bluuebunny/crossref_metadata_2025 huggingface dataset:
Protein structure–based gene expression signatures
Authors: Rahman Rayees , Zatorski Nicole , Hansen Jens , Xiong Yuguang , van Hasselt J. G. Coen , Sobie Eric A. , Birtwistle Marc R. , Azeloglu Evren U. , Iyengar Ravi , Schlessinger Avner
Published: May 2021

Significance

Gene expression signatures (GES) are used to define phenotypes, such as cell and tissue state, or the effects of perturbagens. GES have suffered from vague assessment criteria and limited reproducibility. Here, we show that combining protein structure features with GES using deep learning approaches significantly enhances the reliability of the transcriptomic signatures across datasets representing various phenotypes, including relationships among tissues and drugs.
Reversed-engineered human alveolar lung-on-a-chip model
Authors: Huang Di , Liu Tingting , Liao Junlong , Maharjan Sushila , Xie Xin , Pérez Montserrat , Anaya Ingrid , Wang Shiwei , Tirado Mayer Alan , Kang Zhixin , Kong Weijia , Mainardi Valerio Luca , Garciamendez-Mijares Carlos Ezio , García Martínez Germán , Moretti Matteo , Zhang Weijia , Gu Zhongze , Ghaemmaghami Amir M. , Zhang Yu Shrike
Published: May 2021

Significance

This work reports the development of a physiologically relevant human alveolar lung-on-a-chip model, composed of a three-dimensional (3D) porous hydrogel made of gelatin methacryloyl (GelMA) featuring an inverse opal structure, bonded to a compartmentalized chip device that provides air–liquid interface and cyclic breathing motions. Significantly, this GelMA structure has a high similarity to native human alveolar sacs in that they both possess sac-like pores and interconnecting windows between the sacs, in addition to a stiffness similar to the native human distal lung. We showed through multiscale analyses that our 3D GelMA inverse opal structure was better able to maintain the functions of primary human alveolar epithelial cells in a more in vivo-like manner compared with planar models.
Biallelic splicing variants in the nucleolar 60S assembly factor RBM28 cause the ribosomopathy ANE syndrome
Authors: Bryant Carson J. , Lorea Cláudia F. , de Almeida Hiram Larangeira , Weinert Letícia , Vedolin Leonardo , Pinto e Vairo Filippo , Baserga Susan J.
Published: May 2021

Significance

RBM28 is a human protein essential for proper assembly of the large ribosomal subunit, crucially enabling synthesis of all cellular proteins. Defects in RBM28 cause rare ribosomopathies: alopecia, neurological defects, and endocrinopathy (ANE) syndrome. We investigated an ANE syndrome patient with a clinical presentation consistent with the definition of ANE syndrome but possessing differing genetic variants and molecular pathology. We find one inherited allele is null, clarifying that ANE syndrome is not caused by
RBM28
haploinsufficiency, while the other inherited allele retains enough function to enable survival but preclude proper development. Our results define an underlying pathology of ANE syndrome, further delineating an emerging class of assembly factor ribosomopathies and underscoring the importance of nucleolar processes in human health.
Strategic placement of an obstacle suppresses droplet break up in the hopper flow of a microfluidic soft crystal
Authors: Bick Alison D. , Khor Jian Wei , Gai Ya , Tang Sindy K. Y.
Published: May 2021

Significance

Order can emerge spontaneously from collective interactions in many-body systems. This work reports an unexpected order from the interactions between an obstacle and highly confined water-in-oil drops flowing in a 2D hopper. This geometry-mediated order suppresses droplet break up drastically at the hopper exit in the fast flow limit where no order has been observed before. The results are important to the understanding of out-of-equilibrium many-body systems and can find use in other soft systems such as foams, gels, biological cellular aggregates, and systems with soft long-range interactions, including merging traffic. Practically, the findings can facilitate the design of droplet microfluidic systems for the flow control of these drops as microreactors and extrusion-based 3D printing of emulsion-based materials.
Dysregulation of Amphiregulin stimulates the pathogenesis of cystic lymphangioma
Authors: Yoshida Naofumi , Yamamoto Seiji , Hamashima Takeru , Okuno Noriko , Okita Naruho , Horikawa Shinjiro , Hayashi Masao , Dang Thanh Chung , Nguyen Quang Linh , Nishiyama Koichi , Makino Teruhiko , Ishii Yoko , Tomihara Kei , Shimizu Tadamichi , Shibuya Masabumi , Noguchi Makoto , Sasahara Masakiyo
Published: May 2021

Significance

Several lymphangiogenic factors, such as vascular endothelial growth factor C (VEGF-C), have been known in normal lymphatics development; however, the key molecules and cell types involved in pathological lymphangiogenesis are less well known. We find that dermal fibroblasts in
Pdgfrb
knockout (β-KO) mice highly express Amphiregulin, and such Amphiregulin causes the cyst-like lymphatic vessels observed in the β-KO mice to form. Similarly, in human cystic lymphangioma, fibroblasts surrounding cystic lymphatics, which highly express Amphiregulin, can also induce the expression of Amphiregulin in lymphatic endothelial cells. Collectively, excessive expression of Amphiregulin results in pathogenesis of cystic lymphangioma. These findings suggest Amphiregulin as a fascinating therapeutic target for patients with cystic lymphangioma.
Discovery of a body-wide photosensory array that matures in an adult-like animal and mediates eye–brain-independent movement and arousal
Authors: Shettigar Nishan , Chakravarthy Anirudh , Umashankar Suchitta , Lakshmanan Vairavan , Palakodeti Dasaradhi , Gulyani Akash
Published: May 2021

