bluuebunny/crossref_metadata_2025_split huggingface dataset:
TMS in working memory research
Authors: Johnson Jeffrey S. , Feredoes Eva , Postle Bradley R. 
Published: February 2021

Abstract
This chapter provides a broad overview of research focused on the use of transcranial magnetic stimulation (TMS), both alone and together with neural recording modalities such as magnetic resonance imaging (MRI) and electroencephalography (EEG), to elucidate the cognitive and neural underpinnings of working memory. It first considers research using TMS to create “virtual lesions” in targeted brain areas, with the goal of establishing the causal role, and sometimes the timing, of the targeted area in specific working memory component processes. Next, it highlights research adopting a “perturb-and-measure” approach, in which TMS is used in conjunction with simultaneous neural recording (e.g., functional MRI or EEG) to assess the role of brain excitability and inter-area connectivity in working memory. Finally, research using TMS to assess the role of neural oscillations in working memory is reviewed. Throughout, the chapter highlights how different TMS modalities can be used profitably to clarify the neural bases of working memory and to effect strong tests of predictions derived from psychological models.
Global Legal Institutions
Authors: Sapignoli Maria , Niezen Ronald 
Published: February 2021

AbstractGlobal legal institutions such as UN agencies, the World Bank, and the World Trade Organization have become sites of some of the most innovative research in the social sciences, with implications that carry over into the methods and perspectives of legal scholarship. This chapter presents an outline of the history and methods of ethnography in global legal institutions as well as an account of the main findings of ethnographic work in this context. One of the key findings of ethnographic inquiry is that the structural failings and disenchantment of these institutions are at variance with persistent expressions of hope that are at the foundation of institutional ethics and self-representation. This hope is now being channelled into possibilities opened up by new information and communication technologies. These institutions are capitalizing on digitalization and innovations in technology as sources of decision-making. At the same time, new spaces have been created for private sector involvement in global governance initiatives, most prominently the UN Forum on Business and Human Rights. The UN, together with its corporate partners, is developing powerful information and communications technologies that present both important opportunities and risks in the administration of programmes in which artificial intelligence (AI) and machine learning are essential tools. These initiatives also present an important place for ethnographic research in presenting a clearer picture of the new geography of global governance and its legal frameworks.
Constancy Mechanisms and Distal Content: a Reply to Garson
Authors: Schulte Peter 
Published: February 2021

AbstractSensory perceptions represent things in the outside world. This mundane fact raises a major problem for naturalistic theories of content: the ‘distality problem’. In a previous paper for this journal, I presented a solution to this problem which makes central appeal to constancy mechanisms. Justin Garson, also in this journal, recently criticized my solution and suggested a Dretskean alternative to it. Here, I defend my proposal by arguing, first, that Garson's criticisms ultimately miss the mark, and secondly, that his Dretskean alternative is not viable, because it faces two fundamental problems: the empirical problem and the problem of changing response functions.
Behavioral Test (BAT-Back)
Authors: Holzapfel Sebastian , Schemer Lea , Riecke Jenny , Glombiewski Julia A. 
Published: February 2021

Objectives:
Although several questionnaires assessing fear of movement exist, it is still a challenge to identify individuals who might benefit more from exposure for chronic pain than from other psychological approaches and vice versa. Psychological approaches to chronic pain cannot advance toward the often called-for “tailored approaches” because of limited knowledge about treatment predictors. Our aim was to evaluate the additional predictive value of avoidance behavior based on behavioral observation.

Methods:
This study examined pretreatment self-report and behavioral measures as predictors of treatment outcome for n=43 patients experiencing disabling chronic low back pain, who took part in a randomized controlled trial in which they received 10 to 15 sessions of exposure treatment. Only patients with elevated fear avoidance based on self-report measures were included. Data were analyzed using regression analyses and classification and regression trees.

Results:
Regression analyses showed that higher avoidance behavior at pretreatment as measured by the Behavioral Avoidance Test—Back Pain (BAT-Back) significantly predicted reduction in global disability (with a small to medium effect), but not in specific disability. Self-report measures failed to predict treatment success for both outcome measures. Classification and regression trees divide subgroups who might benefit from exposure treatment through a BAT-Back score of >22 for Pain Disability Index.

