bluuebunny/crossref_metadata_2025 huggingface dataset:
Measurement of mechanical strain based on piezo-avalanche effect
Authors: Perunnilathil Joy Abbin , Kanygin Mikhail , Bahreyni Behraad
Published: May 2019

We report on the use of the breakdown voltage of a pn junction to measure mechanical strain in microstructures. The working principle relies on the dependence of the silicon bandgap on the mechanical stress which affects the current-voltage characteristics of the pn junction. An analytical model is developed and verified experimentally for the phenomenon. A micromechanical device with integrated junctions was designed and fabricated. Mechanical stress was applied onto the structure by subjecting it to mechanical vibrations. It is shown that the breakdown voltage of the device exhibited a high stress sensitivity of about 240 μV/MPa. The mechanical stress can also be measured by monitoring the device current while biased at a constant voltage. In this mode, the steep changes of the junction current in the breakdown region led to nearly a tenfold higher stress sensitivity compared to a piezoresistive sensor. The high sensitivity, simple measurement, and potential for miniaturization for piezo-avalanche sensing make it a promising technique for the measurement of stress in micro- and nanomechanical devices.
Current-induced motion of twisted skyrmions
Authors: Jin Chendong , Zhang Chunlei , Song Chengkun , Wang Jinshuai , Xia Haiyan , Ma Yunxu , Wang Jianing , Wei Yurui , Wang Jianbo , Liu Qingfang
Published: May 2019

Twisted skyrmions, whose helicity angles are different from those of Bloch and Néel skyrmions, have recently been demonstrated in experiments. In this work, we first discuss the origin and the topological properties of twisted skyrmions. Following that, we investigate the current-induced motion of twisted skyrmions by using micromagnetic simulations. It is found that the skyrmion Hall angle of twisted skyrmions driven by the spin Hall effect (SHE) varies continuously with the helicity, which means that the skyrmion Hall angle depends significantly upon the helicity in addition to the dissipative force tensor and the Gilbert damping. More importantly, we demonstrate that the trajectory of the twisted skyrmion can be controlled in a two-dimensional plane with a Gilbert damping gradient, which makes it possible to achieve the SHE-induced motion of twisted skyrmions with zero skyrmion Hall angle. At last, the simulation results demonstrate that the dynamics of twisted skyrmions driven by the spin transfer torque can be described by Thiele's equation, and they are essentially identical to the dynamics of Bloch and Néel skyrmions. Our results provide an understanding of the current-induced motion of twisted skyrmions, which may contribute to the applications of skyrmion-based racetrack memories.
Review of Scientific Instruments New Products
Authors: Mandelis Andreas
Published: May 2019

In order to supplement manufacturers’ information, this department will welcome the submission by our readers of brief communications reporting measurements on the physical properties of materials which supersede earlier data or suggest new research applications.
Respiratory chain inactivation links cartilage-mediated growth retardation to mitochondrial diseases
Authors: Holzer Tatjana , Probst Kristina , Etich Julia , Auler Markus , Georgieva Veronika S. , Bluhm Björn , Frie Christian , Heilig Juliane , Niehoff Anja , Nüchel Julian , Plomann Markus , Seeger Jens M. , Kashkar Hamid , Baris Olivier R. , Wiesner Rudolf J. , Brachvogel Bent
Published: May 2019

In childhood, skeletal growth is driven by transient expansion of cartilage in the growth plate. The common belief is that energy production in this hypoxic tissue mainly relies on anaerobic glycolysis and not on mitochondrial respiratory chain (RC) activity. However, children with mitochondrial diseases causing RC dysfunction often present with short stature, which indicates that RC activity may be essential for cartilage-mediated skeletal growth. To elucidate the role of the mitochondrial RC in cartilage growth and pathology, we generated mice with impaired RC function in cartilage. These mice develop normally until birth, but their later growth is retarded. A detailed molecular analysis revealed that metabolic signaling and extracellular matrix formation is disturbed and induces cell death at the cartilage–bone junction to cause a chondrodysplasia-like phenotype. Hence, the results demonstrate the overall importance of the metabolic switch from fetal glycolysis to postnatal RC activation in growth plate cartilage and explain why RC dysfunction can cause short stature in children with mitochondrial diseases.
Rhizosphere priming of two near-isogenic wheat lines varying in citrate efflux under different levels of phosphorus supply
Authors: Xu Qiao , Wang Xiaojuan , Tang Caixian
Published: May 2019

Backgrounds and Aims

The rhizosphere priming effect (RPE) has been explained from the perspective of microbial responses to root exudates and nutrient availability. This study introduced a chemical process that could also contribute to RPE: root exudates (organic acid ligands) could liberate mineral-protected carbon (C) in soil for microbial degradation.

Methods

Wheat (Triticum aestivum L.) near-isogenic lines varying in citrate efflux were grown for 6 weeks in a C4 soil supplied with either low (10 μg g–1) or high P (40 μg g–1). Total below-ground CO2 was trapped and partitioned for determination of soil organic C decomposition and RPE using a stable isotopic tracing technique. Mineral dissolution was examined by incubating soil with citric ligand at a series of concentrations.

