bluuebunny/crossref_metadata_2025 huggingface dataset:
CAZyme prediction in ascomycetous yeast genomes guides discovery of novel xylanolytic species with diverse capacities for hemicellulose hydrolysis
Authors: Ravn Jonas L. , Engqvist Martin K. M. , Larsbrink Johan , Geijer Cecilia
Published: July 2021

Background

Ascomycetous yeasts from the kingdom fungi inhabit every biome in nature. While filamentous fungi have been studied extensively regarding their enzymatic degradation of the complex polymers comprising lignocellulose, yeasts have been largely overlooked. As yeasts are key organisms used in industry, understanding their enzymatic strategies for biomass conversion is an important factor in developing new and more efficient cell factories. The aim of this study was to identify polysaccharide-degrading yeasts by mining CAZymes in 332 yeast genomes from the phylum Ascomycota. Selected CAZyme-rich yeasts were then characterized in more detail through growth and enzymatic activity assays.

Results

The CAZyme analysis revealed a large spread in the number of CAZyme-encoding genes in the ascomycetous yeast genomes. We identified a total of 217 predicted CAZyme families, including several CAZymes likely involved in degradation of plant polysaccharides. Growth characterization of 40 CAZyme-rich yeasts revealed no cellulolytic yeasts, but several species from the Trichomonascaceae and CUG-Ser1 clades were able to grow on xylan, mixed-linkage β-glucan and xyloglucan. Blastobotrys mokoenaii, Sugiyamaella lignohabitans, Spencermartinsiella europaea and several Scheffersomyces species displayed superior growth on xylan and well as high enzymatic activities. These species possess genes for several putative xylanolytic enzymes, including ones from the well-studied xylanase-containing glycoside hydrolase families GH10 and GH30, which appear to be attached to the cell surface. B. mokoenaii was the only species containing a GH11 xylanase, which was shown to be secreted. Surprisingly, no known xylanases were predicted in the xylanolytic species Wickerhamomyces canadensis, suggesting that this yeast possesses novel xylanases. In addition, by examining non-sequenced yeasts closely related to the xylanolytic yeasts, we were able to identify novel species with high xylanolytic capacities.

Conclusions

Our approach of combining high-throughput bioinformatic CAZyme-prediction with growth and enzyme characterization proved to be a powerful pipeline for discovery of novel xylan-degrading yeasts and enzymes. The identified yeasts display diverse profiles in terms of growth, enzymatic activities and xylan substrate preferences, pointing towards different strategies for degradation and utilization of xylan. Together, the results provide novel insights into how yeast degrade xylan, which can be used to improve cell factory design and industrial bioconversion processes.
Ageing-associated changes in DNA methylation in X and Y chromosomes
Authors: Kananen Laura , Marttila Saara
Published: July 2021

Background

Ageing displays clear sexual dimorphism, evident in both morbidity and mortality. Ageing is also associated with changes in DNA methylation, but very little focus has been on the sex chromosomes, potential biological contributors to the observed sexual dimorphism. Here, we sought to identify DNA methylation changes associated with ageing in the Y and X chromosomes, by utilizing datasets available in data repositories, comprising in total of 1240 males and 1191 females, aged 14–92 years.

Results

In total, we identified 46 age-associated CpG sites in the male Y, 1327 age-associated CpG sites in the male X, and 325 age-associated CpG sites in the female X. The X chromosomal age-associated CpGs showed significant overlap between females and males, with 122 CpGs identified as age-associated in both sexes. Age-associated X chromosomal CpGs in both sexes were enriched in CpG islands and depleted from gene bodies and showed no strong trend towards hypermethylation nor hypomethylation. In contrast, the Y chromosomal age-associated CpGs were enriched in gene bodies, and showed a clear trend towards hypermethylation with age.

Conclusions

Significant overlap in X chromosomal age-associated CpGs identified in males and females and their shared features suggest that despite the uneven chromosomal dosage, differences in ageing-associated DNA methylation changes in the X chromosome are unlikely to be a major contributor of sex dimorphism in ageing. While age-associated CpGs showed good replication across datasets in the present study, only a limited set of previously reported age-associated CpGs were replicated. One contributor to the limited overlap are differences in the age range of individuals included in each data set. Further study is needed to identify biologically significant age-associated CpGs in the sex chromosomes.
A modified protocol for successful miRNA profiling in human precision-cut lung slices (PCLS)
Authors: Niehof Monika , Reamon-Buettner Stella Marie , Danov Olga , Hansen Tanja , Sewald Katherina
Published: July 2021

Objective

Human precision cut lung slices (PCLS) are widely used as an ex vivo model system for drug discovery and development of new therapies. PCLS reflect the functional heterogeneity of lung tissue and possess relevant lung cell types. We thus determined the use of PCLS in studying non-coding RNAs notably miRNAs, which are important gene regulatory molecules. Since miRNAs play key role as mediators of respiratory diseases, they can serve as valuable prognostic or diagnostic biomarkers, and in therapeutic interventions, of lung diseases. A technical limitation though is the vast amount of agarose in PCLS which impedes (mi)RNA extraction by standard procedures. Here we modified our recently published protocol for RNA isolation from PCLS to enable miRNA readouts.

