Straw and chaff spreaders

AE-90

Observation weights unlock bulk RNA-seq tools for zero inflation and single-cell applications

Dropout events in single-cell RNA sequencing (scRNA-seq) cause many transcripts to go undetected and induce an excess of zero read counts, leading to power issues in differential expression (DE) analysis. This has triggered the development of bespoke scRNA-seq DE methods to cope with zero inflation. Recent evaluations, however, have shown that dedicated scRNA-seq tools provide no advantage compared to traditional bulk RNA-seq tools. We introduce a weighting strategy, based on a zero-inflated negative binomial model, that identifies excess zero counts and generates gene-and cell-specific weights to unlock bulk RNA-seq DE pipelines for zero-inflated data, boosting performance for scRNA-seq

Age class composition and growth of Atlantic cod (Gadus morhua) in the shallow water zone of Kongsfjorden, Svalbard

Although Atlantic cod has been observed in Svalbard waters since the 1880s, knowledge about the presence in the Arctic shallow water zone is limited. The regular catch of juvenile Atlantic cod in Kongsfjorden since 2008 is in line with an overall northward shift of boreal fish species toward the Arctic. This is the first study showing the age class composition, growth rates, and stomach content of Atlantic cod in the shallow water zone of Kongsfjorden, Svalbard. From 2012 to 2014 a total of 721 specimens were sampled in 3 to 12 m water depth. The primary age classes were identified as 0+, 1+, and 2+ using otolith age analysis. The different cohorts of these specimens show stable growth rates during the polar day and night. By stomach content analysis, we show that these specimens primarily feed on benthic food sources. These observations support the assumption that the shallow water zone of Kongsfjorden is likely to be a nursery ground for Atlantic cod.publishedVersio

Age class composition and growth of Atlantic cod (Gadus morhua) in the shallow water zone of Kongsfjorden, Svalbard

Although Atlantic cod has been observed in Svalbard waters since the 1880s, knowledge about the presence in the Arctic shallow water zone is limited. The regular catch of juvenile Atlantic cod in Kongs orden since 2008 is in line with an overall northward shift of boreal fish species toward the Arctic. This is the first study showing the age class composition, growth rates, and stomach content of Atlantic cod in the shallow water zone of Kongs orden, Svalbard. From 2012 to 2014 a total of 721 specimens were sampled in 3 to 12 m water depth. The primary age classes were identified as 0+, 1+, and 2+using otolith age analysis. The diferent cohorts of these specimens show stable growth rates during the polar day and night. By stomach content analysis, we show that these specimens primarily feed on benthic food sources. These observations support the assumption that the shallow water zone of Kongs orden is likely to be a nursery ground for Atlantic cod

The impact of performing gastric cancer surgery during holiday periods. A population-based study using Dutch upper gastrointestinal cancer audit (DUCA) data

Existing literature suggests inferior quality of oncologic surgery during holiday periods. This study aimed to investigate the impact of holiday periods on surgical treatment of gastric cancer in the Netherlands. This nationwide study included all gastric cancer patients undergoing potentially curative surgery registered in the Dutch Upper Gastrointestinal Cancer Audit (DUCA). For each patient it was established whether they underwent surgery during or outside the 11 Dutch holiday weeks, based on date and region of surgery. Separate, single-day holidays were not included. Baseline and treatment characteristics were compared using descriptive statistics. Time from diagnosis to treatment and short-term surgical outcomes were compared using multilevel multivariable logistic regression analyses. To prevent bias from recent advancements, analyses were repeated in a recent cohort of patients (2015-2018). Between 2011-2018, 3440 patients were included in the DUCA. Some 555 (16.1%) patients underwent surgery during 11 holiday weeks. There were no differences in patient, tumor and treatment characteristics and time to treatment between holidays and non-holidays. Tumor-positive resection margins (R1/R2 vs R0) occurred more frequent during holidays (aOR:1.47, 95%CI:1.07-2.04). Subgroup analyses in a recent cohort of patients also found higher tumor-positive resection margins (aOR:1.59, 95%CI:1.01-2.43) and higher failure-to-rescue rates (aOR:2.55, 95%CI:1.18-5.49) during holidays. Even though time to treatment and patient, tumor and treatment characteristics were comparable between holidays and non-holidays, tumor-positive resection margin and failure to-rescue rates were higher during holidays. This suggests that steps must be taken to keep specialized and dedicated gastric cancer expertise up to standard during holiday periods. (C)& nbsp;2022 The Author(s). Published by Elsevier Inc.& nbsp;& nbsp

