bluuebunny/crossref_metadata_2025 huggingface dataset:
Does Prior Breast Augmentation Affect Outcomes After Mastectomy With Reconstruction? An Analysis of Postoperative Complications and Reoperations
Authors: Hammond Jacob B. , Foley Brittany M. , James Sheridan , Rebecca Alanna M. , Teven Chad M. , Kruger Erwin A. , Kosiorek Heidi E. , Cronin Patricia A. , Bernard Robert W. , Pockaj Barbara A. , Casey William J.
Published: November 2020

Background

The purpose of this study is to evaluate how prior breast augmentation impacts rates of complications and risk for reoperation after mastectomy with concurrent breast reconstruction.

Methods

Patients undergoing nipple-sparing, skin-sparing, or simple mastectomy with implant-based reconstruction from 2008 to 2018 were identified in a prospective database. Postoperative complications and reoperations were then analyzed comparing patients with prior augmentation to patients without history of previous breast surgery.

Results

A total of 468 patients were identified with a median follow-up of 4 years. Of these, 72 had prior augmentation mammoplasty. These patients underwent nipple-sparing (52, 72%), skin-sparing (15, 21%), or simple (5, 7%) mastectomy with immediate direct-to-implant (46, 61%) or tissue expander (26, 35%) reconstruction. On univariate analysis, this cohort had a lower body mass index (23.3 vs 25.3, P = 0.003), a higher rate of nipple-sparing mastectomy (72% vs 54%, P = 0.01), and a higher prevalence of stage I disease (44% vs 33%, P = 0.04). Differences in age, comorbidities, reconstructive techniques, tumor size, and neoadjuvant/adjuvant therapies were not significant. Overall complication rate between patients with or without prior augmentation did not significantly differ (51% vs 50%, P = 0.83); no significant differences in rates of surgical site infection, hematoma, mastectomy skin flap/wound necrosis, nipple complications, implant loss, or capsular contracture were found. Analysis of reoperations between patients with and without prior augmentation revealed no significant differences in average number of subsequent planned, unplanned, or total reoperations. On multivariate analysis, prior breast augmentation was found to be associated with significantly increased risk for undergoing ≥1 unplanned reoperation (odds ratio, 2.28; 95% confidence interval, 1.28–4.05, P = 0.005).

Conclusions

Prior augmentation mammoplasty does not significantly affect rates of postoperative complications after mastectomy with concurrent reconstruction. Although prior augmentation does not affect number of subsequent reoperations on average, it does increase the risk of experiencing 1 or more unplanned reoperation after mastectomy with reconstruction.
Does Water-Jet Force Affect Cryopreserved Adipose-Derived Stem Cells? Evidence of Improved Cell Viability and Fat Graft Survival
Authors: Qu Yaping , Luan Jie , Mu Dali , Wang Qian , Li Zifei , Liu Tong , Fu Su
Published: November 2020

Background

Adipose tissue harvested by liposuctions is an available source of adipose-derived stem cells (ASCs). Water-jet–assisted liposuction is a favorable method for fat collection with little mechanical damage. This study aimed to investigate whether or not the water-jet–assisted liposuction made a difference in the biological characteristics of cryopreserved ASCs and fat graft survival in cell-assisted lipotransfer.

Methods

Human lipoaspirates were obtained from the abdomen or thighs of 20 female participants for body contouring. A single surgeon randomly harvested 50 mL of adipose tissue by the water-jet–assisted liposuction and the conventional liposuction, respectively. Adipose-derived stem cells were isolated from lipoaspirates and then cryopreserved for 4 weeks. Cryopreserved ASCs were used to examine the surface markers, cell proliferation, migration, and adipogenic differentiation in vitro. The fat survival of ASCs-enriched grafts from different liposuctions was measured in animal models.

Results

The cryopreserved ASCs with the water-jet assistance had better capacities of cell proliferation, migration, and adipogenic differentiation and achieved a better survival result of ASCs-enriched fat grafting.

Conclusions

Cryopreservation of ASCs with the water-jet force showed more excellent biological characteristics. The water-jet–assisted liposuction was superior to the conventional liposuction in obtaining ASCs and fat survival of coimplantation with grafts.
The Role of a Deep Neuromuscular Block in the Treatment of Mandibular Subcondylar Fractures
Authors: Bonavolontà Paola , Orabona Giovanni Dell’Aversana , Cama Antonia , Maglitto Fabio , Abbate Vincenzo , Romano Antonio , Piombino Pasquale , Iaconetta Giorgio , Califano Luigi
Published: November 2020

Mandibular fractures are the third most frequents maxillo-facial fractures. Most frequent site is the subcondylar region. Different approaches to reach subcondylar region, have been described. In the study was evaluated the advantages of neuromuscular block during endoscopic surgery for subcondylar fractures. Twenty-five patients affected by subcondylar fractures were enrolled in this study and divided in 2 groups; group A: patients who received an intraoperative booster of curare during surgical procedure and group B patients who underwent surgery treated without the intraoperative booster of curare. All patients were treated successfully by endoscope-assisted transoral approach. The analysis of time required for surgery showed a reduction in group A comparing to group B. The mean time for surgery for the patients in group B with displacement between 0° and 45° was 170 minutes, and for 45° to 90° was 230 minutes. In group A, the mean time was 117.5 minutes for patients with condylar displacement between 0° and 45°, and 147.5 minutes for the other group. In conclusion, deep neuromuscular block seems to improve the surgical conditions in patients undergoing subcondylar endoscopic assisted surgery, further study needs to assess this surgical technique in order to better define this surgical protocol.
Significance of Uncinate Duct Dilatation in IPMNs
Authors: AlMasri Samer S. , Zenati Mazen S. , Dasyam Anil , Singhi Aatur D. , Lee Kenneth K. , Bartlett David L. , Slivka Adam , Mcgrath Kevin , Chennat Jennifer , Fasanella Kenneth E. , Khalid Asif , Brand Randall E. , Sarkaria Savreet , Das Rohit , Hogg Melissa E. , Zeh Herbert J. , Paniccia Alessandro , Zureikat Amer H.
Published: November 2020

