bluuebunny/crossref_metadata_2025 huggingface dataset:
Perpendicular drill bit alignment provides a practical guidance to determine the appropriate suture anchor insertion angle during acetabular labral repair
Authors: Ismailoglu Abdul Veli , Ozdogmus Omer , Karaman Muhammed Ilkay , Kayaalp Asim , Kocaoglu Baris
Published: August 2021

The safe acetabular rim angle is an anatomical measurement used to determine the safety margin when inserting suture anchors. The purpose of the present study was to find out whether aligning the drill bit perpendicularly during arthroscopic surgery can provide a reference point for determining an appropriate angle to facilitate the suture anchor insertion and to prevent extra- and intra-articular perforations. One hundred computed tomographic hips were used to reconstruct three-dimensional acetabular hip models. Each model was radially sectioned at the 4 o’clock, 3 o’clock and anterior inferior iliac spine (AIIS) positions (that corresponded mainly to the 2:20 clock position). A perpendicular reference line, representing a perpendicular drill bit alignment, was drawn for each position within the acetabular model, and its relation to the safe acetabular rim angle was measured. The length of the perpendicular reference line and the effect of gender on measurements were also evaluated. The mean safe acetabular rim angle at the 3 o’clock position was significantly smaller compared to other clock positions (P < 0.001). The perpendicular reference line was located out of the safe acetabular rim angle in 28 cases (%28), mostly in female acetabula at the 3 o’clock position, and relative to the perpendicular reference line the required minimal angle was 4° ± 2.3° to place the anchor in the safe acetabular rim angle to avoid extra-articular perforation. The perpendicular reference line was shortest at the 3 o’clock position, and its mean length was shorter in female acetabula at all clock positions (P < 0.001). Aligning the drill bit perpendicular to the acetabular opening plane during an arthroscopic anchor placement is a practical way to estimate and target the position of the safe acetabular rim angle to avoid anchor perforations. Based on measurements from a perpendicularly aligned drill bit, the drill bit should be directed towards the joint minimally by 4° to avoid extra-articular perforations and maximally by 30° to avoid intra-articular perforations.
Pararhodonellum marinum gen. nov., sp. nov., isolated from deep-sea sediment
Authors: Song Lei , Liu Hongcan , Huang Ying , Dai Xin , Zhou Yuguang
Published: August 2021

A Gram-stain-negative, non-motile bacterial strain, designated SW124T, was isolated from a deep-sea sediment sample collected from the Indian Ocean. SW124T was aerobic and catalase-positive. The strain grew at 4–40 °C (optimum, 30 °C), at pH 5.0–8.6 (optimum, pH 7.0) and in the presence of 0.5–9.5 % (w/v) NaCl (optimum, 3.0%). The results of comparative analyses of the 16S rRNA gene sequence indicated that SW124T was grouped in the vicinity of the genus

Rhodonellum

in the family

Cyclobacteriaceae

. The quinone system contained menaquinone MK-7. The predominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 3 (comprising C16 : 1ω7c and/or C16 : 1ω6c). SW124T contained phosphatidylethanolamine (PE) as the major polar lipid. The genomic DNA G+C content of SW124T was 41.7 mol%. On the basis of its phenotypic characteristics and phylogenetic data, we propose that strain SW124T (=CGMCC 1.16171T=KCTC 82235T) represents a novel species of a novel genus, with the name Pararhodonellum marinum gen. nov., sp. nov.
Anxiety disorders and age-related changes in physiology
Authors: Mutz Julian , Hoppen Thole H. , Fabbri Chiara , Lewis Cathryn M.
Published: August 2021

Background

Anxiety disorders are leading contributors to the global disease burden, highly prevalent across the lifespan, and associated with substantially increased morbidity and early mortality.

Aims

The aim of this study was to examine age-related changes across a wide range of physiological measures in middle-aged and older adults with a lifetime history of anxiety disorders compared to healthy controls.

Method

The UK Biobank study recruited >500,000 adults, aged 37–73, between 2006–2010. We used generalised additive models to estimate non-linear associations between age and hand-grip strength, cardiovascular function, body composition, lung function and heel bone mineral density in cases and in controls.

Results

The main dataset included 332,078 adults (mean age = 56.37 years; 52.65% females). In both sexes, individuals with anxiety disorders had a lower hand-grip strength and blood pressure, while their pulse rate and body composition measures were higher than in healthy controls. Case-control differences were larger when considering individuals with chronic and/or severe anxiety disorders, and differences in body composition were modulated by depression comorbidity status. Differences in age-related physiological changes between female anxiety disorder cases and healthy controls were most evident for blood pressure, pulse rate and body composition, while in males for hand-grip strength, blood pressure and body composition. Most differences in physiological measures between cases and controls decreased with increasing age.

Conclusions

Individuals with a lifetime history of anxiety disorders differed from healthy controls across multiple physiological measures, with some evidence of case-control differences by age. The differences observed varied by chronicity/severity and depression comorbidity.
External validation of 4C ISARIC mortality score in the setting of a Saudi Arabian ICU. Retrospective study
Authors: Mumtaz Shahzad A. , Shahzad Saima A. , Ahmed Intekhab , Alodat Mohammed A. , Gharba Mohamed , Saif Zohdy A. , Mady Ahmed F. , Mahmood Waqas , Mhawish Huda , Abdulmowla Majd M. , Aletreby Waleed
Published: August 2021

COVID-19 pandemic has burdened healthcare systems, necessitating the development of mortality prediction scores to guide clinical decisions and resource allocation. 4C ISARIC mortality score was developed and validated on a British cohort.

