bluuebunny/crossref_metadata_2025 huggingface dataset:
No Light Perception Vision in Neuro-Ophthalmology Practice
Authors: Garg Anubhav , Margolin Edward , Micieli Jonathan A.
Published: August 2021

Background:

To determine differential diagnosis and visual outcomes of patients with no light perception (NLP) vision related to neuro-ophthalmic conditions.

Methods:

Retrospective case series of patients seen at tertiary neuro-ophthalmology practices. Patients were included if they had NLP vision any time during their clinical course. Outcome measures were final diagnosis, treatment, and visual outcome.

Results:

Seventy-two eyes of 65 patients were included. The average age was 57.6 (range 18–93) years, and 58% were women. The Most common diagnosis (21 patients) was compressive optic neuropathy (CON) with meningioma being the most common culprit (12). Other diagnoses included optic neuritis (ON) (11 patients), infiltrative optic neuropathies (8), posterior ischemic optic neuropathy (7), nonarteritic anterior ischemic optic neuropathy (4), arteritic anterior ischemic optic neuropathy (3), ophthalmic artery occlusion (3), nonorganic vision loss (3), radiation-induced optic neuropathy (2), cortical vision loss (1), retinitis pigmentosa with optic disc drusen (1), and infectious optic neuropathy (1). Ten patients recovered vision: 7 ON, 2 infiltrative optic neuropathy, and 1 CON. Corticosteroids accelerated vision recovery in 7 of the 11 patients with ON to mean 20/60 (0.48 logMAR) over 9.0 ± 8.6 follow-up months. Eleven patients deteriorated to NLP after presenting with at least LP; their diagnoses included CON (3), ophthalmic artery occlusion (2), infiltration (2), ON (1), posterior ischemic optic neuropathy (1), arteritic anterior ischemic optic neuropathy (1), and radiation-induced optic neuropathy (1).

Conclusions:

NLP vision may occur because of various diagnoses. Vision recovery was mainly seen in patients with ON. Serious systemic conditions may present or relapse with NLP vision, which clinicians should consider as an alarming sign in patients with known malignancies.
Advanced materials design based on waste wood and bark
Authors: Wenig Charlett , Dunlop John W. C. , Hehemeyer-Cürten Johanna , Reppe Friedrich J. , Horbelt Nils , Krauthausen Karin , Fratzl Peter , Eder Michaela
Published: August 2021

Trees belong to the largest living organisms on Earth and plants in general are one of our main renewable resources. Wood as a material has been used since the beginning of humankind. Today, forestry still provides raw materials for a variety of applications, for example in the building industry, in paper manufacturing and for various wood products. However, many parts of the tree, such as reaction wood, branches and bark are often discarded as forestry residues and waste wood, used as additives in composite materials or burned for energy production. More advanced uses of bark include the extraction of chemical substances for glues, food additives or healthcare, as well as the transformation to advanced carbon materials. Here, we argue that a proper understanding of the internal fibrous structure and the resulting mechanical behaviour of these forest residues allows for the design of materials with greatly varying properties and applications. We show that simple and cheap treatments can give tree bark a leather-like appearance that can be used for the construction of shelters and even the fabrication of woven textiles.

This article is part of the theme issue ‘Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)’.
Life cycle assessment (LCA): informing the development of a sustainable circular bioeconomy?
Authors: Sevigné-Itoiz Eva , Mwabonje Onesmus , Panoutsou Calliope , Woods Jeremy
Published: August 2021

The role of life cycle assessment (LCA) in informing the development of a sustainable and circular bioeconomy is discussed. We analyse the critical challenges remaining in using LCA and propose improvements needed to resolve future development challenges. Biobased systems are often complex combinations of technologies and practices that are geographically dispersed over long distances and with heterogeneous and uncertain sets of indicators and impacts. Recent studies have provided methodological suggestions on how LCA can be improved for evaluating the sustainability of biobased systems with a new focus on emerging systems, helping to identify environmental and social opportunities prior to large R&D investments. However, accessing economies of scale and improved conversion efficiencies while maintaining compatibility across broad ranges of sustainability indicators and public acceptability remain key challenges for the bioeconomy. LCA can inform, but not by itself resolve this complex dimension of sustainability. Future policy interventions that aim to promote the bioeconomy and support strategic value chains will benefit from the systematic use of LCA. However, the LCA community needs to develop the mechanisms and tools needed to generate agreement and coordinate the standards and incentives that will underpin a successful biobased transition. Systematic stakeholder engagement and the use of multidisciplinary analysis in combination with LCA are essential components of emergent LCA methods.