Significance

This study highlights the breathtaking sophistication of form and function possible with eye-independent light-sensory systems. We have discovered a body-wide sensory organization of unique photoreceptor cells that allows even head-removed flatworms to move like intact animals, revealing the mechanistic framework underpinning one of the most sensitive eye–brain-independent photoresponses known. Distinct from the ocular system, the body-wide sensory array matures in adult-like animals, can trigger arousal of intact animals from a “resting-state” and employs “noncanonical” opsins. Our discovery of a body-wide network of photoreceptor cells triggering coordinated movement is intriguing and conceptualizes how “dispersed”-sensory nodes may network to control outputs typically through a centralized brain. Our work illustrates how eye-independent systems can deeply influence animal physiology and behavior.
A simple expression for the strength of selection on recombination generated by interference among mutations
Authors: Roze Denis
Published: May 2021

Significance

Recombination between parental chromosomes during meiosis represents an important source of genetic novelty and is thought to be the main evolutionary benefit of sexual reproduction. However, the evolutionary forces driving the rapid evolution of recombination rates demonstrated by comparisons between populations or closely related species remain obscure. This article provides mathematical quantification of the selective advantage of a mutation increasing the genetic map length (average number of cross-overs occurring at meiosis) of a whole genome due to the increased efficiency of selection against deleterious alleles. It shows that the advantage of recombination can be expressed as a simple expression of the mutation rate per unit map length, providing a simple way of evaluating its plausible order of magnitude.
Phylogenomic conflict coincides with rapid morphological innovation
Authors: Parins-Fukuchi Caroline , Stull Gregory W. , Smith Stephen A.
Published: May 2021

Significance

We demonstrate that instances of high gene-tree conflict (discordance in phylogenetic signal across genes) in mammals, birds, and several major plant clades correspond to rate increases in morphological innovation. We suggest that gene-tree conflict and rapid phenotypic change across major clades of vascular plants, mammals, and birds are often the result of coincident population processes (e.g., changes in population size, rapid speciation, and incomplete lineage sorting). Closer examination of these coincident patterns will contribute to a stronger understanding of the microevolutionary dynamics underlying the emergence of phenotypic patterns typically only observable over deep time. Our findings indicate that patterns of gene-tree conflict, occurring episodically across the Tree of Life, offer clues toward understanding the population-level processes driving major evolutionary transitions.
Fast and pervasive transcriptomic resilience and acclimation of extremely heat-tolerant coral holobionts from the northern Red Sea
Authors: Savary Romain , Barshis Daniel J. , Voolstra Christian R. , Cárdenas Anny , Evensen Nicolas R. , Banc-Prandi Guilhem , Fine Maoz , Meibom Anders
Published: May 2021

Significance

Coral reefs are in catastrophic decline worldwide, in part due to increasingly warm surface waters that cause mass coral bleaching and mortality. However, corals in the northern Red Sea and Gulf of Aqaba have shown no sign of bleaching, despite local seawater temperature rising faster than the global average. We show that the exceptional heat tolerance of the common symbiotic reef-building coral
Stylophora pistillata
from the Gulf of Aqaba is based on a rapid gene expression response and recovery pattern when exposed to heat stress up to 32 °C. Such temperatures are not anticipated to occur in the region within this century, giving real hope for the preservation of at least one major coral reef ecosystem for future generations.
Physical tuning of galectin-3 signaling
Authors: Farhadi Shaheen A. , Liu Renjie , Becker Matthew W. , Phelps Edward A. , Hudalla Gregory A.
Published: May 2021

Significance

The family of carbohydrate-binding proteins known as galectins receive considerable attention for their ability to modulate cell behavior in both normal and pathological settings. Galectin-3, for instance, can crosslink membrane glycans to initiate, amplify, attenuate, or inhibit signal transduction pathways that lead to cell differentiation, proliferation, or death. However, understanding structure–function relationships of galectin-3 is challenged by its promiscuous glycan-binding properties and assembly into oligomers with undefined number of subunits or “valency.” Here, we address these challenges by providing a toolbox of synthetic galectin-3 oligomers with tunable valency. Cell-based studies with these oligomers suggest a role for physical size as a structural determinant of galectin-3 signaling function, in addition to the increased binding strength typically associated with multivalency.
Echolocating bats rely on an innate speed-of-sound reference
Authors: Amichai Eran , Yovel Yossi
Published: May 2021

Significance

Animals rely on their senses to survive and reproduce. Sensory systems are subject to a trade-off between the advantage of flexibility that often comes with a cost of a prolonged learning period and the advantage of innateness, which is less successful in dealing with altered environments. Most bat species rely on echolocation—emitting sound signals and analyzing the returning echoes. An object’s distance can be assessed using echolocation given a reference to the speed of sound. Since bats experience a range of speeds of sound, we tested whether the encoding of the speed of sound is innate or learned. We found that bats’ reference to the speed of sound is innate and that it is not flexible during adulthood.
A global carbon and nitrogen isotope perspective on modern and ancient human diet
Authors: Bird Michael I. , Crabtree Stefani A. , Haig Jordahna , Ulm Sean , Wurster Christopher M.
Published: May 2021