Objectives

External validation of the score in the setting of a large Saudi Arabian ICU.

Method

Retrospective chart review of COVID-19 patients admitted to ICU of King Saud Medical City, Riyadh, Saudi Arabia. Collecting data to calculate the score, then fitting a ROC curve against known patients’ outcome.

Results

Cohort included 1493 patients with 38% mortality, AUC of the score was 0.81 (95% CI: 0.79 – 0.83, p < 0.001), correctly classifying 72.67% of the cohort. Cut-off value of > 9 had sensitivity of 70.5% (95% CI: 66.6 – 74.3), specificity 73.97% (95% CI: 71 – 76.8), positive predictive value 62.4% (95% CI: 59.5 – 65.2), and negative predictive value 80.2% (95% CI: 78.2 – 82.4).

Conclusion

4C ISARIC mortality risk score performed well with a good discriminatory ability for critically ill patients admitted to ICU in our setting. Cut-off > 9 was the optimal criterion.
Genetic Risk for Hemochromatosis is Associated with Movement Disorders
Authors: Loughnan Robert , Ahern Jonathan , Thompkins Cherisse , Palmer Clare E. , Sugrue Leo , Iversen John , Thompson Wesley , Andreassen Ole , Jernigan Terry , Dale Anders , Boyle Mary ET , Fan Chun Chieh
Published: August 2021

Hereditary hemochromatosis (HH) is an autosomal recessive genetic disorder that can lead to iron overload, causing oxidative damage to affected organs. HH type 1 is predominantly associated with homozygosity for the mutation p.C282Y. Previous case studies have reported tentative links between HH and movement disorders, e.g., Parkinson’s disease, and basal ganglia abnormalities on magnetic resonance imaging. We investigated the impact of p.C282Y homozygosity: on whole brain T2 intensity differences, a measure of iron deposition, and; on measures of movement abnormalities and disorders within UK Biobank. The neuroimaging analysis (154 p.C282Y homozygotes, 595 matched controls) showed that p.C282Y homozygosity was associated with decreased T2 signal intensity in motor circuits (basal ganglia, thalamus, red nucleus, and cerebellum; Cohen’s d > 1) consistent with substantial iron deposition. Across the whole UK Biobank (2,889 p.C282Y homozygotes, 496,968 controls), we found a significant enrichment for movement abnormalities in male homozygotes (OR (95% CI) = 1.82 (1.27-2.61), p=0.001), but not females (OR (95% CI) = 1.10 (0.69-1.78), p=0.71). Among the 31 p.C282Y homozygote males with a movement disorder only 7 had a concurrent HH diagnosis. These findings indicate susceptibility to iron overload in subcortical structures in p.C282Y homozygotes, and confirmed an increased risk of movement abnormalities and disorders in males. Given the effectiveness of early treatment in HH, screening for p.C282Y homozygosity in high risk individuals may offer a potential avenue to reduce iron accumulation in the brain and limit additional risk for the development of movement disorders among males.
Point-of-care semiquantitative test for adherence to tenofovir alafenamide or tenofovir disoproxil fumarate
Authors: Sevenler Derin , Niu Xin , Dossantos Sandy , Toner Mehmet , Cressey Tim R. , Sandlin Rebecca , Drain Paul
Published: August 2021

Synopsis

Objective

Objective measurement of antiretrovirals may aid clinical interventions for improving adherence to HIV prevention or treatment regimens. A point-of-care urine test could provide real-time information about recent adherence to regimens containing tenofovir disoproxil fumarate (TDF) or tenofovir alafenamide (TAF). We developed a lateral flow immunoassay (LFA) and enzyme-linked immunoassay (ELISA) for urinary tenofovir.

Methods

Intensity of the LFA test line was quantified using an optical reader and visually scored 0 – 5 by two independent people, using a reference card. The sensitivity and specificity of both the ELISA and LFA were determined for two different tenofovir concentration cutoffs for TDF and TAF adherence—1,500 ng/mL and 150 ng/mL, respectively. To validate the assays, we measured 586 urine samples from 28 individuals collected as part of a study of tenofovir pharmacokinetics in adults, which were also measured by mass spectrometry as ground truth.

Results

Both the LFA signal and ELISA signal were each strongly correlated to drug concentrations (0.91 and 0.92 respectively). The LFA signal and ELISA were highly sensitive and specific at both thresholds (LFA se/sp TDF 89%/96%, TAF 90%/96%; ELISA se/sp TDF 94%/94%, TAF 92%/84%). Visual scoring of the LFA was also highly sensitive and specific at both the TDF and TAF thresholds (se/sp TDF 91%/94%, TAF 87%/90%).

