bluuebunny/crossref_metadata_2025 huggingface dataset:
The ancillary N-terminal region of the yeast AP-1 transcription factor Yap8 contributes to its DNA binding specificity
Authors: Maciaszczyk-Dziubinska Ewa , Reymer Anna , Vijay Kumar Nallani , Białek Wojciech , Mizio Katarzyna , Tamás Markus J. , Wysocki Robert
Published: April 2019

Activator protein 1 (AP-1) is one of the largest families of basic leucine zipper (bZIP) transcription factors in eukaryotic cells. How AP-1 proteins achieve target DNA binding specificity remains elusive. In Saccharomyces cerevisiae, the AP-1-like protein (Yap) family comprises eight members (Yap1 to Yap8) that display distinct genomic target sites despite high sequence homology of their DNA binding bZIP domains. In contrast to the other members of the Yap family, which preferentially bind to short (7-8 bp) DNA motifs, Yap8 binds to an unusually long DNA motif (13 bp). It has been unclear what determines this unique specificity of Yap8. In this work, we use molecular and biochemical analysis combined with computer-based structural design and molecular dynamics simulations of Yap8-DNA interactions to better understand the structural basis of DNA binding specificity determinants. We identify specific residues in the N-terminal tail preceding the basic region, which define stable association of Yap8 with the ACR3 promoter. We propose that the N-terminal tail directly interacts with DNA and stabilizes Yap8 binding to the 13 bp motif. Thus, beside the core basic region, the adjacent N-terminal region contributes to alternative DNA binding selectivity within the AP-1 family.
Integrase-mediated differentiation circuits improve evolutionary stability of burdensome and toxic functions in E. coli
Authors: Williams Rory. L , Murray Richard M.
Published: April 2019

Advances in synthetic biology, bioengineering, and computation allow us to rapidly and reliably program cells with increasingly complex and useful functions. However, because the functions we engineer cells to perform are typically unnecessary for cellular survival and burdensome to cell growth, they can be rapidly lost due to the processes of mutation and natural selection. To improve the evolutionary stability of engineered functions in a general manner, we developed an integrase-recombination-based differentiation gene circuit in Escherichia coli. In this system, differentiated cells uniquely carry out burdensome or toxic engineered functions but have limited capacity to grow (terminal differentiation), preventing the propagation of selectively advantageous loss of function mutations that inevitably arise. To experimentally implement terminal differentiation, we co-opted the R6K plasmid system, using differentiation to simultaneously activate T7 RNAP-driven expression of arbitrary engineered functions, and inactivate expression of π protein (an essential factor for R6K plasmid replication), thereby allowing limitation of differentiated cell growth through antibiotic selection. We experimentally demonstrate terminal differentiation increases both duration and magnitude of high-burden T7 RNAP-driven expression, and that its evolutionary stability can be further improved with strategic redundancy. Using burdensome overexpression of a fluorescent protein as a model engineered function, our terminal differentiation circuit results in a ~2.8-fold (single-cassette) and ~4.2-fold (two-cassette) increase of total fluorescent protein produced compared to high-burden naive expression in which all cells inducibly express T7 RNAP. Finally, we demonstrate that differentiation can enable the expression of even toxic functions, a feat not achieved to our knowledge by any other strategy for addressing long-term evolutionary stability. Overall, this study provides an effective generalizable strategy for protecting engineered functions from evolutionary degradation.
A Method for Cost-Effective and Rapid Characterization of Engineered T7-based Transcription Factors by Cell-Free Protein Synthesis Reveals Insights into the Regulation of T7 RNA Polymerase-Driven Expression
Authors: McManus John B. , Murray Richard M. , Emanuel Peter A. , Lux Matthew W.
Published: April 2019

The T7 bacteriophage RNA polymerase (T7 RNAP) serves as a model for understanding RNA synthesis, as a tool for protein expression, and as an actuator for synthetic gene circuit design in bacterial cells and cell-free extract. T7 RNAP is an attractive tool for orthogonal protein expression in bacteria owing to its compact single subunit structure and orthogonal promoter specificity. Understanding the mechanisms underlying T7 RNAP regulation is important to the design of engineered T7-based transcription factors, which can be used in gene circuit design. To explore regulatory mechanisms for T7 RNAP-driven expression, we developed a rapid and cost-effective method to characterize engineered T7-based transcription factors using cell-free protein synthesis and an acoustic liquid handler. Using this method, we investigated the effects of the tetracycline operator’s proximity to the T7 promoter on the regulation of T7 RNAP-driven expression. Our results reveal a mechanism for regulation that functions by interfering with the transition of T7 RNAP from initiation to elongation and validates the use of the method described here to engineer future T7-based transcription factors.

Highlights

Development of a rapid and cost-effective method for screening synthetic promoters.

Insights into the regulation of engineered T7-based transcription factors and T7 RNAP enzyme kinetics.