Objective:

To evaluate the significance of UDD in IPMNs.

Background:

The uncinate process of the pancreas has an independent ductal drainage system. International consensus guidelines of IPMNs still consider it as a branch-duct, even though it is the main drainage system for the uncinate process.

Methods:

A retrospective review of all surgically treated IPMNs at our institution after 2008 was performed. Preoperative radiological studies were reviewed by an abdominal radiologist who was blinded to the pathological results. In addition to the Fukuoka criteria, presence of UDD was recorded. Using multivariate analysis, the pathological significance of UDD in predicting advanced neoplasia [high grade dysplasia or invasive carcinoma (HGD/ IC)] was determined.

Results:

Two hundred sixty patients were identified (mean age at diagnosis was 68 years and 49% were females): 122 (47%) had HGD/IC. UDD was noted in 59 (23%), of which 36 (61%) had HGD/IC (P < 0.003). On multivariate analysis, UDD was an independent predictor of HGD/IC (odds ratio = 2.99, P < 0.04). Subgroup analysis on patients with IPMNs confined to the dorsal portion of the gland (n = 161), also demonstrated UDD to be a significant predictor of HGD/IC in those remote lesions (odds ratio: 4.41, P = 0.039).

Conclusions:

This is the largest study to evaluate the significance of UDD in IPMNs and shows it to be a high-risk feature. This association persisted for remote IPMNs limited to the dorsal pancreas, suggesting UDD may be associated with an aggressive phenotype even in remote IPMN lesions.
A More Extensive Lymphadenectomy Enhances Survival After Neoadjuvant Chemoradiotherapy in Locally Advanced Esophageal Adenocarcinoma
Authors: Sihag Smita , Nobel Tamar , Hsu Meier , Tan Kay See , Carr Rebecca , Janjigian Yelena Y. , Tang Laura H. , Wu Abraham J. , Bott Matthew J. , Isbell James M. , Bains Manjit S. , Jones David R. , Molena Daniela
Published: November 2020

Objective:

We sought to determine the extent of lymphadenectomy that optimizes staging and survival in patients with locally advanced EAC treated with neoadjuvant chemoradiotherapy followed by esophagectomy.

Summary of Background Data:

Several studies have found that a more extensive lymphadenectomy leads to better disease-specific survival in patients treated with surgery alone. Few studies, however, have investigated whether this association exists for patients treated with neoadjuvant chemoradiotherapy.

Methods:

We examined our prospective database and identified patients with EAC treated with neoadjuvant chemoradiotherapy followed by esophagectomy between 1995 and 2017. Overall survival (OS) and DFS were estimated using Kaplan-Meier methods, and a multivariable Cox proportional hazards model was used to identify independent predictors of OS and DFS. The relationship between the total number of nodes removed and 5-year OS or DFS was plotted using restricted cubic spline functions.

Results:

In total, 778 patients met the inclusion criteria. The median number of excised nodes was 21 (interquartile range, 16–27). A lower number of excised lymph nodes was independently associated with worse OS and DFS (OS: hazard ratio, 0.98; confidence interval, 0.97–1.00; P = 0.013; DFS: hazard ratio, 0.99; confidence interval, 0.98–1.00; P = 0.028). Removing 25 to 30 lymph nodes was associated with a 10% risk of missing a positive lymph node. Both OS and DFS improved with up to 20 to 25 lymph nodes removed, regardless of treatment response.

Conclusions:

The optimal extent of lymphadenectomy to enhance both staging and survival after chemoradiotherapy, regardless of treatment response, is approximately 25 lymph nodes.
Intimate Partner Violence Among Surgeons: We are Not Immune
Authors: Stein Sharon L. , Bliggenstorfer Jonathan T. , Ofshteyn Asya , Henry Marion C. , Turner Patricia , Bass Barbara , Hollands Celeste , Steinhagen Emily , Crandall Marie
Published: November 2020

Objective:

The incidence and risk factors for IPV are not well-studied among surgeons. We sought to fill this gap in knowledge by surveying surgeons to estimate the incidence and identify risk factors associated with IPV.

Summary of Background Data:

An estimated 36.4% of women and 33.6% of men in the United States have experienced IPV. Risk factors include low SES, non-White ethnicity, psychiatric disorders, alcohol and drug abuse, and history of childhood abuse. Families with higher SES are not exempt from IPV, yet there is very little data examining incidence and risk factors among these populations.

Methods:

An anonymous online survey targeting US-based surgeons was distributed through 4 major surgical societies. Demographics, history of abuse, and related factors were assessed. Chi-square analysis and multivariable logistic regression were utilized to evaluate for potential risk factors of IPV.