Conclusions

Our rapid semi-quantitative test can measure TFV concentrations relevant to both TAF or TDF adherence, which may support adherence-promoting interventions across a range of HIV care settings.
Anti-PF4 levels of patients with VITT do not reduce 4 months following AZD1222 vaccination
Authors: Nicolson Phillip L.R. , Montague Samantha J. , Smith Christopher W. , Lodwick Clare S. , Stoneley Charlotte , Roberts Matthew , Watson Steve P. , Lowe Gillian C. , Lester William A.
Published: August 2021

Background

Anti-Platelet Factor 4 (PF4) IgG antibodies that activate platelets via FcγRIIa have been shown to be an important part of the pathophysiology of vaccine-induced immune thrombocytopenia and thrombosis (VITT). There is now extensive literature on its presentation and initial management. There is no literature however on what happens to these patients following discharge.

Methods

We collected clinical data and samples from seven patients presenting with VITT and followed them up for 82-145 days. We also collected clinical samples from them at last follow-up. Testing for anti-PF4/heparin antibodies was done using an anti-PF4/heparin enzymatic immunoassay. Flow Cytometry was used to look at FcγRIIa levels on patient platelets. Light Transmission Aggregometry with patient serum and healthy donor / patient platelets was used to analyse platelet responsiveness, in the presence and absence of PF4.

Findings

All patients were discharged on direct oral anticoagulants. Two patients remain completely symptom free, three have ongoing headaches, two have residual neurological deficits. Two patients developed mild thrombocytopenia and worsening headache (but without cerebral venous sinus thrombosis) and were retreated, one of these with rituximab. All patients, except the one treated with rituximab, had similar anti-PF4 antibody titres at 80-120 days to their levels at diagnosis. Platelets from patients at follow-up had normal levels of FcγRIIa and had normal responses to thrombin and collagen-related-peptide. Patient serum from diagnosis strongly activated healthy donor platelets in the presence of PF4. Serum from follow-up was much weaker at stimulating platelets, even in the presence of PF4.

Interpretation

This study shows that despite similar PF4 antibody titres at diagnosis and during follow-up, there are further differences in patient serum, that are not apparent from currently used testing, that result in lower levels of platelet activation during the follow-up period. Further understanding of these factors are important in order to assess duration of anticoagulation for these patients.

Funding

This work was supported by an Accelerator Grant (AA/18/2/34218) from the British Heart Foundation (BHF) and by a National Institute for Health Research (NIHR) grant.

Key points

PF4 antibody titres do not reduce up to 4-months post ChAdOx1 nCoV-19 in patients with VITT

Despite similar PF4 antibody titres, diagnostic serum is more potent at activating platelets in the presence of PF4 than follow-up serum.
Fall 2021 Resurgence and COVID-19 Seroprevalence in Canada Modelling waning and boosting COVID-19 immunity in Canada A Canadian Immunization Research Network Study
Authors: Dick David W. , Childs Lauren , Feng Zhilan , Li Jing , Röst Gergely , Buckeridge David L , Ogden Nick H , Heffernan Jane M
Published: August 2021

There is a threat of COVID-19 resurgence in Fall 2021 in Canada. To understand the probability and severity of this threat, quantification of the level of immunity/protection of the population is required. We use an age-structured model including infection, vaccination and waning immunity to estimate the distribution of immunity to COVID-19 in the Canadian population. By late Summer 2021, coinciding with the end of the vaccination program, we estimate that 60 − 80% of the Canadian population will have some immunity to COVID-19. Model results show that this level of immunity is not sufficient to stave off a Fall 2021 resurgence. The timing and severity of a resurgence, however, varies in magnitude given multiple factors: relaxation of non-pharmaceutical interventions such as social distancing, the rate of waning immunity, the transmissibility of variants of concern, and the protective characteristics of the vaccines against infection and severe disease. To prevent large-scale resurgence, booster vaccination and/or re-introduction of public health mitigation may be needed.
Detecting orientation of Brain MR scans using deep learning
Authors: Singhal Chinmay , Gupta Nihit , Stein Anouk , Zhou Quan , Chen Leon , Shih George
Published: August 2021

Abstract

There has been a steady escalation in the impact of Artificial Intelligence (AI) on Healthcare along with an increasing amount of progress being made in this field. While many entities are working on the development of significant deep learning models for the diagnosis of brain-related diseases, identifying precise images needed for model training and inference tasks is limited due to variation in DICOM fields which use free text to define things like series description, sequence and orientation [1]. Detecting the orientation of brain MR scans (Axial/Sagittal/Coronal) remains a challenge due to these variations caused by linguistic barriers, human errors and de-identification - essentially rendering the tags unreliable [2, 3, 4]. In this work, we propose a deep learning model that identifies the orientation of brain MR scans with near perfect accuracy.
Premature infants display discriminable behavioural, physiological and brain responses to noxious and non-noxious stimuli
Authors: van der Vaart Marianne , Hartley Caroline , Baxter Luke , Mellado Gabriela Schmidt , Andritsou Foteini , Cobo Maria M. , Fry Ria Evans , Adams Eleri , Fitzgibbon Sean , Slater Rebeccah
Published: August 2021