Significance

The carbon and nitrogen isotope composition of human tissues can be used to infer dietary information. We transformed isotope compositions of 13,666 modern and ancient analyses to make them comparable on a common scale. This reveals that the isotope dietary breadth of modern humans is highly compressed when compared to populations predating the development in 1910 of modern industrial fertilizer by the Haber–Bosch method. However, modern humans that still use “traditional” subsistence strategies retain remarkably similar isotope dietary breadth to all pre-Haber–Bosch human populations. Increased reliance on industrial agriculture and pastoralism is resulting in a cascade of “rewiring” to remaining food webs globally that can reduce the resilience of global ecosystems in the face of accelerating environmental change.
Intranasal vaccination with influenza HA/GO-PEI nanoparticles provides immune protection against homo- and heterologous strains
Authors: Dong Chunhong , Wang Ye , Gonzalez Gilbert X. , Ma Yao , Song Yufeng , Wang Shelly , Kang Sang-Moo , Compans Richard W. , Wang Bao-Zhong
Published: May 2021

Significance

A noninvasive intranasal (i.n.) influenza vaccine can induce mucosal immune responses in respiratory tracts, preventing infection at the portal of virus entry. However, the absence of appropriate mucosal adjuvants at present hinders the development of such a vaccine. Here, we developed polyethyleneimine-functionalized two-dimensional graphene oxide nanoparticles (GP) that showed high antigen-loading capacities and superior immunoenhancing properties. Robust and broadly reactive immune responses were induced with i.n. immunization with GP-HA nanoparticles, conferring protection against homologous and heterologous viruses. With versatility and flexibility, GP nanoparticles can be easily adapted for constructing mucosal vaccines of different respiratory pathogens.
Conditional sanctioning in a legume–
Rhizobium
mutualism
Authors: Westhoek Annet , Clark Laura J. , Culbert Michael , Dalchau Neil , Griffiths Megan , Jorrin Beatriz , Karunakaran Ramakrishnan , Ledermann Raphael , Tkacz Andrzej , Webb Isabel , James Euan K. , Poole Philip S. , Turnbull Lindsay A.
Published: May 2021

Significance

Legumes, like peas, beans, and lentils, are high in protein because they form associations with specialized nitrogen-fixing bacteria. Plants provide the bacteria with carbon and receive nitrogen in return, but some bacterial strains provide more nitrogen than others. We show that pea plants supply resources to strains that are poor at fixing nitrogen only if they have no other choice. If a better strain is present, resources are withheld. This indicates that legumes can make conditional decisions, giving them remarkable control over their symbiotic partners. This knowledge could allow selection of plants that are better at discriminating among strains and improve understanding of soil bacterial populations. Both could help to increase yields in agricultural settings, where poor fixers are common.
Compliant 3D frameworks instrumented with strain sensors for characterization of millimeter-scale engineered muscle tissues
Authors: Zhao Hangbo , Kim Yongdeok , Wang Heling , Ning Xin , Xu Chenkai , Suh Judy , Han Mengdi , Pagan-Diaz Gelson J. , Lu Wei , Li Haibo , Bai Wubin , Aydin Onur , Park Yoonseok , Wang Jiaojiao , Yao Yao , He Yishan , Saif M. Taher A. , Huang Yonggang , Bashir Rashid , Rogers John A.
Published: May 2021

Significance

Tissue-on-chip systems offer important capabilities in engineering of living tissues for diverse biomedical applications in disease model studies, drug screening, and regenerative medicine. Conventional approaches use two-dimensional layouts that cannot suppport interfaces to geometrically complex three-dimensional (3D) tissue constructs in a deterministic fashion. Here, we present concepts in engineering systems that allow intimate contact with and stable mechanical coupling to 3D tissues for high-precision measurements of tissue contractility, as demonstrated in 3D, millimeter-scale engineered skeletal muscle tissues. These compliant, 3D frameworks instrumented with advanced sensors and other functional electronics, may significantly enhance the capabilities of tissue-on-chip systems.
Pharmacological modulation of T cell immunity results in long-term remission of autoimmune arthritis
Authors: Huang Yi-Shu , Tseng Wen-Yi , Clanchy Felix I. L. , Topping Louise M. , Ogbechi Joy , McNamee Kay , Perocheau Dany , Chiang Nien-Yi , Ericsson Peter , Sundstedt Anette , Xue Zhong-Tian , Salford Leif G. , Sjögren Hans-Olov , Stone Trevor W. , Lin Hsi-Hsien , Luo Shue-Fen , Williams Richard O.
Published: May 2021

Significance

Chronic inflammatory diseases are characterized by an imbalance between pathogenic T effector cells and regulatory T cells. In this report, we demonstrate that decitabine, a cytosine analog, has a rapid and sustained therapeutic effect in animal models of rheumatoid arthritis. Decitabine selectively targets T effector cells expressing ENT1, a nucleoside transporter, and generates robust regulatory T cells with the capacity to suppress immune-driven inflammation. This study identifies a path toward resetting tolerance in autoimmune disease using a repurposed drug.
Manipulating placebo analgesia and nocebo hyperalgesia by changing brain excitability
Authors: Tu Yiheng , Wilson Georgia , Camprodon Joan , Dougherty Darin D. , Vangel Mark , Benedetti Fabrizio , Kaptchuk Ted J. , Gollub Randy L. , Kong Jian
Published: May 2021