This article is part of the theme issue ‘Bio-derived and bioinspired sustainable advanced materials for emerging technologies (part 1)’.
Comparative genomics of Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) reveals lineage-specific host adaptation of ST432
Authors: Uelze Laura , Borowiak Maria , Deneke Carlus , Fischer Jennie , Flieger Antje , Simon Sandra , Szabó István , Tausch Simon H. , Malorny Burkhard
Published: August 2021

Unlike most

Salmonella enterica

subsp.

diarizonae

, which are predominantly associated with cold-blooded animals such as reptiles, the serovar IIIb 61:k:1,5,(7) (termed SASd) is regarded as host-adapted to sheep. The bacterium is rarely associated with disease in humans but, nevertheless, SASd isolates are sporadically obtained from human clinical samples. It is unclear whether these transmissions are directly linked to sheep or whether transmissions may, for example, occur through other domestic animals also carrying SASd. For this reason, we utilized whole-genome sequencing to investigate a set of 119 diverse SASd isolates, including sheep-associated and human-associated isolates, as well as isolates obtained from other matrices. We discovered that serovar IIIb 61:k:1,5,(7) is composed of two distinct lineages defined by their sequence types ST432 and ST439. These two lineages are distinguished by a number of genetic features, as well as their prevalence and reservoir. ST432 appears to be the more prevalent sequence type, with the majority of isolates investigated in this study belonging to ST432. In contrast, only a small number of isolates were attributed to ST439. While ST432 isolates were of sheep, human or other origin, all ST439 isolates with source information available, were obtained from human clinical samples. Regarding their genetic features, lineage ST432 shows increased pseudogenization, harbours a virB/D4 plasmid that encodes a type IV secretion system (T4SS) and does not possess the iro gene cluster, which encodes a salmochelin siderophore for iron acquisition. These characteristics likely contribute to the ability of ST432 to persistently colonize the intestines of sheep. Furthermore, we found isolates of the lineage ST432 to be highly clonal, with little variation over the sampling period of almost 20 years. We conclude from the genomic comparisons that SASd underlies a microevolutionary process and that it is specifically lineage ST432 that should be considered as host-adapted to sheep.
Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants
Authors: Du Shuo , Liu Pulan , Zhang Zhiying , Xiao Tianhe , Yasimayi Ayijiang , Huang Weijin , Wang Youchun , Cao Yunlong , Xie Xiaoliang Sunney , Xiao Junyu
Published: August 2021

The spread of the SARS-CoV-2 variants could seriously dampen the global effort to tackle the COVID-19 pandemic. Recently, we investigated the humoral antibody responses of SARS-CoV-2 convalescent patients and vaccinees towards circulating variants, and identified a panel of monoclonal antibodies (mAbs) that could efficiently neutralize the B.1.351 (Beta) variant. Here we investigate how these mAbs target the B.1.351 spike protein using cryo-electron microscopy. In particular, we show that two superpotent mAbs, BD-812 and BD-836, have non-overlapping epitopes on the receptor-binding domain (RBD) of spike. Both block the interaction between RBD and the ACE2 receptor; and importantly, both remain fully efficacious towards the B.1.617.1 (Kappa) and B.1.617.2 (Delta) variants. The BD-812/BD-836 pair could thus serve as an ideal antibody cocktail against the SARS-CoV-2 VOCs.
Spike protein multiorgan tropism suppressed by antibodies targeting SARS-CoV-2
Authors: Brady Molly , Combs Abigail , Venkatraman Chethana , Solorzano Alexander , Johnson Angelique , McQuaid Conor , Rahman Akib , Leyva Hannah , Edmund Kwok Wing-Chi , Wood Ronald W , Deane Rashid
Published: August 2021