Pain assessment in preterm infants is challenging, as behavioural, autonomic and neurophysiological measures of pain are reported to be less sensitive and specific than in term infants. Understanding the pattern of preterm infants’ noxious-evoked responses is vital to improve pain assessment in this group. This study investigated the discriminability and development of multi-modal noxious-evoked responses in infants aged 28-40 weeks postmenstrual age. A classifier was trained to discriminate responses to a noxious heel lance from a non-noxious control in 47 infants, using measures of facial expression, brain activity, heart rate and limb withdrawal, and tested in two independent cohorts with a total of 98 infants. The model discriminates responses to the noxious from the non-noxious procedure from 28 weeks onwards with an overall accuracy of 0.77-0.83 and an accuracy of 0.78-0.79 in the 28-31 week group. Noxious-evoked responses have distinct developmental patterns. Heart rate responses increase in magnitude with age, while noxious-evoked brain activity undergoes three distinct developmental stages, including a previously unreported transitory stage consisting of a negative event-related potential between 30-33 weeks postmenstrual age. These findings demonstrate that while noxious-evoked responses change across early development, infant responses to noxious and non-noxious stimuli are discriminable from 28 weeks onwards.
Lifelong association of disorders related to military trauma with subsequent Parkinson’s disease
Authors: Scott Gregory D. , Neilson Lee E. , Woltjer Randy , Quinn Joseph F. , Lim Miranda M.
Published: August 2021

Background

Trauma-related disorders such as traumatic brain injury (TBI) and posttraumatic stress disorder (PTSD) are emerging as risk factors for Parkinson’s Disease (PD), but their association with development of PD and independence from comorbid disorders remains unknown. This case-control study examines TBI and PTSD related to early trauma in military veterans.

Methods

PD was identified by ICD code, recurrent PD-specific prescriptions, and availability of 5+ years of earlier records. Validation was performed by chart review by a movement disorder-trained neurologist. Controls were matched 4:1 by age, duration of preceding health care, race, ethnicity, birth year, and sex. TBI and PTSD were identified by ICD code and onset based on active duty. Association and interaction were measured for TBI and PTSD with PD going back sixty years. Interaction was measured for comorbid disorders.

Results

71,933 cases and 287,732 controls were identified. TBI and PTSD increased odds of subsequent PD at all preceding five-year intervals back to year -60 (OR range: 1.5 [1.4,1.7] to 2.1 [2.0,2.1]). TBI and PTSD showed synergism (synergy index range: 1.14 [1.09,1.29] to 1.28 [1.09,1.51]) and additive association (OR range: 2.2 [1.6,2.8] to 2.7 [2.5,2.8]). Chronic pain and migraine showed greatest synergy with PTSD and TBI. Effect sizes for trauma-related disorders were comparable to established prodromal disorders.

Discussion

TBI and PTSD are associated with later PD and are synergistic with chronic pain and migraine. These findings provide evidence for TBI and PTSD as risk factors preceding PD by decades and could aid in prognostic calculation and earlier intervention.
Using historical museum samples to examine divergent and parallel evolution in the invasive starling
Authors: Stuart Katarina C. , Sherwin William B. , Austin Jeremy J. , Bateson Melissa , Eens Marcel , Brandley Matthew C. , Rollins Lee A.
Published: August 2021

1.

During the Anthropocene, Earth has experienced unprecedented habitat loss, native species decline, and global climate change. Concurrently, greater globalisation is facilitating species movement, increasing the likelihood of alien species establishment and propagation. There is a great need to understand what influences a species’ ability to persist or perish within a new or changing environment. Examining genes that may be associated with a species’ invasion success or persistence informs invasive species management, assists with native species preservation, and sheds light on important evolutionary mechanisms that occur in novel environments. This approach can be aided by coupling spatial and temporal investigations of evolutionary processes. Here we use the common starling,Sturnus vulgaris,to identify parallel and divergent evolutionary change between contemporary native and invasive range samples and their common ancestral population. To do this, we use reduced-representation sequencing of native samples collected recently in north-western Europe and invasive samples from Australia, together with museum specimens sampled in the UK during the mid-19thCentury. We found evidence of parallel selection on both continents, possibly resulting from common global selective forces such as exposure to pollutants (e.g. TCDD) and food carbohydrate content. We also identified divergent selection in these populations, which might be related to adaptive changes in response to the novel environment encountered in the introduced Australian range. Interestingly, signatures of selection are equally as common within both invasive and native range contemporary samples. Our results demonstrate the value of including historical samples in genetic studies of invasion and highlight the ongoing and occasionally parallel role of adaptation in both native and invasive ranges.
Child Mortality in England During the First Year of the COVID-19 Pandemic
Authors: Odd David , Stoianova Sylvia , Williams Tom , Fleming Peter , Luyt Karen
Published: August 2021

OBJECTIVES

The aim of this analysis was to quantify the relative risk of childhood deaths across the whole of England during the first year of the COVID pandemic, compared to a similar period of 2019.

DESIGN

This work is based on data collected by the National Child Mortality Database (NCMD) which collates data on all children who die in England. The number of deaths, and their characteristics, from 1st April 2020 until 31st of March 2021 (2020-21), were compared to those from the same period of 2019-20. Relative risk and excess mortality were derived for deaths in 2020-21 vs 2019-20.

SETTING

All deaths reported to NCMD in England of children under 18 years of age, between April 2019 and March 2021.

PARTICIPANTS

6490 deaths of children, under the age of 18 years, reported to the NCMD over the study period.

