bluuebunny/crossref_metadata_2025_split huggingface dataset:
P13: CHARACTERISATION OF THE TUMOUR MICROENVIRONMENT IN MESENCHYMAL GASTRIC TUMOURS USING SINGLE-CELL RNA SEQUENCING
Authors: Harrington J , Lloyd M , Mabrouk N , Walker R , Grace B , Underwood T 
Published: April 2021

Abstract

Introduction
Gastric mesenchymal tumours are a rare group of neoplasms, which include gastrointestinal stromal tumours (GISTs) and leiomyomas. To date, there is limited information on the tumour microenvironment (TME) in these neoplasms, despite the TME widely known to influence the hallmarks of cancer. In this study we used single cell RNA sequencing (scRNAseq) to profile individual cells of the TME in GIST and leiomyoma.

Method
The two gastric mesenchymal tumours and two normal gastric samples were analysed using DropSeq, where single cell transcriptomes are captured onto barcoded beads using a microfluidic device before next generation sequencing. For comparison, we performed bulk RNA-sequencing and CIBERSORT to estimate the abundance of 22 immune cell populations. Furthermore, we used immunohistochemistry to elucidate the presence and location of several immune cells.

Result
Both neoplasms had diverse immune and stromal cell populations with a greater proportion of macrophages but less B cells than normal gastric tissue. ScRNAseq was able to identify subpopulations of B cells and T cells not detected with CIBERSORT. Interstitial cells of cajal, believed to be the pre-cursor to GISTs, were observed through scRNAseq and confirmed through immunohistochemistry.

Conclusion
To our knowledge, this is the first study to utilise scRNAseq on GISTs and leiomyomas, which enabled characterisation of the TME at a cellular level. Using this platform in future studies will enable better characterisation of the TME and may inform the discovery of therapeutic targets.

Take-home message
Single cell RNA sequencing enables the ability to explore the tumour microenvironment of mesenchymal tumours at an enhanced resolution, paving the way for potential future therapeutic targets.
P20: DOES PRE-OP MRI FOLLOWING NEOADJUVANT LONG COURSE CHEMO-RADIOTHERAPY IN RECTAL CANCER AFFECT R0 RESECTION RATE?
Authors: Borucki JP , Jones KL , Stearns AT 
Published: April 2021

Abstract

Introduction
Neoadjuvant long course chemo-radiotherapy (LCCR) is the standard of care for locally advanced rectal cancer. In June 2013 this institution implemented preoperative MRI post LCCR in an attempt to improve the R0 resection rate. The aims of this projects were to audit the compliance with the new policy and to assess whether it had an impact on the R0 resection rate.

Method
All patients who underwent resection after LCCR between June 2013 and February 2017 had their clinical notes audited to assess compliance with the standard ‘all patients who have undergone LCCR should receive MRI imaging of the rectum unless clinically contraindicated’. To assess effectiveness of the intervention the R0 resection rate of patients who had received the preoperative MRI was compared to those who had not between the period January 2008 and February 2017. The data was entered and stored onto a larger departmental database so that it could be used in future for other projects.

Result
33 out of 88 (37.5%) of eligible patients received post LCCR MRI rectum prior to resection although a further two patients had a preoperative CT scan. The R0 resection rate in patients who had pre-operative MRI was 88% compared to 89% in those who did not (p=1).

Conclusion
The rate of patients who received pre-operative MRI following LCCR was 37.5%. Whilst this shows significant room for improvement, data collected regarding effectiveness of the intervention shows that it makes no difference to R0 resection rate.

Take-home message
Pre-op MRI following LCCR does not improve R0 resection rate in locally advanced rectal cancer.
P23: ENHANCED RECOVERY PROGRAMME – DOES PREOPERATIVE EDUCATION REDUCE LENGTH OF HOSPITAL STAY (LOS) IN PRIMARY HIP & KNEE ARTHROPLASTY
Authors: Ahmad M , Rahman H , Awan N 
Published: April 2021

Abstract

Introduction
Total knee and hip arthroplasty significantly improve quality of life in people suffering from end-stage hip & knee arthritides. Enhanced recovery programs have shown improved outcomes following elective arthroplasty by decreasing patients anxiety, postoperative pain and reducing the length of hospital stay (LOS). The aim of our study is to evaluate the impact of preoperative education programs on length of hospital stay in patients undergoing hip & knee arthroplasty.