Validation of this method by comparison with the T7 RNAP kinetic model.
An improved method to produce clinical scale natural killer cells from human pluripotent stem cells
Authors: Zhu Huang , Kaufman Dan S.
Published: April 2019

Human natural killer (NK) cell-based adoptive anti-cancer immunotherapy has gained intense interest with many clinical trials actively recruiting patients to treat a variety of both hematological malignancies and solid tumors. Most of these trials use primary NK cells isolated either from peripheral blood (PB-NK cells) or umbilical cord blood (UCB-NK cells), though these sources require NK cell collection for each patient leading to donor variability and heterogeneity in the NK cell populations. In contrast, NK cells derived human embryonic stem cells (hESC-NK cells) or induced pluripotent stem cells (hiPSC-NK cells) provide more homogeneous cell populations that can be grown at clinical scale, and genetically engineered if desired. These characteristics make hESC/iPSC-derived NK cells an ideal cell population for developing standardized, “off-the-shelf” immunotherapy products. Additionally, production of NK cells from undifferentiated human pluripotent stem cells enables studies to better define pathways that regulate human NK cell development and function. Our group previously established a stromal-free, two-stage culture system to derive NK cells from hESC/hiPSC in vitro followed by clinical-scale expansion of these cells using interleukin-21 expressing artificial antigen-presenting cells. However, prior to differentiation, this method requires single cell adaption of hESCs/hiPSCs which takes months. Recently we optimized this method by adapting the mouse embryonic fibroblast-dependent hESC/hiPSC to feeder-free culture conditions. These feeder-free hESC/hiPSCs are directly used to generate hemato-endothelial precursor cells. This new method produces mature, functional NK cells with higher efficiency to enable rapid production of an essentially unlimited number of homogenous NK cells that can be used for standardized, targeted immunotherapy for the treatment of refractory cancers and infectious diseases.
Targeted mRNA demethylation using an engineered dCas13b-ALKBH5 fusion protein
Authors: Li Jiexin , Chen Zhuojia , Chen Feng , Ling Yuyi , Peng Yanxi , Luo Nan , Wang Hongsheng
Published: April 2019

Studies on biological functions ofN6-methyladenosine (m6A) modification in mRNA have sprung up in recent years. Here we construct and characterize a CRISPR-Cas13b-based tool for the first time that targeted m6A methylation of mRNA by fusing the catalytically dead Type VI-B Cas13 enzyme from Prevotella sp.P5-125 (dPspCas13b) with the m6A demethylase ALKBH5, which is named as dm6ACRISPR. Subsequently, such system is shown to specific demethylase the m6A of target mRNA such as CYB5A to increase its mRNA stability. In addition, the dm6ACRISPR system appeared to afford efficient demethylation of the target genes with tenuous off-target effects. Together, we provide a programmable andin vivomanipulation tool to study mRNA modification and its potential biological functions of specific gene.
A How-To guide to: Quantitative high-speed video profiling to discriminate between variants of primary ciliary dyskinesia
Authors: Chioccioli M. , Feriani L. , Nguyen Q. , Kotar J. , Dell S. D. , Mennella V. , Amirav I. , Cicuta P.
Published: April 2019

This document presents detailed steps to analysing the waveforms of beating cilia, measured in high speed video microscopy. We show that in the case of PCD caused by mutations inDNAH11andHYDINthe classification by a handful of parameters describing ciliary dynamics allows to distinguish the genotype, as well as (much more easily) distinguishing healthy from PCD samples. This document is intended to complement the brief highlight (1) and presents the details of the datasets used in that letter.
Normal development and fertility of Fut1, Fut2, and Sec1 triple knockout mice
Authors: Chen Jiaxi , Su Zhipeng , Zhang Chunlei , Li Fenge , Hwu Patrick , Wang Zhen , Wang Yanping , Li Yunsen , Tong Jiao , Chen Chunchao , Zhou Dapeng
Published: April 2019

The fucose alpha(1,2) galactose structure (H antigen) is synthesized by α1,2 fucosyltransferases Fut1, Fut2 and Sec1. H antigen has been reported to be involved in cancer progression, neurite migration, synaptic plasticity, host-microbe interaction, blastocyst implantation, and the maintenance of gut microbiome. Genetic depletion of Fut1 or Fut2 only cause defects of alpha1,2 fucosylation in limited tissues because of enzyme redundancy. In this study, we generated mice with deficiencies in Fut1, Fut2, and Sec1 genes to deplete H antigen through BAC Engineering for the generation of ES Cell-Targeting construct. The homogenous triple knockout mice showed no significant decrease of viability or development. Mass spectrometry and Western blot analysis confirmed the absence of H blood group antigen in multiple organs. These results indicate normal development and fertility of mice devoid of blood group H. The fine pathophysiological alterations in these mice remain to be carefully studied, and they may serve as valuable tools to study gut microbiome and host-microbe interactions.
Intertwined trade-offs coordinateDrosophilamidgut mitosis vs. endoreplication and host defense vs. dysplasia
Authors: Tamamouna Vasilia , Panagi Myrofora , Theophanous Andria , Demosthenous Maria , Michail Maria , Papadopoulou Markella , Teloni Savvas , Pitsouli Chrysoula , Apidianakis Yiorgos
Published: April 2019

Inflammatory signaling supports host defense against infection, not only through immune cells, but also via regeneration of damaged tissue. Heightened regeneration, nevertheless, predisposes for all types of cancer and thus a trade-off exists between regeneration capacity and long-term tissue homeostasis. Here, we study the role of tissue-intrinsic regenerative inflammatory signaling in stem cell mitosis of the adultDrosophilamidgut at the baseline and the infected state and its impact on intestinal host defense to infection and stem cell-mediated dysplasia. Through a quantitative genetics screen we find that stem cell mitosis is positively linked with the expression ofeiger, Delta, upd3andveinin the midgut, as well as with dysplasia and host defense, but negatively with enterocyte endoreplication. We provide evidence that intertwined trade-offs fine-tune midgut homeostasis, according to which stem cell mitosis throughcyclin Ein stem cells promotes the optimal host defense to infection, unless dysplasia ensues. However,cyclin Ein enteroblasts promotes enterocyte endoreplication and counterbalances stem cell mitosis and dysplasia, providing an alternative but less efficient mechanism to support host defense.
UNC-45A is preferentially expressed in epithelial cells and binds to and co-localizes with interphase MTs
Authors: Habicht Juri , Mooneyham Ashley , Shetty Mihir , Zhang Xiaonan , Shridhar Vijayalakshmi , Winterhoff Boris , Zhang Ying , Cepela Jason , Starr Timothy , Lou Emil , Bazzaro Martina
Published: April 2019