Significance

Although previous studies have extensively studied the neurobiological mechanisms of placebo and nocebo effects, ways to manipulate these effects to yield further benefits remain relatively unknown. We combined simultaneous repeated transcranial direct current stimulation (tDCS)-fMRI, an expectancy manipulation model, and task-based fMRI to investigate the modulatory effects of anodal and cathodal tDCS at the right dorsolateral prefrontal cortex on placebo analgesia and nocebo hyperalgesia. Our results suggest that active tDCS has the potential to boost placebo and blunt nocebo effects and modulate brain activity and connectivity associated with placebo analgesia and nocebo hyperalgesia. These findings provide deeper understanding of mechanistic manipulation of placebo and nocebo effects and may lead to improved clinical outcomes in medical practice.
DNA-inspired nanomaterials for enhanced endosomal escape
Authors: Lee Jinhyung , Sands Ian , Zhang Wuxia , Zhou Libo , Chen Yupeng
Published: May 2021

To realize RNA interference (RNAi) therapeutics, it is necessary to deliver therapeutic RNAs (such as small interfering RNA or siRNA) into cell cytoplasm. A major challenge of RNAi therapeutics is the endosomal entrapment of the delivered siRNA. In this study, we developed a family of delivery vehicles called Janus base nanopieces (NPs). They are rod-shaped nanoparticles formed by bundles of Janus base nanotubes (JBNTs) with RNA cargoes incorporated inside via charge interactions. JBNTs are formed by noncovalent interactions of small molecules consisting of a base component mimicking DNA bases and an amino acid side chain. NPs presented many advantages over conventional delivery materials. NPs efficiently entered cells via macropinocytosis similar to lipid nanoparticles while presenting much better endosomal escape ability than lipid nanoparticles; NPs escaped from endosomes via a “proton sponge” effect similar to cationic polymers while presenting significant lower cytotoxicity compared to polymers and lipids due to their noncovalent structures and DNA-mimicking chemistry. In a proof-of-concept experiment, we have shown that NPs are promising candidates for antiviral delivery applications, which may be used for conditions such as COVID-19 in the future.
Internet of Things Design on Chili Plants
Authors: Hardyanto R. Hafid , Ciptadi Prahenusa Wahyu , Mukhayat Nurdin
Published: May 2021

This study aims to develop system application in chili plants. Chili is a fruit commodity that cannot be released in daily needs. This plant is widely used to meet the need for vitamins and minerals necessary for growth and health. Many factors influence the development of plant cultivation, for example temperature, soil pH, humidity, the need for irradiation or light intensity used, and other factors. All of these are a combination that must be known in order to produce good chili plant growth. This study aims to produce a system design for monitoring the growth of chili plants based on the internet of things. The method used in this study uses a waterfall. The results of the study resulted in an IoT design on chili plants that is ready to be tested on a large scale.
Utilization of Information Technology for Kudus Local Values
Authors: Khamidah Noor , Utaminingsih Sri , Kanzunnudin Mohammad
Published: May 2021

The purpose of this research is to discribe the local wisdom value about rebo wekasam in jepang village, the terminology of Rebo Wekasan is special Rebo (Wednesday) because it doesn’t look like another Wednesday. Its term is understandable, because Rebo Wekasan is last Wednesday in Shofar, second month in hijriyyah calendar. This research is using qualitative approach. Technic of data collecting is using literature review, interview, observation, recording, taping, and photography. The result showed that rebo wekasan tradition is having local wisdom value. The value itself is consisting of leadership value, devotion value, tradition value and cultural value.
Photocatalytic Activity of Ag-ZnO Nanocomposites Integrated Essential Ginger Oil Fabricated by Green Synthesis Method
Authors: Abbas Asaad M. , Abid M. A. , Abbas Khaldoon N. , Aziz Wisam J. , Salim A. A.
Published: May 2021

Facile and eco-friendly green synthesis route was used to fabricate pure ZnO nanoparticles (NPs) and silver doped ZnO nanocomposites (Ag-ZnO NCPs) using essential ginger oil (EGO) as reduction agent. These Ag-ZnO NCPs were determined and characterized via various analytical tools such as X-ray diffraction, FESEM, and UV-Vis spectrophotometer. X-ray diffraction patterns confirmed the crystallinity of single ZnO that showed a hexagonal wurtizite (HW) structure with preferential orientation in the (100) direction and the Ag NPs verified face center cubic (FCC) structure with preferred orientation in the (111) direction. The FESEM images exposed uniformly distributed triangle cages of ZnO NPs and nanowires shape of Ag-ZnO NCPs. The UV-Vis absorption band of as-synthesized Ag-ZnO NCPs showed sharp and minor peaks at 395 nm and 550 nm. Photocatalytic activity of Ag-ZnO NCPs was obtained through methylene orange (MO) dye degradation tests, which exhibited remarkable photodegradation efficiency around ≈ 90% after 150 min under UV light. In contrast, single ZnO revealed photodegradation efficiency ≈ 84% at 150 min UV light exposure. These Ag-ZnO NCPs can offer a great potential for large demands of semiconductor applications.
Stern-Volmer Mechanistic Study on Transition Metals Embedded onto Optical Fibre for Dissolved Oxygen Sensing And Monitoring: A Systematic Literature Review
Authors: Shamsudin M S , Syuhada A , Rusop M , Mohamad F , Harun S W , Aziz M S
Published: May 2021