RESULTS

Children who died between April 2020 and March 2021 had similar demographics to those who died in 2019-20. Overall, there were 356 (198 to 514) fewer deaths in 2020-21 than in 2019-20 (RR 0.90 (0.85-0.94), p<0.001). Repeating the analysis by category of death, suggested that deaths from infection (RR 0.49 (0.38-0.64)) and from other underlying medical conditions (RR 0.75 (0.68-0.82)) were lower in 2020-21 than 2019-20, and weak evidence (p=0.074) that this was also true of deaths from substance abuse.

CONCLUSIONS

Childhood mortality in England during the first year of the SARS-CoV-2 pandemic was the lowest on record, with over 300 fewer deaths than the preceding 12 months. The greatest reduction was seen in children less than 10 years old. It is important that we learn from this effect, that potentially offers alternative ways to improve the outcome for the most vulnerable children in our society.
A compilation of fecal microbiome shotgun metagenomics from hospitalized patients undergoing hematopoietic cell transplantation
Authors: Yan Jinyuan , Liao Chen , Taylor Bradford P. , Fontana Emily , Amoretti Luigi A. , Wright Roberta J. , Dai Anqi , Waters Nicholas , Peled Jonathan U. , Taur Ying , Perales Miguel-Angel , Siranosian Benjamin A. , Bhatt Ami S. , van den Brink Marcel R.M. , Pamer Eric G. , Schluter Jonas , Xavier Joao B.
Published: August 2021

Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study how the human gut microbiome changes in response to perturbations, and how the resulting changes in the microbiome feedback on its living host. We previously compiled a large-scale longitudinal dataset of stool microbiome compositions from these patients and associated metadata1. In that dataset the microbiome analysis was limited to the taxonomic composition of the bacterial population obtained from 16S rRNA gene sequencing. Here, we augment those data with shotgun metagenomic sequences from a nested subset of 395 stool samples. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC2 to be analyzed without the users having to download or transfer the files. We provide examples that show how shotgun sequencing enriches microbiome analyses beyond the taxonomic composition such as the analysis of gene functions including virulence factors and antibiotic resistances, and the assembly of genomes from metagenomic data.
A deep learning-based iterative digital pathology annotation tool
Authors: Jaber Mustafa I. , Song Bing , Beziaeva Liudmila , Szeto Christopher W. , Spilman Patricia , Yang Phil , Soon-Shiong Patrick
Published: August 2021

Well-annotated exemplars are an important prerequisite for supervised deep learning schemes. Unfortunately, generating these annotations is a cumbersome and laborious process, due to the large amount of time and effort needed. Here we present a deep-learning-based iterative digital pathology annotation tool that is both easy to use by pathologists and easy to integrate into machine vision systems. Our pathology image annotation tool greatly reduces annotation time from hours to a few minutes, while maintaining high fidelity with human-expert manual annotations. Here we demonstrate that our active learning tool can be used for a variety of pathology annotation tasks including masking tumor, stroma, and lymphocyte-rich regions, among others. This annotation automation system was validated on 90 unseen digital pathology images with tumor content from the CAMELYON16 database and it was found that pathologists’ gold standard masks were re-produced successfully using our tool. That is, an average of 2.7 positive selections (mouse clicks) and 8.0 negative selections (mouse clicks) were sufficient to generate tumor masks similar to pathologists’ gold standard in CAMELYON16 test WSIs. Furthermore, the developed image annotation tool has been used to build gold standard masks for hundreds of TCGA digital pathology images. This set was used to train a convolutional neural network for identification of tumor epithelium. The developed pan-cancer deep neural network was then tested on TCGA and internal data with comparable performance. The validated pathology image annotation tool described herein has the potential to be of great value in facilitating accurate, rapid pathological analysis of tumor biopsies.
Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland soil
Authors: Fossum Christina , Estera-Molina Katerina , Yuan Mengting , Herman Don , Chu-Jacoby Ilexis , Nico Peter , Morrison Keith , Pett-Ridge Jennifer , Firestone Mary
Published: August 2021

Plant roots and the organisms that surround them are a primary source for stabilized organic C, particularly in grassland soils, which have a large capacity to store organic carbon belowground. To quantify the flow and fate of plant fixed carbon (C) in a Northern California annual grassland, we tracked plant carbon from a five-day 13CO2 pulse field labeling for the following two years. Soil and plant samples were collected immediately after the pulse labeling, and again at three days, four weeks, six months, one year, and two years. Soil organic matter was fractionated using a sodium polytungstate density gradient to separate the free-light fraction (FLF), occluded-light fraction (OLF), and heavy fraction (HF). Using isotope ratio mass spectrometry, we measured 13C enrichment and total C content for plant shoots, roots, soil, soil dissolved organic carbon (DOC), and the FLF, OLF, and HF. The HF was further analyzed by solid state 13C NMR spectroscopy.

At the end of the labeling period, the largest amount of 13C was recovered in plant shoots (60%), but a substantial amount (40%) was already found belowground in roots, soil, and soil DOC. Density fractionation of 4-week soil samples (from which living roots were removed) indicated that the highest isotope enrichment was in the mineral-rich heavy fraction, with similar enrichment of the FLF and OLF. At the 6-month sampling, after the dry summer period during which plants senesced and died, the amount of label in the FLF increased such that it was equal to that in the HF. By the 1-year sampling, 13C in the FLF had declined substantially and continued to decline by the 2-year sampling. 13C recovery in the OLF and HF, however, was qualitatively stable between sampling times. By the end of the 2-year experiment, 69% of remaining label was in the HF, 18% in the FLF and 13% in the OLF.

