bluuebunny/crossref_metadata_2025 huggingface dataset:
A case report of esophageal metastasis from breast cancer
Authors: Xu Huijun , Yang Yang , Wu Shusheng , Ke Lihong , Yan Ying , Niu Jiayu , Luo Huiqing , Chen Wenju , Li Huimin , Hu Xiaoxiu , Cao Lulu , Li Mengge , He Yifu
Published: September 2021

Introduction:

The common metastatic sites of breast carcinoma are the lymph nodes, liver, lungs and bone. Breast cancer metastasis to esophagus is a rarity with an incidence of 0.03% to 0.6%.

Patient concerns:

A 63-year-old woman presented with worsening dysphagia of 13 months duration. Thirteen years before, the patient had a right modified radical mastectomy and radiotherapy treatment for breast carcinoma.

Diagnosis:

Barium swallow presented a stricture of 4 cm length in the midthoracic esophagus. On endoscopy, a stricture was found in the esophageal lumen at the 28th centimeter. Biopsy showed metastatic esophageal carcinoma.

Interventions and outcomes:

Chemotherapy with gemcitabine and capecitabine was provided as the treatment. After treatment, her dysphagia markedly improved.

Conclusion:

Esophageal involvement in metastatic breast cancer is rare. Dysphagia after breast cancer treatment can indicate metastasis. Histopathologic examination is required to confirm the diagnosis.
A new smoking cessation ‘cascade’ among women with or at risk for HIV infection
Authors: Breger Tiffany L. , Westreich Daniel , Edmonds Andrew , Edwards Jessie K. , Zalla Lauren C. , Cole Stephen R. , Ramirez Catalina , Ofotokun Igho , Kassaye Seble G. , Brown Todd T. , Konkle-Parker Deborah , Jones Deborah L. , D'Souza Gypsyamber , Cohen Mardge H. , Tien Phyllis C. , Taylor Tonya N. , Anastos Kathryn , Adimora Adaora A.
Published: September 2021

Objectives:

The aim of this study was to define a smoking cessation ‘cascade’ among USA women with and without HIV and examine differences by sociodemographic characteristics.

Design:

An observational cohort study using data from smokers participating in the Women's Interagency HIV Study between 2014 and 2019.

Methods:

We followed 1165 women smokers with and without HIV from their first study visit in 2014 or 2015 until an attempt to quit smoking within approximately 3 years of follow-up, initial cessation (i.e. no restarting smoking within approximately 6 months of a quit attempt), and sustained cessation (i.e. no restarting smoking within approximately 12 months of a quit attempt). Using the Aalen-Johansen estimator, we estimated the cumulative probability of achieving each step, accounting for the competing risk of death.

Results:

Forty-five percent of smokers attempted to quit, 27% achieved initial cessation, and 14% achieved sustained cessation with no differences by HIV status. Women with some post-high school education were more likely to achieve each step than those with less education. Outcomes did not differ by race. Thirty-six percent [95% confidence interval (95% CI): 31–42] of uninsured women attempted to quit compared with 47% (95% CI: 44–50) with Medicaid and 49% (95% CI: 41–59) with private insurance.

Conclusion:

To decrease smoking among USA women with and without HIV, targeted, multistage interventions, and increased insurance coverage are needed to address shortfalls along this cascade.
Inorganically modified particles FeAl-LDH@SiO
2
as reinforcement in poly (methyl) methacrylate matrix composite
Authors: Vuksanović Marija M. , Egelja Adela , Barudžija Tanja , Tomić Nataša , Petrović Miloš , Marinković Aleksandar , Radojević Vesna , Heinemann Radmila Jančić
Published: September 2021

Silica particles were obtained from rice husk to which layered double hydroxide particles were deposited (weight ratio 1 : 1). Fe
2+
-Al
3+
layered double hydroxides (FeAl-LDH) were synthesized by co-precipitation with ratios Fe : Al of 3 : 1 in the presence of SiO
2
particles from the rice husk. Characterization of the synthesized FeAl-LDH@SiO
2
particles was performed by X-ray diffraction, Fourier transforms infrared spectroscopy (FTIR) and scanning electron microscopy with EDS. Prepared FeAl-LDH@SiO
2
particles were used as reinforcing agents in 1, 3 and 5 wt% quantity in poly (methyl) methacrylate matrix. The aim of this study was to examine whether FeAl-LDH@SiO
2
particles affect the mechanical properties of polymer composite materials. The morphology of the composites was examined using a field emission scanning electron microscope. Microindentation, tensile and impact testing determined the mechanical properties of the obtained composites.
Transient processes in a gas/plate structure in the case of light loading
Authors: Mironov Mikhail A. , Shanin Andrey V. , Korolkov Andrey I. , Kniazeva Kseniia S.
Published: September 2021

The problem of a pulse excitation in an acoustic half-space with a flexible wall described by a thin plate equation is studied. The solution is written as a double Fourier integral. A novel technique of estimation of this integral is developed. The surface of integration is deformed in such a way that the integrand is exponentially small everywhere except the neighbourhoods of several ‘special points’ that provide field components. Special attention is paid to the pulse associated with the coincidence point of the branches of the dispersion diagram of the acoustic medium and the plate. This pulse is shown to be a harmonic wave of a finite duration.
From temporal network data to the dynamics of social relationships
Authors: Gelardi Valeria , Le Bail Didier , Barrat Alain , Claidiere Nicolas
Published: September 2021