Results

The modified method relies on the separation of lysis and precipitation steps, and a clean-up procedure with specific magnetic beads. We obtained successfully quality miRNA amenable for downstream applications such as RTqPCR and whole transcriptome miRNA analysis. Comparison of miRNA profiles in PCLS with published data from human lung, identified all important miRNAs regulated in IPF, COPD, asthma or lung cancer. Therefore, this shows suitability of the method for analyzing miRNA targets and biomarkers in the valuable human PCLS model.
Antigen-specific response of CD4+ T cells and hepatic lymph node cells to Fasciola hepatica-derived molecules at the early and late stage of the infection in sheep
Authors: Pérez-Caballero Raúl , Martínez-Moreno F. Javier , Corripio-Miyar Yolanda , McNeilly Tom N. , Cwiklinski Krystyna , Dalton John P. , Zafra Rafael , Pérez José , Martínez-Moreno Álvaro , Buffoni Leandro
Published: July 2021

The immunomodulatory capacity of F. hepatica antigens is probably one of the main reasons for the development of a driven non-protective Th2 immune response. In this study, we analysed the cellular response of hepatic lymph node cells and CD4+ T cells in terms of proliferative response, efficiency of antigen presentation and cytokine production, to F. hepatica-derived molecules, at early and late stages of the infection. Thirty-one sheep were allocated into five groups and were slaughtered at 16 dpi and 23 wpi. In order to analyse antigen-specific response, the following F. hepatica recombinant molecules were used: rFhCL1, rFhCL2, rFhCL3, rFhCB1, rFhCB2, rFhCB3, rFhStf-1, rFhStf-2, rFhStf-3 and rFhKT1. A cell proliferation assay using hepatic lymph node cells and an antigen presentation cell assay using CD4+ T cells were performed. At 16 dpi, all molecules but rFhStf-2 and rFhKT1 elicited a significant cell proliferative response on hepatic lymph node cells of infected animals. At both early and late stage of the infection, antigen presentation of rFhCB3 and rFhCL2 resulted in higher stimulation index of CD4+ T cells which was IL-2 mediated, although no statistically significant when compared to uninfected animals. Significant cytokine production (IL-4, IL-10 and IFN-γ) was conditioned by the antigen-specific cell stimulation. No CD4+ T cell exhaustion was detected in infected sheep at the chronic stage of the infection. This study addressed antigen-specific response to F. hepatica-derived molecules that are involved in key aspects of the parasite survival within the host.
Geometry calibration in wireless acoustic sensor networks utilizing DoA and distance information
Authors: Gburrek Tobias , Schmalenstroeer Joerg , Haeb-Umbach Reinhold
Published: July 2021

Due to the ad hoc nature of wireless acoustic sensor networks, the position of the sensor nodes is typically unknown. This contribution proposes a technique to estimate the position and orientation of the sensor nodes from the recorded speech signals. The method assumes that a node comprises a microphone array with synchronously sampled microphones rather than a single microphone, but does not require the sampling clocks of the nodes to be synchronized. From the observed audio signals, the distances between the acoustic sources and arrays, as well as the directions of arrival, are estimated. They serve as input to a non-linear least squares problem, from which both the sensor nodes’ positions and orientations, as well as the source positions, are alternatingly estimated in an iterative process. Given one set of unknowns, i.e., either the source positions or the sensor nodes’ geometry, the other set of unknowns can be computed in closed-form. The proposed approach is computationally efficient and the first one, which employs both distance and directional information for geometry calibration in a common cost function. Since both distance and direction of arrival measurements suffer from outliers, e.g., caused by strong reflections of the sound waves on the surfaces of the room, we introduce measures to deemphasize or remove unreliable measurements. Additionally, we discuss modifications of our previously proposed deep neural network-based acoustic distance estimator, to account not only for omnidirectional sources but also for directional sources. Simulation results show good positioning accuracy and compare very favorably with alternative approaches from the literature.
Commutators of log-Dini-type parametric Marcinkiewicz operators on non-homogeneous metric measure spaces
Authors: Xiangxing Tao , Qiange Zhang
Published: July 2021

Let $(\mathcal{X}, d, \mu )$
(
X
,
d
,
μ
)
be a non-homogeneous metric measure space, which satisfies the geometrically doubling condition and the upper doubling condition. In this paper, the authors prove the boundedness in $L^{p} (\mu )$

L
p

(
μ
)
of mth-order commutators $\mathcal{M}^{\rho }_{b,m}$

M

b
,
m

ρ

generated by the Log-Dini-type parametric Marcinkiewicz integral operators with RBMO functions on $(\mathcal{X}, d, \mu )$
(
X
,
d
,
μ
)
. In addition, the boundedness of the mth-order commutators $\mathcal{M}^{\rho }_{b,m}$

M

b
,
m

ρ

on Morrey spaces $M^{q}_{p}(\mu )$

M
p
q

(
μ
)
, $1< p \leq q< \infty $
1
<
p
≤
q
<
∞
, is also obtained for the parameter $0<\rho <\infty $
0
<
ρ
<
∞
.
Development of a web-based contact tracing and point-of-care-testing workflow for SARS-CoV-2 at a German University Hospital
Authors: Zirbes Julian , Sterr Christian M. , Steller Marcus , Dapper Laura , Nonnenmacher-Winter Claudia , Günther Frank
Published: July 2021

Introduction

In late 2019, a novel coronavirus was detected in China. Supported by its respiratory transmissibility, even by people infected without symptomatic disease, this coronavirus soon began to rapidly spread worldwide.