While the total 13C content of the HF did not change significantly from the 4-week to the 2-year sample time, 13C NMR spectroscopic analysis of spring HF samples from 2018, 2019, and 2020 suggests that the relative proportion of aliphatic/alkyl functional groups declined in the newly formed SOC over the 2-year period. Simultaneously, aromatic and carbonyl functional groups increased, and the proportion of carbohydrate groups remained relatively constant. In summary, our results indicate that initial associations between minerals and root-derived organic matter are significant and form rapidly; by 4 weeks, a substantial amount (17%) of the total plant-derived 13C had become associated with the heavy fraction (HF) of soil. While the majority of annual C input cycles rapidly (<2-year timescale), a sizeable proportion (∼12% of the original inputs) persisted for 2 years.
Lipid droplet structural remodeling in adipose tissue upon caloric excess
Authors: Zhou Weinan , Bandara Sarith R , Leal Cecilia , Anakk Sayeepriyadarshini
Published: August 2021

Excess calories are stored as triacylglycerols (TAG) and cholesteryl esters (CE) in lipid droplets (LD), and during obesity, LD expansion occurs. X-ray scattering of adipose tissue uncovered that LDs comprise two TAG packing domains: a disordered core and a multilamellar shell. The number of TAG layers increases upon diet-induced obesity and is adipose depot-specific. Further, collagen was highly oriented in brown but randomly dispersed in white fat. We discovered that the body’s surfactant, bile acids (BAs) stimulate remodeling of LD size. Deleting the BA receptor, Farnesoid X receptor (FXR) reduced a hydrophilic BA, β muricholic acid (β-MCA), and enlarged the adipocytes. BA composition is a critical determinant of overall hydrophobicity index and solubilization ability. Accordingly, we found that the obesogenic diet reduced a hydrophobic BA, chenodeoxycholic acid (CDCA). Taken together, these findings implicate that BAs, tissue niches, and diet influence LD structural remodeling.

Lipid droplets (LDs) pack triacylglycerols (TAGs) with altered dimensions and exhibit distinct collagen orientation between the white and brown fat depots and are remodeled by bile acids (BAs) such that deletion of BA-receptor, Farnesoid X receptor (FXR) results in adipocyte hypertrophy.
Chasing the structural diversity of the transcription regulator Mycobacterium tuberculosis HigA2
Authors: Richardson William , Kang Gyun Won , Lee Hee Joong , Kwon Kang Mu , Kim Saron , Kim Hyo Jung
Published: August 2021

Transcription factors are the primary regulators of gene expression and recognize specific DNA sequences under diverse physiological conditions. Although they are vital for many important cellular processes, it remains unclear when and how transcription factors and DNA interact. The antitoxin from a toxin–antitoxin system is an example of negative transcriptional autoregulation: during expression of the cognate toxin it is suppressed through binding to a specific DNA sequence. In the present study, the antitoxin HigA2 from Mycobacterium tuberculosis M37Rv was structurally examined. The crystal structure of M. tuberculosis HigA2 comprises three sections: an N-terminal autocleavage region, an α-helix bundle which contains an HTH motif, and a C-terminal β-lid. The N-terminal region is responsible for toxin binding, but was shown to cleave spontaneously in its absence. The HTH motif performs a key role in DNA binding, with the C-terminal β-lid influencing the interaction by mediating the distance between the motifs. However, M. tuberculosis HigA2 exhibits a unique coordination of the HTH motif and no DNA-binding activity is detected. Three crystal structures of M. tuberculosis HigA2 show a flexible alignment of the HTH motif, which implies that the motif undergoes structural rearrangement to interact with DNA. This study reveals the molecular mechanisms of how transcription factors interact with partner proteins or DNA.
Structural characterization of hexameric shell proteins from two types of choline-utilization bacterial microcompartments
Authors: Ochoa Jessica M. , Mijares Oscar , Acosta Andrea A. , Escoto Xavier , Leon-Rivera Nancy , Marshall Joanna D. , Sawaya Michael R. , Yeates Todd O.
Published: August 2021

Bacterial microcompartments are large supramolecular structures comprising an outer proteinaceous shell that encapsulates various enzymes in order to optimize metabolic processes. The outer shells of bacterial microcompartments are made of several thousand protein subunits, generally forming hexameric building blocks based on the canonical bacterial microcompartment (BMC) domain. Among the diverse metabolic types of bacterial microcompartments, the structures of those that use glycyl radical enzymes to metabolize choline have not been adequately characterized. Here, six structures of hexameric shell proteins from type I and type II choline-utilization microcompartments are reported. Sequence and structure analysis reveals electrostatic surface properties that are shared between the four types of shell proteins described here.
New restraints and validation approaches for nucleic acid structures in PDB-REDO
Authors: de Vries Ida , Kwakman Tim , Lu Xiang-Jun , Hekkelman Maarten L. , Deshpande Mandar , Velankar Sameer , Perrakis Anastassis , Joosten Robbie P.
Published: August 2021