Results:

Eight hundred eighty-two practicing surgeons and trainees completed the survey, of whom 536 (61%) reported experiencing some form of behavior consistent with IPV. The majority of respondents were women (74.1%, P = 0.004). Emotional abuse was most common (57.3%), followed by controlling behavior (35.6%), physical abuse (13.1%), and sexual abuse (9.6%).

History of mental illness, [odds ratio (OR) 2.32, P < 0.001], alcohol use (frequent/daily OR 1.76, P = 0.035 and occasional OR 1.78, P = 0.015), childhood physical abuse (OR 1.96, P = 0.020), childhood emotional abuse (OR 1.76, P = 0.008), and female sex (OR 1.46, P = 0.022) were associated with IPV.

Conclusions:

As the first national study of IPV among surgeons, this analysis demonstrates surgeons experience IPV and share similar risk factors to the general population.
The effect of intracerebral structure volumes on idiopathic intracranial hypertension
Authors: Ozkal Birol , Ozen Ozkan
Published: November 2020

Background

This aim of this study was to assess the effect of idiopathic intracranial hypertension (IIH) in the development of intracranial hypertension by measuring patients’ cerebrospinal fluid (CSF), brain, and segment volumes. IIH is a disease of unknown cause characterized by chronic CSF pressure elevation and papillary edema. Under the Monro–Kellie doctrine, efforts have been made to explain the disease through an increase in the volumes of one or two of brain, blood or CSF in the intracranial cavity, although these have not been completely successful.

Methods

Twelve IIH patients diagnosed based on the modified Dandy criteria and 15 age- and sex-compatible healthy controls were included in the study. Cases’ 3D T1 sequence images were evaluated using the voxel-based volumetric analysis system (volBrain). Intracranial cavity extraction, macrostructures, and subcortical structure volumes were measured and compared.

Results

No statistically significant differences were observed between control cases’ and IIH patients’ CSF, cerebrum, cerebellum, brainstem, and subcortical structure volumes.

Conclusion

IIH arises from a chronic cause that does not impair the volumetric balance between structures inside the intracerebral cavity.
Elevated Skin pH Is Associated With an Increased Permeability to Synthetic Urine
Authors: Koudounas Sofoklis , Bader Dan L. , Voegeli David
Published: November 2020

PURPOSE:

The aim of this study was to investigate the permeability of the skin following cleansing activities and its susceptibility to synthetic urine penetration.

SUBJECTS AND SETTING:

Ten healthy volunteers (aged 22-58 years) participated in the study, which was conducted in a university bioengineering laboratory.

METHODS:

Tape stripping and sodium lauryl sulfate were used to simulate the physical and chemical irritation exacerbated by frequent cleansing activities, respectively. An untreated site also was selected to evaluate responses of intact skin. Synthetic urine was then applied for a period of 2 hours. Measurements of transepidermal water loss and skin pH were taken at baseline and after each challenge. To quantify the permeability of the skin following exposure, desorption curves of transepidermal water loss were measured and skin surface water loss was calculated.

RESULTS:

Chemically irritated skin, characterized by increased pH (7.34 ± 0.22), demonstrated an increased permeability to urine, as reflected by a significant increase in mean skin surface water loss (46,209 ± 15,596 g/m2) compared to both the intact (14,631 ± 6164 g/m2) and physically irritated (14,545 ± 4051 g/m2) skin (P = .005 in both cases). In contrast, the differences between the intact and physically irritated skin were not significant (P = .88).

CONCLUSION:

Permeability of the skin to irritants is influenced by the status of the skin and its acid mantle. These highlight the need to reevaluate the frequency of cleansing activities, along with the choice of product in clinical settings, favoring the use of pH-balanced cleansers.
An Early Assessment of Curfew and Second COVID-19 Lock-down on Virus Propagation in France
Authors: Baunez Christelle , Degoulet Mickael , Luchini Stéphane , Pintus Patrick A. , Teschl Miriam
Published: November 2020

This note provides an early assessment of the reinforced measures to curb the COVID-19 pandemic in France, which include a curfew of selected areas and culminate in a second COVID-19-related lock-down that started on October 30, 2020 and is still ongoing. We analyse the change in virus propagation across age groups and across départements using an acceleration index introduced in Baunez et al. (2020). We find that while the pandemic is still in the acceleration regime, acceleration decreased notably with curfew measures and this more rapidly so for the more vulnerable population group, that is, for people older than 60. Acceleration continued to decline under lock-down, but more so for the active population under 60 than for those above 60. For the youngest population aged 0 to 19, curfew measures did not reduce acceleration but lock-down does. This suggests that if health policies aim at protecting the elderly population generally more at risk to suffer severe consequences from COVID-19, curfew measures may be effective enough. However, looking at the departmental map of France, we find that curfews have not necessarily been imposed in départements where acceleration was the largest.