Key Results

High P increased RPE (81 %), shoot (32 %) and root biomass (57 %), root-derived CO2-C (20 %), microbial biomass C (28 %) and N (100%), soil respiration (20 %) and concentrations of water-extractable P (30 %), Fe (43 %) and Al (190 %), but decreased inorganic N in the rhizosphere. Compared with Egret-Burke, wheat line Egret-Burke TaMATE1B with citrate efflux had lower inorganic N, microbial biomass C (16 %) and N (30 %) in the rhizosphere but greater RPE (18 %), shoot biomass (12 %) and root-derived CO2-C (low P 36 %, high P 13 %). Egret-Burke TaMATE1B also had higher concentrations of water-extractable P, Fe and Al in the rhizosphere, indicating the release of mineral-protected C. In addition, citrate ligand facilitated Fe and Al release from soil, with their concentrations rising with increasing ligand concentration and incubation time.

Conclusions

While high P supply increased microbial growth and RPE possibly due to higher total root exudation, citrate efflux from the root might have facilitated the liberation of mineral-bound C, leading to the higher RPE under Egret-Burke TaMATE1B. Mineral dissolution may be an important process that regulates RPE and should be considered in future RPE research.
Rotation equivariant and invariant neural networks for microscopy image analysis
Authors: Chidester Benjamin , Zhou Tianming , Do Minh N , Ma Jian
Published: May 2019

Motivation

Neural networks have been widely used to analyze high-throughput microscopy images. However, the performance of neural networks can be significantly improved by encoding known invariance for particular tasks. Highly relevant to the goal of automated cell phenotyping from microscopy image data is rotation invariance. Here we consider the application of two schemes for encoding rotation equivariance and invariance in a convolutional neural network, namely, the group-equivariant CNN (G-CNN), and a new architecture with simple, efficient conic convolution, for classifying microscopy images. We additionally integrate the 2D-discrete-Fourier transform (2D-DFT) as an effective means for encoding global rotational invariance. We call our new method the Conic Convolution and DFT Network (CFNet).

Results

We evaluated the efficacy of CFNet and G-CNN as compared to a standard CNN for several different image classification tasks, including simulated and real microscopy images of subcellular protein localization, and demonstrated improved performance. We believe CFNet has the potential to improve many high-throughput microscopy image analysis applications.

Availability and implementation

Source code of CFNet is available at: https://github.com/bchidest/CFNet.

Supplementary information

Supplementary data are available at Bioinformatics online.
Assumption of Responsibility: Four Questions
Authors: Nolan Donal
Published: May 2019

Although the assumption of responsibility concept pervades the English law of negligence, its meaning remains hazy and its significance contested. While the courts employ the language of assumption of responsibility on a regular basis, no clear judicial definition of it has emerged. And commentators are divided as to whether assumption of responsibility is a distinct ground on which liability is imposed, or merely a foil for policy arguments – or for another, more general, test for the recognition of duties of care. Matters are complicated by the fact that assumption of responsibility does not fit neatly within the orthodox categories of ‘tort’ and ‘contract’, but hovers uncertainly between the two. The aim of this article is to try to bring some clarity to the controversies surrounding assumption of responsibility. Four questions frame the analysis. What does assumption of responsibility mean? When does it matter? Why do we need it? And where does it belong? Although the answers to some of these questions are necessarily tentative, at least one conclusion should become clear, namely that assumption of responsibility is a meaningful and distinctive basis on which to impose negligence liability.
Right ventricular free-wall scar: an exceptional source of post-infarction ventricular tachycardia. A case report
Authors: Tritto Massimo , Renzullo Elvira , Zagari Domenico , Moretti Paolo
Published: May 2019

Background 

In patients with coronary artery disease, ventricular tachycardia (VT) is usually related to left ventricular (LV) post-infarction scars.

Case summary

A case of a 78-year-old man with post-infarction VT originating from the right ventricular (RV) free wall is described. Following recurrent episodes of VT with left bundle branch block morphology and left superior axis deviation, a patient with prior myocardial infarction was submitted to catheter ablation. Two areas of abnormal bipolar electrograms were observed at 3D electroanatomical mapping: one located at the basal aspect of the posterior and postero-septal LV, and the other one extending from the antero-lateral to the posterior mid-basal RV free wall. Ventricular late potentials (LPs) were recorded within both scars, but only pacing from those located in the RV resulted in long stimulus-to-QRS latency and optimal pace-mapping. Accordingly, this substrate was deemed the culprit of the clinical VT. Radiofrequency catheter ablation aimed at eliminating all LPs recorded from both scars was effective in preventing VT recurrences at follow-up.

Discussion

A post-infarction RV free-wall scar may exceptionally be responsible of VT occurrence. Right ventricular mapping should be considered in selected cases based on 12-lead electrocardiogram VT morphology and prior RV infarct.
Familial spontaneous pneumothorax: importance of screening for Birt–Hogg–Dubé syndrome
Authors: Liu Yanguo , Xing Huajie , Huang Yu , Meng Shushi , Wang Jun
Published: May 2019

OBJECTIVES

The goal of this study was to investigate the prevalence of Birt–Hogg–Dubé (BHD) syndrome in patients with familial spontaneous pneumothorax (FSP) and the clinical characteristics of pneumothorax related to BHD syndrome compared with those of primary spontaneous pneumothorax.