Networks are well-established representations of social systems, and temporal networks are widely used to study their dynamics. However, going from temporal network data (i.e. a stream of interactions between individuals) to a representation of the social group’s evolution remains a challenge. Indeed, the temporal network at any specific time contains only the interactions taking place at that time and aggregating on successive time-windows also has important limitations. Here, we present a new framework to study the dynamic evolution of social networks based on the idea that social relationships are interdependent: as the time we can invest in social relationships is limited, reinforcing a relationship with someone is done at the expense of our relationships with others. We implement this interdependence in a parsimonious two-parameter model and apply it to several human and non-human primates’ datasets to demonstrate that this model detects even small and short perturbations of the networks that cannot be detected using the standard technique of successive aggregated networks. Our model solves a long-standing problem by providing a simple and natural way to describe the dynamic evolution of social networks, with far-reaching consequences for the study of social networks and social evolution.
Photosynthesis from stolen chloroplasts can support sea slug reproductive fitness
Authors: Cartaxana Paulo , Rey Felisa , LeKieffre Charlotte , Lopes Diana , Hubas Cédric , Spangenberg Jorge E. , Escrig Stéphane , Jesus Bruno , Calado Gonçalo , Domingues Rosário , Kühl Michael , Calado Ricardo , Meibom Anders , Cruz Sónia
Published: September 2021

Some sea slugs are able to steal functional chloroplasts (kleptoplasts) from their algal food sources, but the role and relevance of photosynthesis to the animal host remain controversial. While some researchers claim that kleptoplasts are slowly digestible ‘snacks’, others advocate that they enhance the overall fitness of sea slugs much more profoundly. Our analysis shows light-dependent incorporation of
13
C and
15
N in the albumen gland and gonadal follicles of the sea slug
Elysia timida
, representing translocation of photosynthates to kleptoplast-free reproductive organs. Long-chain polyunsaturated fatty acids with reported roles in reproduction were produced in the sea slug cells using labelled precursors translocated from the kleptoplasts. Finally, we report reduced fecundity of
E. timida
by limiting kleptoplast photosynthesis. The present study indicates that photosynthesis enhances the reproductive fitness of kleptoplast-bearing sea slugs, confirming the biological relevance of this remarkable association between a metazoan and an algal-derived organelle.
Whole genome sequencing reveals great diversity of Vibrio spp in prawns at retail
Authors: Janecko Nicol , Bloomfield Samuel J. , Palau Raphaëlle , Mather Alison E.
Published: September 2021

Consumption of prawns as a protein source has been on the rise worldwide with seafood identified as the predominant attributable source of human vibriosis. However, surveillance of non-cholera

Vibrio

is limited both in public health and in food. Using a population- and market share-weighted study design, 211 prawn samples were collected and cultured for

Vibrio

spp. Contamination was detected in 46 % of samples, and multiple diverse

Vibrio

isolates were obtained from 34 % of positive samples. Whole genome sequencing (WGS) and phylogenetic analysis illustrated a comprehensive view of

Vibrio

species diversity in prawns available at retail, with no known pathogenicity markers identified in

Vibrio parahaemolyticus

and

V. cholerae

. Antimicrobial resistance genes were found in 77 % of isolates, and 12 % carried genes conferring resistance to three or more drug classes. Resistance genes were found predominantly in

V. parahaemolyticus

, though multiple resistance genes were also identified in

V. cholerae

and

V. vulnificus

. This study highlights the large diversity in

Vibrio

derived from prawns at retail, even within a single sample. Although there was little evidence in this study that prawns are a major source of vibriosis in the UK, surveillance of non-cholera

Vibrio

is very limited. This study illustrates the value of expanding WGS surveillance efforts of non-cholera Vibrios in the food chain to identify critical control points for food safety through the production system and to determine the full extent of the public health impact.
Persistence of robust humoral immune response in COVID-19 convalescent individuals over 12 months after infection
Authors: Miyakawa Kei , Kubo Sousuke , Jeremiah Sundararaj Stanleyraj , Go Hirofumi , Yamaoka Yutaro , Ohtake Norihisa , Kato Hideaki , Ikeda Satoshi , Mihara Takahiro , Matsuba Ikuro , Sanno Naoko , Miyakawa Masaaki , Shinkai Masaharu , Miyazaki Tomoyuki , Ogura Takashi , Ito Shuichi , Kaneko Takeshi , Yamamoto Kouji , Goto Atsushi , Ryo Akihide
Published: September 2021