JEL Classification Numbers

I18; H12
Lack of immune homology with vaccine preventable pathogens suggests childhood immunizations do not protect against SARS-CoV-2 through adaptive cross-immunity
Authors: Guo Weihua , Lee Kyle O. , Lee Peter P.
Published: November 2020

Abstract (Summary)

Recent epidemiological studies have investigated the potential effects of childhood immunization history on COVID-19 severity. Specifically, prior exposure to Bacillus Calmette–Guérin (BCG) vaccine, oral poliovirus vaccine (OPV), or measles vaccine have been postulated to reduce COVID-19 severity – putative mechanism is via stimulation of the innate immune system to provide broader protection against non-specific pathogens. While these epidemiological results remain inconclusive, we sought to investigate the potential role of adaptive immunity via cross-reactivity between vaccine preventable diseases (VPDs) with SARS-CoV-2. We implemented a comprehensive exploration of immune homology (including sequence homology, immune epitopes, and glycosylation patterns) between SARS-CoV-2 and all pathogens with FDA-approved vaccines. Sequence homology did not reveal significant alignments of protein sequences between SARS-CoV-2 with any VPD pathogens, including BCG-related strains. We also could not identify any shared T or B cell epitopes between SARS-CoV-2 and VPD pathogens among either experimentally validated epitopes or predicted immune epitopes. For N-glycosylation (N-glyc), while sites with the same tripeptides could be found between SARS-CoV-2 and certain VPD pathogens, their glycosylation potentials and positions were different. In summary, lack of immune homology between SARS-CoV-2 and VPD pathogens suggests that childhood immunization history (i.e., BCG vaccination or others) does not provide protection from SARS-CoV-2 through adaptive cross-immunity.

Highlights

Comprehensive exploration of immune homology for SARS-CoV-2 with 34 vaccine preventable pathogens covering all FDA-approved vaccines.

Little to no immune homology between SARS-CoV-2 and VPD pathogens: insignificant aligned protein sequences, unmapped immune epitopes, or matched N-glycosylation sites with different glycosylation potentials and positions.

BCG vaccination is unlikely to confer SARS-CoV-2 protection through adaptive cross-immunity.

Graphic summary
Plasma Markers of Disrupted Gut Permeability in Severe COVID-19 Patients
Authors: Giron Leila B. , Dweep Harsh , Yin Xiangfan , Wang Han , Damra Mohammad , Goldman Aaron R. , Gorman Nicole , Palmer Clovis S. , Tang Hsin-Yao , Shaikh Maliha W. , Forsyth Christopher B. , Balk Robert A. , Zilberstein Netanel F , Liu Qin , Kossenkov Andrew , Keshavarzian Ali , Landay Alan , Abdel-Mohsen Mohamed
Published: November 2020

A disruption of the crosstalk between the gut and the lung has been implicated as a driver of severity during respiratory-related diseases. Lung injury causes systemic inflammation, which disrupts gut barrier integrity, increasing the permeability to gut microbes and their products. This exacerbates inflammation, resulting in positive feedback. We aimed to test whether severe Coronavirus disease 2019 (COVID-19) is associated with markers of disrupted gut permeability. We applied a multi-omic systems biology approach to analyze plasma samples from COVID-19 patients with varying disease severity and SARS-CoV-2 negative controls. We investigated the potential links between plasma markers of gut barrier integrity, microbial translocation, systemic inflammation, metabolome, lipidome, and glycome, and COVID-19 severity. We found that severe COVID-19 is associated with high levels of markers of tight junction permeability and translocation of bacterial and fungal products into the blood. These markers of disrupted intestinal barrier integrity and microbial translocation correlate strongly with higher levels of markers of systemic inflammation and immune activation, lower levels of markers of intestinal function, disrupted plasma metabolome and glycome, and higher mortality rate. Our study highlights an underappreciated factor with significant clinical implications, disruption in gut functions, as a potential force that may contribute to COVID-19 severity.
Multi-state network meta-analysis of progression and survival data
Authors: Jansen Jeroen P. , Incerti Devin , Trikalinos Thomas A.
Published: November 2020

Multiple randomized controlled trials, each comparing a subset of competing interventions, can be synthesized by means of a network meta-analysis to estimate relative treatment effects between all interventions in the evidence base. Here we focus on estimating relative treatment effects for time-to-event outcomes. Cancer treatment effectiveness is frequently quantified by analyzing overall survival (OS) and progression-free survival (PFS). We introduce a method for the joint network meta-analysis of PFS and OS that is based on a time-inhomogeneous tri-state (stable, progression, and death) Markov model where time-varying transition rates and relative treatment effects are modeled with parametric survival functions or fractional polynomials. The data needed to run these analyses can be extracted directly from published survival curves. We demonstrate use by applying the methodology to a network of trials for the treatment of non-small-cell lung cancer. The proposed approach allows the joint synthesis of OS and PFS, relaxes the proportional hazards assumption, extends to a network of more than two treatments, and simplifies the parameterization of decision and cost-effectiveness analyses.
Trecode: a FAIR eco-system for the analysis and archiving of omics data in a combined diagnostic and research setting
Authors: Kerstens Hindrik HD , Hehir-Kwa Jayne Y , van de Geer Ellen , van Run Chris , Verwiel Eugène TP , van der Leest Douwe , Tops Bastiaan BJ , Kemmeren Patrick
Published: November 2020

Motivation

The increase in speed, reliability and cost-effectiveness of high-throughput sequencing has led to the widespread clinical application of genome (WGS), exome (WXS) and transcriptome analysis. WXS and RNA sequencing is now being implemented as standard of care for patients and for patients included in clinical studies. To keep track of sample relationships and analyses, a platform is needed that can unify metadata for diverse sequencing strategies with sample metadata whilst supporting automated and reproducible analyses. In essence ensuring that analysis is conducted consistently, and data is Findable, Accessible, Interoperable and Reusable (FAIR).