Background

Many countries have implemented different infection control and containment strategies due to ongoing community transmission. In this context, contact tracing as well as adequate testing and consequent quarantining of high-risk contacts play leading roles in containing the virus by interrupting infection chains. This approach is especially important in the hospital setting where contacts often cannot be avoided and physical distance is usually not possible. Furthermore, health care workers (HCWs) usually have contact with a variety of vulnerable people, making it essential to identify infections among hospital employees as soon as possible to interrupt the rapid spread of SARS-CoV-2 in the facility. Several electronic tools for contact tracing, such as specific software or mobile phone apps, are available for the public health sector. In contrast, contact tracing in hospitals often has to be carried out without helpful electronic tools, and an enormous amount of human resources is typically required.

Aim

For rapid contact tracing and effective infection control and management measures for HCWs in hospitals, adapted technical solutions are needed.

Methods

In this study, we report the development of our containment strategy to a web-based contact tracing and rapid point-of-care-testing workflow.

Results/conclusion

Our workflow yielded efficient control of the rapidly evolving situation during the SARS-CoV-2 pandemic from May 2020 until January 2021 at a German University Hospital.
Performances of NIPT for copy number variations at different sequencing depths using the semiconductor sequencing platform
Authors: Yang Jiexia , Wu Jing , Peng Haishan , Hou Yaping , Guo Fangfang , Wang Dongmei , Ouyang Haoxin , Wang Yixia , Yin Aihua
Published: July 2021

Objective

To evaluate the performance of noninvasive prenatal testing (NIPT) and NIPT-PLUS for the detection of genome-wide microdeletion and microduplication syndromes (MMSs) at different sequencing depths. The NIPT sequencing depth was 0.15X, and the data volume was 3 million reads; the NIPT-PLUS sequencing depth was 0.4X, and the data volume was 8 million reads.

Methods

A cohort of 50,679 pregnancies was recruited. A total of 42,969 patients opted for NIPT, and 7710 patients opted for NIPT-PLUS. All high-risk cases were advised to undergo invasive prenatal diagnosis and were followed up.

Results

A total of 373 cases had a high risk of a copy number variation (CNV) as predicted by NIPT and NIPT-PLUS: NIPT predicted 250 high-risk CNVs and NIPT-PLUS predicted 123. NIPT-PLUS increased the detection rate by 1.02% (0.58% vs 1.60%, p < 0.001). A total of 291 cases accepted noninvasive prenatal diagnosis, with 197 cases of NIPT and 94 cases of NIPT-PLUS. The PPV of CNV > 10 Mb for NIPT-PLUS was significantly higher than that for NIPT (p = 0.02). The total PPV of NIPT-PLUS was 12.56% higher than that of NIPT (43.61% vs 30.96%, p = 0.03).

Conclusion

NIPT-PLUS had a better performance in detecting CNVs in terms of the total detection rate and total PPV. However, great care must be taken in presenting results and providing appropriate counseling to patients when deeper sequencing is performed in clinical practice.
Intestinal microbiota and active systemic lupus erythematosus: a systematic review
Authors: Vieira Juliana Rosa Pires , Rezende Andréa Toledo de Oliveira , Fernandes Marcos Rassi , da Silva Nilzio Antonio
Published: July 2021

Background

Systemic Lupus Erythematosus (SLE) is an autoimmune disease, characterized by being multi-systemic and, therefore, reaching various organs and affecting mainly young women. Its pathogenesis comprehends many factors, including the interaction between microbiota and immune system. This systematic review assessed the relationship between intestinal microbiota and SLE in activity, highlighting microbiota representative patterns regarding quantity and diversity.

Methods

This study considered researches carried out in patients with SLE, with no restriction of age or gender, which fulfilled the classification criteria of either Systemic Lupus International Collaborating Clinic (SLICC), American College of Rheumatology (ACR) or European League Against Rheumatism (EULAR) and used the Systemic Lupus Erythematosus Disease Activity Index (SLEDAI) to classify disease in activity or remission were included. The search was carried out from October, 2020 to January, 2021 using the following databases: Medline via Pubmed, Scopus, and Embase. Five papers were included with a total of 288 participants with SLE.

Results

Regarding microbiota in patients with SLE in activity, there was significant increase in the following genera: Lactobacillus, Streptococcus, Megasphaera, Fusobacterium, Veillonella, Oribacterium, Odoribacter, Blautia, and Campylobacter. On the other hand, decrease in Faecalibacterium and Roseburia genera as well as Ruminococcus gnavus species was observed in remission cases, showing differences between the microbiota profile in SLE in activity and in remission.

Conclusions

Results suggest that dysbiosis may be involved in the disease activity process.

Trial registration

CRD42021229322.
Risk factors for the flare of systemic lupus erythematosus and its influence on prognosis: a single-center retrospective analysis
Authors: Zeng Xiaohong , Zheng Ling , Rui Hongbing , Kang Rihui , Chen Junmin , Chen Huaning , Liu Jizan
Published: July 2021

Objectives

To explore the risk factors for systemic lupus erythematosus (SLE) flare and their impact on prognosis.

Methods

The clinical characteristics, laboratory results, and treatment plans of 121 patients with SLE flare were retrospectively analyzed. Ninety-eight SLE outpatients with sustained remission during the same period were selected as controls. Logistic multivariate regression analysis was employed to screen for risk factors for SLE flare.

Results

Infection, thrombocytopenia, arthritis, anti-nucleosome antibodies positive, anti-β2-glycoprotein I (IgG) antibodies positive, and patient’s self-discontinuation of medicine maintenance therapy might be risk factors for SLE flare. Patients who discontinued medicine maintenance therapy by themselves had a significantly higher rate of severe SLE flare than patients with regular medicine maintenance therapy (P = 0.033). The incidence of anemia associated with SLE (P = 0.001), serositis (P = 0.005), and pulmonary hypertension (P = 0.003) in patients who discontinued medicine maintenance therapy were significantly higher than patients with regular medicine maintenance therapy. SLE patients with regular medicine maintenance therapy for less than 3 years had a higher risk of pulmonary hypertension than those with regular medicine maintenance therapy longer than 3 years (P = 0.034).