SARS-CoV-2 infection elicits varying degrees of protective immunity conferred by neutralizing antibodies (nAbs). Here we report the persistence of nAb responses over 12 months after infection despite its decreasing trend noticed from 6 months. The study included sera from 358 individuals who had been infected with SARS-CoV-2 between January and May 2020. Samples were collected at 6 and 12 months after onset. The titers of IgG to the viral nucleocapsid protein (NP) and receptor-binding domain of the spike protein (RBD) were measured by CLEIA. The nAb titer was determined using lentivirus-based pseudovirus or authentic virus. Antibody titers of NP-IgG, RBD-IgG, and nAbs were higher in severe and moderate cases than in mild cases at 12 months after onset. While the nAb levels were likely to confer adequate protection against wild-type viral infection, the neutralization activity to recently circulating variants in some of the mild cases (∼30%) was undermined, implying the susceptibility of reinfection to the variants of concerns (VOCs). COVID-19 convalescent individuals have robust humoral immunity even at 12 months after infection albeit that the medical history and background of patients could affect the function and dynamics of antibody response to the VOCs.
Altered prefrontal signaling during inhibitory control in a salient drug context in human cocaine addiction
Authors: Ceceli Ahmet O. , Parvaz Muhammad A. , King Sarah , Schafer Matthew , Malaker Pias , Sharma Akarsh , Alia-Klein Nelly , Goldstein Rita Z.
Published: September 2021

Drug addiction is characterized by impaired Response Inhibition and Salience Attribution (iRISA), where the salience of drug cues is postulated to overpower that of other reinforcers with a concomitant decrease in self-control. However, the neural underpinnings of the interaction between the salience of drug cues and inhibitory control in drug addiction remain unclear. We developed a novel stop-signal fMRI task where the stop-signal reaction time (SSRT—a classical inhibitory control measure) was tested under different salience conditions (modulated by drug, food, threat or neutral words) in individuals with cocaine use disorder (CUD; n=26) vs. demographically matched healthy control participants (HC; n=26). Despite similarities in drug cue-related SSRT and valence and arousal word ratings between groups, dorsolateral prefrontal cortex (dlPFC) activity was diminished during the successful inhibition of drug versus food cues in CUD, and was correlated with lower frequency of recent use, lower craving, and longer abstinence (Z>3.1, p<.05 corrected). Results suggest altered involvement of cognitive control regions (e.g., dlPFC) during inhibitory control under a drug context, relative to an alternative reinforcer, in CUD. Supporting the iRISA model, these results elucidate the direct impact of drug-related cue-reactivity on the neural signature of inhibitory control in drug addiction.
Availability and readiness of healthcare facilities and their effects on long-acting modern contraception use in Bangladesh: Analysis of linked data
Authors: Khan Md Nuruzzaman , Islam M Mofizul , Akter Shahinoor
Published: September 2021

Aim

Evidence on the availability and accessibility of health facilities and their impacts on long-acting modern contraceptives (LAMC) use in low- and middle-Income countries are scarce. This study examined the influence of the availability and readiness of health facilities in determining the use of LAMC in Bangladesh.

Methods

We linked data of the Bangladesh Demographic and Health Survey and the Health Facility Survey using the administrative-boundary linkage method. Mixed effect multilevel logistic regression was conducted. The sample comprised 10,938 married women of 15-49 years of age, who were fertile but did not desire a child within two years of the date of survey. The outcome variable was the current use of LAMC (yes, no) and the explanatory variables were health facility-, individual-, household- and community-level factors.

Results

Nearly 34% of participants used LAMC with significant variations across areas in Bangladesh. The average distance between the nearest LAMC-providing health facilities and women’s homes was 6.36 km, higher in the Sylhet division (8.34 km) and lower in the Dhaka division (4.34 km). Increased scores for the management (adjusted odds ratio (AOR) 1.59; 95% CI, 1.21-2.42) and infrastructure (AOR, 1.44; 95% CI, 1.01-1.69) of health facilities were positively associated with the overall uptake of LAMC. AORs for women to report using LMAC were 2.16 (95% CI, 1.18-3.21) and 1.74 (95% CI, 1.15-3.20), respectively, for per unit increase in the availability and readiness scores to provide LAMC at the nearest health facilities. Nearly 27% decline in the likelihood of LAMC uptake was observed for every kilometer increase in the average regional-level distance between women’s homes and the nearest health facilities.

Conclusion

The availability of health facilities close to residence and their improved management, infrastructure, and readiness to provide LAMC play a significant role in increasing LAMC uptake among women. Policies and programs should prioritize increasing the availability and accessibility of health facilities that provide LAMC services.
Impact of long-COVID on health-related quality of life in Japanese COVID-19 patients
Authors: Tsuzuki Shinya , Miyazato Yusuke , Terada Mari , Morioka Shinichiro , Ohmagari Norio , Beutels Philippe
Published: September 2021

Background

The empirical basis for a quantitative assessment of the disease burden imposed by long-COVID is currently scant. We aimed to assess the disease burden caused by long-COVID in Japan.

Methods

We conducted a cross sectional self-report questionnaire survey. The questionnaire was mailed to 530 eligible patients, who were recovered from acute COVID-19 in April 2021. Answers were classified into two groups; participants who have no symptom and those who have any ongoing symptoms that lasted longer than four weeks at the time of the survey. We compared health-related quality of life scores estimated by the EQ-5D-3L questionnaire between these two groups after adjusting basic characteristics of the participants by propensity score matching.