Method
Retrospective data was collected from a consecutive series of 520 patients' charts and Irish National Orthopedic Register (INOR) who underwent Hip or Knee arthroplasty from January 1, 2018, to December 31, 2018, in Our Lady Hospital, Navan. The length of stay study compared two hundred and twenty-six patients in the Educational Group (EG) who attended the Hip & Knee School (Preoperative Education Class) with 294 patients in the Conventional Group (CG) who did not attend the hip and knee educational programme.

Result
We identified that Length of Hospital Stay decreased to 5.2 days in Educational Group from 5.5 days in Conventional Group (P-value equals to 0.26, statistically insignificant, t = 1.1093 df = 518), with a mean difference of only 0.3 days (95% confidence interval).

Conclusion
Preoperative education does not reduce the length of hospital stay in primary hip & knee arthroplasty.

Take-home message
Preoperative education has no role in reducing hospital stay in Arthroplasty patients.
P28: LAPAROSCOPIC VERSUS ULTRASOUND-GUIDED TRANSVERSUS ABDOMINIS PLANE BLOCK IN LAPAROSCOPIC COLORECTAL SURGERY - A SYSTEMATIC REVIEW AND META-ANALYSIS
Authors: Copperthwaite A , Sahebally S , Devane L , McCawley N , Burke J , McNamara D 
Published: April 2021

Abstract

Introduction
A multimodal approach to peri-operative analgesia represents a cornerstone of enhanced recovery programmes in minimally invasive colorectal surgery. Transversus abdominis plane (TAP) block is an emerging anaesthetic technique that may reduce postoperative opiod analgesic requirements. It can be performed laparoscopically or percutaneously. We performed a systematic review and meta-analysis to compare the effectiveness of laparoscopic versus ultrasound-guided TAP block in laparoscopic colorectal surgery.

Method
PubMed, EMBASE and Cochrane databases were searched for relevant articles from inception until November 2019. All studies that compared laparoscopic (LTB) versus ultrasound-guided (UTB) TAP blocks in laparoscopic colorectal resections were included. The primary outcome measure was narcotic consumption at 24 hours postoperatively, while secondary outcomes included pain scores, operative time, postoperative nausea and vomitting (PONV) and complication rates. Random effects models were used to calculate pooled effect size estimates.

Result
Three randomised controlled trials and one retrospective study were included capturing 309 patients. On random effects analysis, there were no significant differences in narcotic consumption between LTB and UTB (Mean difference -8.12 mg, 95% CI=-22.13 to 5.89, p=0.26). LTB was associated with significantly lower pain scores (Mean difference -0.49, 95% CI=-0.96 to -0.02, p=0.04). There were no differences in operative time (Mean difference -6.67 mins, 95% CI=-29.4 to 16.06, p=0.57), PONV (OR=0.97, 95% CI=0.36 to 2.65, p=0.96) or complication (OR=1.30, 95% CI=0.64 to 2.64, p=0.47) rates.

Conclusion
LTB is associated with significantly less pain at 24 hours postoperatively but similar narcotic usage, PONV, operative time and complication rates, compared to UTB.

Take-home message
Laparoscopic transversus abdominis plane block is shown to leave patients with less pain at 24 hours post-op compared to ultrasound guided methods in colorectal patients.
Achievement Rank Affects Performance and Major Choices in College
Authors: Elsner Benjamin , Isphording Ingo E , Zölitz Ulf 
Published: April 2021

AbstractIn this paper we study how a student's ordinal rank in a peer group affects performance and specialisation choices in university. By exploiting data with repeated random assignment of students to teaching sections, we find that a higher rank increases performance and the probability of choosing related follow-up courses and majors. We document two types of dynamic effect. First, earlier ranks are less important than later ranks. Second, responses to rank changes are asymmetric: improvements in rank raise performance, while decreases in rank have no effect. Rank effects partially operate through students’ expectations about future grades.
Probable Mechanisms Underlying Interallelic Complementation and Temperature-Sensitivity of Mutations at the shibire Locus of Drosophila melanogaster
Authors: Grant Deanna , Unadkat Shilpa , Katzen Alisa , Krishnan K S , Ramaswami Mani 
Published: April 2021