Dissolved oxygen (DO) concentration is the most critical parameter to evaluate water quality, commonly addressed in global freshwater, and seawater aquacultures. Research trends and patterns on optical fibre for environmental DO sensing and monitoring, specifically, photonics, are rising and revolutionilising the current practices. Transition metals have emerged as a promising material for use in determining DO concentration in the water. Their unusual physicochemical and optical properties enable them to be used as an oxygen-sensitive dye and a so-called waveguide in thin-film that can be easily integrated with optical fibre. Thus, the selection of transition metals is important in the early phase of this research to design the optical-based transducers for DO sensing and monitoring. The DO concentration needs to be accurately measured in real-time, as its change is a continuous dynamic process. Gaps were identified utilising various transition metals embedded onto optical fibre for the in-situ determination of DO concentration in the water, contributing new knowledge for future scholarly work. The detection mechanism of DO concentration in the water with various transition metals is briefly outlined and concludes by addressing the real world’s laboratory-scale challenges. In short, we focus on the Stern-Volmer model for mechanistic study on transition metals for DO sensing and monitoring.
Deep Learning: Classification and Automated Detection Earlier of Alzheimer’s Disease Using Brain MRI Images
Authors: Kadhim Karrar A. , Mohamed Farhan , Khudhair Zaid Nidhal
Published: May 2021

Alzheimer’s disease (AD) progression can be avoided by conducting diagnosis beforehand. This diagnosis acquired quick preventive care which could be possibly done by specialists. Fast and accurate evaluation at the earliest and most challenging stage were required to detect in the diagnosis of AD. In this paper, previous studies were reviewed into a better approach that recognizes the presence of disease in sagittal magnetic resonance automatically (MRI) images that are unusually used. The MRI brain images were used to identify and distinguish characteristics using a range of characteristics recognition techniques. The review of research papers on Alzheimer’s Disease published in reputable journals from 2017 to 2020 were presented and discussion of various strategies related to the latest tools used in early diagnosis is our main focus in this study, which could enable researchers to understand current algorithms and techniques in this area, and eventually develop new and more effective algorithms.
Multilayer SiC/C Thin Film Coating on Fiber Tip for Raman Probe Application
Authors: Samsudin Nur Nabilah , Omar Muhammad Firdaus
Published: May 2021

A novel technique in the fabrication of an optical filter that is made up of multilayer thin film is introduced in this study. Multiple layers of silicon carbide and carbon with high and low refractive index materials respectively will be deposited alternatively with a various thickness on a glass substrate by radio frequency magnetron sputtering of 99% purity of silicon carbide as the target. The variation of structure and optical properties of the films are studied by using X-ray reflectivity (XRR), Raman scattering spectroscopy, and UV–vis-NIR spectroscopy until it reached the desired results and meet the specification as Raman optical filter. The thin film is then placed on a multimode fiber tip as Raman edge filter. Raman fingerprint of specific alcohol (ethanol) obtained is tested using a fabricated filter with the standard spectrum. The preliminary result of SiC thin film fabrication for 30, 60 and 90 minutes by sputtering process showed rate of deposition obtained is 3.17nm/min. The results demonstrate that the optical properties of silicon carbide thin film can be monitored by modifying the condition of silicon carbide and carbon deposition.
Influence of Coating Thickness of Polyimide for Moisture Sensing
Authors: Rohizad Siti Nur Aizatti , Daud Suzairi , Noorden Ahmad Fakhrurrazi Ahmad
Published: May 2021

This work focused on the effect of existence of polyimide coated fibre Bragg grating (FBG) for moisture sensing in stingless bee. The moisture sensitive material namely polyimide (PI) was used to improve the sensitivity of the fibre optic sensor. By taking the benefits from amine groups in 3-(aminopropyl) triethoxysilane (APTES), PI is coated onto the segment of FBG through covalent interaction. Different thickness of PI coated FBG as well as determination and optimization of the designated sensor has been done. 3 layers of polyimide coating were used to improve the sensitivity of moisture sensing, and the sensitivity of coated fibre been analysed.
A novel hybrid feature extraction method using LTP, TFCM, and GLCM
Authors: Najjar Fallah H. , Al-Jawahry Hassan M. , Al-Khaffaf Mustafa Saleh , Al-Hasani Ahmed T.
Published: May 2021

Image classification and feature extraction have been studied extensively and used efficiently in several applications. This paper suggests a novel method by combining three main methods for texture feature extraction. The proposed method is based on Local Ternary Pattern (LTP), Texture Feature Coding Method (TFCM), and Gray Level Cooccurrence Matrix (GLCM). We have entitled our method as GCLTP which is stand for Gray Coding Local Ternary Pattern. The combination of LTP, TFCM, and GLCM is assigned a unique value used to extract the features of an image. GCLTP is tested using images are taken from the Brodatz database. A set of 22 features were extracted from images. GCLTP is experimentally accomplished a high accuracy in classification by using the most known classifiers.
All-Optical Tuning of Au Nanocluster Functionalized Microfibre Coil Resonator
Authors: Yin Yu , Li Shi , Wang Pengfei
Published: May 2021

An all-optical tunable microfibre coil resonator (MCR) functionalized using Au nanoclusters (AuNCs) was investigated and demonstrated. The MCR was manufactured by winding tapered fibre on a hollow rod of low refractive index polycarbonate (PC) resin to form a fluidic channel, and the AuNCs aqueous solution was injected into the channel to complete the functionalization process. The resonance wavelength and extinction ratio can be tuned using a pump laser with wavelength of 808 nm due to the photo-thermal effect and photon generated carriers from strong absorption of AuNCs at 808 nm, resulting light-matter interaction and providing all-optical tuning properties, including variations of resonance wavelength and extinction ratio. The variation rate of the resonance wavelength and extinction ratio were determined as 69 pm/mW and 0.459 dBm/mW. The response times of the MCR functionalized with the AuNCs are 11.99 s (rising) and 11.41 s (falling). The AuNCs functionalized MCR has several advantages compared to other tunable resonator devices, including easy fabrication, high tuning efficiency, low cost and all-fibre construction.
Temperature sensitivity of FBG coating with zinc oxide and silicon carbide
Authors: Mansor N F , Raja Ibrahim R K
Published: May 2021