UNC-45A is a ubiquitously expressed protein highly conserved throughout evolution. Most of what we currently know about UNC-45A pertains to its role as a regulator of the actomyosin system. However, emerging studies from both our and other laboratories support a role of UNC-45A outside of actomyosin regulation. This includes studies showing that UNC-45A: regulates gene transcription, co-localizes and biochemically co-fractionates with gamma tubulin and regulates centrosomal positioning, is found in the same subcellular fractions where MT-associated proteins are, and is a mitotic spindle-associated protein with MT destabilizing activity in absence of the actomyosin system.

Here, we extended our previous findings and show that UNC45A is variably expressed across a spectrum of cell lines with the highest level being found in HeLa cells and in ovarian cancer cells inherently paclitaxel-resistant. Furthermore, we show that UNC-45A is preferentially expressed in epithelial cells, localizes to mitotic spindles in clinical tumor specimens of cancer and co-localizes and co-fractionates with MTs in interphase cells independent of actin or myosin.

In sum, we report alteration of UNC45A localization in the setting of chemotherapeutic treatment of cells with paclitaxel, and localization of UNC45A to MTs both in vitro and in vivo. These findings will be important to ongoing and future studies in the field that further identify the important role of UNC45A in cancer and other cellular processes.
A rapid and accurate MinION-based workflow for tracking species biodiversity in the field
Authors: Maestri Simone , Cosentino Emanuela , Paterno Marta , Freitag Hendrik , Garces Jhoana M. , Marcolungo Luca , Alfano Massimiliano , Njunjić Iva , Schilthuizen Menno , Slik Ferry , Menegon Michele , Rossato Marzia , Delledonne Massimo
Published: April 2019

Genetic markers (DNA barcodes) are often used to support and confirm species identification. Barcode sequences can be generated in the field using portable systems based on the Oxford Nanopore Technologies (ONT) MinION platform. However, to achieve a broader application, current proof-of-principle workflows for on-site barcoding analysis must be standardized to ensure reliable and robust performance under suboptimal field conditions without increasing costs. Here we demonstrate the implementation of a new on-site workflow for DNA extraction, PCR-based barcoding and the generation of consensus sequences. The portable laboratory features inexpensive instruments that can be carried as hand luggage and uses standard molecular biology protocols and reagents that tolerate adverse environmental conditions. Barcodes are sequenced using MinION technology and analyzed with ONTrack, an original de novo assembly pipeline that requires as few as 500 reads per sample. ONTrack-derived consensus barcodes have high accuracy, ranging from 99,8% to 100%, despite the presence of homopolymer runs. The ONTrack pipeline has a user-friendly interface and returns consensus sequences in minutes. The remarkable accuracy and low computational demand of the ONTrack pipeline, together with the inexpensive equipment and simple protocols, make the proposed workflow particularly suitable for tracking species under field conditions.
Crystal structure and Hirshfeld surface analysis of (μ-2-{4-[(carboxylatomethyl)carbamoyl]benzamido}acetato-κ2
O:O′)bis[bis(1,10-phenanthroline-κ2
N,N′)copper(II)] dinitrate N,N′-(1,4-phenylenedicarbonyl)diglycine monosolvate octahydrate
Authors: Pook Niels-Patrick , Adam Arnold , Gjikaj Mimoza
Published: April 2019

The centrosymmetric binuclear complex cation of the title compound, [Cu2(C12H10N2O6)(C12H8N2)4](NO3)2·C12H12N2O6·8H2O, is composed of a CuII atom with a distorted trigonal–bipyramidal coordination environment defined by four N atoms from two bidentate 1,10-phenanthroline ligands and one oxygen atom from one-half of the monodentate N,N′-(1,4-phenylenedicarbonyl)diglycinate anion. The asymmetric unit is completed by one-half of the N,N′-(1,4-phenylenedicarbonyl)diglycine solvent molecule, which is located on a centre of inversion, by one nitrate counter-anion and four water molecules. In the crystal, the cationic complexes are linked via intermolecular π–π stacking and through lone-pair...π interactions involving the N,N′-(1,4-phenylenedicarbonyl)diglycinate anion and the phenanthroline ligands. The N,N′-(1,4-phenylenedicarbonyl)diglycine solvent molecule is involved in classical and non-classical hydrogen-bonding interactions, as well as π–π stacking interactions. The centroid-to-centroid distances between aromatic entities are in the range 3.5402 (5)–4.3673 (4) Å. The crystal structure is stabilized by further C—H...O contacts as well as by O—H...O and N—H...O hydrogen bonds between water molecules, the nitrate anions, the N,N′-(1,4-phenylenedicarbonyl)diglycinate ligands, N,N′-(1,4-phenylenedicarbonyl)diglycine solvent molecules and phenanthroline ligands, giving rise to a supramolecular framework. A Hirshfeld surface analysis was carried out to quantify these interactions.
D-Glutamic acid hydrochloride
Authors: Fox-Uribe Leonardo Y. , Hernández-Paredes Javier , Soberanes Yedith , Valenzuela-Chavira Ignacio , Garcia-Orozco Karina D. , Ochoa-Leyva Adrian , Lara Karen Ochoa , Navarro Rosa Elena , Sotelo-Mundo Rogerio R.
Published: April 2019