Abstract
The shibire locus of Drosophila melanogaster encodes dynamin, a GTPase required for the fission of endocytic vesicles from plasma membrane. Biochemical studies indicate that mammalian dynamin is part of a complex containing multiple dynamin subunits and other polypeptides. To gain insight into sequences of dynamin critical for its function, we have characterized in detail a collection of conditional and lethal shi alleles. We describe a probable null allele of shi and show that its properties are distinct from those of two classes of lethal alleles (termed I and II) that show intergroup, interallelic complementation. Sequenced class I alleles, which display dominant properties, carry missense mutations in conserved residues in the GTPase domain of dynamin. In contrast, the sequenced class II alleles, which appear completely recessive, carry missense mutations in conserved residues of a previously uncharacterized “middle domain” that lies adjacent to the GTPase region. These data suggest that critical interactions mediated by this middle domain are severely affected by the class II lethal mutations; thus, the mutant sequences should be very useful for confirming the in vivo relevance of interactions observed in vitro. Viable heteroallelic combinations of shi lethals show rapid and reversible temperature-sensitive paralytic phenotypes hitherto only described for the ts alleles of shi. When taken together with the molecular analysis of shi mutations, these observations suggest that the GTPase domain of dynamin carries an intrinsically temperature-sensitive activity: hypomorphic mutations that reduce this activity at low temperatures result in conditional temperature-sensitive phenotype. These observations explain why screens for conditional paralytic mutants in Drosophila inevitably recover ts alleles of shi at high frequencies.
Topoisomerase I Is Essential in Cryptococcus neoformans: Role in Pathobiology and as an Antifungal Target
Authors: Del Poeta Maurizio , Toffaletti Dena L , Rude Thomas H , Dykstra Christine C , Heitman Joseph , Perfect John R 
Published: April 2021

Abstract
Topisomerase I is the target of several toxins and chemotherapy agents, and the enzyme is essential for viability in some organisms, including mice and drosophila. We have cloned the TOP1 gene encoding topoisomerase I from the opportunistic fungal pathogen Cryptococcus neoformans. The C. neoformans topoisomerase I contains a fungal insert also found in topoisomerase I from Candida albicans and Saccharomyces cerevisiae that is not present in the mammalian enzyme. We were unable to disrupt the topoisomerase I gene in this haploid organism by homologous recombination in over 8000 transformants analyzed. When a second functional copy of the TOP1 gene was introduced into the genome, the topoisomerase I gene could be readily disrupted by homologous recombination (at 7% efficiency). Thus, topoisomerase I is essential in C. neoformans. This new molecular strategy with C. neoformans may also be useful in identifying essential genes in other pathogenic fungi. To address the physiological and pathobiological functions of the enzyme, the TOP1 gene was fused to the GAL7 gene promoter. The resulting GAL7::TOP1 fusion gene was modestly regulated by carbon source in a serotype A strain of C. neoformans. Modest overexpression of topoisomerase I conferred sensitivity to heat shock, γ-rays, and camptothecin. In contrast, alterations in topoisomerase I levels had no effect on the toxicity of a novel class of antifungal agents, the dicationic aromatic compounds (DACs), indicating that topoisomerase I is not the target of DACs. In an animal model of cryptococcal meningitis, topoisomerase I regulation was not critically important to established infection, but may impact on the initial stress response to infection. In summary, our studies reveal that topoisomerase I is essential in the human pathogen C. neoformans and represents a novel target for antifungal agents.
The Aspergillus nidulans uvsB Gene Encodes an ATM-Related Kinase Required for Multiple Facets of the DNA Damage Response
Authors: Hofmann Amy F , Harris Steven D 
Published: April 2021

Abstract
In Aspergillus nidulans, uvsB and uvsD belong to the same epistasis group of DNA repair mutants. Recent observations suggest that these genes are likely to control cell cycle checkpoint responses to DNA damage and incomplete replication. Consistent with this notion, we show here that UVSB is a member of the conserved family of ATM-related kinases. Phenotypic characterization of uvsB mutants shows that they possess defects in additional aspects of the DNA damage response besides checkpoint control, including inhibition of septum formation, regulation of gene expression, and induced mutagenesis. The musN227 mutation partially suppresses the poor growth and DNA damage sensitivity of uvsB mutants. Although musN227 partially suppresses several uvsB defects, it does not restore checkpoint function to uvsB mutants. Notably, the failure of uvsB mutants to restrain septum formation in the presence of DNA damage is suppressed by the musN227 mutation. We propose that UVSB functions as the central regulator of the A. nidulans DNA damage response, whereas MUSN promotes recovery by modulating a subset of the response.
Identification of a Mutant Locus by Noncomplementation of a Transposon Insertion Library in Saccharomyces cerevisiae
Authors: Wiatrowski Heather A , Carlson Marian 
Published: April 2021