METHODS

A total of 37 families diagnosed with FSP from 2007 to 2017 were enrolled in this study. The FLCN gene, which is responsible for BHD syndrome, was sequenced using the Sanger method in 25 probands. For the patients with confirmed BHD syndrome-related pneumothorax, clinical characteristics including the median onset age of pneumothorax, the male-to-female ratio, the mean height and body mass index (BMI) and the recurrence rate after different treatment modalities were obtained and compared with those of patients with primary spontaneous pneumothorax.

RESULTS

Of the 25 probands with FSP, 16 [64.0%, 95% confidence interval (CI) 43.8–84.2%] harboured FLCN germline mutations. In the patients with BHD syndrome-related pneumothorax, the median onset age of pneumothorax was 34 years; the male-to-female ratio was 1.3:1; and the mean height and BMI were 167.0 ± 8.6 cm and 23.6 ± 3.4 kg/m2, respectively. These characteristics were significantly different from those in patients with primary spontaneous pneumothorax from the same centre. The recurrence rate of BHD syndrome-related pneumothorax after conservative therapy was 53.1% (95% CI 38.6–67.5%) compared with 9.1% (95% CI 0–19.4%) after surgical treatment.

CONCLUSIONS

BHD syndrome is one of the most common causes of FSP. Patients with FSP should be recommended for mutation screening for the FLCN gene to facilitate early diagnosis and proper intervention.
Parallel Molecular Evolution in Pathways, Genes, and Sites in High-Elevation Hummingbirds Revealed by Comparative Transcriptomics
Authors: Lim Marisa C W , Witt Christopher C , Graham Catherine H , Dávalos Liliana M
Published: May 2019

High-elevation organisms experience shared environmental challenges that include low oxygen availability, cold temperatures, and intense ultraviolet radiation. Consequently, repeated evolution of the same genetic mechanisms may occur across high-elevation taxa. To test this prediction, we investigated the extent to which the same biochemical pathways, genes, or sites were subject to parallel molecular evolution for 12 Andean hummingbird species (family: Trochilidae) representing several independent transitions to high elevation across the phylogeny. Across high-elevation species, we discovered parallel evolution for several pathways and genes with evidence of positive selection. In particular, positively selected genes were frequently part of cellular respiration, metabolism, or cell death pathways. To further examine the role of elevation in our analyses, we compared results for low- and high-elevation species and tested different thresholds for defining elevation categories. In analyses with different elevation thresholds, positively selected genes reflected similar functions and pathways, even though there were almost no specific genes in common. For example, EPAS1 (HIF2α), which has been implicated in high-elevation adaptation in other vertebrates, shows a signature of positive selection when high-elevation is defined broadly (>1,500 m), but not when defined narrowly (>2,500 m). Although a few biochemical pathways and genes change predictably as part of hummingbird adaptation to high-elevation conditions, independent lineages have rarely adapted via the same substitutions.
Barriers to accessing maternal healthcare among ethnic minority women in Western China: a qualitative evidence synthesis
Authors: Huang Yuan , Martinez-Alvarez Melisa , Shallcross David , Pi Li , Tian Fan , Pan Jay , Ronsmans Carine
Published: May 2019

Quantitative evidence suggests that ethnic disparities in maternal healthcare use are substantial in Western China, but the reasons for these remain under-researched. We undertook a systematic review of English and Chinese databases between January 1, 1990 and February 23, 2018 to synthesize qualitative evidence on barriers faced by ethnic minority women in accessing maternal healthcare in Western China. Four English and 6 Chinese language studies across 8 provinces of Western China and 13 ethnic minority groups were included. We adapted the ‘Three Delays’ framework and used thematic synthesis to categorize findings into six themes. Studies reported that ethnic minority women commonly held traditional beliefs and had lower levels of education, which limited their willingness to use maternal health services. Despite the existence of different financial protection schemes for services related to delivery care, hospital birth was still too costly for some rural households, and some women faced difficulties navigating reimbursement procedures. Women who lived remotely were less likely to go to hospital in advance of labour because of difficulties in arranging accommodation; they often only sought care if pregnancies were complicated. Poor quality of care in health facilities, particularly misunderstandings between doctors and patients due to language barriers or differences in socio-economic status, and clinical practices that conflicted with local fears and traditional customs, were reported. The overall evidence is weak however: authors treated different ethnicities as if they belonged to one homogeneous group and half of the studies failed in methodological rigour. The current evidence base is very limited and poor in quality, so much more research elucidating the nature of ‘ethnicity’ as a set of barriers to maternal healthcare access is needed. Addressing the multiple barriers associated with ethnicity will require multi-faceted solutions that adequately reflect the specific local context.
Promoting Inclusion, Diversity, Access, and Equity Through Enhanced Institutional Culture and Climate
Authors: Piggott Damani A , Cariaga-Lo Liza
Published: May 2019

Advancing the health of all members of the global community remains core to the mission of the infectious diseases profession. Training, research, healthcare-delivery, and other infectious diseases–related institutions play a central role in meeting this goal. The promotion of inclusion, diversity, access, and equity (IDA&E) is critical to harnessing the full range of human creativity, innovation, and talent necessary to realizing the education, research, patient care, and service missions that constitute the principal objectives of such institutions. Strong and positive institutional cultures and climates are essential to achieving these IDA&E goals. We discuss opportunity gaps that exist in leveraging institutional culture and climate to optimize IDA&E. We further identify effective strategies to address these gaps and achieve excellence in education, research, patient care, and service in infectious diseases and the broader healthcare and biomedical space. We discuss the importance of both local and global context in conceptualizing IDA&E to best achieve these aims.
The Territorialization of Cyberspace*
Authors: Lambach Daniel
Published: May 2019