The absolute structure of D-glutamic acid hydrochloride [systematic name: (R)-1,3-dicarboxypropan-1-aminium chloride], C5H10NO4
+·Cl−, has been determined by single-crystal X-ray diffraction at room temperature using Cu Kα radiation.
Exploring the role of risk and corruption on bank stability: evidence from Pakistan
Authors: Ali Muhammad , Sohail Amna , Khan Lubna , Puah Chin-Hong
Published: April 2019

Purpose

This paper aims to explore the impact of liquidity risk, credit risk, funding risk and corruption on bank stability of the banking system in Pakistan.

Design/methodology/approach

The empirical analysis is confined to 24 retail banks, which include 5 Islamic and 19 conventional banks during the period of 2007-2015.

Findings

The findings of this study suggest that bank size, liquidity risk, funding risk and corruption exert a positive impact on bank stability. Additionally, the authors find a negative relationship between credit risk and bank stability.

Originality/value

As per the knowledge of the authors, the present research is the first attempt that discusses the issues of bank stability related to risk and corruption faced by the banking system.
Sustaining open innovation through a “Center of Excellence”
Authors: Richard Elizabeth E. , Davis Jeffrey R. , Paik Jin H. , Lakhani Karim R.
Published: April 2019

Purpose

This paper presents NASA’s experience using a Center of Excellence (CoE) to scale and sustain an open innovation program as an effective problem-solving tool and includes strategic management recommendations for other organizations based on lessons learned.

Design/methodology/approach

This paper defines four phases of implementing an open innovation program: Learn, Pilot, Scale and Sustain. It provides guidance on the time required for each phase and recommendations for how to utilize a CoE to succeed. Recommendations are based upon the experience of NASA’s Human Health and Performance Directorate, and experience at the Laboratory for Innovation Science at Harvard running hundreds of challenges with research and development organizations.

Findings

Lessons learned include the importance of grounding innovation initiatives in the business strategy, assessing the portfolio of work to select problems most amenable to solving via crowdsourcing methodology, framing problems that external parties can solve, thinking strategically about early wins, selecting the right platforms, developing criteria for evaluation, and advancing a culture of innovation. Establishing a CoE provides an effective infrastructure to address both technical and cultural issues.

Originality/value

The NASA experience spanned more than seven years from initial learnings about open innovation concepts to the successful scaling and sustaining of an open innovation program; this paper provides recommendations on how to decrease this timeline to three years.
Case of severe bullous erythema including intertrigo‐like eruptions with angioedema induced by pegylated liposomal doxorubicin
Authors: Totsuka Michiru , Watanabe Yuko , Asai Chika , Takahashi Saki , Ishikawa Hideyuki , Takamura Naoko , Hagiwara Mayumi , Aihara Michiko
Published: April 2019

Pegylated liposomal doxorubicin (PLD) is an anthracycline anticancer agent used in ovarian cancer and a form of doxorubicin enclosed in pegylated liposomes. There are only a few reports on intertrigo‐like eruptions caused by PLD. We describe the first case of severe bullous erythema, including intertrigo‐like eruptions with angioedema, induced by PLD in Japan. We present the case of a 53‐year‐old woman who was diagnosed with stage IIIC ovarian cancer. After receiving three cycles of PLD, the patient developed swelling of the upper lip and painful erythema with blisters and erosions on the axilla, upper back, flank and wrists. The patient was diagnosed with angioedema and severe skin lesions, including intertrigo‐like eruptions induced by PLD. Although treatment with oral prednisolone and topical steroids was effective against these eruptions, the administration of PLD was discontinued because of its ineffectiveness against the primary disease. Several risk factors, such as obesity, perspiration and racial differences, may contribute toward a severe manifestation such as that seen in our patient. Moreover, our case was the first accompanied by angioedema. The mechanism of coexistence of intertrigo‐like eruptions and angioedema is not clear; further studies are required to clarify the pathological mechanism of intertrigo‐like eruptions.
Effects of stand age, richness and density on productivity in subtropical forests in China
Authors: Ouyang Shuai , Xiang Wenhua , Wang Xiangping , Xiao Wenfa , Chen Liang , Li Shenggong , Sun Han , Deng Xiangwen , Forrester David I. , Zeng Lixiong , Lei Pifeng , Lei Xiangdong , Gou Mengmeng , Peng Changhui
Published: April 2019

Forest productivity may be determined not only by biodiversity but also by environmental factors and stand structure attributes. However, the relative importance of these factors in determining productivity is still controversial for subtropical forests.

Based on a large dataset from 600 permanent forest inventory plots across subtropical China, we examined the relationship between biodiversity and forest productivity and tested whether stand structural attributes (stand density in terms of trees per ha, age and tree size) and environmental factors (climate and site conditions) had larger effects on productivity. Furthermore, we quantified the relative importance of environmental factors, stand structure and diversity in determining forest productivity.

Diversity, together with stand structure and site conditions, regulated the variability in forest productivity. The relationship between diversity and forest productivity did not vary along environmental gradients. Stand density and age were more important modulators of forest productivity than diversity.