Results

349 participants reported no symptoms and 108 reported any symptoms at the time of the survey. The participants who reported any symptoms showed a lower value on a Visual Analogue Scale (median 70 [IQR 60-80]) and on the EQ-5D-3L (median 0.81 [IQR 0.77-1.0]) than those reporting no symptoms (median 85 [IQR 75-90] and 1.0 [IQR 1.0-1.0], respectively). After adjusting for background characteristics, these trends did not change substantially (Visual Analog Scale: median 70 [IQR 60-80] vs 80 [IQR 77-90], EQ-5D-3L: median 0.81 [IQR 0.76-1.0] vs 1.0 [IQR 1.0-1.0]).

Conclusions

Due to their long duration, long-COVID symptoms represent a substantial disease burden expressed in impact on health-related quality of life.

Trial registration

Not applicable.
Rhizobial adhesives enhance nodule formation in sunn hemp
Authors: Rai Qulina , Choudhury Robin , Soti Pushpa , Racelis Alexis
Published: September 2021

Inoculation of legume seed with rhizobacteria before planting is an efficient and convenient way of introducing effective rhizobacteria to soil vicinity of legume root and ensuring nitrogen fixation in cover cropped field. However, there are still challenges in identifying the proper seed coating technique to ensure microbial survival in adverse environmental conditions and maintaining the symbiotic relation with plants. The objectives of this study are firstly, to analyze the effectiveness of different sticking agents aiding inoculation of Bradyrhizobium japonicum L. in sunn hemp seeds to enhance root nodule formation. Secondly, to observe nodulation pattern over time as affected by the treatment and lastly to check if there is significant difference between main root and lateral root nodulation pattern due to the treatments. Two similar field studies were conducted in fall 2019 and summer 2020 using four sticking agents: water, peanut oil, 10% jaggery solution, and 40% gum arabic solution. The fall study showed no significant differences among total nodules across treatments, but percentage of active nodules was highest in the oil treatment and lowest in the water treatment. In the summer study, significantly higher total nodules were seen in the jaggery treatment and the lowest was in water treatment again, however, there were no differences in percentage of total active nodules across treatments. Interestingly, the trend across weeks showed gum arabic treatment exhibiting higher main root nodulation and jaggery treatment exhibiting higher lateral root nodulation. Overall, water as an adhesive was less effective in aiding nodulation compared to other treatments. Peanut oil and jaggery showed better performance as adhesives aiding active nodulation and could be more effective than gum arabic or water.
DenVar: Density-based Variation analysis of multiplex imaging data
Authors: Seal Souvik , Vu Thao , Ghosh Tusharkanti , Wrobel Julia , Ghosh Debashis
Published: September 2021

Multiplex immunohistochemistry (mIHC) and multiplexed ion beam imaging (MIBI) platforms have become increasingly popular for studying complex single-cell biology in the tumor microenvironment (TME) of cancer subjects. Studying the intensity of the proteins that regulate important cell-functions, often known as functional markers, in the TME becomes extremely crucial for subject-specific assessment of risks, such as risk of recurrence and risk of death. The conventional approach requires selection of two thresholds, one to define the cells of the TME as positive or negative for a particular functional marker, and the other to classify the subjects based on the proportion of the positive cells. The selection of the thresholds has a large impact on the results and an arbitrary selection can lead to an incomprehensible conclusion. In light of this problem, we present a threshold-free distance between the subjects based on the probability densities of the functional markers. The distance can be used to classify the subjects into meaningful groups or can be used in a linear mixed model setup for testing association with clinical outcomes. The method gets rid of the subjectivity bias of the thresholding-based approach, enabling an easier but interpretable analysis of these types of data. With the proposed method, we analyze a lung cancer dataset from an mIHC platform, finding the difference in the density of functional marker HLA-DR to be significantly associated with the overall survival. The approach is also applied on an MIBI triple-negative breast cancer dataset to analyze effects of multiple functional markers. Finally, we demonstrate the reliability of our method through extensive simulation studies.
An ensemble deep learning framework to refine large deletions in linked-reads
Authors: Hu Yunfei , Mangal Sanidhya V , Zhang Lu , Zhou Xin
Published: September 2021

The detection of structural variants (SVs) remains challenging due to inconsistencies in detected breakpoints and biological complexity of some rearrangements. Linked-reads have demonstrated their superiority in diploid genome assembly and SV detection. Recently developed tools Aquila and Aquila_stLFR use a reference sequence and linked-reads to generate a high quality diploid genome assembly, using which they then detect and phase personal genetic variations. However, they both produce a substantial proportion of false positive deletion SV calls. To take full advantage of linked-reads, an effective downstream filtering and refinement framework is needed pressingly. In this work, we propose AquilaDeepFilter to filter large deletion SVs from Aquila and Aquila_stLFR. AquilaDeepFilter relies on a deep learning ensemble approach by integrating six state-of-the-art CNN backbones. The filtering of deletion SVs is formulated as a binary classification task on image data that are generated through the extraction of multiple alignment signals, including read depth, split reads and discordant read pairs. Three linked-reads libraries sequenced from the well-studied sample NA24385 and the gold standard of GiaB benchmark were used to perform thorough experiments on our proposed method. The results demonstrated that AquilaDeepFilter could increase the precision rate of Aquila while the recall rate of Aquila decreased only slightly, and the overall F1 improved by 20%. Furthermore, AquilaDeepFilter outperformed another deep learning based method for SV filtering, DeepSVFilter. Even though we designed AquilaDeepFilter for linked-reads, the framework could also be used to improve SV detection on short reads.
Risk scores for predicting HIV incidence among adult heterosexual populations in sub-Saharan Africa: a systematic review and meta-analysis
Authors: Jia Katherine M. , Eilerts Hallie , Edun Olanrewaju , Lam Kevin , Howes Adam , Thomas Matthew L. , Eaton Jeffrey W.
Published: September 2021