While there is clinical evidence of severe acute respiratory syndrome coronavirus 2 multiorgan tropism in severely infected coronavirus 19 patients, it’s unclear if there is differential multiorgan biodistribution and organ uptake in healthy young individuals, a group that usually has asymptomatic to moderate coronavirus 19 symptoms. In addition, for antibody therapies and vaccines that target the spike protein, it’s unclear if these reduce severe acute respiratory syndrome coronavirus 2 or spike protein multiorgan tropism equally. We used fluorescently labeled spike protein near infrared fluorescence to study viral behavior, using an in vivo dynamic imaging system, in young mice. We found a spike protein body-wide biodistribution followed by a slow regional elimination, except for the liver, which showed an accumulation. Spike protein uptake was highest for the lungs, and this was followed by kidney, heart and liver, but, unlike the choroid plexus, it was not detected in the brain parenchyma or cerebrospinal fluid. Thus, the brain vascular barriers were effective in restricting the entry of spike protein into brain parenchyma in young healthy mice. While both anti-angiotensin converting enzyme 2 and anti-spike protein antibodies suppressed spike protein biodistribution and organ uptake, anti-spike protein antibody was more effective. By extension, our data support the efficacy of these antibodies on severe acute respiratory syndrome coronavirus 2 biodistribution kinetics and multiorgan tropism that could determine coronavirus 19 organ-specific outcomes.
The Effect of Incarceration on Tuberculosis Treatment Outcomes in Brazil: a Retrospective Cohort Study
Authors: O’Marr Jamieson , Gonçalves Crhistinne , Arakaki-Sanchez Denise , Pelissari Daniele Maria , Costa Fernanda Dockhorn , Croda Julio , Walter Katharine S. , Andrews Jason R.
Published: August 2021

Background

Tuberculosis notifications in Latin American prisons have more than doubled over the past two decades; however, treatment outcomes and their determinants among incarcerated individuals in this region are not well understood.

Methods

Newly diagnosed drug-susceptible tuberculosis cases reported to Brazil’s Sistema de Informação de Agravos de Notificação (SINAN) between January 2015 and December 2017 were included. Multivariate logistic regression was used to assess socioeconomic and clinical factors associated with treatment success among incarcerated individuals.

Results

Incarcerated individuals (n=17,776) had greater treatment success than non-incarcerated individuals (n=160,728; 82.2% vs 75.1%, p<0.0001), including after adjusting for demographic and clinical risk factors (adjusted Odds Ratio [aOR]: 1.27; 95% CI: 1.19-1.34). These differences were partially mediated by increased use of directly observed therapy among incarcerated individuals (DOT) (61% vs 47%, p<0.001), which was associated with greater efficacy in the incarcerated population (aOR 2.56 vs aOR 2.17; p<0.001). DOT was associated with improved treatment success among incarcerated subpopulations at elevated risk of poor outcomes.

Conclusion

Tuberculosis treatment success among incarcerated individuals in Brazil is higher than non-incarcerated individuals, but both fall below WHO targets. Expanding the use of DOT and services for socially and medically vulnerable individuals may improve outcomes in carceral settings.
STAT3 expression in dendritic cells protects mice from colitis by a gut microbiome-dependent mechanism
Authors: Liu Jianyun , Szilágyi Keely L. , Capitano Maegan L. , Iyer Abhirami K. , He Jiefeng , Olson Matthew R. , Du Jianguang , Van Der Pol William , Morrow Casey , Zhou Baohua , Kaplan Mark H. , Dent Alexander L. , Brutkiewicz Randy R.
Published: August 2021

An imbalance in gut homeostasis results in local and systemic pathogenesis. It is still not well-understood how the immune system interacts with the gut microbiome and maintains a delicate balance. Here, we utilized a mouse model in which STAT3 expression is deleted in CD11c+ (i.e., dendritic) cells (STAT3 cKO); these mice developed an ulcerative colitis-like disease, colon carcinoma and myelodysplastic syndrome-like disease. Circulating IgE levels in STAT3 cKO mice were significantly elevated. The gut microbiome was indispensable for the observed pathogenesis, as treatment with broad-spectrum antibiotics or cross-fostering STAT3 cKO pups with mothers harboring a different microbiome prevented disease development. Gut microbiome analyses suggested that decreased commensal bacteria and increased pathogenic bacteria most likely contributed to disease. Our data suggest that STAT3 controls the manifestation of inflammation in the gut caused by the microbiome. Therefore, we conclude that a deficiency of STAT3 in DCs is sufficient to trigger uncontrolled inflammation and the development of inflammatory bowel disease.
Human centromere formation activates transcription and opens chromatin fibre structure
Authors: Naughton Catherine , Huidobro Covadonga , Catacchio Claudia R. , Buckle Adam , Grimes Graeme R. , Nozawa Ryu-Suke , Purgato Stefania , Rocchi Mariano , Gilbert Nick
Published: August 2021