Conclusions

The accompanying thrombocytopenia, arthritis, anti-nucleosome antibodies positive and anti-β2-glycoprotein I (IgG) antibodies positive at the onset of SLE may affect the prognosis of SLE. Patient’s self-discontinuation of medicine maintenance therapy is the main cause of SLE flare, which may induce severe flare in SLE patients and lead to a significantly higher incidence of pulmonary hypertension.
Mathematical modeling of the impact of treatment on the dynamics of typhoid
Authors: Nyaberi Halson O. , Musaili Jane S.
Published: July 2021

In this paper, we propose a mathematical model for the transmission of typhoid which analyzes the impact of treatment of the infected individuals on the dynamics of the disease. The model consists of human population and pathogen population. The human population is subdivided into three compartments, namely susceptible individuals, infected individuals, and recovered individuals and pathogen population comprises one compartment. We derived the basic reproduction number $${\mathcal {R}}_0$$

R
0

, and analyzed the dynamical behaviors of both disease free equilibrium and endemic equilibrium by the theory of ordinary differential equations. Using MATLAB, we carried out numerical simulation and the findings indicate that effective treatment is adequate in eradicating typhoid fever.
Frequency-domain reflection waveform inversion with generalized internal multiple imaging
Authors: Wang Guanchao , Guo Qiang , Alkhalifah Tariq , Wang Shangxu
Published: July 2021

Full-waveform inversion (FWI) has the potential to provide a high-resolution detailed model of the earth’s subsurface, but it often fails to do so if the starting model differs significantly from the true one. Reflection waveform inversion (RWI) is a popular method for building a sufficiently accurate initial model for FWI. In traditional RWI, the low-wavenumber updates are always computed and captured by smearing the data misfit along the reflection path with the help of migration/demigration. However, the success of RWI relies heavily on accurately reproducing the data in demigration. Thus, we have introduced a new generalized internal multiple imaging-based RWI (GIMI-RWI) implementation, in which we avoid the Born modeling and update the primary reflection kernel directly. In GIMI-RWI, we store one reflection kernel for each source-receiver pair, preserving the unique wavepath for every single source-receiver trace. Subsequently, the convolution between the data residuals and the corresponding reflection kernel can build the tomographic velocity updates. In this situation, the long-wavelength tomographic updates are free of migration footprints and will contribute a smoother background velocity to reduce the cycle-skipping risk and stabilize the followed FWI process. In addition, the GIMI-RWI method is source independent because it entirely relies on the data. Using a synthetic example extracted from the Sigsbee2A model, we find the reliable performance of the GIMI-RWI technique.
FSH Level and Changes in Bone Mass and Body Composition in Older Women and Men
Authors: Wu Karin C , Ewing Susan K , Li Xiaojuan , Sigurðsson Sigurður , Guðnason Vilmundur , Kado Deborah M , Hue Trisha F , Woods Gina N , Veldhuis-Vlug Annegreet G , Vittinghoff Eric , Zaidi Mone , Rosen Clifford J , Lang Thomas , Kim Tiffany Y , Schwartz Ann V , Schafer Anne L
Published: July 2021

Context

FSH may have independent actions on bone remodeling and body fat regulation. Cross-sectionally, we have shown that serum FSH is associated with bone mineral density (BMD) and body fat in older postmenopausal women, but it remains unknown whether FSH predicts bone and fat changes.

Objective

We examined whether baseline FSH level is associated with subsequent bone loss or body composition changes in older adults.

Setting, Design, Participants

We studied 162 women and 158 men (mean age 82 ± 4 years) from the Age, Gene/Environment Susceptibility (AGES)-Bone Marrow Adiposity cohort, a substudy of the AGES-Reykjavik Study of community-dwelling older adults. Skeletal health and body composition were characterized at baseline and 3 years later.

Main Outcomes

Annualized change in BMD and body composition by dual-energy X-ray absorptiometry (DXA) and quantitative computed tomography (QCT). Models were adjusted for serum estradiol and testosterone levels.

Results

There was no evidence for an association between baseline FSH level and change in BMD or body composition by DXA or QCT. For femoral neck areal BMD, adjusted mean difference (95% CI) per SD increase in FSH was 1.3 (-0.7 to 3.3) mg/cm2/y in women, and -0.2 (-2.6 to 2.2) mg/cm2/y in men. For visceral fat, adjusted mean difference (95% CI) per SD increase in FSH was 1.80 (-0.03 to 3.62) cm2/y in women, and -0.33 (-3.73 to 3.06) cm2/y in men.

Conclusions

Although cross-sectional studies and studies in perimenopausal women have demonstrated associations between FSH and BMD and body composition, in older adults, FSH level is not associated with bone mass or body composition changes.
Interleukin-2 Transiently Inhibits Pulsatile Growth Hormone Secretion in Young but not Older Healthy Men
Authors: Roelfsema Ferdinand , Yang Rebecca , Veldhuis Johannes D
Published: July 2021

Context

Interleukin-2 (IL-2), a proinflammatory cytokine, has been used to treat malignancies. Increased cortisol and adrenocorticotropin (ACTH) were noted, but growth hormone (GH) secretion was not investigated in detail.