Introduction

Several HIV risk scores have been developed to identify individuals for prioritised HIV prevention in sub-Saharan Africa. We systematically reviewed HIV risk scores to: (i) identify factors that consistently predicted incident HIV infection, (ii) review inclusion of community-level HIV risk in predictive models, and (iii) examine predictive performance.

Methods

We searched nine databases from inception until February 15, 2021 for studies developing and/or validating HIV risk scores among the heterosexual adult population in sub-Saharan Africa. Studies not prospectively observing seroconversion or recruiting only key populations were excluded. Record screening, data extraction, and critical appraisal were conducted in duplicate. We used random-effects meta-analysis to summarise hazard ratios and the area under the receiver-operating characteristic curve (AUC-ROC).

Results

From 1563 initial search records, we identified 14 risk scores in 13 studies. Seven studies were among sexually active women using contraceptives enrolled in randomised-controlled trials, three among adolescent girls and young women (AGYW), and three among cohorts enrolling both men and women. Consistently identified HIV prognostic factors among women were younger age (pooled adjusted hazard ratio: 1.62 [95% Confidence Interval: 1.17, 2.23], compared to above-25), single/not cohabiting with primary partners (2.33 [1.73, 3.13]) and having sexually transmitted infections (STIs) at baseline (HSV-2: 1.67 [1.34, 2.09]; curable STIs: 1.45 [1.17; 1.79]). Among AGYW only STIs were consistently associated with higher incidence, but studies were limited (n=3). Community-level HIV prevalence or unsuppressed viral load strongly predicted incidence but were only considered in three of 11 multi-site studies. The AUC-ROC ranged from 0.56 to 0.79 on the model development sets. Only the VOICE score was externally validated by multiple studies, with pooled AUC-ROC 0.626 [0.588, 0.663] (I2: 64.02%).

Conclusions

Younger age, non-cohabiting, and recent STIs were consistently identified as predicting future HIV infection. Both community HIV burden and individual factors should be considered to quantify HIV risk. However, HIV risk scores had only low-to-moderate discriminatory ability and uncertain generalisability, limiting their programmatic utility.

Further evidence on the relative value of specific risk factors, studies populations not restricted to ‘at-risk’ individuals, and data outside South Africa will improve the evidence base for risk differentiation in HIV prevention programmes.

PROSPERO Number

CRD42021236367
Pollutants corrupt resilience pathways of aging in the nematode C. elegans
Authors: Scharf Andrea , Limke Annette , Guehrs Karl-Heinz , von Mikecz Anna
Published: September 2021

Delaying aging while prolonging health and lifespan is a major goal in aging research. While many resources have been allocated to find positive interventions with promising results, negative interventions such as pollution and their accelerating effect on age-related degeneration and disease have been mostly neglected. Here, we used the short-lived model organism C. elegans to analyze whether two candidate pollutants interfere with positive interventions by corrupting general aging pathways. We took advantage of the immense data sets describing the age-related remodeling of the proteome including increased protein insolubilities to complement our analysis. We show that the emergent pollutant silica nanoparticles (NP) and the classic xenobiotic inorganic mercury reduce lifespan and cause a premature protein aggregation phenotype. Silica NPs rescaled the longevity effect of genetic interventions targeting the IGF-1/insulin-like signaling pathway. Comparative mass spectrometry revealed that increased insolubility of proteins with important functions in proteostasis is a shared phenotype of intrinsic- and pollution-induced aging supporting the hypothesis that proteostasis is a central resilience pathway controlling lifespan and aging. The presented data demonstrate that pollutants corrupt intrinsic aging pathways, which results in premature aging phenotypes. Reducing pollution is therefore an important step to increase healthy aging and prolong life expectancies on a population level in humans and animals.
Distinct Expansion of Group II Introns Depends on the Type of Intron-encoded Protein and Genomic Signatures in Prokaryotes
Authors: Miura Masahiro C. , Nagata Shohei , Tamaki Satoshi , Tomita Masaru , Kanai Akio
Published: September 2021