There are widespread worries about the impending fragmentation of the internet. Reviewing the IR literature on cyberspace and internet governance, this paper demonstrates that these debates rest on very traditional understandings of territory and the state, focusing on ways that hard-shelled “power containers” are recreated in cyberspace. Using a practice-oriented conceptual framework drawing on insights from critical geography, the paper highlights how state, corporate, and private actors deterritorialize and reterritorialize cyberspace. Results indicate that there are multiple ways to territorialize cyberspace beyond the reconstruction of the “national territory” and that a multitude of actors engage in territorializing practices. This allows for a more nuanced reevaluation of the “internet fragmentation” discourse.
Dust attenuation, dust emission, and dust temperature in galaxies at z ≥ 5: a view from the FIRE-2 simulations
Authors: Ma Xiangcheng , Hayward Christopher C , Casey Caitlin M , Hopkins Philip F , Quataert Eliot , Liang Lichen , Faucher-Giguère Claude-André , Feldmann Robert , Kereš Dušan
Published: May 2019

We present a suite of 34 high-resolution cosmological zoom-in simulations consisting of thousands of haloes up to $M_{\rm halo}\sim 10^{12}\, \mathrm{M}_{\odot }$ ($M_{\ast }\sim 10^{10.5}\, \mathrm{M}_{\odot }$) at z ≥ 5 from the Feedback in Realistic Environments project. We post-process our simulations with a three-dimensional Monte Carlo dust radiative transfer code to study dust attenuation, dust emission, and dust temperature within these simulated z ≥ 5 galaxies. Our sample forms a tight correlation between infrared excess (IRX ≡ FIR/FUV) and ultraviolet (UV)-continuum slope (βUV), despite the patchy, clumpy dust geometry shown in our simulations. We find that the IRX–βUV relation is mainly determined by the shape of the attenuation law and is independent of its normalization (set by the dust-to-gas ratio). The bolometric IR luminosity (LIR) correlates with the intrinsic UV luminosity and the star formation rate (SFR) averaged over the past 10 Myr. We predict that at a given LIR, the peak wavelength of the dust spectral energy distributions for z ≥ 5 galaxies is smaller by a factor of 2 (due to higher dust temperatures on average) than at z = 0. The higher dust temperatures are driven by higher specific SFRs and SFR surface densities with increasing redshift. We derive the galaxy UV luminosity functions (UVLFs) at z = 5–10 from our simulations and confirm that a heavy attenuation is required to reproduce the observed bright-end UVLFs. We also predict the IR luminosity functions (IRLFs) and UV luminosity densities at z = 5–10. We discuss the implications of our results on current and future observations probing dust attenuation and emission in z ≥ 5 galaxies.
Designing and implementing at-scale programs to improve complementary feeding
Authors: Frongillo Edward A
Published: May 2019

Advancing knowledge about how to improve complementary feeding at large scale is a high priority. This article identifies strategies for designing and implementing programs to improve complementary feeding at large scale, drawing on lessons learned from three initiatives: Alive & Thrive, which implemented large-scale programs in 3 countries; a low-burden intervention in Mexico that used scripted messages; and Estrategia Integral de Atención a la Nutrición, which is introducing large-scale programs tied to Mexico’s conditional cash transfer program. These initiatives illustrate different ways of designing and implementing large-scale programs, with lessons about the importance of having partnerships and alliances; well-grounded understanding from research; a public health strategy; scalable program modes and elements; using existing systems where possible; monitoring, learning, and evaluating; and adopting a model aimed at successfully implementing programs at scale. Improving complementary feeding globally is challenging because of the complex behaviors involved, and the development of specific programs geared to complementary feeding is necessary. Designing and implementing such specific programs at large scale is achievable with the intention, commitment, appropriate strategies, and financial support to do so from the outset.
Sedentary behaviors in children and adolescents with type 1 diabetes, depending on the insulin therapy used
Authors: Czenczek-Lewandowska Ewelina , Leszczak Justyna , Weres Aneta , Baran Joanna , Wyszyńska Justyna , Grzegorczyk Joanna , Lewandowski Bogumił , Mazur Artur
Published: May 2019

Assessment of sedentary behaviors in children and adolescents with type 1 diabetes (T1D), relative to the method of insulin therapy used, and in comparison to healthy controls.

The study group consisted of 215 children with T1D, including 109 (50.7%) insulin pen and 106 (49.3%) insulqsain pump users. The control group comprised 115 healthy children. The subjects’ sedentary time was measured with a tri-axial accelerometer ActiGraph GT3X+, used continuously for 7 days.

The diabetes group was characterized by a significantly higher “% in sedentary time” score (P = .024) and a lower “mean daily breaks in sedentary time” result (P = .007), which means that they spent much more time on sedentary activities compared to the control group. There were no significant differences between the children using insulin pump and insulin pen in the “% in sedentary time” score (P = .294) and “mean daily breaks in sedentary time” (P = .251).