Discussion:
There is some preliminary evidence that pretreatment avoidance behavior might be an indicator for reduction in global disability after exposure treatments in patients experiencing disabling chronic low back pain and elevated fear avoidance. We identified preliminary cutoff scores that need further investigation.
Endoscopic Shielding With Platelet-rich Plasma After Resection Of Large Colorectal Lesions
Authors: Lorenzo-Zúñiga Vicente , Moreno de Vega Vicente , Bartolí Ramón 
Published: February 2021

Background:
Platelet-rich plasma (PRP) has demonstrated efficacy as submucosal injection before endoscopic mucosal resection or local injection after endoscopic submucosal dissection of nonpedunculated colorectal lesions.

Methods:
The EndoPRP study was a prospective single-center study to analyze the efficacy of PRP shield after endoscopic mucosal resection of large nonpedunculated colorectal lesio with impossible clip closure, assessed by the incidence of delayed bleeding (DB) and delayed perforation, and percentage of mucosal restoration after 4 weeks (mucosal healing rate).

Results:
Shielding technique with PRP was performed in 4 patients, aged 52 to 80, with 4 lesions at rectum (mean size 53.7±20.6 mm, range 35 to 80 mm). DB occurred in 1 lesion (25% of all lesions), no required blood transfusion or endoscopic treatment. No postoperative delayed perforation occurred. Mucosal healing rate was of 78.6% after 4 weeks.

Conclusions:
PRP shield failed in prevent DB, probably due to migration and failure in the adherence in large wounds. Future comparative studies are needed to confirm these data.
Quality of Life Outcomes Following Single-stage Laparoscopic Common Bile Duct Exploration Versus 2-stage Endoscopic Sphincterotomy Followed by Laparoscopic Cholecystectomy in Management of Cholelithiasis With Choledocholithiasis
Authors: Asuri Krishna , Jain Mayank , Maheshwari Parteek , Prakash Om , Kumar Subodh , Garg Pramod , Sagar Rajesh , Bansal Virinder K. 
Published: February 2021

Introduction:
With various studies in the literature showing laparoscopic common bile duct (CBD) exploration to have equal or similar results when compared with endoscopic sphincterotomy (EST) clearance, decision-making in regard to the treatment modality to be used may become debatable. Thus, quality of life (QoL) data may assist both the patient and the clinician in deciding the management of the disease. The present prospective randomized trial was undertaken to compare QoL of patients undergoing treatment with these 2 approaches.

Methodology:
The study was conducted March 1, 2013, to September 31, 2016. Consecutive patients with CBD stones were randomized to either laparoscopic CBD exploration with cholecystectomy (group I) and EST followed by laparoscopic cholecystectomy (group II). Diagnosis was confirmed preoperatively using magnetic resonance cholangiopancreatography and/or endoscopic ultrasound. QoL scores were assessed by World Health Organization Quality of Life—Brief Version (WHOQOL-BREF), European Organization for Research and Treatment of Cancer Core Quality of Life Questionnaire C30 (EORTC QLQ-C30), and Hospital Anxiety and Depression Scale (HADS) questionnaires.

Results:
A total of 77 patients with concomitant gallstones and CBD stones were finally recruited (38 patients in group I and 39 patients in group II). The demographic and clinical profiles were similar in both the groups. On EORTC QLQ-C30 questionnaire, there was significant improvement in physical, emotional, and role functioning in both the groups (P<0.01) with no intergroup variation preprocedure or postprocedure. Patients in both the groups reported similar WHOQOL scores with significant improvement postprocedure and minimal intergroup variation. Both the depression and anxiety scores on HADS were comparable between the 2 groups preoperatively and at 3 months postoperatively.