Abstract
We describe a new approach for identifying the gene corresponding to a mutation in Saccharomyces cerevisiae. A library of mTn-lacZ/LEU2 insertions is tested for failure to complement the mutation, and the noncomplementing insertion is used to obtain sequence. This approach offers an alternative to cloning by complementation with a plasmid library.
Genetic Analysis of a Synaptic Calcium Channel in Drosophila: Intragenic Modifiers of a Temperature-Sensitive Paralytic Mutant of cacophony
Authors: Brooks I M , Felling R , Kawasaki F , Ordway R W 
Published: April 2021

Abstract
Our previous genetic analysis of synaptic mechanisms in Drosophila identified a temperature-sensitive paralytic mutant of the voltage-gated calcium channel α1 subunit gene, cacophony (cac). Electrophysiological studies in this mutant, designated cacTS2, indicated cac encodes a primary calcium channel α1 subunit functioning in neurotransmitter release. To further examine the functions and interactions of cac-encoded calcium channels, a genetic screen was performed to isolate new mutations that modify the cacTS2 paralytic phenotype. The screen recovered 10 mutations that enhance or suppress cacTS2, including second-site mutations in cac (intragenic modifiers) as well as mutations mapping to other genes (extragenic modifiers). Here we report molecular characterization of three intragenic modifiers and examine the consequences of these mutations for temperature-sensitive behavior, synaptic function, and processing of cac pre-mRNAs. These mutations may further define the structural basis of calcium channel α1 subunit function in neurotransmitter release.
Evolution of MHC Class II Eβ Diversity Within the Genus Peromyscus
Authors: Richman Adam D , Herrera L Gerardo , Nash Deanna 
Published: April 2021

Abstract
Progress in understanding the evolution of variation at the MHC has been slowed by an inability to assess the relative roles of mutation vs. intragenic recombination in contributing to observed polymorphism. Recent theoretical advances now permit a quantitative treatment of the problem, with the result that the amount of recombination is at least an order of magnitude greater than that of mutation in the history of class II genes. We suggest that this insight allows progress in evaluating the importance of other factors affecting the evolution of the MHC. We investigated the evolution of MHC class II Eβ sequence diversity in the genus Peromyscus. We find evidence for extensive recombination in the history of these sequences. Nevertheless, it appears that intragenic recombination alone is insufficient to account for evolution of MHC diversity in Peromyscus. Significant differences in silent variation among subgenera arose over a relatively short period of time, with little subsequent change. We argue that these observations are consistent with the effects of historical population bottleneck(s). Population restrictions may explain general features of MHC evolution, including the large amount of recombination in the history of MHC genes, because intragenic recombination may efficiently regenerate allelic polymorphism following a population constriction.
Gene Silencing Triggered by Non-LTR Retrotransposons in the Female Germline of Drosophila melanogaster
Authors: Robin Stéphanie , Chambeyron Séverine , Bucheton Alain , Busseau Isabelle 
Published: April 2021

Abstract
Several studies have recently shown that the activity of some eukaryotic transposable elements is sensitive to the presence of homologous transgenes, suggesting the involvement of homology-dependent genesilencing mechanisms in their regulation. Here we provide data indicating that two non-LTR retrotransposons of Drosophila melanogaster are themselves natural triggers of homology-dependent gene silencing. We show that, in the female germline of D. melanogaster, fragments from the R1 or from the I retrotransposons can mediate silencing of chimeric transcription units into which they are inserted. This silencing is probably mediated by sequence identity with endogenous copies of the retrotransposons because it does not occur with a fragment from the divergent R1 elements of Bombyx mori, and, when a fragment of I is used, it occurs only in females containing functional copies of the I element. This silencing is not accompanied by cosuppression of the endogenous gene homologous to the chimeric transcription unit, which contrasts to some other silencing mechanisms in Drosophila. These observations suggest that in the female germline of D. melanogaster the R1 and I retrotransposons may self-regulate their own activity and their copy number by triggering homology-dependent gene silencing.
The Drosophila roX1 RNA Gene Can Overcome Silent Chromatin by Recruiting the Male-Specific Lethal Dosage Compensation Complex
Authors: Kelley Richard L , Kuroda Mitzi I 
Published: April 2021