The T1D is a serious encumbrance, leading to longer duration of sedentary time, in comparison to healthy controls. The type of insulin therapy did not significantly affect the percentage of the wear-day spent in sedentary time and mean daily breaks in sedentary time.
Pyoderma Gangrenosum After Abdominal Free Tissue Transfer for Breast Reconstruction
Authors: Li Wai-Yee , Andersen James C. , Jung Jae , Andersen James S.
Published: May 2019

Introduction

Pyoderma gangrenosum following free tissue transfer for breast reconstruction is rare. This unusual ulcerative condition is frequently misdiagnosed, leading to inappropriate debridement and escalation of the subsequent wound through pathergy. Once diagnosed, treatment with immunosuppressive agents, including corticosteroids, results in an initial rapid response, but prolonged treatment is required. There is a paucity of literature regarding how to approach future surgery.

Methods

This was a retrospective case review from a single center over a 17-year period. All patients diagnosed with postsurgical pyoderma gangrenosum after free tissue transfer from the abdomen for breast reconstruction were included.

Results

Of 456 free tissue transfers from the abdomen for breast reconstruction, 8 women who underwent 13 free flaps were diagnosed with postsurgical pyoderma gangrenosum in 10 flaps. The surgeries performed included transverse rectus abdominis muscle (n = 5), deep inferior epigastric perforator (n = 4) and superficial inferior epigastric artery (n = 4) flaps. Mean age at diagnosis was 52.8 years, and 3 patients had preexisting autoimmune conditions: type 2 diabetes mellitus, dermatomyositis, and Graves disease. The mean time of presentation of wound symptoms was 3.9 days after surgery, and mean time diagnosis was made was 9.4 days.

Conclusions

Pyoderma gangrenosum after autologous breast reconstruction is a rare, but serious, complication that is worsened by misdiagnosis and inappropriate debridement. We present a case series of 8 patients and emphasize the importance of early recognition and treatment with immune suppression. We include a treatment algorithm to manage these patients, once the diagnosis is suspected. Future surgery can be considered with a fully informed patient and careful collaboration with dermatology colleagues.
Role of the Wound, Ostomy and Continence Nurse in Continence Care: 2018 Update
Authors: Berke Christine , Conley Mary Jo , Netsch Deb , Franklin Lynette , Goodman Eric , Shephard Cindy , Thompson Donna
Published: May 2019

The Wound, Ostomy and Continence Nurses Society believes the tri-specialty certified nurse (Certified Wound Ostomy Continence Nurse [CWOCN]) or advanced practice tri-specialty certified nurse (Certified Wound Ostomy Continence Nurse-Advanced Practice [CWOCN-AP]) possesses unique knowledge, expertise for assessment, and first-line management of incontinence as well as for prevention of incontinence. The CWOCN or CWOCN-AP provides care and consultation in the treatment of potential and actual skin complications through absorption, and containment, in persons with urinary, fecal, or dual incontinence. This executive summary describes the role of the CWOCN or CWOCN-AP in the delivery of continence care across care settings. The original statement is available at https://cdn.ymaws.com/www.wocn.org/resource/collection/6D79B935-1AA0-4791-886F-E361D29F152D/Role_of_Continence_Nurse__2018_.pdf.
A Clostridia-rich microbiota contributes to increased excretion of bile acids in diarrhea-predominant irritable bowel syndrome
Authors: Zhao Ling , Yang Wei , Chen Yang , Huang Fengjie , Lu Lin , Lin Chengyuan , Huang Tao , Ning Ziwan , Zhai Lixiang , Zhong Linda LD , Lam Waiching , Yang Zhen , Zhang Xuan , Cheng Chungwah , Han Lijuan , Qiu Qinwei , Shang Xiaoxiao , Huang Runyue , Ren Zhenxing , Chen Dongfeng , Sun Silong , El-Nezami Hani , Lu Aiping , Fang Xiaodong , Jia Wei , Bian Zhaoxiang
Published: May 2019

Objective

An excess of fecal bile acids (BAs) is thought to be one of the mechanisms for diarrhea-predominant irritable bowel syndrome (IBS-D). However, the factors causing excessive BA excretion remains unclear. Given the importance of gut microbiota in BA metabolism, we hypothesized that gut dysbiosis might contribute to excessive BA excretion in IBS-D.

Design

Metabolomic and metagenomic analyses were performed of specimens from 290 IBS-D patients and 89 healthy volunteers. By transplanting human microbiota and manipulating specific microbiome species in mice, the effects of microbiota on host BA metabolism were assessed at metabolic, genetic and protein levels. Effects of individual and mixed BAs on enterohepatic feedback pathways were also tested in vitro and in vivo.

Results

Total fecal BAs were excessively excreted in 24.5% of IBS-D patients. Their fecal metagenomes showed increased abundances of Clostridia and BA-transforming genes (hdhA and bais). The increases of Clostridia bacteria (e.g. C. scindens) were positively associated with the levels of fecal BAs and serum 7α-hydroxy-4-cholesten-3-one (C4), while being negatively correlated with serum fibroblast growth factor 19 (FGF19). Both Clostridia-rich human microbiota and C. scindens enhanced levels of serum C4 and hepatic conjugated BAs in mice recipients and reduced ileal FGF19 expression. Inhibition of Clostridium species by vancomycin yielded opposite findings. Clostridia-derived BAs (e.g. conjugated and free ursodeoxycholic acid) significantly suppressed intestinal FGF19 expression.