Impacts of artificial light at night in marine ecosystems—A review

The globally widespread adoption of Artificial Light at Night (ALAN) began in the mid-20th century. Yet, it is only in the last decade that a renewed research focus has emerged into its impacts on ecological and biological processes in the marine environment that are guided by natural intensities, moon phase, natural light and dark cycles and daily light spectra alterations. The field has diversified rapidly from one restricted to impacts on a handful of vertebrates, to one in which impacts have been quantified across a broad array of marine and coastal habitats and species. Here, we review the current understanding of ALAN impacts in diverse marine ecosystems. The review presents the current state of knowledge across key marine and coastal ecosystems (sandy and rocky shores, coral reefs and pelagic) and taxa (birds and sea turtles), introducing how ALAN can mask seabird and sea turtle navigation, cause changes in animals predation patterns and failure of coral spawning synchronization, as well as inhibition of zooplankton Diel Vertical Migration. Mitigation measures are recommended, however, while strategies for mitigation were easily identified, barriers to implementation are poorly understood. Finally, we point out knowledge gaps that if addressed would aid in the prediction and mitigation of ALAN impacts in the marine realm

Postoperative intensive care unit stay after minimally invasive esophagectomy shows large hospital variation:Results from the Dutch Upper Gastrointestinal Cancer Audit

Item does not contain fulltextINTRODUCTION: The value of routine intensive care unit (ICU) admission after minimally invasive esophagectomy (MIE) has been questioned. This study aimed to investigate Dutch hospital variation regarding length of direct postoperative ICU stay, and the impact of this hospital variation on short-term surgical outcomes. MATERIALS AND METHODS: Patients registered in the Dutch Upper Gastrointestinal Cancer Audit (DUCA) undergoing curative MIE were included. Length of direct postoperative ICU stay was dichotomized around the national median into short ICU stay ( ≤ 1 day) and long ICU stay ( > 1 day). A case-mix corrected funnel plot based on multivariable logistic regression analyses investigated hospital variation. The impact of this hospital variation on short-term surgical outcomes was investigated using multilevel multivariable logistic regression analyses. RESULTS: Between 2017 and 2019, 2110 patients from 16 hospitals were included. Median length of postoperative ICU stay was 1 day [hospital variation: 0-4]. The percentage of short ICU stay ranged from 0 to 91% among hospitals. Corrected for case-mix, 7 hospitals had statistically significantly higher short ICU stay rates and 6 hospitals had lower rates. ICU readmission, in-hospital/30-day mortality, failure to rescue, postoperative pneumonia, cardiac complications and anastomotic leakage were not associated with hospital variation in length of ICU stay. Total length of hospital stay was significantly shorter in hospitals with relatively short ICU stay. CONCLUSION: This study showed significant hospital variation in postoperative length of ICU stay after MIE. Short ICU stay was associated with shorter overall hospital admission and did not negatively impact short-term surgical outcomes. More selected use of ICU resources could result in a national significant cost reduction

Anti-proliferative action of vitamin D in MCF7 is still active after siRNA-VDR knock-down

Background: The active form of Vitamin D, 1,25-dihydroxyvitamin D3(1,25D), has strong anti-proliferative effects, yet the molecular mechanisms underneath this effect remain unclear. In contrast, the molecular mechanism of 1,25D for the regulation of calcium homeostasis has principally been resolved, demonstrating a pivotal role for the vitamin D receptor (VDR). Results: We first addressed the question whether the anti-proliferative effects of 1,25D are influenced by VDR. Knockdown of VDR by siRNA did not affect the anti-proliferative effects of 1,25D in MCF7 breast cancer cells. This unanticipated finding led us to take an alternative approach using genome wide screens to study the molecular mechanisms of 1,25D in proliferation. For that purpose, four independently developed and stable 1,25D resistant MCF7 cell lines were analyzed. Array CGH identified a copy number alteration in a region of 13.5 Mb at chromosome 11q13.4-14.1 common to all four 1,25D resistant cell lines. Expression arrays revealed that no single gene was differentially expressed between the sensitive and resistant cells, but multiple membrane receptor signaling pathways were altered in the 1,25D resistant cell lines. Importantly, in the genome wide experiments neither VDR, CYP24A1 nor other known vitamin D signaling pathway genes were associated with 1,25D resistance. Conclusion: In conclusion, siRNA and genome wide studies both suggest that the anti-proliferative effects of 1,25D in MCF7 breast tumor cell lines do not rely on classical Vitamin D pathway per se

On embeddings of CAT(0) cube complexes into products of trees

We prove that the contact graph of a 2-dimensional CAT(0) cube complex ${\bf X}$ of maximum degree $\Delta$ can be coloured with at most $\epsilon(\Delta)=M\Delta^{26}$ colours, for a fixed constant $M$. This implies that ${\bf X}$ (and the associated median graph) isometrically embeds in the Cartesian product of at most $\epsilon(\Delta)$ trees, and that the event structure whose domain is ${\bf X}$ admits a nice labeling with $\epsilon(\Delta)$ labels. On the other hand, we present an example of a 5-dimensional CAT(0) cube complex with uniformly bounded degrees of 0-cubes which cannot be embedded into a Cartesian product of a finite number of trees. This answers in the negative a question raised independently by F. Haglund, G. Niblo, M. Sageev, and the first author of this paper.Comment: Some small corrections; main change is a correction of the computation of the bounds in Theorem 1. Some figures repaire