Objective

We quantified GH secretion after a single subcutaneous injection of IL-2 in 17 young and 18 older healthy men in relation to dose, age, and body composition.

Methods

This was a placebo-controlled, blinded, prospectively randomized, crossover study. At 20:00 hours IL-2 (3 or 6 million units/m2) or saline was injected subcutaneously. Lights were off between 23:00 and 07:00 hours. Blood was sampled at 10-minute intervals for 24 hours. Outcome measures included convolution analysis of GH secretion.

Results

GH profiles were pulsatile under both experimental conditions and lower in older than young volunteers. Since the effect of IL-2 might be time limited, GH analyses were performed on the complete 24-hour series and the 6 hours after IL-2 administration. Total and pulsatile 24-hour GH secretion decreased nonsignificantly. Pulsatile secretion fell over the first 6 hours after IL-2 (P = .03), with visceral fat as a covariate (P = .003), but not age (P = .10). Plots of cumulative 2-hour bins of GH pulse mass showed a distinction by treatment and age groups: A temporary GH decrease of 32% and 28% occurred in the first 2-hour bins after midnight (P = .02 and .04) in young participants, whereas in older individuals no differences were present at any time point.

Conclusion

This study demonstrates that IL-2 temporarily diminishes GH secretion in young, but not older, men.
Type 2 Diabetes and Change in Total Hip Bone Area and Bone Mineral Density in Swedish Men and Women Older Than 55 Years
Authors: Mitchell Adam , Fall Tove , Melhus Håkan , Lind Lars , Michaëlsson Karl , Byberg Liisa
Published: July 2021

Context

In a cross-sectional study, we found an association between type 2 diabetes mellitus (T2DM) and smaller bone area together with greater bone mineral density (BMD) at the total hip.

Objective

This work aims to investigate these associations longitudinally, by studying T2DM status (no T2DM n = 1521, incident T2DM n = 119, or prevalent T2DM n = 106) in relation to changes in total hip bone area and BMD.

Methods

In 3 cohorts, the Swedish Mammography Cohort Clinical (SMCC; n = 1060), Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS; n = 483), and Uppsala Longitudinal Study of Adult Men (ULSAM; n = 203), with repeat assessment of T2DM status and dual energy x-ray absorptiometry (DXA) measurements of total hip bone area and BMD on average 8 years apart, a linear regression model was used to assess the effect of T2DM status on change in bone area and BMD at the total hip.

Results

After meta-analysis, the change in bone area at the total hip was 0.5% lower among those with incident T2DM compared to those without T2DM (–0.18 cm2; 95% CI, –0.30 to –0.06). The change in bone area was similar among those with prevalent T2DM compared to those without (0.00 cm2; 95% CI, –0.13 to 0.13). For BMD, the combined estimate was 0.004 g/cm2 (95% CI, –0.006 to 0.014) among those with incident T2DM and 0.010 g/cm2 (95% CI, –0.000 to 0.020) among those with prevalent T2DM, compared to those without T2DM.

Conclusion

Those with incident T2DM have a lower expansion in bone area at the total hip compared to those without T2DM.
Keratin 8 mutations in transgenic mice predispose to lung injury
Authors: Kim Sujin , Lim Younglan , Lee So-Young , Yoon Han-Na , Yi Hayan , Jang Kwi-Hoon , Ku Nam-On
Published: July 2021

Keratin 8 (K8) is the cytoskeletal intermediate filament protein of simple-type epithelia. Mutations in K8 predispose the affected individual and transgenic mouse to liver disease. However, the role of K8 in the lung has not been reported in mutant transgenic mouse models. Here, we investigated the susceptibility of two different transgenic mice expressing K8 Gly62–Cys (Gly62 replaced with Cys) or Ser74–Ala (Ser74 replaced with Ala) to lung injury. The mutant transgenic mice were highly susceptible to two independent acute and chronic lung injuries compared with control mice. Both K8 Gly62–Cys mice and K8 Ser74–Ala mice showed markedly increased mouse lethality (∼74% mutant mice versus ∼34% control mice) and more severe lung damage, with increased inflammation and apoptosis, under L-arginine-mediated acute lung injury. Moreover, the K8 Ser74–Ala mice had more severe lung damage, with extensive hemorrhage and prominent fibrosis, under bleomycin-induced chronic lung injury. Our study provides the first direct evidence that K8 mutations predispose to lung injury in transgenic mice.
TAPAS: Towards Automated Processing and Analysis of multi-dimensional bioimage data
Authors: Gilles Jean-François , Boudier Thomas
Published: July 2021

Modern microscopy is based on reproducible quantitative analysis, image data should be batch-processed by a standardized system that can be shared and easily reused by others. Furthermore, such system should require none or minimal programming from the users.

We developed TAPAS (Towards an Automated Processing and Analysis System). The goal is to design an easy system for describing and exchanging processing workflows. The protocols are simple text files comprising a linear list of commands used to process and analyse the images. An extensive set of 60 modules is already available, mostly based on the tools proposed in the 3D ImageJ Suite.

We propose a wizard, called TAPAS menu, to help the user design the protocol by listing the available modules and the parameters associated. Most modules will have default parameters values for most common tasks. Once the user has designed the protocol, he/she can apply the protocol to a set of images, that can be either stored locally or on a OMERO database.