Conclusion

The Clostridia-rich microbiota contributes to excessive BA excretion in IBS-D patients. This study provided the basis for more precise clinical diagnosis and management for IBS-D.
Revisiting the decay of scientific email addresses
Authors: Rodriguez-Esteban Raul , Vishnyakova Dina , Rinaldi Fabio
Published: May 2019

Email is the primary means of communication for scientists. However, scientific authors change email address over time. Using a new method, we have calculated that approximately 18% of all authors’ contact email addresses in MEDLINE are invalid. While an unfortunate number, it is, however, lower than previously estimated. To mitigate this problem, institutions should provide email forwarding and scientific authors should use more stable email addresses. In fact, a steadily growing share already use free private email addresses: 32% of all new addresses in MEDLINE in 2018 were of this kind.
Genome-Wide Association Study of Resistance to Bean Fly and Population Structure of Market Classes of Common Bean
Authors: Ojwang Pascal P. Okwiri , Eldridge Tilly , Corredor-Moreno Pilar , Njung'e Vincent
Published: May 2019

Common bean (Phaesolus vulgaris L.) distribution across eastern, central and southern Africa region is widely driven by choice of grain types, which is affecting the genetic composition and adaptation to target production environments for biotic and abiotic constraints. Two bean fly species, Ophiomyia spencerella and Ophiomyia phaseoli are harmful insect pests of beans causing significant yield losses. Our objectives were to assess the population structure of common bean germplasm of different market classes and to identify polymorphic loci associated with resistance to O. spencerella. The study was carried out on a diversity panel of 284 genotypes using 9040 SNP markers. The genotypes were differentiated in to 14 distinct clusters. The mean FST of 0.4849, revealed major differentiation among the populations. Andean gene pool was more diverse compared to Mesoamerica gene pool which could be attributed to preference for large seeded cultivars. Multi-dimensional scaling and structure analyses revealed admixture among seed types. From genome wide association studies (GWAS), major genomic regions associated with O. spencerella resistance were identified on chromosome 1 (Pv01). The most significant SNP on Pv01 was aligned to gene PHAVU_001G075500g that is related to the Interleukin-1 receptor-associated kinase (IRAK) pathway, critical in regulating inherent immune responses to disease infection and insect herbivore attack. The diversity uncovered on the basis of market classes of beans and the presence of QTL regions associated with resistance to bean fly could serve as a valuable genetic resource for improvement of beans of different seed types in eastern and southern Africa region.
Recording temporal data onto DNA with minutes resolution
Authors: Bhan Namita J , Strutz Jonathan , Glaser Joshua , Kalhor Reza , Boyden Edward , Church George , Kording Konrad , Tyo Keith E.J.
Published: May 2019

Recording biological signals can be difficult in three-dimensional matrices, such as tissue. We present a DNA polymerase-based strategy that records temporal biosignals locally onto DNA to be read out later, which could obviate the need to extract information from tissue on the fly. We use a template-independent DNA polymerase, terminal deoxynucleotidyl transferase (TdT) that probabilistically adds dNTPs to single-stranded DNA (ssDNA) substrates without a template. We show thatin vitro, the dNTP-incorporation preference of TdT changes with the presence of Co2+, Ca2+, Zn2+and temperature. Extracting the signal profile over time is possible by examining the dNTP incorporation preference along the length of synthesized ssDNA strands like a molecular ticker tape. We call this TdT-based untemplated recording of temporal local environmental signals (TURTLES). We show that we can determine the time of Co2+addition to within two minutes over a 60-minute period. Further, TURTLES has the capability to record multiple fluctuations. We can estimate the rise and fall of an input Co2+pulse to within three minutes. TURTLES has at least 200-fold better temporal resolution than all previous DNA-based recording techniques.
Relationship Between Motor Capacity of the Contralesional and Ipsilesional Hand Depends on the Side of Stroke
Authors: Varghese Rini , Winstein Carolee J.
Published: May 2019

There is considerable evidence that after a stroke, ipsilesional deficits increase as contralesional impairment increases. Here, we asked if the relationship between the motor capacities of the two limbs differs based on the side of stroke. Forty-two pre-morbidly right-handed chronic stroke survivors (left hemisphere damage, LHD = 21) with mild-to-moderate paresis performed distal items of the Wolf Motor Function Test (dWMFT). We found that compared to RHD, the relationship between contralesional arm impairment (Upper Extremity Fugl-Meyer, UEFM) and ipsilesional hand motor capacity was stronger (R2LHD= 0.42; R2RHD < 0.01; z = 2.12; p = 0.03) and the slope was steeper (t = −2.03; p = 0.04) in LHD. Similarly, the relationship between contralesional dWMFT and ipsilesional hand motor capacity was stronger (R2LHD= 0.65; R2RHD= 0.09; z = 2.45; p = 0.01) and the slope was steeper (t = 2.03; p = 0.04) in LHD compared to RHD. Multiple regression analysis confirmed the presence of an interaction between contralesional UEFM and side of stroke (β3= 0.66 ± 0.30; p = 0.024) but only trended towards significance for the interaction between contralesional dWMFT and side of stroke (β3= −0.51 ± 0.34; p = 0.05). Results were confirmed after removal of potential outliers. Our findings suggest that the relationship between contra- and ipsi-lesional motor capacity depends on the side of stroke, such that the inter-limb relationship is stronger for stroke survivors with left hemisphere damage compared to those with right hemisphere damage.
GABAA receptor-mediated currents and hormone mRNAs in cells expressing more than one hormone transcript in intact human pancreatic islets
Authors: Korol Sergiy V. , Jin Zhe , Birnir Bryndis
Published: May 2019