Abstract
The Drosophila MSL complex consists of at least six proteins and two noncoding roX RNAs that mediate dosage compensation. It acts to remodel the male's X chromatin by covalently modifying the amino terminal tails of histones. The roX1 and roX2 genes are thought to be nucleation sites for assembly and spreading of MSL complexes into surrounding chromatin where they roughly double the rates of transcription. We generated many transgenic stocks in which the roX1 gene was moved from its normal location on the X to new autosomal sites. Approximately 10% of such lines displayed unusual sexually dimorphic expression patterns of the transgene's mini-white eye-color marker. Males often displayed striking mosaic pigmentation patterns similar to those seen in position-effect variegation and yet most inserts were in euchromatic locations. In many of these stocks, female mini-white expression was very low or absent. The male-specific activation of mini-white depended upon the MSL complex. We propose that these transgenes are inserted in several different types of repressive chromatin environments that inhibit mini-white expression. Males are able to overcome this silencing through the action of the MSL complex spreading from the roX1 gene and remodeling the local chromatin to allow transcription. The potency with which an ectopic MSL complex overcomes silent chromatin suggests that its normal action on the X must be under strict regulation.
Phenotypic Analysis of Separation-of-Function Alleles of MEI-41, Drosophila ATM/ATR
Authors: Laurençon Anne , Purdy Amanda , Sekelsky Jeff , Hawley R Scott , Su Tin Tin 
Published: April 2021

Abstract
ATM/ATR kinases act as signal transducers in eukaryotic DNA damage and replication checkpoints. Mutations in ATM/ATR homologs have pleiotropic effects that range from sterility to increased killing by genotoxins in humans, mice, and Drosophila. Here we report the generation of a null allele of mei-41, Drosophila ATM/ATR homolog, and the use of it to document a semidominant effect on a larval mitotic checkpoint and methyl methanesulfonate (MMS) sensitivity. We also tested the role of mei-41 in a recently characterized checkpoint that delays metaphase/anaphase transition after DNA damage in cellular embryos. We then compare five existing mei-41 alleles to the null with respect to known phenotypes (female sterility, cell cycle checkpoints, and MMS resistance). We find that not all phenotypes are affected equally by each allele, i.e., the functions of MEI-41 in ensuring fertility, cell cycle regulation, and resistance to genotoxins are genetically separable. We propose that MEI-41 acts not in a single rigid signal transduction pathway, but in multiple molecular contexts to carry out its many functions. Sequence analysis identified mutations, which, for most alleles, fall in the poorly characterized region outside the kinase domain; this allowed us to tentatively identify additional functional domains of MEI-41 that could be subjected to future structure-function studies of this key molecule.
Change of the Heterogametic Sex From Male to Female in the Frog
Authors: Ogata M , Ohtani H , Igarashi T , Hasegawa Y , Ichikawa Y , Miura I 
Published: April 2021

Abstract
Two different types of sex chromosomes, XX/XY and ZZ/ZW, exist in the Japanese frog Rana rugosa. They are separated in two local forms that share a common origin in hybridization between the other two forms (West Japan and Kanto) with male heterogametic sex determination and homomorphic sex chromosomes. In this study, to find out how the different types of sex chromosomes differentiated, particularly the evolutionary reason for the heterogametic sex change from male to female, we performed artificial crossings between the West Japan and Kanto forms and mitochondrial 12S rRNA gene sequence analysis. The crossing results showed male bias using mother frogs with West Japan cytoplasm and female bias using those with Kanto cytoplasm. The mitochondrial genes of ZZ/ZW and XX/XY forms, respectively, were similar in sequence to those of the West Japan and Kanto forms. These results suggest that in the primary ZZ/ZW form, the West Japan strain was maternal and thus male bias was caused by the introgression of the Kanto strain while in the primary XX/XY form and vice versa. We therefore hypothesize that sex ratio bias according to the maternal origin of the hybrid population was a trigger for the sex chromosome differentiation and the change of heterogametic sex.