Synthesis. Diversity had significant and positive effects on productivity in species‐rich subtropical forests, but the effects of stand density and age were also important. Our work highlights that while biodiversity conservation is often important, the regulation of stand structure can be even more important to maintain high productivity in subtropical forests.
Specific class of intrapartum antibiotics relates to maturation of the infant gut microbiota: a prospective cohort study
Authors: Coker MO , Hoen AG , Dade E , Lundgren S , Li Z , Wong AD , Zens MS , Palys TJ , Morrison HG , Sogin ML , Baker ER , Karagas MR , Madan JC
Published: April 2019

Objective

To evaluate the potential impact of intrapartum antibiotics, and their specific classes, on the infant gut microbiota in the first year of life.

Design

Prospective study of infants in the New Hampshire Birth Cohort Study (NHBCS).

Settings

Rural New Hampshire, USA.

Population or sample

Two hundred and sixty‐six full‐term infants from the NHBCS.

Methods

Intrapartum antibiotic use during labour and delivery was abstracted from medical records. Faecal samples collected at 6 weeks and 1 year of age were characterised by 16S rRNA sequencing, and metagenomics analysis in a subset of samples.

Exposures

Maternal exposure to antibiotics during labour and delivery.

Main outcome measure

Taxonomic and functional profiles of faecal samples.

Results

Infant exposure to intrapartum antibiotics, particularly to two or more antibiotic classes, was independently associated with lower microbial diversity scores as well as a unique bacterial community at 6 weeks (GUnifrac, P = 0.02). At 1 year, infants in the penicillin‐only group had significantly lower α diversity scores than infants not exposed to intrapartum antibiotics. Within the first year of life, intrapartum exposure to penicillins was related to a significantly lower increase in several taxa including Bacteroides, use of cephalosporins was associated with a significantly lower rise over time in Bifidobacterium and infants in the multi‐class group experienced a significantly higher increase in Veillonella dispar.

Conclusions

Our findings suggest that intrapartum antibiotics alter the developmental trajectory of the infant gut microbiome, and specific antibiotic types may impact community composition, diversity and keystone immune training taxa.

Tweetable abstract

Class of intrapartum antibiotics administered during delivery relates to maturation of infant gut microbiota.
Clomiphene citrate and neural tube defects: a meta‐analysis of controlled observational studies
Authors: Auffret M , Cottin J , Vial T , Cucherat M
Published: April 2019

Background

At the end of the 1980s, several studies suggested a potential increased risk of neural tube defects (NTDs) with ovulation induction/fertility drugs, especially with clomiphene citrate (CC). A previous meta‐analysis of observational studies evaluating the risk of NTDs associated with the use of CC performed in 1995 found a risk ratio of 1.08 (95% CI 0.76–1.51). Since then, additional studies have been published and the risk of NTDs associated with periconceptional CC exposure may have changed.

Objective

To perform an updated quantitative meta‐analysis of the risk of NTDs associated with periconceptional CC exposure.

Search strategy

MEDLINE, Web of Science, and Scopus were searched (October 2018).

Selection criteria

Comparative cohort and case–control studies investigating the risk of NTDs after periconceptional CC exposure.

Data collection and analysis

Pooled effect sizes with corresponding 95% CIs were calculated using random effects models, comparing the risk of NTDs between pregnancies exposed and not exposed to CC.

Main results

Thirteen studies met the inclusion criteria, totalling 218 819 pregnancies. Periconceptional exposure to CC was not significantly associated with an increased risk of NTDs (pooled odds ratio 1.21, 95% CI 0.88–1.66). No heterogeneity between studies was observed (I2 = 26%). A funnel plot and asymmetry test were not suggestive of publication bias.

Conclusion

Our meta‐analysis confirms that exposure to CC before or in early pregnancy was associated with a 21% increased risk of NTD in relation to CC exposure; however, this increased risk is not statistically significant.

Tweetable abstract

A new meta‐analysis finds that clomiphene citrate exposure before or in early pregnancy is not associated with an increased risk of NTDs.
Reimagining Sutherland 80 years after white‐collar crime*
Authors: Simpson Sally S.
Published: April 2019

Eighty years ago, Edwin H. Sutherland conceptualized and defined white‐collar crime. In this article, I engage retrospectively with Sutherland's ideas and work to emphasize important aspects that continue to guide research today; to note where he was prescient as well as shortsighted. I center this discussion around “corporate crime” or crimes by business. Four main themes are discussed: 1) law and official responses to corporate offending—the data problem, 2) corporate crime and the life cycle of organizations, 3) psychological and trait‐based explanations, and 4) consequences of definitional ambiguity.
Innovative microscale workflow from fungi cultures to Cell Wall‐Degrading Enzyme screening
Authors: Raulo Roxane , Heuson Egon , Siah Ali , Phalip Vincent , Froidevaux Renato
Published: April 2019