Human centromeres appear as constrictions on mitotic chromosomes and form a platform for kinetochore assembly in mitosis. Biophysical experiments led to a suggestion that repetitive DNA at centromeric regions form a compact scaffold necessary for function, but this was revised when neocentromeres were discovered on non-repetitive DNA. To test whether centromeres have a special chromatin structure we have analysed the architecture of a neocentromere. Centromere formation is accompanied by RNA pol II recruitment and active transcription to form a decompacted, negatively supercoiled domain enriched in ‘open’ chromatin fibres. In contrast, centromerisation causes a spreading of repressive epigenetic marks to surrounding regions, delimited by H3K27me3 polycomb boundaries and divergent genes. This flanking domain is transcriptionally silent and partially remodelled to form ‘compact’ chromatin, similar to satellite-containing DNA sequences, and exhibits genomic instability. We suggest transcription disrupts chromatin to provide a foundation for kine-tochore formation whilst compact pericentromeric heterochromatin generates mechanical rigidity.
Rational Design of Self-assembling Artificial Proteins Utilizing a Micelle-Assisted Protein Labeling Technology (MAPLabTech): Testing the Scope
Authors: Reddy Mullapudi Mohan , Bhandari Pavankumar , Sandanaraj Britto S
Published: August 2021

Self-assembling artificial proteins (SAPs) have gained enormous interest in recent years due to their applications in different fields. Synthesis of well-defined monodisperse SAPs is accomplished predominantly through genetic methods. However, the last decade witnessed the use of few chemical technologies for that purpose. In particular, micelle-assisted protein labeling technology (MAPLabTech) has made huge progress in this area. The first generation MAPLabTech focused on site-specific labeling of the active-site residue of serine proteases to make SAPs. Further, this methodology was exploited for labeling of N-terminal residue of a globular protein to make functional SAPs. In this study, we describe the synthesis of novel SAPs by developing a chemical method for site-specific labeling of a surface-exposed cysteine residue of globular proteins. In addition, we disclose the synthesis of redox- and pH-sensitive SAPs and their systematic self-assembly and dis-assembly studies using complementary biophysical studies. Altogether these studies further expand the scope of MAPLabTech in different fields such as vaccine design, targeted drug delivery, diagnostic imaging, biomaterials, and tissue engineering.
Individual-level specialisation and interspecific resource partitioning in bees revealed by pollen DNA metabarcoding
Authors: Klečka Jan , Mikát Michael , Koloušková Pavla , Hadrava Jiří , Straka Jakub
Published: August 2021

It is increasingly recognised that intraspecific variation in traits, such as morphology, behaviour, or diet is both ubiquitous and ecologically important. While many species of predators and herbivores are known to display high levels of between-individual diet variation, there is a lack of studies on pollinators. It is important to fill in this gap because individual-level specialisation of flower-visiting insects is expected to affect their efficiency as pollinators with consequences for plant reproduction. Accordingly, the aim of our study was to quantify the level of individual-level specialisation and foraging preferences, as well as interspecific resource partitioning, across different temporal scales in three co-occurring species of bees of the genusCeratina(Hymenoptera: Apidae: Xylocopinae),C.chalybea,C.nigrolabiata, andC.cucurbitina. We conducted a field experiment where we provided artificial nesting opportunities for the bees and combined a short-term mark-recapture study with the dissection of the bees’ nests to obtain repeated samples from individual foraging females and complete pollen provisions from their nests. Hence, we could study variation of the composition of pollen collected by the bees at different temporal scales. We used DNA metabarcoding based on the ITS2 locus to identify the composition of the pollen samples. We found that the composition of pollen carried on the bodies of female bees and stored in the brood provisions in their nests significantly differed among the three co-occurring species. At the intraspecific level, individual females consistently differed in their level of specialisation and in the composition of pollen carried on their bodies and stored in their nests. Our study thus provides evidence of consistent individual-level specialisation in pollinators across multiple temporal scales. We also demonstrate that higher generalisation at the species level stemmed from larger among-individual variation in diets as observed in other types of consumers, such as predators. Our study thus reveals how specialisation and foraging preferences of bees change from the scale of individual foraging bouts to complete pollen provisions accumulated in their nests over their lifetime. Such multi-scale view of foraging behaviour is necessary to improve our understanding of the functioning of plant-flower visitor communities.
Downregulation of Neurodevelopmental Gene Expression in iPSC-Derived Cerebral Organoids Upon Infection by Human Cytomegalovirus
Authors: O’Brien Benjamin S. , Mokry Rebekah L. , Schumacher Megan L. , Pulakanti Kirthi , Rao Sridhar , Terhune Scott S. , Ebert Allison D.
Published: August 2021