An extensive documentation including the list of modules, various tutorials and link to the source code is available at https://imagej.net/TAPAS.
Pancreatic cancer incidence trends in the United States from 2000-2017: Analysis of Surveillance, Epidemiology and End Results (SEER) database
Authors: Ali Hassam , Pamarthy Rahul , Vallabhaneni Meghana , Sarfraz Shiza , Ali Hadiqa , Rafique Hamza
Published: July 2021

Background: Recent incidence trends of pancreatic cancers were reviewed by demographics and histologic type to observe any new findings.

Methods: Data was used from the Surveillance, Epidemiology, and End Results (SEER) registry 18 (2000-2017) and it underwent temporal trend analysis. Pancreatic cancer incidence rates were reported based on histological subtype and demographics.

Results: The incidence rate of white males increased significantly during 2000-2017 (annual percent change (APC) = 3.5%) compared to previously reported APCs. The incidence of white females grew from an APC of 1.29% to 2.9%. Rates among black ethnicity increased with an APC of 4.2%. Rates among Hispanics and other ethnicities also showed increment. The rates for ductal adenocarcinoma showed a positive trend in all races, with the APC ≥ 6 % for females and APC ≥ 6.5 % for males. The rates of non-secretory endocrine tumors showed a decline in both genders of all five races in recent years after showing an initial positive trend till 2010. Rates for pancreatic adenocarcinoma continued to rise in all ethnicities from 2000-2017. Interestingly, there was a rise in carcinoid type pancreatic neuroendocrine tumors (PNETs) in all ethnicities. Cumulatively, males had a higher incidence than females; male to female Incidence Risk Ratio (IRRs) was 1.32. The IRR was > 1 for age groups ≥ 35 years. The male to female IRRs was less than 1 for cystic adenocarcinoma, secretory endocrine, and solid pseudopapillary carcinomas (IRR = 0.5, 0.9, and 0.2 respectively, confidence intervals 0.4–0.6 and 0.9-1.3, 0.2–0.3, respectively).

Conclusion: Pancreatic cancer incidence continued to rise in the years 2000-2017. However, incidence differed by demographics and histologic type. Interestingly, recent years discerned a rise in PNETs (carcinoid type) which has not been reported previously.
Engagement and social acceptance in genome editing for human benefit: Reflections on research and practice in a global context
Authors: Barbosa Sebastián , Pare Toe Lea , Thizy Delphine , Vaz Manjulika , Carter Lucy
Published: July 2021

While there are both practical and ethical reasons for public engagement in science and innovation, real-world detailed examples of engagement practice and the lessons to come from these are still hard to find. This paper showcases three contextually diverse case studies of engagement practice. Case 1 recounts the experiences of a government-funded initiative to involve scientists and policy makers as science communicators for the purpose of engaging the Argentine public on gene editing. Case 2 describes the research methodologies used to elicit diverse stakeholder views in the face of political uncertainty and institutional distrust in India. Finally, case 3 unpacks the tensions and gaps with existing international guidelines for ensuring local voices are respected in community decision-making in Burkina Faso. Each case shares its own compelling rationale for selecting the engagement method chosen and details the challenges encountered along the way. Each case shares its vision for creating legitimate opportunities for broader societal involvement in the planning, conduct and delivery of responsible science. These cases demonstrate the nuances, sensitivities and challenges of engaging with publics and broader stakeholders in discussions about genome editing for human benefit.
Kidney Exchange: An Operations Perspective
Authors: Ashlagi Itai , Roth Alvin E.
Published: July 2021

Many patients in need of a kidney transplant have a willing but incompatible (or poorly matched) living donor. Kidney exchange programs arrange exchanges among such patient-donor pairs, in cycles and chains of exchange, so that each patient receives a compatible kidney. Kidney exchange has become a standard form of transplantation in the United States and a few other countries, in large part because of continued attention to the operational details that arose as obstacles were overcome and new obstacles became relevant. We review some of the key operational issues in the design of successful kidney exchange programs. Kidney exchange has yet to reach its full potential, and the paper further describes some open questions that we hope will continue to attract attention from researchers interested in the operational aspects of dynamic exchange.

This paper was accepted by David Simchi-Levi, Special Section of Management Science: 65th Anniversary.
A Casa do Brasil de Lisboa: uma associação de Acolhida
Authors: Karam Brum Ceres
Published: July 2021

O artigo aborda a experiência realizada entre 2016 e 2021, na Casa do Brasil de Lisboa (CBL), focalizando aspectos de sua história e atuação no universo do associativismo imigrante em Portugal. A discussão que perpassa este texto destaca a casa como um lugar de simbolização coletiva e individual que extrapola sua dimensão de moradia, remetendo as noções de casa-nação, territorialização/ (des)territorialização de identidades e solidariedade imigrante na Europa.
Aprendendo a ser mulher no cárcere
Authors: Alves Araújo Isabela Cristina , Hordones Chaves Luana
Published: July 2021

Com o propósito de abordar as expectativas dos papéis de gênero no sistema prisional, tratamos, neste artigo, de temas relacionados à maternidade, à sexualidade, às relações conjugais e ao cotidiano nas prisões. Para tanto, analisamos os dados qualitativos e quantitativos de uma pesquisa realizada nas unidades prisionais femininas da Região Metropolitana de Belo Horizonte. Como resultado, temos que os tradicionais papéis de gênero regem, em grande medida, a experiência de ser mulher no cárcere.
Midwives' experiences of performing obstetric ultrasounds in maternity care: a systematic review
Authors: Bwanga Osward , Mwase Gabriel , Kaunda Happiness Chanda
Published: July 2021

Background/aims

Ultrasound scans, often performed by midwives, play a vital role in the management of pregnancy, but there is a lack of literature on midwives' experience of this task. This study aimed to systematically review the experiences of midwives when performing obstetrical ultrasounds in maternity care.