This study aimed at developing a complete miniaturized high‐throughput screening workflow for the evaluation of the Cell Wall‐Degrading Enzyme (CWDE) activities produced by any fungal strain directly cultivated on raw feedstock in a submerged manner. In this study, wheat straw was selected as model substrate as it represents an important carbon source but yet poorly valorised to yield high added value products. Fungi were grown in a microbioreactor in a high‐throughput (HT) way to replace the fastidious shaking flask cultivations. Both approaches were compared in order to validate our new methodology. The range of CWDE activities produced from the cultures was assayed using AZO‐died and pNP‐linked substrates in an SBS plate format using a Biomek FXp pipetting platform. As highlighted in this study, it was shown that the CWDE activities gathered from the microbioreactor cultivations were similar or higher to those obtained from shake flasks cultures, with a lower standard deviation on the measured values, making this new method much faster than the traditional one and suitable for HT CWDE production thanks to its pipetting platform compatibility. Also, the results showed that the enzymatic activities measured were the same when doing the assay manually or using the automated method.
Clinical analysis of EGFR‐positive non‐small cell lung cancer patients treated with first‐line afatinib: A Nagano Lung Cancer Research Group
Authors: Sonehara Kei , Kobayashi Takashi , Tateishi Kazunari , Morozumi Nobutoshi , Yoshiike Fumiaki , Hachiya Tsutomu , Ono Yasushi , Takasuna Keiichirou , Agatsuma Toshihiko , Masubuchi Takeshi , Matsuo Akemi , Tanaka Hozumi , Morikawa Akio , Hanaoka Masayuki , Koizumi Tomonobu
Published: April 2019

Background

In the LUX‐Lung 3 and LUX‐Lung 6 trials, afatinib improved overall survival in previously untreated patients with EGFR 19del mutated non‐small cell lung cancer (NSCLC) compared to chemotherapy. The appropriate management of adverse events and dose reduction of afatinib are important for EGFR‐positive NSCLC patients. We conducted a retrospective and observational study of patients treated with first‐line afatinib for EGFR‐positive NSCLC in Nagano prefecture, Japan, focusing on efficacy and toxicities.

Methods

We retrospectively collected the medical records of NSCLC patients initially treated with afatinib between May 2014 and March 2018.

Results

A total of 62 patients with a median age of 67 years and a median body surface area (BSA) of 1.57 m2 were included. The overall response rate was 87.7% and median progression‐free survival (PFS) was 15.7 months. The median PFS was similar between standard initial dose (40 mg) and reduced initial doses (30 and 20 mg) (15.7 vs. 14.2 months; P = 0.978). The frequency of dose reduction and the discontinuation rate in the 40 mg daily dose group was higher in patients with BSA < 1.58 m2 (100%) compared to BSA ≥ 1.58 m2 (68.2%) (P = 0.014). The frequency of diarrhea was higher in patients with BSA < 1.58 m2 (93.5%) compared to BSA ≥ 1.58 m2 (71.0%) (P = 0.02).

Conclusion

In real‐world clinical practice, first‐line afatinib was well managed and was equally as effective as in previous clinical trials of EGFR‐positive NSCLC. BSA is considered a predictive marker for appropriate afatinib dose reduction.
Chronic epididymitis and leptin and their associations with semen characteristics in men with infertility
Authors: Xin Song , Hao Ye , Zhi‐Peng Ma , Nanhe Lin , Bin Chen
Published: April 2019

Problem

The aim of this study was to ascertain the associations between serum leptin levels and chronic epididymitis and semen parameters in patients with infertility.

Method of study

A total of 846 patients who were diagnosed as primary infertility were enrolled and divided into four groups. The general information, blood lipids, reproductive hormones, and semen parameters were collected. Receiver operating characteristic (ROC) curves of leptin were plotted for diagnosis of the poor sperm quality. We used Student'sttest and the chi‐squared test to analyze their relationships and used logistic regression analysis to evaluate potential confounding factors.

Results

Receiver operating characteristic curve revealed that leptin had better sensitivity and specificity at the concentration of 6.02 (0.565 and 0.917). Isolated epididymitis or elevated leptin had no effect on sperm concentration and sperm membrane function, but the combination of these conditions would reduce the concentration and normal morphology rate both (P = 0.002,P = 0.005). Epididymitis or elevated leptin can affect the motility of sperms, the former presented more significance (P = 0.000), and the co‐existence would further reduce the sperm motility (P = 0.001).

Conclusion

Low sperm motility and sperm normal morphology were found to be associated with chronic epididymitis and high leptin. Simultaneously suffering from chronic epididymitis and high leptin could produce a more serious effect on sperm quality.
Mast cell–induced immunopathology in recurrent pregnancy losses
Authors: Derbala Youssef , Elazzamy Haidy , Bilal Mahmood , Reed Rachel , Salazar Garcia Maria Dinorah , Skariah Annie , Dambaeva Svetlana , Fernandez Emilio , Germain Alfredo , Gilman‐Sachs Alice , Beaman Kenneth , Kwak‐Kim Joanne
Published: April 2019

Problem

Mast cells (MC) have been known to play an important role in inflammation and angiogenesis by secreting numerous mediators, such as proteases, gelatinases, and proteoglycans. Three different MC subtypes were found in the endometrial layers of the uterus. In this study, we aim to investigate the role of endometrial MCs in recurrent pregnancy losses (RPL).

Method of study

Endometrial biopsy was performed 5‐7 days post‐ovulation (implantation window) in women with a history of two or more RPL (n = 46) and normal fertile women (n = 10). Quantitative RT‐PCR was performed to detect the expression of various mast cell mediators. Endometrial samples were evaluated using immunohistochemistry for c‐kit receptor (CD117) and tryptase (MC activation marker).