Group II introns (G2Is) are self-splicing ribozymes that have retroelement characteristics in prokaryotes. Although G2Is are considered an important factor in the evolution of prokaryotes, comprehensive analyses of these introns among the tens of thousands of prokaryotic genomes currently available are still limited. Here, we developed a bioinformatic pipeline that systematically collects G2Is and applied it to prokaryotic genomes. We found that in bacteria, 25% (447 of 1,790) of the total representative species had an average of 5.3 G2Is, and in archaea, 9% (28 of 296) of the total representative species had an average of 3.0 G2Is. The greatest number of G2Is per species was 101 in Arthrospira platensis (phylum Cyanobacteriota). A comprehensive sequence analysis of the intron-encoded protein (IEP) in each G2I sequence was conducted and resulted in the addition of three new IEP classes (U1–U3) to the previous classification. This analysis suggested that about 30% of all IEPs are noncanonical IEPs. The number of G2Is per species was defined almost at the phylum level, and the type of IEP was associated as a factor in the G2I increase, i.e. there was an explosive increase in G2Is with bacterial C-type IEPs in the phylum Firmicutes and in G2Is with CL-type IEPs in the phylum Cyanobacteriota. We also systematically analyzed the relationship between genomic signatures and the mechanism of these increases in G2Is. This is the first study to systematically characterize G2Is in the prokaryotic phylogenies.
CNpare: matching DNA copy number profiles
Authors: Chaves-Urbano Blas , Hernando Bárbara , Garcia Maria J , Macintyre Geoff
Published: September 2021

Selecting the optimal cancer cell line for an experiment can be challenging given the diversity of lines available. Cell lines are often chosen based on their tissue of origin, however, the results of large-scale pan-cancer studies suggest that matching lines based on molecular features may be more appropriate. Existing approaches are available for matching lines based on gene expression, DNA methylation or low resolution DNA copy number features. However, a specific tool for computing similarity based on high resolution genome-wide copy number profiles is lacking. Here, we present CNpare, which identifies similar cell line models based on genome-wide DNA copy number. CNpare compares copy number profiles using four different similarity metrics, quantifies the extent of genome differences between pairs, and facilitates comparison based on copy number signatures. CNpare incorporates a precomputed database of 1,170 human cancer cell line profiles for comparison. In an analysis of separate cultures of 304 cell line pairs, CNpare identified the matched lines in all cases. CNpare provides a powerful solution to the problem of selecting the best cell line models for cancer research, especially in the context of studying chromosomal instability.
Critical role of DNA unwinding and Cas9 conformational changes in modelling off-target effects
Authors: Khakimzhan Aset , Noireaux Vincent
Published: September 2021

CRISPR-Cas9 off-target effects interfere with the ability to accurately perform genetic edits. To predict off-target effects CRISPR-Cas9 researchers perform high throughput guide RNA mismatch and bulge experiments and then use the data to fit thermodynamic binding models. While impactful from an engineering perspective such models are not based on the experimentally observed target interrogation process and thus incorrectly measure the energetic effects mismatches have on the system. In this work we convert an experimentally deduced qualitive model of target interrogation to a linear ODE model and demonstrate that the mismatch tolerance patterns observed in experiments do not need to be caused by differences in energetic penalties of mismatches but rather are emergent effects of the timing and coordination of target DNA unwinding and Cas9 conformational changes.
Microbiological quality assessment of five common foods sold at different points of sale in Burkina-Faso
Authors: Compaore Muller K. A , Kpoda Dissinviel Stéphane , Bazie Bazoin S. R. , Ouedraogo Marcelline , Yakoro Alphonse , Nikiema Fulbert , Belemlougri Asseto , Meda Romaric , Bande Moumouni , Barro Nicolas , Kabre Elie
Published: September 2021

The aim of the present study was to assess the microbial quality of five different types of food such as bread, pasta, rice with sauce, beans and milk sold in five localities of Burkina Faso. One hundred and one (101) samples were collected and microbial quality were assessed by evaluating the food hygiene indicators such as total aerobic mesophilic flora, total coliforms, thermotolerant coliforms, yeast and mould. Food safety indicators such as Escherichia coli, Salmonella, coagulase-positive staphylococci, Clostridium perfringens and Bacillus cereus were checked too. All samples were analyzed under ISO methods.

The results showed that 73.27% of samples were satisfactory while 14.85% were acceptable and 11.88% were not satisfactory according to international standards. Among the food safety indicators sought, Escherichia coli was detected in two samples and Bacillus cereus in four samples. Most of the analyzed food exhibited good hygiene behavior within the acceptable limits and the highest of not satisfactory rate was observed in milk powder and rice with sauce. Ouagadougou samples record the highest number of not satisfactory samples.

Despite the general quality was satisfactory, the presence of specific microorganisms such as coliforms is indicative of the poor hygiene surrounded these foods. It is therefore necessary to train and follow up the vendors in the handling of equipment, hand-washing practices and selling environment hygiene for better improvement of the quality of the street foods.
Somatic IDH1 variant (p.R132C) in an adult male with Maffucci syndrome
Authors: Brown Natasha J. , Ye Zimeng , Stutterd Chloe , Jayasinghe Sureshni I. , Schneider Amy , Mullen Saul , Mandelstam Simone A. , Hildebrand Michael S.
Published: September 2021