Methods

Online databases, journals and cited references were searched, with no date limit. Thematic analysis was used to synthesise the findings.

Results

A total of eight studies were included. The five themes identified were 1) the benefits of ultrasound in maternity care, 2) access to and performing an obstetric ultrasound, 3) the relationship between midwives and ultrasound experts, 4) ethical and legal issues and 5) education and training for midwives. Midwives' positive experiences were usually a result of access to obstetric ultrasound and adequate support from obstetricians and radiologists. Negative experiences were caused by ethical and legal complications, as well as a lack of ultrasound equipment and training.

Conclusions

There is a need to support midwives in performing basic obstetric ultrasounds, through education and training, to improve maternity care.
Wound prevalence survey in a regional integrated care organisation in the midwest of Ireland
Authors: Meagher Helen , Keane Niamh , Egan Siobhan , Sheikhi Ali , Moloney Michael A. , Kavanagh Eamon
Published: July 2021

Background/aims:

The aim of this clinical audit was to determine the point prevalence of wounds over a 1-week period during April 2019 in the midwest Regional Integrated Care Organisation (RICO), which has a population of 379 452. The RICO consists of six hospitals, a public health nursing service across three counties, community residential settings, nine older person's service sites, community health centres and one prison.

Method:

A peer-reviewed, purpose-designed data collection tool was used to gather demographic and wound data on each patient with a wound in the midwest RICO. Anonymised data were collected by the nurse undertaking routine wound care on one occasion during the 1-week study period. There were no exclusion criteria for this study; all patients with a wound were eligible for inclusion. Ethical approval was obtained.

Results:

Completed data collection forms were returned for 791 patients who had a combined total of 1164 wounds. Data were analysed using SPSS version 21 to produce descriptive statistics. A point prevalence of 0.2% of the total RICO population had a wound, with a mean of 1.47 wounds per patient. Some 51% of the cohort was female. The median age was 75 years (range 3–101 years, standard deviation=19.881). Leg ulcers were the most common wound type, with a prevalence of 0.07% (33.7% of the cohort).

Conclusions:

This clinical wound prevalence audit supports previous studies in relation to wound statistics in Ireland and will be useful for resource planning in an ageing population.
What does the future hold for learning and development in care homes?
Authors: Ashurst Adrian
Published: July 2021

In a world forever changed by the COVID-19 pandemic, Adrian Ashurst discusses the importance of reviewing the way in which staff receive their induction and ongoing training in a care home setting.
Digital Andragogical Competences of Ecuadorian Higher Education Teachers during the COVID-19 Pandemic
Authors: Velazco Derling Jose Mendoza , Cejas Mercedes Navarro , Martinez Magda Francisca Cejas , Naranjo Paola Gabriela Vinueza , Falcón Vladimir Vega
Published: July 2021

The changes brought about in higher education by the Coronavirus disease (COVID-19) pandemic require effective action. Teachers must be trained to work on university platforms. The study allows us to analyse the current educational problems, which are found in many countries, not only in Ecuador. The research aimed to determine the virtual andragogical competencies of Ecuadorian university education during the COVID-19 pandemic. A mixed research approach was used. A quantitative analysis was applied first, followed by a qualitative analysis. The sample selection was participatory and non-probabilistic. The sample consisted of 1003 active higher education teachers in Ecuador. A questionnaire of 106 questions divided into four variables was applied. A multiple analysis of variance (MANOVA) was performed. The analyses demonstrated the need to apply four integral competencies. First the teacher must "Know how to be", through continuous ICT training. After the teacher has been trained, he/she must "Know". This process involves mastering educational technology. After updating knowledge, they must "Know how to live together". Develop critical and constructive communication. Then "Know how to do" by applying an effective guiding methodology. Teacher training under the competency-based approach is seen as a viable alternative.
Resonant fiber optical gyroscope using the single-mode fiber ring resonator
Authors: Liu Lu , Liu Shuang , Qian Weiwen , Li Hanzhao , Ma Huilian
Published: July 2021

This paper provides a scheme for realizing high-accuracy, low-cost resonant fiber optical gyroscopes (RFOGs) with single-mode (SM) fibers. The temperature-related polarization noise, which deteriorates the bias stability of the RFOG, has been suppressed thanks to a much longer birefringence beat length of SM fibers. It is also helpful to improve the theoretical sensitivity of the RFOG because of the very low loss of the SM fiber components. A transmissive 39-m-long SM fiber ring resonator (FRR) is fabricated. The measured finesse is 58.7, and its total loss is calculated to be less than 0.3 dB. Using this SM-FRR as the sensing element, an RFOG is then set up that achieves an angular random walk of

0.0039

∘

/

√

h

and a bias stability of 0.05°/h. The experimental results show that the SM-FRR scheme would be a good candidate for producing high-accuracy and low-cost RFOGs.
Deep-ROCS: from speckle patterns to superior-resolved images by deep learning in rotating coherent scattering microscopy
Authors: Saguy Alon , Jünger Felix , Peleg Aviv , Ferdman Boris , Nehme Elias , Rohrbach Alexander , Shechtman Yoav
Published: July 2021