The quality of macromolecular structure models crucially depends on refinement and validation targets, which optimally describe the expected chemistry. Commonly used software for these two procedures has been designed and developed in a protein-centric manner, resulting in relatively few established features for the refinement and validation of nucleic acid-containing structure models. Here, new nucleic acid-specific approaches implemented in PDB-REDO are described, including a new restraint model using noncovalent geometries (base-pair hydrogen bonding and base-pair stacking) as refinement targets. New validation routines are also presented, including a metric for Watson–Crick base-pair geometry normality (Z
bpG). Applying the PDB-REDO pipeline with the new restraint model to the whole Protein Data Bank (PDB) demonstrates an overall positive effect on the quality of nucleic acid-containing structure models. Finally, we discuss examples of improvements in the geometry of specific nucleic acid structures in the PDB. The new PDB-REDO models and pipeline are available at https://pdb-redo.eu/.
How do I get the most out of my protein sequence using bioinformatics tools?
Authors: Pereira Joana , Alva Vikram
Published: August 2021

Biochemical and biophysical experiments are essential for uncovering the three-dimensional structure and biological role of a protein of interest. However, meaningful predictions can frequently also be made using bioinformatics resources that transfer knowledge from a well studied protein to an uncharacterized protein based on their evolutionary relatedness. These predictions are helpful in developing specific hypotheses to guide wet-laboratory experiments. Commonly used bioinformatics resources include methods to identify and predict conserved sequence motifs, protein domains, transmembrane segments, signal sequences, and secondary as well as tertiary structure. Here, several such methods available through the MPI Bioinformatics Toolkit (https://toolkit.tuebingen.mpg.de) are described and how their combined use can provide meaningful information on a protein of unknown function is demonstrated. In particular, the identification of homologs of known structure usingHHpred, internal repeats usingHHrepID, coiled coils usingPCOILSandDeepCoil, and transmembrane segments usingQuick2Dare focused on.
Stage-I Shariah compliant Macaulay’s duration model testing
Authors: Shah Syed Alamdar Ali , Sukmana Raditya , Fianto Bayu Arie
Published: August 2021

Purpose

The purpose of this study is to develop, test and examine econometric methodology for Sharīʿah-compliant duration models of Islamic banks.

Design/methodology/approach

The research evaluates all existing duration models from Sharīʿah’s perspective and develops a four-stage framework for testing Sharīʿah-compliant duration models. The econometric methodology consists of multiple regression, Johansen co-integration, error correction model, vector error correction model (VECM) and threshold vector error models (TVECM).

Findings

Regressions analysis suggests that returns on earning assets and interbank offered rates are significant factors for calculating the duration of earning assets, whereas returns paid on return bearing liabilities and average interbank rates of deposits are significant factors for duration of return bearing liabilities. VECM suggests that short run duration converges into long run duration and TVECM suggests that management of assets and liabilities also plays a significant role that can bring about a change of about 15% in respective durations.

Practical implications

Sharīʿah-compliant duration models will improve risk and Sharīʿah efficiency, which will ultimately improve market capitalization and returns stability of Islamic banks in the long run.

Originality/value

Sharīʿah-compliant duration models testing provides insight into how various factors, namely, rates of return, benchmark rates and managerial skills of Islamic bank risk managers impact durations of assets and liabilities. It also explains the future course of action for Sharīʿah-compliant duration model testing.
Anti-money laundering in the United Kingdom: new directions for a more effective regime
Authors: Pontes Rafael , Lewis Nick , McFarlane Paul , Craig Patrick
Published: August 2021

Purpose

This paper aims to provide a more nuanced understanding of the effectiveness of the anti-money laundering (AML) regime in the UK and explore opportunities to improve policy and performance.

Design/methodology/approach

Qualitative research design using semi-structured interviews and a focus group with practitioners from both public and private sectors.

Findings

This paper identifies preventive measures are underfunded by the public sector; there is a disconnect between the regulatory requirement and the regulators’ supervisory approach leading to the ineffective application of the risk-based approach; and authorities have limited ability to stop low-utility reports. Increased collaboration across institutions and sectors, better utilisation of innovative technologies and a sustainable funding plan are needed to drive a collective response to money laundering.

Research limitations/implications

Few practitioners in the industry have the knowledge and expertise to discuss the topic at a strategic level and participants were limited (n = 8).

Practical implications

This paper adds to the growing corpus of research showing that the AML regime in the UK is ineffective and needs reform.

Social implications

This paper encourages practitioners to improve the AML regime, this research contributes to the reform of the existing measures against financial crime.

Originality/value

This paper presents new data from AML practitioners to provide a better understanding of the limitations of the AML regime in the UK.
Does regulatory enforcement improve continuing disclosure? The municipal securities market case of the Municipalities Continuing Disclosure Cooperation (MCDC) initiative
Authors: Abbas Yulianti , Johnson Craig L.
Published: August 2021

Purpose

This paper analyzes the impact of increased federal regulatory enforcement from the SEC's Municipalities Continuing Disclosure Cooperation (MCDC) initiative on municipal debt issuers continuing disclosure practices.