Maffucci syndrome is a rare, highly variable somatic mosaic condition, and well-known cancer-related gain-of-function variants in either the IDH1 or IDH2 genes have been found in the affected tissues of most reported individuals. Features include benign enchondroma and spindle-cell hemangioma, with a recognized increased risk of various malignancies. Fewer than 200 affected individuals have been reported; therefore, accurate estimates of malignancy risk are difficult to quantify and recommended surveillance guidelines are not available. The same gain-of-function IDH1 and IDH2 variants are also implicated in a variety of other benign and malignant tumors. An adult male presented with several soft palpable lesions on the right upper limb. Imaging and histopathology raised the possibility of Maffucci syndrome. DNA was extracted from peripheral blood lymphocytes and tissue surgically resected from a spindle-cell hemangioma. Sanger sequencing and droplet digital polymerase chain reaction (PCR) analysis of the IDH1 gene were performed. We identified a somatic mosaic c.394C > T (p.R132C) variant in exon 5 of IDH1, in DNA derived from hemangioma tissue at ∼17% variant allele fraction. This variant was absent in DNA derived from blood. This variant has been identified in the affected tissue of most reported individuals with Maffucci syndrome. Although this individual has a potentially targetable variant, and there is a recognized risk of malignant transformation in this condition, a decision was made not to intervene with an IDH1 inhibitor. The reasons and prospects for therapy in this condition are discussed.
Laboratory exploration of mineral precipitates from Europa's subsurface ocean
Authors: Thompson Stephen P. , Kennedy Hilary , Butler Benjamin M. , Day Sarah J. , Safi Emmal , Evans Aneurin
Published: September 2021

The precipitation of hydrated phases from a chondrite-like Na–Mg–Ca–SO4–Cl solution is studied usingin situsynchrotron X-ray powder diffraction, under rapid- (360 K h−1,T= 250–80 K,t= 3 h) and ultra-slow-freezing (0.3 K day−1,T = 273–245 K,t= 242 days) conditions. The precipitation sequence under slow cooling initially follows the predictions of equilibrium thermodynamics models. However, after ∼50 days at 245 K, the formation of the highly hydrated sulfate phase Na2Mg(SO4)2·16H2O, a relatively recent discovery in the Na2Mg(SO4)2–H2O system, was observed. Rapid freezing, on the other hand, produced an assemblage of multiple phases which formed within a very short timescale (≤4 min, ΔT= 2 K) and, although remaining present throughout, varied in their relative proportions with decreasing temperature. Mirabilite and meridianiite were the major phases, with pentahydrite, epsomite, hydrohalite, gypsum, blödite, konyaite and loweite also observed. Na2Mg(SO4)2·16H2O was again found to be present and increased in proportion relative to other phases as the temperature decreased. The results are discussed in relation to possible implications for life on Europa and application to other icy ocean worlds.
Visualizing lithium ions in the crystal structure of Li3PO4 by in situ neutron diffraction
Authors: Manawan Maykel , Kartini Evvy , Avdeev Maxim
Published: September 2021

Li3PO4 is known to demonstrate Li+ ionic conductivity, making it a good candidate for solid electrolytes in all-solid batteries. Understanding the crystal structure and its connection to Li+ diffusion is essential for further rational doping to improve the ionic transport mechanism. The purpose of this study is to investigate this mechanism using anisotropic displacement parameters (ADPs), nuclear density distribution and bond valence mapping. In situ neutron powder diffraction experiments have been performed using the high-resolution powder diffractometer ECHIDNA at the OPAL reactor, Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, NSW, Australia. The ADPs and nuclear density distribution were determined from the analysis of neutron diffraction data using the Rietveld method, whereas the bond valence map was calculated from the refined structure. The crystal structure remained unchanged as the temperature was increased (3, 100, 300 and 400 K). However, the ADPs show a greater increase in anisotropy in the a and b axes compared with the c axis, indicating the tendency of the ionic movement. By combining nuclear density distribution and bond valence mapping, the most likely lithium-ion diffusion in the crystal structure can be visualized.
Cryo-TEM simulations of amorphous radiation-sensitive samples using multislice wave propagation
Authors: Himes Benjamin , Grigorieff Nikolaus
Published: September 2021

Image simulation plays a central role in the development and practice of high-resolution electron microscopy, including transmission electron microscopy of frozen-hydrated specimens (cryo-EM). Simulating images with contrast that matches the contrast observed in experimental images remains challenging, especially for amorphous samples. Current state-of-the-art simulators apply post hoc scaling to approximate empirical solvent contrast, attenuated image intensity due to specimen thickness and amplitude contrast. This practice fails for images that require spatially variable scaling, e.g. simulations of a crowded or cellular environment. Modeling both the signal and the noise accurately is necessary to simulate images of biological specimens with contrast that is correct on an absolute scale. The `frozen plasmon' method is introduced to explicitly model spatially variable inelastic scattering processes in cryo-EM specimens. This approach produces amplitude contrast that depends on the atomic composition of the specimen, reproduces the total inelastic mean free path as observed experimentally and allows for the incorporation of radiation damage in the simulation. These improvements are quantified using the matched filter concept to compare simulation and experiment. The frozen plasmon method, in combination with a new mathematical formulation for accurately sampling the tabulated atomic scattering potentials onto a Cartesian grid, is implemented in the open-source software package cisTEM.
Selected solid-state behaviour of three di-tert-butyl-substituted N-salicylideneaniline derivatives: temperature-induced phase transitions and chromic behaviour
Authors: Mason Helen E. , Howard Judith A. K. , Sparkes Hazel A.
Published: September 2021