Human cytomegalovirus (HCMV) is a beta herpesvirus that, upon congenital infection, can cause severe birth defects including vision and hearing loss, microcephaly, and seizures. Currently, no approved treatment options exist for in utero infections. We previously demonstrated that HCMV infection decreases calcium signaling responses and alters neuronal differentiation in induced pluripotent stem cell (iPSC) derived neural progenitor cells (NPCs). Here we aimed to determine the impact of infection on the transcriptome in developing human neurons using iPSC-derived 3-dimensional cerebral organoids. We infected iPSC-derived cerebral organoids with HCMV encoding eGFP and sorted cell populations based on GFP signal strength. Significant transcriptional downregulation was observed including in key neurodevelopmental gene pathways in both the GFP (+) and intermediate groups. Interestingly, the GFP (-) group also showed downregulation of the same targets indicating a mismatch between GFP expression and viral infection. Using a modified HCMV virus destabilizing IE 1 and 2 proteins, we still observed significant downregulation of neurodevelopmental gene expression in infected neural progenitor cells. Together, these data indicate that IE viral proteins are not the main drivers of neurodevelopmental gene dysregulation in HCMV infected neural tissues suggesting therapeutically targeting IE gene expression is insufficient to restore neural differentiation and function.
Classification and clustering of RNA crosslink-ligation data reveal complex structures and homodimers
Authors: Zhang Minjie , Fischer-Hwang Irena T. , Li Kongpan , Bai Jianhui , Chen Jian-Fu , Weissman Tsachy , Zou James Y. , Lu Zhipeng
Published: August 2021

The recent development and application of methods based on the general principle of “crosslinking and proximity ligation” (crosslink-ligation) are revolutionizing RNA structure studies in living cells. However, extracting structure information from such data presents unique challenges. Here we introduce a set of computational tools for the systematic analysis of data from a wide variety of cross-link-ligation methods, specifically focusing on read mapping, alignment classification and clustering. We design a new strategy to map short reads with irregular gaps at high sensitivity and specificity. Analysis of previously published data reveals distinct properties and bias caused by the crosslinking reactions. We perform rigorous and exhaustive classification of alignments and discover 8 types of arrangements that provide distinct information on RNA structures and interactions. To deconvolve the dense and inter-twined gapped alignments, we develop a network/graph-based tool CRSSANT (Crosslinked RNA Secondary Structure Analysis using Network Techniques), which enables clustering of gapped alignments and discovery of new alternative and dynamic conformations. We discover that multiple crosslinking and ligation events can occur on the same RNA, generating multi-segment alignments to report complex high level RNA structures and multi-RNA interactions. We find that alignments with overlapped segments are produced from potential homodimers and develop a new method for their de novo identification. Analysis of overlapping alignments revealed potential new homodimers in cellular noncoding RNAs and RNA virus genomes in the Picornaviridae family. Together, this suite of computational tools enables rapid and efficient analysis of RNA structure and interaction data in living cells.
Multi-run Concrete Autoencoder to Identify Prognostic lncRNAs for 12 Cancers
Authors: Mamun Abdullah Al , Tanvir Raihanul Bari , Sobhan Masrur , Mathee Kalai , Narasimhan Giri , Holt Gregory E , Mondal Ananda Mohan
Published: August 2021