Conclusion:
Single-stage management of patients with gallbladder and CBD stones and EST followed by laparoscopic cholecystectomy were similar in terms of improvement in QoL.
Comparison of Converse Ω Anastomosis and Extracorporeal Anastomosis After Laparoscopic Distal Gastrectomy for Gastric Cancer
Authors: Tsuchiya Nobuhiro , Kunisaki Chikara , Kubo Hirokazu , Sato Sho , Tanaka Yusaku , Sato Kei , Miyamoto Hiroshi , Watanabe Jun , Takeda Kazuhisa , Kosaka Takashi , Akiyama Hirotoshi , Endo Itaru , Misumi Toshihiro 
Published: February 2021

Background:
Converse Ω anastomosis is a recently developed technique of delta-shaped anastomosis for intracorporeal gastroduodenostomy to simplify the anastomotic procedures and reduce their potential risks. This study aimed to evaluate the safety and effectiveness of converse Ω anastomosis, comparing it with conventional extracorporeal Billroth-I anastomosis after laparoscopic distal gastrectomy (LDG) for gastric cancer.

Patients and Methods:
Among 169 gastric cancer patients who underwent LDG with Billroth-I anastomosis anastomosis between April 2013 and March 2018, we selected 100 patients by propensity score matching (50 in the converse Ω anastomosis group and 50 in the extracorporeal anastomosis group). Patients’ characteristics, intraoperative outcomes, postoperative complications, and survival time were compared between the 2 groups.

Results:
Median anastomosis time was significantly longer in the converse Ω group than in the extracorporeal group (40.0 vs. 30.5 min, P=0.005). However, the total procedure time did not differ significantly between the groups. Intraoperative blood loss volume was significantly lower in the converse Ω group than in the extracorporeal anastomosis group (40 vs. 120 mL, P<0.001). There were no significant differences in the number of dissected lymph nodes, postoperative morbidity, mortality, or length of hospital stay. The postoperative body mass index and the prognostic nutritional index did not differ between the groups 1 year after surgery. There were no significant differences in overall survival and relapse-free survival between the 2 groups.

Conclusions:
Converse Ω anastomosis is feasible and safe. This novel technique can be adopted as a treatment option for reconstruction after LDG in patients with early-stage gastric cancer. Therefore, the risks and benefits of converse Ω anastomosis after LDG should be confirmed in larger cohorts.
Germaphobia! Does our Relationship with, and Knowledge of Biodiversity Affect our Attitudes Towards Microbes?
Authors: Robinson Jake M. , Cameron Ross , Jorgensen Anna 
Published: February 2021

AbstractGermaphobia –– a pathological aversion to microorganisms –– could be contributing to an explosion in human immune-related disorders via mass sterilisation of surfaces and reduced exposure to biodiversity. Loss of biodiversity and our connectedness to nature, along with poor microbial literacy may be augmenting the negative consequences of germaphobia on ecosystem health. In this study, we created an online questionnaire to acquire data on attitudes towards, and knowledge of microbes. We collected data on nature connectedness and interactions with nature and explored the relationships between these variables. We found a significant association between attitudes towards microbes and both duration and frequency of visits to natural environments. A higher frequency of visits to nature per week, and a longer duration spent in nature per visit, significantly associated with positive attitudes towards microbes. We found no association between nature connectedness and attitudes towards microbes. We found a significant relationship between knowledge of ‘lesser known’ microbial groups (e.g., identifying that fungi, algae, protozoa, and archaea are microbes) and positive attitudes towards microbes. However, we also found that people who correctly identified viruses as being microbes expressed less positive views of microbes overall –– this could potentially be attributed to a ‘COVID-19 effect’. Our results suggest that basic microbial literacy and nature engagement may be important in reducing/preventing germaphobia. The results also suggest that a virus-centric phenomenon (e.g., COVID-19) could increase broader germaphobia. As the rise of immune-related disorders and mental health conditions have been linked to germaphobia, reduced biodiversity, and non-targeted sterilisation, our findings point to a feasible strategy to potentially help ameliorate these negative consequences. A greater emphasis on microbial literacy and promoting time spent in nature could be useful in promoting resilience in human health and more positive/constructive attitudes towards the foundations of our ecosystems – the microorganisms.
A user manual to measure gas diffusion kinetics in plants: Pneumatron construction, operation and data analysis
Authors: Trabi C.L. , Pereira L. , Guan X. , Miranda M.T. , Bittencourt P.R.L. , Oliveira R.S. , Ribeiro R.V. , Jansen S. 
Published: February 2021