In pancreatic islets the major cell-types are α, β and δ cells, secreting the hormones glucagon (GCG), insulin (INS) and somatostatin (SST), respectively. The GABA (γ-aminobutyric acid) signalling system is expressed in human pancreatic islets. We have previously used single-cell RT-PCR in combination with current recordings to correlate expression of single hormone transcript with functional GABAA receptor (iGABAAR) properties in islets. Here we extended these studies to islet cells from non-diabetic and type 2 diabetic donors that express mRNAs for more than one hormone. We detected cells expressing double (α/β, α/δ, β/δ cell-types) and triple (α/β/δ cell-type) hormone transcripts. The most common mixed-identity cell-type was the α/β group where the cells could be grouped into β- and α-like subgroups. The β-like cells had low GCG/INS expression ratio (< 0.6) and significantly higher frequency of single-channel iGABAAR openings than the α-like cells where the GCG/INS expression ratio was high (> 1.2). The difference in expression levels and single channel iGABAAR characteristics varied in the α/β/δ cell-type. No correlation was observed between the cell-types identity with time in culture or cell size. Clearly, multiple hormone transcripts can be expressed in islet cells whereas iGABAAR functional properties appear α or β cell specific.
Conserved pheromone production, response and degradation byStreptococcus mutans
Authors: Ricomini Filho Antonio Pedro , Khan Rabia , Åmdal Heidi Aarø , Petersen Fernanda C.
Published: May 2019

Streptococcus mutans, a bacterium with high cariogenic potential, coordinates competence for natural transformation and bacteriocin production via the XIP and CSP pheromones. CSP is effective in inducing bacteriocin responses, but not competence in chemically defined media (CDM). This is in contrast to XIP, which is a strong inducer of competence in CDM, but can also stimulate bacteriocin genes as a late response. Inter-connections between the pathways activated by the two pheromones have been characterized in certain detail inS. mutansUA159, but it is mostly unknown whether such findings are representative for the species. In this study, we used bioassays based on luciferase reporters for the bacteriocin genecipBand the alternative sigma factorsigXto investigate variousS. mutansisolates for production and response to CSP and XIP pheromones in CDM. Similar toS. mutansUA159, endogenous CSP was undetectable in the culture supernatants of all tested strains. During optimization of the bioassay using thecipBreporter, we discovered that the acivity of exogenous CSP used as a standard was reduced over time duringS. mutansgrowth. Using a FRET-CSP reporter peptide, we found thatS. mutansUA159 was indeed able to degrade CSP, and that such proteolytic activity was not significantly different in isogenic mutants with deletion of the protease genehtrA, or the competence genessigX, oppD, andcomR. CSP proteolysis was also detected in all the wild type strains, indicating that such activity is conserved inS. mutans. For the XIP pheromone, endogenous production was observed in the supernatants of all 34 tested strains at peak concentrations in culture supernatants that varied between 200 nM and 26000 nM. Transformation in the presence of exogenous XIP was detected in all, but one, of the isolates. The efficiency of transformation varied, however, among the different strains, and for those with the highest transformation rates, endogenous XIP peak concentrations in the supernatants were above 2000 nM XIP. We conclude that XIP production and inducing effect on transformation, as well as proteolytic activity leading to the inactivation of CSP are conserved functions among differentS. mutansisolates. Understanding the functionality and conservation of pheromone systems inS. mutansmay lead to novel strategies to prevent or treat unbalances in oral microbiomes that may favour diseases.
Decrease in within-trial variability contributes to a decrease in across-trial variability of neural firing in the primate cortex during neural computations
Authors: Sendhilnathan Naveen , Basu Debaleena , Murthy Aditya
Published: May 2019

The conventional approach to understanding neural responses underlying complex computations is to study across-trial averages of repeatedly performed computations from single neurons. When a brain region performs complex computations, such as processing stimulus related information or motor planning, it has been repeatedly shown through measures such as the Fano factor (FF) that neural variability across trials in the network decreases. However, in reality, multiple neurons contribute to a common computation on a single trial, rather than a single neuron contributing to a computation on multiple trials. Therefore, on individual trials the concept of FF loses significance. In this study, we extended previous work using measures of variability that are confined to a single trial and found that neurons perform a common computation, they briefly fire with increased regularity in spike timings, with similar inter-spike interval durations. We propose that this decrease in within-trial variability in neural spiking contributes to a decrease in across-trial variability in neural firing rates during network level computations. We confirmed our hypothesis by testing it on the activity of frontal eye field neurons recorded as two monkeys performed a memory-guided saccade task, and also on simulated spike trains. Furthermore, this phenomenon also has important behavioral correlates: the reaction time of the animal was faster when the within-trial variability was lower. We show that a decrease in within-trial variability is linked to a decrease in across-trial variability in neural response and indicates stationarity of neural network variability across time.