The synthesis, single-crystal structures and chromic behaviour of three related Schiff bases, namely, (E)-2,4-di-tert-butyl-6-{[(4-fluorophenyl)imino]methyl}phenol, C21H26FNO, 1, (E)-2,4-di-tert-butyl-6-{[(4-chlorophenyl)imino]methyl}phenol, C21H26ClNO, 2, and (E)-6-{[(4-bromophenyl)imino]methyl}-2,4-di-tert-butylphenol, C21H26BrNO, 3, are reported. Two polymorphs of 1 were obtained, which were found to have different photochromic properties. Schiff bases 2 and 3 were found to be isostructural and underwent a phase transition upon cooling which was attributed to the dynamic disorder in one of the tert-butyl groups resolving at low temperature. All of the structures were found to exist in the enol rather than the keto form based on the C—O(H) and imine C=N bond lengths, and contained an intramolecular O—H...N hydrogen bond alongside weaker intermolecular C—H...O contacts.
Development of career capital during expatriation: partners' perspectives
Authors: Kanstrén Kaisu , Suutari Vesa
Published: September 2021

Purpose

The purpose of this qualitative study is to examine the effects of expatriation on the development of career capital among the partners of expatriates.

Design/methodology/approach

The study draws on in-depth interviews with 30 Finnish partners of expatriates.

Findings

The results reflect the various learning experiences reported by partners of expatriates that developed their career capital during expatriation. The learning experiences related to the experience of living abroad itself and to the specific activities undertaken when abroad. The extent to which partners developed knowing-why, knowing-how and knowing-whom career capital was found to partly reflect their situation abroad as stay-at-home partners or as employees in less-demanding or more-demanding jobs. Though the experiences were developmental for all partners as have been reported among expatriates, the authors also identified several aspects in which partners' experiences differed from the typical developmental experiences of expatriates.

Practical implications

The results also highlight the influence of initiative, an active role and career self-management skills in partners' career capital development.

Originality/value

This paper advances the understanding of how expatriation affects expatriate partners' career capital, a topic that has not previously been studied in-depth.
Human resources, organizational learning and due diligence: avoiding the honeymoon hangover effect in mergers & acquisitions
Authors: Lattuch Frank , Ruppert Enno
Published: September 2021

Purpose

Mergers & acquisitions (M&As) can be an effective way to expand into new markets or business opportunities. Yet, a considerable number of failed M&As can be attributed to disregarded human resource (HR) concerns. In particular, an organization’s leadership tends to hail the advantages of a merger or acquisition during the early stages, raising employees’ expectations (honeymoon effect). Many documented failures in such corporate transactions indicate organizational members’ declining satisfaction following a deal (hangover effect).

Design/methodology/approach

Drawing on in-depth interviews with senior M&A experts (n = 12) at a global big-four accountancy firm and focus group sessions with their respective clients, this study investigates in two cases the interplay between HR issues and M&A transactions and infers effective risk management actions.

Findings

A honeymoon hangover after a transaction may appear in organizations if HR issues are neglected. Study results provide notable implications for HR departments and HR professionals facing a merger or acquisition. These implications include (1) focusing on HR risks, (2) involving HR executives to manage the HR due diligence efforts, (3) setting up transition teams that communicate well, (4) creating policies for learning and knowledge sharing, (5) developing new competencies for the NewCo, (6) being sensitive to cultural differences and (7) considering legal aspects.

Research limitations/implications

The two transactions studied revealed patterns that are important for successful change. However, we should not underestimate the individual perspective in M&As. Further studies with interview data directly from stakeholders are important to analyze further the relationships between HR due diligence, organizational learning, effective knowledge transfer, and culture. Due to our research approach, we cannot claim that the results can be generalizable to all major M&As. Further research is needed to measure the impact of the HR Due Diligence aspects outlined on M&A success.

Originality/value

Although M&As have been much researched, relatively little has been written on practical managerial adaptation from a human resource perspective and its implications for organizational learning. This article helps address this imbalance by providing a people-oriented approach for effectively managing M&As from beginning to integration.
Exploration of employability perceptions with blended multi-criteria decision-making methods
Authors: Castro-Lopez Adrian , Monteiro Sílvia , Bernardo Ana B. , Almeida Leandro S.
Published: September 2021

Purpose

The purpose of this paper is to explore employment perception of students as a relevant indicator of higher education quality, using blended multi-criteria decision-making methods.

Design/methodology/approach

The differential impact of these variables was analyzed in this paper taking a sample of 641 students and six higher education lecturers identified as experts on young vocational careers. The traditional study of student behavior and perceptions of employability does not incorporate the uncertainty associated with multi-criteria decision processes and is therefore less adapted to the human reasoning process. This research applies traditional techniques together with fuzzy techniques capable of managing more effectively the uncertainty associated with student actions and behaviors.

Findings

This research shows that it is important to consider previous work experience, academic achievement and soft skills developed during education experiences. In this way, this research shows the lecturers how to adapt their pedagogical practices according to students' perceptions of employability and assess their students' perceptions of employability. In addition, lecturers will be able to incorporate the uncertainty associated with decision-making processes to optimize employability perception.

Originality/value

Higher education-related research on uncertainty environments as multi-criteria decision problems is still in early stages. The incorporation of the uncertainty associated with decision-making processes to this field allows to optimize employability perception thanks to its adaptation to real human behavior in the adoption of decisions.