Results

We present “Trecode”, a framework that records both clinical and research sample (meta) data and manages computational genome analysis workflows executed for both settings. Thereby achieving tight integration between analyses results and sample metadata. With complete, consistent and FAIR (meta) data management in a single platform, stacked bioinformatic analyses are performed automatically and tracked by the database ensuring data provenance, reproducibility and reusability which is key in worldwide collaborative translational research.

Availability and implementation

The Trecode data model, codebooks, NGS workflows and client programs are currently being cleared from local compute infrastructure dependencies and will become publicly available in spring 2021.

Contact

p.kemmeren@prinsesmaximacentrum.nl
Intranasal Administration of ACIS KEPTIDE™ Prevents SARS-CoV2-Induced Acute Toxicity in K18-hACE2 Humanized Mouse Model of COVID-19: A Mechanistic Insight for the Prophylactic Role of KEPTIDE™ in COVID-19
Authors: Gottschalk Gunnar , Keating James F , Kesler Kris , Knox Konstance , Roy Avik
Published: November 2020

Previously, we have demonstrated that ACIS KEPTIDE™, a chemically modified peptide, selectively binds to ACE-2 receptor and prevents the entry of SARS-CoV2 virionsin vitroin primate kidney Cells. However, it is not known if ACIS KEPTIDE™ attenuates the entry of SARS-CoV2 virusin vivoin lung and kidney tissues, protects health, and prevent death once applied through intranasal route. In our current manuscript, we demonstrated that the intranasal administration of SARS-CoV2 (1*106) strongly induced the expression of ACE-2, promoted the entry of virions into the lung and kidney cells, caused acute histopathological toxicities, and mortality (28%). Interestingly, thirty-minutes of pre-treatment with 50 μg/Kg Body weight ACIS normalized the expression of ACE-2 via receptor internalization, strongly mitigated that viral entry, and prevented mortality suggesting its prospect as a prophylactic therapy in the treatment of COVID-19. On the contrary, the peptide backbone of ACIS was unable to normalize the expression of ACE-2, failed to improve the health vital signs and histopathological abnormalities. In summary, our results suggest that ACIS is a potential vaccine-alternative, prophylactic agent that prevents entry of SARS-CoV2in vivo, significantly improves respiratory health and also dramatically prevents acute mortality in K18-hACE2 humanized mice.

Highlights

ACIS KEPTIDE stimulates the internalization of ACE-2 receptor (Fig. 2) and buffers the membrane localization of ACE-2 receptors (Fig. 2, 6 & 8). Intranasal inoculation of SARS-CoV2 upregulates the expression of ACE-2 in lung epithelium (Fig.6) and kidney tubular cells (Fig.8). ACIS KEPTIDE normalizes the expression of ACE-2 in the kidney tubular cells of virus-treated K18-hACE2mice (Fig. 8).

ACIS KEPTIDE™completely preventsthe entry of SARS-CoV2 in Bronchiolar epithelium (Fig.6), alveolar parenchyma (Fig. 6), and kidney tubular cells (Fig.8).

ACIS KEPTIDE™ improves the pulmonary (Fig. 5) and renal pathological changes (Fig. 7) caused by the SARS-CoV2 virus insult.

Intranasal administration of 0.05% Beta-propiolactone (βPL)-inactivated SARS-CoV2 (1 *106) causes significant death (28%) in K18-hACE2 humanized mice after 24 hrs of intranasal inoculation (Supplemental videos) suggesting that SARS-CoV2 doesnotrequire its infective properties and genetic mechanism to be functional to cause mortality.

The peptide backbone of ACIS KEPTIDE™ provides much less and insignificant protection in the prevention of pathological changes in Lungs (Fig.5 & 6) and Kidney (Fig.7 & 8). Peptide failed to normalize the upscaled expression of ACE-2 in kidney tubular cells (Fig.8) of SARS-CoV2-treated K18-hACE2 mice.
Combining climatic and genomic data improves range-wide tree height growth prediction in a forest tree
Authors: Archambeau Juliette , Garzón Marta Benito , Barraquand Frédéric , de Miguel Vega Marina , Plomion Christophe , González-Martínez Santiago C.
Published: November 2020

Population response functions based on climatic and phenotypic data from common gardens have long been the gold standard for predicting quantitative trait variation in new environments. However, prediction accuracy might be enhanced by incorporating genomic information that captures the neutral and adaptive processes behind intra-population genetic variation. We used five clonal common gardens containing 34 provenances (523 genotypes) of maritime pine (Pinus pinasterAiton) to determine whether models combining climatic and genomic data capture the underlying drivers of height-growth variation, and thus improve predictions at large geographical scales. The plastic component explained most of the height-growth variation, probably resulting from population responses to multiple environmental factors. The genetic component stemmed mainly from climate adaptation, and the distinct demographic and selective histories of the different maritime pine gene pools. Models combining climate-of-origin and gene pool of the provenances, and positive-effect height-associated alleles (PEAs) captured most of the genetic component of height-growth and better predicted new provenances compared to the climate-based population response functions. Regionally-selected PEAs were better predictors than globally-selected PEAs, showing high predictive ability in some environments, even when included alone in the models. These results are therefore promising for the future use of genome-based prediction of quantitative traits.
Chest CT features of COVID-19 in the region of Abu Dhabi, UAE- A single institute study
Authors: Saeed Ghufran Aref , Al Helali Abeer Ahmed , Almazrouei Safaa , Shah Asad , Ahmed Luai A.
Published: November 2020

OBJECTIVE

Our aim is to investigate high resolution CT features of COVID-19 infection in Abu Dhabi, UAE, and to compare the diagnostic performance of CT scan with RT-PCR test.