This work aims to evaluate the sensitivity of coated FBG in measuring non-thermal plasma temperature inside a dielectric barrier discharge reactor. The FBG sensor were coated with Zinc Oxide (ZnO) and Silicon Carbide (SiC) by using magnetron sputtering technique. Both materials are insulator hence suitable to probe temperature inside the plasma reactor. Results revealed that the temperature sensitivity of and SiC coated FBG were 12.6 pm/°C and 12.37 pm/°C, respectively (suggested to put both 2 decimal places). This means temperature sensitivity of ZnO is higher than bare FBG (12.43 pm/°C) while SiC coated FBG shows the lowest. The values show slightly different between each other and give less significant in sensitivity value. When applied it inside plasma, spectroscopic diagnostic result shows stable plasma throughout the time.
Preparation and Characterization of Biodegradable Polylactic Acid (PLA) Film for Food Packaging Application: A Review
Authors: Malek N S A , Faizuwan M , Khusaimi Z , Bonnia N N , Rusop M , Asli N A
Published: May 2021

Biodegradable PLA which is produced by polymerization of lactic acid derived from the starch of plants is a good candidate for replacing the current petroleum-based polymers such as polystyrene (PS) or Polypropylene (PP) in food packaging application. These petroleum-based polymers do contribute to large-scale environmental pollution as it is a non-degradable polymer. Being classified as Generally Recognized As Safe (GRAS) for the food contact applications, PLA film for food packaging application can be synthesized in lab-scale and mass production by using solvent casting and injection molding which are common for the thermoplastic fabrication with the fast production and low in cost. The characterization methods used for the PLA film analysis can be done by the Universal Tensile machine (UTS) in which the main characteristics of the polymer film compatibility and its performance with the combined materials have been discussed in comparison with those of pure polymer films.
Investigating the Effects of Threatening Language, Message Framing, and Reactance in Opt-Out Organ Donation Campaigns
Authors: Miller Jordan , McGregor Lesley , Currie Sinéad , O’Carroll Ronan E
Published: May 2021

Background

Under opt-out organ donation policies, individuals are automatically considered to have agreed to donate their organs in the absence of a recorded opt-out decision. Growing evidence suggests that the language used within organ donation campaigns influences donor intentions and decision-making.

Purpose

As awareness campaigns to promote opt-out consent in the UK are ongoing, the objectives of this study were to investigate the effect of language and message framing used in opt-out organ donation campaigns on donor intentions and psychological reactance.

Methods

Individuals from Scotland and England (N = 1,350) completed this online experiment. Participants were randomized to view one of four messages, designed in the format of a newspaper article, which described the upcoming opt-out system. This followed a 2 × 2 design whereby the degree of threatening language (high threat vs. low threat) and message framing (loss vs. gain) of the newspaper article was experimentally manipulated. Measures of intention (pre-exposure and postexposure) and postmessage reactance (threat to freedom and anger and counter-arguing) were obtained.

Results

A mixed analysis of variance revealed a significant Group × Time interaction on donor intentions; post hoc analysis revealed that intentions significantly decreased for individuals exposed to the High threat × Loss frame article but significantly increased for those exposed to the High threat × Gain frame article.

Conclusions

In campaigns to promote opt-out legislation, high-threat language combined with loss-frame messages should be avoided. If high-threat language is used, gain-frame messaging that highlights the benefits of organ donation should also be incorporated.
Are presymptomatic SARS-CoV-2 infections in nursing home residents unrecognised symptomatic infections? Sequence and metadata from weekly testing in an extensive nursing home outbreak
Authors: van den Besselaar Judith H , Sikkema Reina S , Koene Fleur M H P A , van Buul Laura W , Oude Munnink Bas B , Frénay Ine , Witt René te , Koopmans Marion P G , Hertogh Cees M P M , Buurman Bianca M
Published: May 2021

Background

Sars-CoV-2 outbreaks resulted in a high case fatality rate in nursing homes (NH) worldwide. It is unknown to which extent presymptomatic residents and staff contribute to the spread of the virus.

Aims

To assess the contribution of asymptomatic and presymptomatic residents and staff in SARS-CoV-2 transmission during a large outbreak in a Dutch NH.

Methods

Observational study in a 185-bed NH with two consecutive testing strategies: testing of symptomatic cases only, followed by weekly facility-wide testing of staff and residents regardless of symptoms. Nasopharyngeal and oropharyngeal testing with RT-PCR for SARs-CoV-2, including sequencing of positive samples, was conducted with a standardised symptom assessment.

Results

185 residents and 244 staff participated. Sequencing identified one cluster. In the symptom-based test strategy period, 3/39 residents were presymptomatic versus 38/74 residents in the period of weekly facility-wide testing (P-value < 0.001). In total, 51/59 (91.1%) of SARS-CoV-2 positive staff was symptomatic, with no difference between both testing strategies (P-value 0.763). Loss of smell and taste, sore throat, headache or myalga was hardly reported in residents compared to staff (P-value <0.001). Median Ct-value of presymptomatic residents was 21.3, which did not differ from symptomatic (20.8) or asymptomatic (20.5) residents (P-value 0.624).