New & Noteworthy

During computations, neural variability across trials decreases. In reality, multiple neurons contribute to a common computation on a single trial, rather than a single neuron contributing to a computation on multiple trials. We found that when a network of neurons performs a common computation, they briefly fire with increased regularity in spike timings. We propose that this decrease in within-trial variability in neural spiking contributes to a decrease in the observed across-trial variability.
Anabolic SIRT4 exerts retrograde control over TORC1 signalling by glutamine sparing in the mitochondria
Authors: Shaw Eisha , Talwadekar Manasi , Mohan Nitya , Acharya Aishwarya , Kolthur-Seetharam Ullas
Published: May 2019

Anabolic and catabolic signalling mediated via mTOR and AMPK have to be intrinsically coupled to mitochondrial functions for maintaining homeostasis and mitigate cellular/organismal stress. Although, glutamine is known to activate mTOR, if/how differential mitochondrial utilization of glutamine impinges on mTOR signalling is less explored. Mitochondrial SIRT4, which unlike other sirtuins is induced in a fed state, is known to inhibit catabolic signalling/pathways through AMPK-PGC1a/SIRT1-PPARa axis and negatively regulate glutamine metabolism via TCA cycle. However, physiological significance of SIRT4 functions during a fed state is still unknown. Here, we establish SIRT4 as key anabolic factor that activates TORC1 signalling and regulates lipogenesis, autophagy and cell proliferation. Mechanistically, we demonstrate that the ability of SIRT4 to inhibit anaplerotic conversion of glutamine to α-ketoglutarate potentiates TORC1. Interestingly, we also show that mitochondrial glutamine sparing or utilization is critical for differentially regulating TORC1 under fed and fasted conditions. Moreover, we conclusively show that differential expression of SIRT4 during fed and fasted states is vital for coupling mitochondrial energetics and glutamine utilization with anabolic pathways. These significant findings also illustrate that SIRT4 integrates nutrient inputs with mitochondrial retrograde signals to maintain a balance between anabolic and catabolic pathways.
Grazing‐induced patchiness, not grazing intensity, drives plant diversity in European low‐input pastures
Authors: Tonn Bettina , Densing Eva M. , Gabler Jessica , Isselstein Johannes
Published: May 2019

Livestock grazing at low stocking rates is widely recommended to maintain grassland biodiversity. However, empirical evidence of grazing‐intensity effects on plant diversity is contradictory. Explicitly considering the small‐scale heterogeneity of short, frequently grazed and tall, rarely grazed patches typical of low‐input grazing systems may be crucial to the understanding of paddock‐scale grazing effects.

We studied three patch types (short, intermediate, tall) within an unfertilised long‐term cattle grazing experiment in Lower Saxony, Germany, comparing three paddock‐scale grazing intensities. We analysed soil nutrient concentrations and recorded vegetation composition at a total of 135 plots. We determined species richness, Simpson diversity, Simpson evenness and beta diversity of individual plots (plot scale) and patch types within paddocks (patch scale). To quantify paddock‐scale diversity, we resampled plot‐scale species composition across a gradient of relative proportions of short and tall patches within a paddock.

Patch type, not paddock‐scale grazing intensity, was the main driver of plant diversity at both plot and patch scale. Short patches were more diverse than tall patches, but the effect was not strongly mediated by the lower soil nutrient concentrations in the short patches. By contrast, both patch type and grazing intensity affected vegetation composition at plot and patch scale.

Beta‐diversity within and between patch types was independent of grazing intensity; consequently, paddock‐scale diversity was determined by the relative proportion of short versus tall patches. Higher alpha diversity of short patches compared to tall patches was more important than beta diversity between the two patch types in shaping paddock‐scale diversity. Consequently, with increasing short‐patch proportion, paddock‐scale diversity increased.

Synthesis and applications. Our study identifies the grazing‐induced patch structure as the most important driver of plant diversity across different grazing intensities in low‐input, that is, unfertilised and continuously stocked, pastures. To optimise grazing management for biodiversity, understanding plant‐diversity responses to grazing at the patch scale is indispensable. Our results suggest that, in unfertilised, continuously stocked European pastures, trade‐offs between biodiversity and agronomic production may be small, as short patches, whose proportion increases with stocking rate, also had the highest plant diversity.
Wearable devices for cardiac arrhythmia detection: a new contender?
Authors: Sajeev Jithin K. , Koshy Anoop N. , Teh Andrew W.
Published: May 2019

There has been increased consumer uptake of smart devices and wearable technology. They facilitate non‐invasive, ambulatory assessment of numerous cardiac indices, including the heart rate and rhythm. Several studies have reported on the utility and deficiencies of these devices in identifying and monitoring cardiac arrhythmias. The rapid uptake of these consumer devices has the potential to generate vast amounts of biometric data. This coupled with gaps in knowledge pertaining to the optimal management of conditions such as sub clinical atrial fibrillation, may result in unnecessary and expensive downstream testing. An improved understanding of this nascent field by the clinician is vital.
Sonoanatomy revisited: the long thoracic nerve
Authors: Chang Ke-Vin , Wu Wei-Ting , Mezian Kamal , Naňka Ondřej , Özçakar Levent
Published: May 2019

The long thoracic nerve (LTN) arises from the C5, C6 and C7 roots and innervates the serratus anterior muscle. Scapular winging is the landmark manifestation of LTN neuropathy and may develop after an accidental injury during selective cervical nerve root or inter-scalene brachial plexus blocks. Although its sonoanatomy has been described in the previous literature, how to gradually identify the entire nerve course has rarely been discussed. In this regard, the present paper aims to elaborate the scanning method of the LTN from its origin to its distal segment.