Long non-coding RNA plays a vital role in changing the expression profiles of various target genes that leads to cancer development. Thus, identifying prognostic lncRNAs related to different cancers might help in developing cancer therapy. To discover the critical lncRNAs that can identify the origin of different cancers, we proposed to use the state-of-the-art deep learning algorithm Concrete Autoencoder (CAE) in an unsupervised setting, which efficiently identifies a subset of the most informative features. However, CAE does not identify reproducible features in different runs due to its stochastic nature. We proposed a multi-run CAE (mrCAE) to identify a stable set of features to address this issue. The assumption is that a feature appearing in multiple runs carries more meaningful information about the data under consideration. The genome-wide lncRNA expression profiles of 12 different types of cancers, a total of 4,768 samples available in The Cancer Genome Atlas (TCGA), were analyzed to discover the key lncRNAs. The lncRNAs identified by multiple runs of CAE were added to the final list of key lncRNAs, which are capable of identifying 12 different cancers. Our results showed that mrCAE performs better in feature selection than single-run CAE, standard autoencoder (AE), and other state-of-the-art feature selection techniques. This study discovered a set of top-ranking 128 lncRNAs that could identify the origin of 12 different cancers with an accuracy of 95%. Survival analysis showed that 76 of 128 lncRNAs have the prognostic capability in differentiating high- and low-risk groups of patients in different cancers. The proposed mrCAE outperformed AE, which select latent features and were thought to be the best tools for dimensionality reduction. By selecting actual features instead of pseudo-features, mrCAE can be valuable for precision medicine. The identified prognostic lncRNAs (this work), mRNAs, miRNAs, and DNA methylated genes (future work) can lead to biomarkers and therapies for different cancers.
Claudin-5 binder enhances focused ultrasound-mediated opening in anin vitroblood-brain barrier model
Authors: Chen Liyu , Sutharsan Ratneswary , Lee Jonathan LF , Cruz Esteban , Asnicar Blaise , Palliyaguru Tishila , Leinenga Gerhard , Götz Jürgen
Published: August 2021

Rationale

The blood-brain barrier (BBB) while functioning as a gatekeeper of the brain, impedes cerebral drug delivery. An emerging technology to overcome this limitation is focused ultrasound (FUS). When FUS interacts with intravenously injected microbubbles (FUS+MB), the BBB opens, transiently allowing the access of therapeutic agents into the brain. However, the ultrasound parameters need to be tightly tuned: when the acoustic pressure is too low there is no opening, and when it is too high, bleeds can occur. We therefore asked whether BBB permeability can be increased by combining FUS+MBwith a second modality such that in a clinical setting lower acoustic pressures could be potentially used.

Methods

Given that FUS achieves BBB opening by the disruption of tight junction (TJ) proteins such as claudin-5 of brain endothelial cells, we generated a stable MDCK II cell line (eGFP-hCldn5-MDCK II) that expresses fluorescently tagged human claudin-5. Two claudin-5 binders, mC5C2 (a peptide) and cCPEm (a truncated form of an enterotoxin), that have been reported previously to weaken the barrier, were synthesized and assessed for their abilities to enhance the permeability of cellular monolayers. We then performed a comparative analysis of single and combination treatments.

Results

We successfully generated a novel cell line that formed functional monolayers as validated by an increased transendothelial electrical resistance (TEER) reading and a low (< 0.2%) permeability to sodium fluorescein (376 Da). We found that the binders exerted a time- and concentration-dependent effect on BBB opening when incubated over an extended period, whereas FUS+MBcaused a rapid barrier opening followed by recovery after 12 hours within the tested pressure range. Importantly, preincubation with cCPEm prior to FUS+MBtreatment resulted in greater barrier opening compared to either FUS+MBor cCPEm alone as measured by reduced TEER values and an increased permeability to fluorescently labelled 40 kDa dextran (FD40).

Conclusion

The data suggest that pre-incubation with clinically suitable binders to TJ proteins may be a general strategy to facilitate safer and more effective ultrasound-mediated BBB opening in cellular and animal systems and potentially also for the treatment of human diseases of the brain.
Scalable clustering with supervised linkage methods
Authors: Anibal James , Day Alexandre G. , Bahadiroglu Erol , O’Neill Liam , Phan Long , Peltekian Alec , Erez Amir , Kaplan Mariana , Altan-Bonnet Grégoire , Mehta Pankaj
Published: August 2021