METHODS

Data of consecutive patients who were suspected to have COVID-19 infection and presented to our hospital, was collected from March 2, 2020, until April 12, 2020. All patients underwent RT-PCR test; out of which 53.8% had chest CT scan done. Using RT-PCR as a standard reference, the sensitivity and specify of CT scan was calculated. We also analyzed the most common imaging findings in patients with positive RT-PCR results.

RESULTS

The typical HRCT findings were seen in 50 scans (65.8%) out of total positive ones; 44 (77.2%) with positive RT-PCR results and 6 (31.6%) with negative results. The peripheral disease distribution was seen in 86%, multilobe involvement in 70%, bilateral in 82%, and posterior in 82% of the 50 scans.

The ground glass opacities were seen in 50/74 (89.3%) of positive RT-PCR group. The recognized GGO patterns in these scans were: rounded 50%, linear 38%, and crazy-paving 24%.

Using RT-PCR as a standard of reference, chest HRCT scan revealed sensitivity of 68.8% and specificity of 70%.

CONCLUSION

The commonest HRCT findings in patients with COVID-19 pneumonia were peripheral, posterior, bilateral, multilobe rounded ground glass opacities.
Melt into the group Electrophysiological Evidence of Gestalt Perception of Human Dyad
Authors: Mersad Karima , Caristan Céline
Published: November 2020

It has been shown recently that the human brain has dedicated networks for perception of human bodies in synchronous motion or in situation of interaction. However, below motion and interaction, how does the brain process a simple plurality of humans in close positioning? We used EEG frequency tagging technique to investigate integration of human dyad elements in a global percept. We presented to participants images of two silhouettes, a man and a woman flickering at different frequencies (5.88 vs.7.14Hz). Clear response at these stimulation frequencies reflected response to dyad parts, both when the dyad was presented upright and inverted. However, an emerging intermodulation component (7.14 + 5.88 = 13.02 Hz), a nonlinear response regarded as an objective signature of holistic representation, was significantly enhanced in upright relatively to inverted position. Inversion effect was significant only for the intermodulation component as opposed to stimulation frequencies revealing that dyad configuration perception overrides structural properties of dyad elements. Inversion effect was not significant for a pair of non-human objects. Our results show that merely facing two humans in close positioning leads to perceptually bind them and suggest that the perception of individuals is of different nature when they form a plurality.
Set-Min sketch: a probabilistic map for power-law distributions with application tok-mer annotation
Authors: Shibuya Yoshihiro , Belazzougui Djamal , Kucherov Gregory
Published: November 2020

Abstract

Motivation

In many bioinformatics pipelines,k-mer counting is often a required step, with existing methods focusing on optimizing time or memory usage. These methods usually produce very large count tables explicitly representingk-mers themselves. Solutions avoiding explicit representation ofk-mers include Minimal Perfect Hash Functions (MPHFs) or Count-Min sketches. The former is only applicable to static maps not subject to updates, while the latter suffers from potentially very large point-query errors, making it unsuitable when counters are required to be highly accurate.

Results

We introduce Set-Min sketch – a sketching technique for representing associative maps inspired by Count-Min sketch – and apply it to the problem of representingk-mer count tables. Set-Min is provably more accurate than both Count-Min and Max-Min – an improved variant of Count-Min for static datasets that we define here. We show that Set-Min sketch provides a very low error rate, both in terms of the probability and the size of errors, at the expense of a very moderate memory increase. On the other hand, Set-Min sketches are shown to take up to an order of magnitude less space than MPHF-based solutions, especially for large values ofk. Space-efficiency of Set-Min takes advantage of the power-law distribution ofk-mer counts in genomic datasets.

Availability

https://github.com/yhhshb/fress
Leveraging Hardy–Weinberg disequilibrium for association testing in case-control studies
Authors: Zhang Lin , Sun Lei
Published: November 2020

In a case-control association study, deviation from Hardy-Weinberg equilibrium (HWE) or Hardy-Weinberg dis-equilibrium (HWD) in the control group is usually considered as evidence for potential genotyping error, and the corresponding SNP is then removed from the study. On the other hand, assuming HWE holds in the study population, a truly associated SNP is expected to be out of HWE in the case group. Efforts have been made in combining association tests with tests of HWE in the cases to increase the power of detecting disease susceptibility loci (Song and Elston (2006), Wang and Shete (2010)). However, these existing methods are ad-hoc and sensitive to model assumptions. Utilizing the recent robust allele-based (RA) regression model for conducting allelic association tests (Zhang and Sun (2020)), here we propose a joint RA test that naturally integrates association evidence from the traditional association test and a test that evaluates the difference in HWD between the case and control groups. The proposed test is robust to genotyping error, as well as to potential HWD in the population attributed to factors that are unrelated to phenotype-genotype association. We provide the asymptotic distribution of the proposed test statistic so that it is easy to implement, and we demonstrate the accuracy and efficiency of the test through extensive simulation studies and an application.
Evaluation of two RT-PCR techniques for SARS-CoV-2 RNA detection in serum for microbiological diagnosis
Authors: Martin Ramirez Alexandra , Zurita Cruz Nelly Daniella , Gutierrez-Cobos Ainhoa , Rodriguez Serrano Diego Anibal , Gonzalez Alvaro Isidoro , Roy Vallejo Emilia , Gomez de Frutos Sara , Fontan Garcia-Rodrigo Leticia , Cardenoso Domingo Laura
Published: November 2020

