22 robotic and 28 open HAIP placements were performed. The median TTFR was 2 days after robotic placement versus 5 days after open HAIP placement (p &lt; 0.001). One patient (4.5%) in the robotic group underwent a conversion to open because of a large bulky tumor leaning on the hilum immobilizing the liver. Postoperative complications were similar—36% (8/22) after robotic placement versus 39% (11/28) after open placement (p = 1.000). The median length of hospital stay was shorter in the robotic group—3 versus 5 days (p &lt; 0.001). All 22 robotic patients initiated HAIP chemotherapy post-surgery, i.e. 93% (26/28) in the open group (p = 0.497). The median time to start HAIP chemotherapy was 14 versus 18 days (p = 0.153). Conclusion: Robotic HAIP placement in patients with unresectable iCCA is a safe and effective procedure and is associated with a significantly shorter TTFR and hospital stay than open HAIP placement.</p

Ab-initio prediction of the electronic and optical excitations in polythiophene: isolated chains versus bulk polymer

We calculate the electronic and optical excitations of polythiophene using the GW approximation for the electronic self-energy, and include excitonic effects by solving the electron-hole Bethe-Salpeter equation. Two different situations are studied: excitations on isolated chains and excitations on chains in crystalline polythiophene. The dielectric tensor for the crystalline situation is obtained by modeling the polymer chains as polarizable line objects, with a long-wavelength polarizability tensor obtained from the ab-initio polarizability function of the isolated chain. With this model dielectric tensor we construct a screened interaction for the crystalline case, including both intra- and interchain screening. In the crystalline situation both the quasi-particle band gap and the exciton binding energies are drastically reduced in comparison with the isolated chain. However, the optical gap is hardly affected. We expect this result to be relevant for conjugated polymers in general.Comment: 15 pages including 4 figures; to appear in Phys. Rev. B, 6/15/200

Upper and lower airway cultures in children with cystic fibrosis: Do not neglect the upper airways

AbstractBackgroundAirways of cystic fibrosis (CF) patients are colonised with bacteria early in life. We aimed to analyse differences between results of simultaneously taken upper airway (UAW) and lower airway (LAW) cultures, to describe clinical characteristics of patients with positive versus negative cultures and to follow up the patients with P. aeruginosa positive UAW cultures.MethodsBacteriological and clinical data from 157 children were collected during annual check up. The number of positive UAW and LAW cultures and correspondence between these results and clinical characteristics were analysed.ResultsPositive LAW and UAW cultures were found in 79.6% and 43.9% of patients respectively (p<0.001). Patients with positive LAW cultures were significantly older (11.9 vs. 9.8years, p<0.05) and had more LAW symptoms (73.6% vs. 46.7%, p<0.05), especially when P. aeruginosa was found. Patients with positive UAW cultures (especially S. aureus) had more nasal discharge (50.7% vs. 25.0%, p<0.001). In 65% of patients with positive UAW and negative LAW culture for P. aeruginosa the next LAW became P. aeruginosa positive.ConclusionUAW cultures and LAW cultures differ in children with CF and there are differences in clinical characteristics between patients with positive versus negative culture results. P. aeruginosa positive UAW cultures appeared to precede positive LAW cultures in a substantial part of patients, suggesting some kind of cross-infection between the UAW and LAW

The Fungal Cell Wall : Structure, Biosynthesis, and Function

N.G. is funded by the Wellcome Trust via a senior investigator award and a strategic award and by the MRC Centre for Medical Mycology. C.M. acknowledges the support of the Wellcome Trust and the MRC. N.G. and C.M. are part of the MRC Centre for Medical Mycology. J.P.L. acknowledges support from ANR, Aviesan, and FRM.Peer reviewedPublisher PD