Conclusions

Symptoms in residents and staff are insufficiently recognised, reported or attributed to a possible SARS-CoV-2 infection. However, residents without (recognised) symptoms showed the same potential for viral shedding as residents with symptoms. Weekly testing was an effective strategy for early identification of SARS-Cov-2 cases, resulting in fast mitigation of the outbreak.
Laboratory Test Ordering Patterns in Pediatrics From Naturopaths and General Practitioners
Authors: Liao Hsuan-Chieh , Astion Michael , Dickerson Jane
Published: May 2021

Objectives

Naturopathic medicine emphasizes prevention and the self-healing process through natural therapies. Naturopathic doctors (NDs) use clinical laboratories as frequently as traditionally trained physicians. Here we evaluated the test-ordering patterns of NDs and general practitioners (GPs).

Methods

A retrospective analysis was performed from a tertiary pediatric hospital. We analyzed tests ordered by NDs who used laboratory services and compared the test ordering patterns with GPs from adolescent medicine, family medicine, or pediatric clinics. Requests were categorized into 10 groups. We determined the tests with the highest ordering frequencies, as well as the percentage of tests that had an abnormal result.

Results

NDs ordered more tests per patient per date of specimen collection compared with GPs. The most frequently ordered tests by NDs were trace elements and toxic metals (23.2% of total), allergens (21.8%), and general chemistry (15.3%). For the same test, the percentage of tests with an abnormal result was significantly lower for NDs than GPs.

Conclusions

We observed different ordering patterns between NDs and GPs. NDs ordered more esoteric tests and had lower rates of abnormal test results compared with GPs. Understanding the patterns of testing from different providers’ specialties is useful to choose effective laboratory stewardship interventions.
Real-time mapping of nanopore raw signals
Authors: Zhang Haowen , Li Haoran , Jain Chirag , Cheng Haoyu , Au Kin Fai , Li Heng , Aluru Srinivas
Published: May 2021

Motivation

Oxford Nanopore Technologies sequencing devices support adaptive sequencing, in which undesired reads can be ejected from a pore in real time. This feature allows targeted sequencing aided by computational methods for mapping partial reads, rather than complex library preparation protocols. However, existing mapping methods either require a computationally expensive base-calling procedure before using aligners to map partial reads or work well only on small genomes.

Results

In this work, we present a new streaming method that can map nanopore raw signals for real-time selective sequencing. Rather than converting read signals to bases, we propose to convert reference genomes to signals and fully operate in the signal space. Our method features a new way to index reference genomes using k-d trees, a novel seed selection strategy and a seed chaining algorithm tailored toward the current signal characteristics. We implemented the method as a tool Sigmap. Then we evaluated it on both simulated and real data and compared it to the state-of-the-art nanopore raw signal mapper Uncalled. Our results show that Sigmap yields comparable performance on mapping yeast simulated raw signals, and better mapping accuracy on mapping yeast real raw signals with a 4.4× speedup. Moreover, our method performed well on mapping raw signals to genomes of size >100 Mbp and correctly mapped 11.49% more real raw signals of green algae, which leads to a significantly higher F1-score (0.9354 versus 0.8660).

Availability and implementation

Sigmap code is accessible at https://github.com/haowenz/sigmap.

Supplementary information

Supplementary data are available at Bioinformatics online.
Engineered microRNA-based regulatory element permits safe high-dose miniMECP2gene therapy in Rett mice
Authors: Sinnett Sarah E , Boyle Emily , Lyons Christopher , Gray Steven J
Published: May 2021

MECP2 gene transfer has been shown to extend the survival of Mecp2−/y knockout mice modelling Rett syndrome, an X-linked neurodevelopmental disorder. However, controlling deleterious overexpression of MECP2 remains the critical unmet obstacle towards a safe and effective gene therapy approach for Rett syndrome. A recently developed truncated miniMECP2 gene has also been shown to be therapeutic after AAV9-mediated gene transfer in knockout neonates.

We show that AAV9/miniMECP2 has a similar dose-dependent toxicity profile to that of a published second-generation AAV9/MECP2 vector after treatment in adolescent mice. To overcome that toxicity, we developed a risk-driven viral genome design strategy rooted in high-throughput profiling and genome mining to rationally develop a compact, synthetic microRNA target panel (miR-responsive auto-regulatory element, ‘miRARE’) to minimize the possibility of miniMECP2 transgene overexpression in the context of Rett syndrome gene therapy. The goal of miRARE is to have a built-in inhibitory element responsive to MECP2 overexpression. The data provided herein show that insertion of miRARE into the miniMECP2 gene expression cassette greatly improved the safety of miniMECP2 gene transfer without compromising efficacy. Importantly, this built-in regulation system does not require any additional exogenous drug application, and no miRNAs are expressed from the transgene cassette.

Although broad applications of miRARE have yet to be determined, the design of miRARE suggests a potential use in gene therapy approaches for other dose-sensitive genes.
Entrainment of Network Activity by Closed-Loop Microstimulation in Healthy Ambulatory Rats
Authors: Averna Alberto , Hayley Page , Murphy Maxwell D , Barban Federico , Nguyen Jimmy , Buccelli Stefano , Nudo Randolph J , Chiappalone Michela , Guggenmos David J
Published: May 2021