Results

Mast cells were present throughout the entire layers of the endometrium; their count was elevated in RPL patients as compared to controls. The gene expression of c‐Kit receptor was not different between the study groups. There are significant increases in the mRNA expression of various mediators, that is, stem cell factor (P = 0.029), tryptase (P = 0.024), heparan sulfate (P = 0.0005), and MMP‐2 (P < 0.0001) in women with RPL as compared to normal controls. Chymase gene expression was not detected in most of the endometrial samples.

Conclusion

This study has shown that MCs are overactive in RPL patients by creating a pro‐inflammatory milieu, suggesting a novel role in the immunopathology of RPL. Future studies are needed to better understand the role of MC in implantation and placental angiogenesis.
Relating glaucomatous visual field loss to retinal oxygen delivery and metabolism
Authors: Aref Ahmad A , Maleki Shervin , Tan Ou , Huang David , Varma Rohit , Shahidi Mahnaz
Published: April 2019

Purpose

To test the hypothesis that visual field (VF) loss is associated with decreased retinal blood flow, oxygen delivery and metabolism, and with increased retinal oxygen extraction fraction (OEF) in glaucomatous individuals.

Methods

Glaucomatous subjects underwent automated perimetry, dual wavelength scanning laser ophthalmoscopy and Doppler optical coherence tomography imaging in order to measure mean deviation, central retinal arterial and venous diameter equivalents (CRAE and CRVE), oxygen saturation levels and total retinal blood flow (TRBF), respectively. Retinal oxygen delivery, metabolism and extraction fraction were derived from measurements of oxygen saturation and blood flow.

Results

Twenty eyes of 14 subjects were included in the study. Mean deviation was on average −13.76 ± 8.70 dB. Mean CRAE and CRVE were 126 ± 28 and 191 ± 35 μm, respectively. Mean TRBF and oxygen delivery were 34.3 ± 11.7 μl/min and 6.5 ± 2.6 μl O2/min, respectively. Mean oxygen metabolism and extraction fraction were 2.1 ± 0.94 μl O2/min and 0.34 ± 0.15, respectively. Visual field (VF) loss was associated with reduced CRAE and CRVE, TRBF and oxygen delivery and associated with increased OEF.

Conclusion

Combined measurements of retinal blood flow and oxygen saturation in glaucomatous individuals suggest VF loss is associated with impaired oxygen delivery and augmented OEF.
The Swedish Neonatal Quality Register – contents, completeness and validity
Authors: Norman Mikael , Källén Karin , Wahlström Erik , Håkansson Stellan ,   The SNQ Collaboration
Published: April 2019

Aim

To describe the Swedish Neonatal Quality Register (SNQ) and to determine its completeness and agreement with other registers.

Methods

SNQ collects data for infants admitted to neonatal units during the first four postnatal weeks. Completeness and registers’ agreement were determined cross‐linking SNQ data with Swedish population registers (the Inpatient, Medical Birth and Cause of Death Registers) for a study period of five years.

Results

In total, 84 712 infants were hospitalised. A total of 52 806 infants occurred in both SNQ and the population registers; 28 692 were only found in the population registers, and 3214 infants were only found in SNQ. Between gestational weeks 24–34, completeness of SNQ was 98–99%. Below and above these gestational ages, completeness was lower. Infants missing in SNQ were term or near‐term in 99% of the cases, and their diagnoses indicated conditions managed in maternity units, or re‐admissions for acute infections, managed in paediatric units. For most diagnoses, the agreement between SNQ and population registers was high, but some (bronchopulmonary dysplasia and grade of hypoxic‐ischaemic encephalopathy) were often missing in the population registers.

Conclusion

SNQ completeness and agreement against other registers, especially for preterm infants, is excellent. SNQ is a valid tool for benchmarking, quality improvement and research.
Urokinase‐type plasminogen activator (uPA) is not essential for epithelial sodium channel (ENaC)‐mediated sodium retention in experimental nephrotic syndrome
Authors: Bohnert Bernhard N. , Daiminger Sophie , Wörn Matthias , Sure Florian , Staudner Tobias , Ilyaskin Alexandr V. , Batbouta Firas , Janessa Andrea , Schneider Jonas C. , Essigke Daniel , Kanse Sandip , Haerteis Silke , Korbmacher Christoph , Artunc Ferruh
Published: April 2019

Aim

In nephrotic syndrome, aberrantly filtered plasminogen (plg) is converted to active plasmin by tubular urokinase‐type plasminogen activator (uPA) and thought to lead to sodium retention by proteolytic activation of the epithelial sodium channel (ENaC). This concept predicts that uPA is an important factor for sodium retention and that inhibition of uPA might be protective in nephrotic syndrome.

Methods

Activation of amiloride‐sensitive currents by uPA and plg were studied in Xenopus laevis oocytes expressing murine ENaC. In doxorubicin‐induced nephrotic mice, uPA was inhibited pharmacologically by amiloride and genetically by the use of uPA‐deficient mice (uPA−/−).

Results

Experiments in Xenopus laevis oocytes expressing murine ENaC confirmed proteolytic ENaC activation by a combination of plg and uPA which stimulated amiloride‐sensitive currents with concomitant cleavage of the ENaC γ‐subunit at the cell surface. Treatment of nephrotic wild‐type mice with amiloride inhibited urinary uPA activity, prevented urinary plasmin formation and sodium retention. In nephrotic mice lacking uPA (uPA−/−), urinary plasmin formation from plg was suppressed and urinary uPA activity absent. However, in nephrotic uPA−/− mice, sodium retention was not reduced compared to nephrotic uPA+/+ mice. Amiloride prevented sodium retention in nephrotic uPA−/− mice which confirmed the critical role of ENaC in sodium retention.