Design/methodology/approach

We analyze the changes in continuing disclosure practices by estimating a series of difference-in-differences regressions based on variables representing issuers' changes in regulatory risk after the MCDC. The continuing disclosure data are hand-collected for 827 cities over a seven-year period.

Findings

The empirical findings indicate that increased regulatory enforcement has a significant impact on continuing disclosure compliance. We find increased enforcement has no impact on issuers that already have a higher probability of being monitored by federal regulators. We also find that an increase in continuing disclosure compliance does not automatically increase continuing disclosure timeliness.

Practical implications

The MCDC lacks monetary penalties for noncompliant bond issuers and no direct regulatory consequences exist for untimely disclosure. Our findings suggest that regulatory enforcement should be followed by adequate sanctions to emphasize the credibility of the enforcement threat and the SEC should consider requiring bond issuers to commit to the timely disclosure of significant information in offering documents.

Originality/value

This paper extends prior studies by analyzing regulatory risk in the market, and the ability of regulation to reduce disclosure compliance deficiencies in the municipal market. By focusing on the MCDC, this study is able to disentangle the impact of regulatory enforcement from the changes in accounting regulation.
Audit committee oversight of external audit: an examination of structural power and behavioural tactics
Authors: Sulaiman Noor Adwa , Mat Yasin Fatimah
Published: August 2021

Purpose

This study aims to examine the structural power wielded by the audit committee (AC) and the various bases of its power, whilst also exploring the behavioural tactics used by the AC to leverage its power in the oversight of the external audit.

Design/methodology/approach

Empirical evidence was drawn from semi-structured interviews with external auditors and AC members in Malaysia.

Findings

The AC’s structural power is derived from its formal and network position in the organisation. The AC possesses three forms of organisational-based power (legitimate, coercive and informational) resultant from its formal position, and these combine with the AC’s personal power (will and expert). The AC uses its personal power base to develop trusting relationships and to promote the exchange of information with other key corporate governance actors in the network position. Furthermore, the AC applies at least four behavioural tactics (assertiveness, ingratiation, rationality and coalition formation) to exercise its bases of power.

Originality/value

This study attempts to describe the AC’s structural sources of power, its organisational and personal power bases, and the behavioural tactics it uses when exerting its power.
Goal orientation and negotiation strategies: an empirical analysis
Authors: Asante-Asamani Abena Emily Ayowa , Elahee Mohammad , MacDonald Jason
Published: August 2021

Purpose

This study aims to examine how negotiators’ goal orientations may affect their negotiation strategy and consequently the negotiation outcomes.

Design/methodology/approach

Using cross-sectional data collected from a Fortune 500 Global firm based in France, this study empirically examines how goal orientations of negotiators may affect their value creation (win-win) and value-claiming (win-lose) negotiation behavior reflecting their desired outcome in a given sales negotiation. In so doing, this study proposes a conceptual model and tests a number of hypotheses using partial least squares structural equation modeling.

Findings

This study shows that learning and performance goal orientations (PGO) are indeed related with two commonly used negotiation strategies: win-win (integrative) and win-lose strategies (distributive) strategies, respectively. The results indicate that while the learning orientation has a positive relationship with a win-win strategy and a negative relationship with a win-lose negotiation strategy, just the opposite is true with the PGO, which is positively related to win-lose strategy and negatively related to win-win strategy.

Originality/value

To the best of the authors’ knowledge, this research represents one of the first attempts to connect goal orientations with negotiations strategies to achieve desired negotiation outcome using data from salespeople with negotiation experience.
Exploring human resource work design, learning mechanism and TQM: through the lens of activity theory and contextual learning theory
Authors: Ajgaonkar Suchitra , Neelam Netra , Behl Abhishek , Dao Le Trung , Lang Le Dang
Published: August 2021

Purpose

This research examines the effects of the context on the relationship between work design, learning mechanism and total quality management (TQM). The exploratory study examines the differential effects in context on how human resources and their activities are strategically managed for achieving TQM. Two theoretical frameworks – activity theory and contextual learning theory – are concurrently used for analysis. Specifically, the manufacturing companies, the authors examine are (1) technology-intensive company which has bought technology from a global foreign establishment (MU1), (2) technology-intensive companies having their own technology (MU2) and (3) labor-intensive units (MU3) of varying organizational sizes.

Design/methodology/approach

This case study-based research consists of 27 in-depth interviews with managers and employees of different hierarchies in each manufacturing unit. The authors interviewed them using semi-structured questions that were pre-validated by five senior HR experts from the manufacturing industry. Document analysis, multiple site visits and website content helped triangulation. The data are coded and analyzed using Dedoose software for qualitative research.

Findings

Activity diagrams for each manufacturing unit provides task and interaction analysis. Within and cross-case analysis address complexity and challenges of contextual reality, influences on work design and learning mechanism. HRD executives must recognize that there may be well-differentiated learning behaviors that align with organizational strategy. The learning behaviors may not be well-differentiated and become very dynamic. This dynamism may be characterized by double loop and single-loop learning feeding into each other.

Practical implications

This study provides substantial practical implications for HRD and other managers in the manufacturing sector.

Originality/value

The new theoretical framework adds to organizational behavior studies through multi-level and cross-contextual approach. It informs strategic combinations and interactions between internal and external context, and learning needs implicating work design and TQM.