As our understanding of volitional motor function increases, it is clear that complex movements are the result of the interactions of multiple cortical regions rather than just the output properties of primary motor cortex. However, our understanding of the interactions among these regions is limited. In this study, we used the activity-dependent stimulation (ADS) technique to determine the short/long-term effects on network activity and neuroplasticity of intracortical connections. ADS uses the intrinsic neural activity of one region to trigger stimulations in a separate region of the brain and can manipulate neuronal connectivity in vivo. Our aim was to compare single-unit neuronal activity within premotor cortex (rostral forelimb area, [RFA] in rats) in response to ADS (triggered from RFA) and randomly-generated stimulation in the somatosensory area (S1) within single sessions and across 21 consecutive days of stimulation. We examined firing rate and correlation between spikes and stimuli in chronically-implanted healthy ambulatory rats during spontaneous and evoked activity. At the end of the treatment, we evaluated changes of synaptophysin expression. Our results demonstrated the ability of ADS to modulate RFA firing properties and to promote synaptogenesis in S1, strengthening the idea that this Hebbian-inspired protocol can be used to modulate cortical connectivity.
A Language of Her Own: Willful Displacement and Nomadic Subjectivity in Jhumpa Lahiri
Authors: walker rebecca
Published: May 2021

In Other Words (2016) is the first of Jhumpa Lahiri’s writings to be published in Italian, charting the journey to self-expression enabled by her twenty-year relationship with this foreign language. Tracing Lahiri’s literary production, this article argues that the autobiographical prose of In Other Words is facilitated by a series of “willful” displacements, reworking and revising the notion of displacement, which is a pervasive theme of Lahiri’s earlier work. Moreover, it is precisely by means of these self-conscious geographical, bodily, linguistic, and literary dislocations that Lahiri articulates a kind of shifting or nomadic subjectivity, where otherness and multiplicity are re-privileged as sources of creative energy and self-affirmation.
Variables affecting the quality of anticoagulation in atrial fibrillation patients newly initiating vitamin K antagonists: insights from the national and multicentre SULTAN registry
Authors: Rivera-Caravaca José Miguel , Badimón Lina , Ferreira-Gonzalez Ignacio , Gómez-Doblas Juan José , Roca-Luque Ivo , Lekuona Iñaki , Jiménez-Candil Javier , Rodríguez-Padial Luis , González-Juanatey Carlos , Calvo-Jambrina Román , Fácila Lorenzo , Ruiz-Ortiz Martín , Anguita Manuel , Marín Francisco
Published: May 2021

Aims

Vitamin K antagonists (VKAs) are effective drugs reducing the risk for stroke in atrial fibrillation (AF), but the benefits derived from such therapy depend on the international normalized ratio (INR) maintenance in a narrow therapeutic range. Here, we aimed to determine independent variables driving poor anticoagulation control [defined as a time in therapeutic range (TTR) <65%] in a ‘real world’ national cohort of AF patients.

Methods and results

The SULTAN registry is a multicentre, prospective study, involving patients with non-valvular AF from 72 cardiology units expert in AF in Spain. At inclusion, all patients naïve for oral anticoagulation were started with VKAs for the first time. For the analysis, the first month of anticoagulation and those patients with <3 INR determinations were disregarded. Patients were followed up during 1 year. A total of 870 patients (53.9% male, the mean age of 73.6 ± 9.2 years, mean CHA2DS2-VASc and HAS-BLED of 3.3 ± 1.5 and 1.4 ± 0.9, respectively) were included in the full analysis set. In overall, 7889 INR determinations were available. At 1-year, the mean TTR was 63.1 ± 22.1% and 49.2% patients had a TTR < 65%. Multivariate Cox regression analysis showed that coronary artery disease [odds ratio (OR) 1.81, 95% confidence interval (CI) 1.14–2.87; P = 0.012] and amiodarone use (OR 1.54, 95% CI 1.01–2.34; P = 0.046) were independently associated with poor quality of anticoagulation (TTR <65%).

Conclusion

This study demonstrated that the quality of anticoagulation in AF patients newly starting VKAs is sub-optimal. Previous coronary artery disease and concomitant use of amiodarone were identified as independent variables affecting the poor quality of VKA therapy during the first year.
Within-Person Associations of Self-Reports of Memory Impairment and Depressive Symptoms in Older Adults: Moderation of Relationships Over Time by Personality
Authors: Mogle Jacqueline , Hill Nikki L , Bratlee-Whitaker Emily , Bhargava Sakshi
Published: May 2021

Objectives

The current study examined within-person associations of self-reports of impaired current memory functioning and perceived decline with depressive symptoms in older adults without cognitive impairment, and whether these associations were moderated by individuals’ levels of neuroticism, conscientiousness, and extraversion.

Methods

Samples were drawn from the Einstein Aging Study, Rush Memory and Aging Project (MAP), Minority Aging Research Study (MARS), Health and Retirement Study (HRS), and National Health and Aging Trends Study (NHATS), with over 8,000 participants (65+ years) included across data sets. In a series of coordinated analyses, multilevel linear models tested within-person relationships over periods of up to 22 years.

Results

Across HRS and NHATS samples, self-reports of impaired current memory functioning covaried with depressive symptoms over time. This association was moderated by neuroticism, such that the association was stronger for individuals with higher levels of neuroticism. Across all samples, perceived memory decline covaried with depressive symptoms over time. This association was moderated by neuroticism in MAP/MARS, HRS, and NHATS, such that the association was stronger for individuals with higher levels of neuroticism.

Discussion

Self-reports of impaired current memory functioning and perceived memory decline are important determinants of older adults’ psychological well-being. In our results, at times when older adults perceive poorer memory functioning or decline, they also tend to report more depressive symptoms. Further, results from two larger data sets suggest that individuals’ level of neuroticism may determine the extent to which self-reports of memory impairment and depressive symptoms covary over time.