Presence of SARS-CoV-2 RNA in serum (viraemia) in COVID-19 patients has been related to poor prognosis and death.
The aim of this study was to evaluate the ability of two commercial reverse real-time-PCR (rRT-PCR) kits, cobas SARS-CoV-2 (Cobas test) and TaqPath COVID-19 CE-IVD RT-PCR Kit (Taqpath test), to detect viraemia in COVID-19 patients and their implementation as routine diagnosis in microbiology laboratory.
This retrospective cohort study was conducted with 203 adult patients admitted to Hospital Universitario de La Princesa, (89 Intensive Care Unit and 114 ward) with at least one serum sample collected in the first 48 hours from admission. A total 265 serum samples were included for study.
Evaluation of both rRT-PCR techniques was performed comparing with the gold standard, a Novel Coronavirus (2019-nCoV) Nucleic Acid Diagnostic Kit; considering at least one target as a positive result.
Comparison of Cobas test and Taqpath test with the gold standard method, showed high values of specificity (93.75 and 92.19 respectively) and Positive Predictive Value (92.92 and 99.88 respectively). Nevertheless, sensitivity (53.72 and 73.63 respectively) and Negative Predictive Value (32.53 and 42.99 respectively) were lower; Kappa values were 0.35 for cobas test and 0.56 for Taqpath test.
For both techniques, differences of viraemia detection between the ICU and non-ICU patients were significant (p<0.001).
Consequently, SARS-CoV-2 viraemia positive results obtained by both rRT-PCR should be considered good tools and may help in handling COVID-19 patients.
Moreover, these methods could be easily integrated in the routine laboratory COVID-19 diagnosis and may open new strategies based on an early COVID-19 treatment.
Transcriptome Profiling of different types of human respiratory tract cells infected by SARS-CoV-2 Highlight an unique Role for Inflammatory and Interferon Response
Authors: Yang Minghui , Lei Luping , Cao Qiumei , Yang Yang , Wang Jun , Jiang Xiao , Huang Kun , Lai Jinzhi , Qing Ling , Wang Yu , Liu Yingxia
Published: November 2020

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease (COVID-19) at the end of 2019 has caused a large global outbreak and now become a major public health issue. Lack of data underlying how the human host interacts with SARS-CoV-2 virus. In the current study, We performed Venn-analysis, Gene ontology (GO), KEGG pathway analysis and Protein-protein interaction analysis of whole transcriptome studies with the aim of clarifying the genes and pathways potentially altered during human respiratory tract cells infected with SARS-CoV-2. We selected four studies through a systematic search of the Gene Expression Omnibus (GEO) database or published article about SARS-CoV-2 infection in different types of respiratory tract cells. We found 36 overlapping upregulated genes among different types of cells after viral infection. Further functional enrichment analysis revealed these DEGs are most likely involved in biological processes related to inflammatory response and response to cytokine, cell component related to extracellular space and I-kappaB/NF-kappaB complex, molecular function related to protein binding and cytokine activity. KEGG pathways analysis highlighted altered conical and casual pathways related to TNF, NF-kappa B, Cytokine-cytokine receptor interaction and IL17 signaling pathways during SARS-CoV-2 infection with CXCL1, CXCL2, CXCL3, CXCL8, CXCL10, IL32, CX3CL1, CCL20, IRF1, NFKB2 and NFKB1A up-regulated which may explain the inflammatory cytokine storms associated with severe cases of COVID-19.
The landscape of autosomal-recessive pathogenic variants in European populations reveals phenotype-specific effects
Authors: Fridman Hila , Yntema Helger G. , Mägi Reedik , Andreson Reidar , Metspalu Andres , Mezzavila Massimo , Tyler-Smith Chris , Xue Yali , Carmi Shai , Levy-Lahad Ephrat , Gilissen Christian , Brunner Han G.
Published: November 2020

The number and distribution of recessive alleles in the population for various diseases are not known at genome-wide-scale. Based on 6447 exome-sequences of healthy, genetically-unrelated Europeans of two distinct ancestries, we estimate that every individual is a carrier of at least 2 pathogenic variants in currently known autosomal recessive (AR) genes, and that 0.8-1% of European couples are at-risk of having a child affected with a severe AR genetic disorder. This risk is 16.5-fold higher for first cousins, but is significantly more increased for skeletal disorders and intellectual disabilities due to their distinct genetic architecture.
C. eleganshermaphrodites undergo semelparous reproductive death
Authors: Kern Carina C. , Srivastava Shivangi , Ezcurra Marina , Hui Nancy , Townsend StJohn , Maczik Dominik , Tse Victoria , Bähler Jürg , Gems David
Published: November 2020