Conclusion

uPA is responsible for the conversion of aberrantly filtered plasminogen to plasmin in the tubular lumen in vivo. However, uPA‐dependent plasmin generation is not essential for ENaC‐mediated sodium retention in experimental nephrotic syndrome.
Sustainable Energy Policy in Southeast Asia: Domestic Variation and Congruence in Policy Discourses
Authors: Taguibao Jalton Garces
Published: April 2019

Southeast Asian governments have maintained “energy self‐reliance” and “energy security” as essential rationales of their macroeconomic policy. Since the availability of energy remains necessary for unabated domestic growth and development, the pursuit for “alternative” sources of energy and the resolve to build sustainable energy systems are constant priorities. Informed by the literature on policy discourse, this article draws attention to the analytical use and significance of policy discourse as a means to examine sustainable energy policies in Southeast Asia, which dominantly adopted an economic lens for “energy supply security.” Policy documents were examined to show the congruence and variation of policy discourses that prompted the governments of Indonesia, the Philippines, and Singapore to institutionalize sustainable energy development from 2000 to 2016—a critical period for the institutionalization of sustainable energy in the region, when domestic renewable energy sectors and systems were simultaneously being established by these governments.
Asylum‐Seeking Work, Precariousness, and the Making of Claimant‐Workers
Authors: Shrestha Tina
Published: April 2019

This article contributes to the anthropological discussion on precariousness and labor precarity, with regard to temporality, potentiality, and subjectivity, by examining how asylum‐seeking accounts intersect with, interrupt, and, above all, inform people's everyday labor activities outside the asylum process. Drawing on my ethnographic research among Nepali migrants and asylum seekers in the United States, I document people's adoption of a familiar sociocultural understanding of “the work of making paper” and retrospective logic to describe their subjective entanglement with the asylum documentation process and their impending labor subordination. I argue that it is through asylum‐seeking work that people participate in and inhabit the precarization process, sustaining and exacerbating, in some cases, their precarious working lives. In this sense, asylum‐seeking work involves a subjective transformation of asylum seekers into precarious “claimant‐workers,” providing the condition of possibility for labor precariousness.
Histopathological evidence for macrophage activation driving post‐transfusion hyperhaemolysis syndrome
Authors: Win Nay , Lucas Sebastian , Hebballi Sangam , McKernan Angela , Hamilton Rosie , Robinson Ivan , Chen Frederick
Published: April 2019

Post‐transfusion hyperhaemolysis syndrome (PTHS) is a rare life‐threatening transfusion complication reported mainly in sickle cell patients. Its pathogenesis is poorly understood. Antibody‐mediated haemolysis and bystander effect have been proposed as putative mechanisms, but in half of cases, red cell antibodies are undetectable, and PTHS develops despite transfusion of cross‐matched compatible RBC. An alternate hypothesis proposes activated macrophages as the main drivers of red cell destruction through direct phagocytosis. We report the histopathological findings of two patients with PTHS showing extensive macrophage expansion and erythrophagocytosis, supportive of macrophage activation driving PTHS. This supports a possible role for novel therapies that target macrophage activation.
Phosphorylated NUB1 distinguishes α‐synuclein in Lewy bodies from that in glial cytoplasmic inclusions in multiple system atrophy
Authors: Tanji Kunikazu , Miki Yasuo , Mori Fumiaki , Kon Tomoya , Kakita Akiyoshi , Takahashi Hitoshi , Wakabayashi Koichi
Published: April 2019

Posttranslational modifications by phosphorylation, ubiquitination, neddylation and other pathways have emerged as major regulators of cellular functions. NEDD8 ultimate buster 1, NUB1, is an adaptor protein, which negatively regulates the levels of the ubiquitin‐like protein NEDD8 as well as neddylated proteins through proteasomal degradation. We previously reported that NUB1 is highly involved in the pathogenesis of synucleinopathy including Parkinson's disease (PD), dementia with Lewy bodies (DLB) and multiple system atrophy (MSA). In general, since phosphorylation is strongly related to the alteration of protein propensity, we examined if the fundamental function of NUB1 can be modulated by its phosphorylation. We created a series of phosphomimic mutants of NUB1. Among them, we found that phosphorylation of NUB1 at S46 (P‐NUB46) efficiently degrades aggregates using a cell‐based assay. Immunohistochemical studies have shown that specific antibodies against P‐NUB46 reacted with Lewy bodies in PD and DLB but not with glial cytoplasmic inclusions in MSA. Moreover, P‐NUB46 levels were significantly higher in the brains of patients with DLB than in control brains, and P‐NUB46 was extracted in an insoluble fraction of DLB. These findings suggest that the phosphorylation of NUB1 is modulated during the pathological process of Lewy body disease.
Increasing earnings inequality and the gender pay gap in Canada: Prospects for convergence
Authors: Fortin Nicole M.
Published: April 2019

This paper retraces the evolution of Canadian women's labour force participation and of the gender earnings ratio across the generations to understand better the prospects for gender convergence in pay. Using data from the public use Labour Force Surveys (LFS) and administrative annual earnings data from the Longitudinal Worker Files (LWF), the paper assesses the role of increasing top earnings inequality in the persistence of the gender pay gap. Having identified a growing role for the under‐representation of women among top earners, the paper then performs an evaluation and critical analysis of existing gender equality policies, centred on horizontal occupational gender segregation, and discusses alternative policies for the future.