AbstractThe Pneumatron device presented measures gas diffusion kinetics in the xylem of plants. The device provides an easy, low-cost, and powerful tool for research on plant water relations. Here, we describe in detail how to construct and operate this device to estimate xylem vulnerability to embolism, and how to analyse pneumatic data. Simple and more elaborated ways of constructing a Pneumatron are shown, either using wires, a breadboard, or a printed circuit board. The instrument is based on an open-source hardware and software system, which allows users to operate it in an automated or semi-automated way. A step-by-step manual and a troubleshooting section are provided. An excel spreadsheet and an R-script are also presented for fast and easy data analysis. This manual should help new users to avoid common mistakes, especially regarding stable measurements of the minimum and maximum amount of gas that can be discharged from xylem tissue.
Single cell transcriptomic analysis reveals cellular diversity of murine esophageal epithelium and age-associated mitochondrial dysfunction
Authors: Kabir Mohammad Faujul , Karami Adam , Cruz-Acuna Ricardo , Klochkova Alena , Saxena Reshu , Mu Anbin , Murray Mary Grace , Keith Kelsey , Madzo Jozef , Huang Hugh , Jelinek Jaroslav , Karakasheva Tatiana , Hamilton Kathryn E. , Muir Amanda B. , Tetreault Marie-Pier , Whelan Kelly A. 
Published: February 2021

ABSTRACTStratified squamous epithelium of the esophagus is comprised of basal keratinocytes that execute a terminal differentiation program in overlying suprabasal and superficial cell layers. Although morphologic progression coupled with expression of specific molecular markers has been characterized along the esophageal epithelial differentiation gradient, the molecular heterogeneity within the cell types along this trajectory has yet to be classified at the level of single cell resolution. To explore the molecular characteristics of esophageal keratinocytes along the squamous differentiation continuum, we performed single cell RNA-Sequencing transcriptomic profiling of 7,972 cells from murine esophageal epithelial sheets. We identified 8 distinct cell clusters in esophageal epithelium, unveiling an unexpected level of diversity, particularly among basal cells. We further mapped the cellular pathways and lineage trajectories within basal, suprabasal, and superficial clusters as well as within the heterogeneous basal cell populations, providing a comprehensive molecular view of esophageal epithelial cells in the context of squamous differentiation. Finally, we explored the impact of tissue aging upon esophageal epithelial cell clusters and demonstrated that mitochondrial dysfunction is a feature of aging in normal esophageal epithelium. These studies provide an unparalleled molecular perspective on murine esophageal keratinocytes that will serve as a valuable resource for dissecting cell type-specific roles in esophageal biology under conditions of homeostasis, aging, and tissue pathology.
A novel antibody against the furin cleavage site of SARS-CoV-2 spike protein: effects on proteolytic cleavage and ACE2 binding
Authors: Spelios Michael G. , Capanelli Jeanne M. , Li Adam W. 
Published: February 2021

AbstractSARS-CoV-2 harbors a unique S1/S2 furin cleavage site within its spike protein, which can be cleaved by furin and other proprotein convertases. Proteolytic activation of SARS-CoV-2 spike protein at the S1/S2 boundary facilitates interaction with host ACE2 receptor for cell entry. To address this, high titer antibody was generated against the SARS-CoV-2-specific furin motif. Using a series of innovative ELISA-based assays, this furin site blocking antibody displayed high sensitivity and specificity for the S1/S2 furin cleavage site, and demonstrated effective blockage of both enzyme-mediated cleavage and spike-ACE2 interaction. The results suggest that immunological blocking of the furin cleavage site may afford a suitable approach to stem proteolytic activation of SARS-CoV-2 spike protein and curtail viral infectivity.
Soil, senescence and exudate utilisation: Characterisation of the Paragon var. spring bread wheat root microbiome
Authors: Prudence Sam , Newitt Jake , Worsley Sarah F. , Macey Michael C. , Murrell J. Colin , Lehtovirta-Morley Laura E. , Hutchings Matthew I. 
Published: February 2021