Ageing in the nematodeCaenorhabditis elegansis unusual in terms of the severity and early onset of senescent pathology, particularly affecting organs involved in reproduction (Ezcurra et al., 2018; Garigan et al., 2002; Herndon et al., 2002). In post-reproductiveC. eleganshermaphrodites, intestinal biomass is converted into yolk leading to intestinal atrophy and yolk steatosis (Ezcurra et al., 2018; Sornda et al., 2019). We recently showed that post-reproductive mothers vent yolk which functions as a milk (yolk milk), supporting larval growth that is consumed by larvae (Kern et al., 2020). This form of massive reproductive effort involving biomass repurposing leading to organ degeneration is characteristic of semelparous organisms (i.e. that exhibit only a single reproductive episode) ranging from monocarpic plants to Pacific salmon where it leads to rapid death (reproductive death) (Finch, 1990; Gems et al., 2020). Removal of the germline greatly increases lifespan in bothC. elegansand Pacific salmon, in the latter case by suppressing semelparous reproductive death (Hsin and Kenyon, 1999; Robertson, 1961). Here we present evidence that reproductive death occurs inC. elegans, and that it is suppressed by germline removal, leading to extension of lifespan. Comparing threeCaenorhabditissibling species pairs with hermaphrodites and females, we show that lactation and massive early pathology only occurs in the former. In each case, hermaphrodites are shorter lived and only in hermaphrodites does germline removal markedly increase lifespan. Semelparous reproductive death has previously been viewed as distinct from ageing; however, drawing on recent theories of ageing (Blagosklonny, 2006; de Magalhães and Church, 2005; Maklakov and Chapman, 2019), we argue that it involves exaggerated versions of programmatic mechanisms that to a smaller extent contribute to ageing in non-semelparous species. Thus, despite the presence of reproductive death, mechanisms of ageing inC. elegansare informative about ageing in general.
Effect of corporate governance attributes on IFRS compliance: evidence from a developing country
Authors: Kabwe Martin , Mwanaumo Erastus , Chalu Henry
Published: November 2020

Purpose

This study aims to analyze the relationship between corporate governance attributes and the International Financial Reporting Standard (IFRS) compliance among Zambian listed companies.

Design/methodology/approach

Data was collected through content analysis of annual reports and audited financial statements of 20 Zambian listed companies for the period 2012 to 2018. This is a longitudinal study which involved panel data analysis. A Hausman test was conducted to select the model to use to run the panel regression analysis.

Findings

The results indicate a positive statistically insignificant relationship between board size, board independence and IFRS compliance. A statistically significant negative relationship between audit committee independence and IFRS compliance. However, there is a positive relationship between board members with accounting and auditing experience, the inclusion of women on the board and IFRS compliance.

Research limitations/implications

Limitation includes the narrow focus on listed companies only which cannot be generalized to other public interest and private companies in Zambia.

Practical implications

The study findings imply that corporate governance attributes such as the inclusion of qualified and experienced Chartered Accountants and women on the board will increase IFRS compliance. The appointment criteria of non-executive directors should be strengthened.

Originality/value

This is the first empirical study to analyze the relationship between IFRS compliance and corporate governance in Zambia. The study also responds to the call by the World Bank (2017) to empirically study IFRS compliance in Zambia and contributes to the scant literature in developing countries on determinants of IFRS compliance.
Urgency of financial technology (Fintech) laws in Indonesia
Authors: Kharisma Dona Budi
Published: November 2020

Purpose

This paper aims to elaborate the reasons why Indonesia needs Law on Fintech. This paper also identifies the flaws in the existing regulations and policies on Fintech, and it also proposes an ideal framework for a fintech law as a strategy to strengthen consumer protection and to accelerate the growth of the digital economy in Indonesia.

Design/methodology/approach

This is normative research with a legal approach. Data were collected through a literature study and analyzed using legal norm method.

Findings

The promising potential and growth of the fintech industry in Indonesia need to be supported by a sound legal framework in the form of Indonesian Law. In regards to fintech, Indonesia does not yet have a specific law on fintech. Existing regulations in the Bank of Indonesia Regulations (PBI) and Indonesia Financial Services Authority Regulations (POJK) only regulate the technical aspects of the industry, thus providing a less sound legal power. Bank of Indonesia (BI) and Indonesia Financial Services Authority (OJK) have limited authority in the making of regulations and the regulations produced by these institutions cannot stipulate criminal provisions. This results in inadequate consumer protection measures. The Investment Alert Task Force reported 2,018 illegal P2P lending, 472 illegal investment companies and 69 illegal pawnbrokers. The accumulation of online lending transactions in December 2019 reached a total of IDR81.50tn, seeing a 259.56% increase from the previous year. Meanwhile, the amount of bad debt reached IDR13.6tn, seeing a 169.48% increase. These reasons illustrate how urgently Indonesia needs Fintech Law.

Research limitations/implications

This research only examines the existing Fintech regulations in Indonesia. The approach method used is normative legal research.

Practical implications

This research is expected to be useful for The House of Representatives of the Republic of Indonesia (DPR), the Ministry of Law and Human Rights, the Indonesia Financial Services Authority (OJK) and Bank of Indonesia (BI) in drafting the Fintech Law.

Social implications

This research is expected to increase protection for consumers, investors and providers of fintech services and accelerate the growth of the digital economy in Indonesia.

Originality/value

Regulating fintech in the Indonesian Law is meant to give legal certainty and better legal protection for consumers, investors and providers of fintech services. Seeing that the value of the Indonesian digital economy in 2019 has reached USD40bn (approximately IDR586tn), Indonesia is philosophically, juridically and sociologically in urgent need of Fintech Law.