Rotating coherent scattering (ROCS) microscopy is a label-free imaging technique that overcomes the optical diffraction limit by adding up the scattered laser light from a sample obliquely illuminated from different angles. Although ROCS imaging achieves 150 nm spatial and 10 ms temporal resolution, simply summing different speckle patterns may cause loss of sample information. In this paper we present Deep-ROCS, a neural network-based technique that generates a superior-resolved image by efficient numerical combination of a set of differently illuminated images. We show that Deep-ROCS can reconstruct super-resolved images more accurately than conventional ROCS microscopy, retrieving high-frequency information from a small number (6) of speckle images. We demonstrate the performance of Deep-ROCS experimentally on 200 nm beads and by computer simulations, where we show its potential for even more complex structures such as a filament network.
Optimal sampled phase-only hologram (OSPOH)
Authors: Tsang P. W. M. , Liu J.-P. , Lam H. , Poon T.-C.
Published: July 2021

A sampled phase-only hologram (SPOH) is the phase component of the hologram of an object image with pixels being sampled with a periodic grid-cross pattern. The reconstructed image of a SPOH is a sparse image with abundant empty voids and degradation in sharpness and contrast. In this paper we proposed a method based on a new sampling scheme, together with stochastic binary search (SBS), to obtain an optimal sampling lattice that can be applied to generate phase-only holograms with enhanced reconstructed image. Experimental results show that with our proposed method, the fidelity and quality of the reconstructed image are increased.
Real-time reception of 106 Gbps PAM-4 transmission over an 80 km SSMF link enabled by CD pre-compensation
Authors: Yang Yanfu , Zhang Qun , Qu Siwei , Zhong Kangping
Published: July 2021

In this study, we report, to the best of our knowledge, the first experimental demonstration of the real-time reception of a 106 Gbps PAM-4 transmission over an 80 km dispersion uncompensated standard single-mode fiber (SSMF) link. In the transmitter, a chromatic dispersion (CD) pre-compensation, aided by an optical IQ modulator, is implemented. The optimization guideline of driver signal amplitudes and bias voltages is proposed to enable optimal CD pre-compensation. In the receiver, a real-time PAM-4 module including simple feed-forward equalization (FFE) is used. After the transmission, the required optical signal-to-noise ratio (OSNR) at a bit error rate (BER) below 3.8 × 10−3 is determined to be 35 dB for 106 Gbps PAM-4 signals. The better BER of 6.9 × 10−4 is achieved successfully compared to the previously reported off-line reception. The demonstration confirms the feasibility of 80 km DCI based on CD pre-compensation under real-time reception.
Performance analysis of dual-frequency lidar in the detection of the complex wind field
Authors: Xu He , Li Jianbing
Published: July 2021

Due to short coherent length of the laser, traditional single frequency lidar (SFL) uses echoes of adjacent samples to retrieve Doppler wind velocity, which inevitably brings about a dilemma of high range resolution and velocity resolution. Dual-frequency lidar (DFL), however, with a frequency difference locating at the radar band, can process the laser echoes with a radar processing framework while maintaining a good wind sensing ability in clear air. In this paper, performances of SFL and DFL are analyzed in terms of different conditions like pulse duration, number of sampling points in processing, wind distribution, signal to noise ratio (SNR), etc. It is shown that, for a complex wind field, DFL has the potential to retrieve the Doppler velocity with high velocity and range resolution, even in a relatively low SNR condition.
Broadband sum frequency generation spectroscopy of dark exciton states in hBN-encapsulated monolayer WSe2
Authors: Kusaba Satoshi , Katagiri Yoshiki , Watanabe Kenji , Taniguchi Takashi , Yanagi Kazuhiro , Naka Nobuko , Tanaka Koichiro
Published: July 2021

We demonstrate that broadband sum frequency generation (SFG) spectroscopy based on a partially incoherent supercontinuum light source can elucidate dark p-series excitons in monolayer WSe2 encapsulated between hexagonal boron nitride (hBN) slabs. The observed 2p exciton peak energy is a few meV higher than that predicted by the Rytova-Keldysh potential model, which is originated from the Berry phase effect. Interestingly, although the radiative relaxation of the 2p exciton is weaker, the 2p exciton peak is broader than the 1s and 2s peaks, which indicates its faster dephasing than the 1s and 2s excitons. Measuring the excitation intensity and temperature dependence, we clarified that this broader linewidth is not caused by excitation- or phonon-induced dephasing, but rather by exciton-electron scattering.
Low cost O-band inter-datacenter interconnect utilizing a 4-bit resolution digital-to-analog converter for PAM-4 signal generation
Authors: Yin Mingzhu , Wang Xiaowu , Zou Dongdong , Wang Wei , Sui Qi , Li Fan
Published: July 2021

In this paper, we experimentally demonstrate the transmission of a 100 Gb/s/λ PAM-4 signal over a 40/80-km single mode fiber (SMF) in the O-band utilizing a 4-bit resolution digital-to-analog converter (DAC) for signal generation. Low resolution DACs are preferred to meet the requirement of low-cost criteria of datacenter interconnects (DCIs). However, large quantization noise introduced by low resolution DACs will deteriorate system performance significantly. Noise shaping (NS) technique is investigated to reduce the quantization noise within the PAM-4 signal band. The experimental results show that the bit error ratio (BER) performance of the signal generated by 4-bit resolution DAC and NS technique will approach that of the signal generated by the 8-bit resolution DAC in the 40/80-km optical fiber transmission system of a 50 Gbaud PAM-4 signal in the O-band, which indicates that our proposed scheme operating in the O-band with a 4-bit resolution DAC and NS technique is a promising candidate for 100 Gbit/s/λ beyond a 40-km Inter-DCI.