AbstractConventional methods of agricultural pest control and crop fertilisation are contributing to a crisis of biodiversity loss, biogeochemical cycle dysregulation, and ecosystem collapse. Thus, we must find ecologically responsible means to control disease and promote crop yields. The root-associated microbiome may contribute to this goal as microbes can aid plants with disease suppression, abiotic stress relief, and nutrient bioavailability. We applied 16S rRNA gene & fungal 18S rRNA gene (ITS2 region) amplicon sequencing to profile the diversity of the bacterial, archaeal & fungal communities associated with the roots of UK elite spring bread wheat varietyTriticum aestivum var.Paragon in different soils and developmental stages. This revealed that community composition shifted significantly for all three groups across compartments. This shift was most pronounced for bacteria and fungi, while we observed weaker selection on the ammonia oxidising archaea-dominated archaeal community. Across multiple soil types we found that soil inoculum was a significant driver of endosphere community composition, however several bacterial families were identified as core enriched taxa in all soil conditions. The most abundant of these wereStreptomycetaceaeandBurkholderiaceae.Moreover, as the plants senesce, both families were reduced in abundance, indicating that input from the living plant was required to maintain their abundance in the endosphere. To understand which microbes are using wheat root exudates in the rhizosphere, root exudates were labelled in a13CO2DNA stable isotope probing experiment. This shows that bacterial taxa within theBurkholderiaceaefamily among other core enriched taxa, such asPseudomonadaceae,were able to use root exudates butStreptomycetaceaewere not. Overall, this work provides a better understanding of the wheat microbiome, including the endosphere community. Understanding crop microbiome formation will contribute to ecologically responsible methods for yield improvement and biocontrol in the future.
Argonaute Binding within Human Nuclear RNA and its Impact on Alternative Splicing
Authors: Chu Yongjun , Yokota Shinnichi , Liu Jing , Kilikevicius Audrius , Johnson Krystal C. , Corey David R. 
Published: February 2021

ABSTRACTMammalian RNA interference (RNAi) is often linked to the regulation of gene expression in the cytoplasm. Synthetic RNAs, however, can also act through the RNAi pathway to regulate transcription and splicing. While nuclear regulation by synthetic RNAs can be robust, a critical unanswered question is whether endogenous functions for nuclear RNAi exist in mammalian cells. Using enhanced crosslinking immunoprecipitation (eCLIP) in combination with RNA sequencing (RNAseq) and multipleAGOknockout cell lines, we mapped AGO2 protein binding sites within nuclear RNA. The strongest AGO2 binding sites were mapped to micro RNAs (miRNAs). The most abundant miRNAs were distributed similarly between cytoplasm and nucleus, providing no evidence for mechanisms that facilitate localization of miRNAs in one compartment versus the other. Beyond miRNAs, most statistically-significant AGO2 binding was within introns. Splicing changes were confirmed by RT-PCR and were recapitulated by synthetic duplex RNAs and miRNA mimics complementary to the sites of AGO2 binding. These data support the hypothesis that miRNAs can control gene splicing. While nuclear RNAi proteins have the potential to be a natural regulatory mechanism, careful study will be necessary to identify critical RNA drivers of normal physiology and disease.
Customized de novo mutation detection for any variant calling pipeline: SynthDNM
Authors: Lian Aojie , Guevara James , Xia Kun , Sebat Jonathan 
Published: February 2021

AbstractMotivationAs sequencing technologies and analysis pipelines evolve, DNM calling tools must be adapted. Therefore, a flexible approach is needed that can accurately identify de novo mutations from genome or exome sequences from a variety of datasets and variant calling pipelines.ResultsHere, we describe SynthDNM, a random-forest based classifier that can be readily adapted to new sequencing or variant-calling pipelines by applying a flexible approach to constructing simulated training examples from real data. The optimized SynthDNM classifiers predict de novo SNPs and indels with robust accuracy across multiple methods of variant calling.AvailabilitySynthDNM is freely available on Github (https://github.com/james-guevara/synthdnm)Contactjsebat@ucsd.eduSupplementary informationSupplementary data are available atBioinformaticsonline.