Data clustering plays a significant role in biomedical sciences, particularly in single-cell data analysis. Researchers use clustering algorithms to group individual cells into populations that can be evaluated across different levels of disease progression, drug response, and other clinical statuses. In many cases, multiple sets of clusters must be generated to assess varying levels of cluster specificity. For example, there are many subtypes of leukocytes (e.g. T cells), whose individual preponderance and phenotype must be assessed for statistical/functional significance. In this report, we introduce a novel hierarchical density clustering algorithm (HAL-x) that uses supervised linkage methods to build a cluster hierarchy on raw single-cell data. With this new approach, HAL-x can quickly predict multiple sets of labels for immense datasets, achieving a considerable improvement in computational efficiency on large datasets compared to existing methods. We also show that cell clusters generated by HAL-x yield near-perfect F1-scores when classifying different clinical statuses based on single-cell profiles. Our hierarchical density clustering algorithm achieves high accuracy in single cell classification in a scalable, tunable and rapid manner. We make HAL-x publicly available at: https://pypi.org/project/hal-x/
Preparing mFc- and hFc-Fusion Proteins from Mammalian Cells
Authors: Greenfield Edward A. , DeCaprio James , Brahmandam Mohan
Published: August 2021

Fc-fusion proteins are composed of an immunoglobulin Fc domain that is directly linked to the antigen of interest. Typically, these vectors will contain an amino-terminal signal sequence that permits trafficking to the cell surface and secretion into the media and a carboxy-terminal Fc receptor that enables purification on Protein A–Sepharose. Fc-fusion proteins have several applications in protein microarrays, oncological therapies, and vaccine and antibody development. Presence of the Fc domain significantly increases the plasma life of the fusion partner, which prolongs therapeutic activity. Furthermore, the Fc domain enhances the solubility and stability of the partner molecule. Because Fc-fusion proteins are secreted into the culture medium, purification by affinity chromatography is relatively easy and cost-effective. Immunizing a murine host with mFc-fusion protein generates an antigen-specific immune response because the Fc domain is recognized as “self” by the host.
Purification of Labeled Oligonucleotides by Chromatography on a Sep-Pak C18 Column
Authors: Green Michael R. , Sambrook Joseph
Published: August 2021

This protocol describes a method for the separation of radiolabeled oligonucleotides from unincorporated radiolabel that takes advantage of the reversible affinity of oligonucleotides for silica gel. This protocol can be used only to purify oligonucleotides carrying a 5′-phosphate group, radiolabeled or unlabeled.
Worldwide research tendencies on probiotics in food science: 1993 to 2021
Authors: Bulut Albayrak Çisem , Duran Mustafa
Published: August 2021

Purpose

This study aimed to identify the main and emerging structural patterns in the growth of the literature on probiotic research in food science, analyze current trends and determine gaps and present future projections.

Design/methodology/approach

A total of 1,301 scientific documents retrieved from Scopus database dated from 1993 to 2021 were analyzed by using bibliometric and scientometric tools.

Findings

The most influencer journals, leading countries and hotspots were identified by scientometric mapping. “Lactic acid bacteria”, “lactobacillus”, “lactobacillus plantarum”, “viability”, “functional foods” and “microencapsulation” were the top keywords that indicate main emerging areas. After a clear understanding of the current situation, future directions can be better projected. Therefore, investigating new probiotic microorganisms with advanced health promoting properties, adapting the new organisms to various food formulations, identifying the probiotic potential of unexplored traditional fermented foods and developing of nondairy probiotic foods can be the studies of the future.

Research limitations/implications

Probiotic concept has been revised during years and valuable knowledge has been accumulated over past decades. The findings demonstrate the development and trends of probiotic related food science researches. This is the first study to address the limitations of prior systematic literature reviews by applying network analysis and guide future works to fill the identified gaps.

Originality/value

The probiotic concept has been revised for years and valuable knowledge has been accumulated. Within the expanding literature, scientometric and bibliometric analysis will provide valuable contribution for identifying the main patterns, analyzing current trends, determining gaps and presenting future projection. This work presents detailed analysis to determine tendencies in probiotic research in food science.
Electronically tunable mixed mode universal filter employing grounded capacitors utilizing highly versatile VD-DVCC
Authors: Faseehuddin Mohammad , Herencsar Norbert , Albrni Musa Ali , Shireen Sadia , Sampe Jahariah
Published: August 2021

Purpose

This paper aims to achieve two main objectives. First, to introduce to the literature a new versatile active building block, namely, voltage differencing differential voltage current conveyor (VD-DVCC) for analog signal processing applications. Second, to design a novel electronically tunable mixed-mode universal filter. The designed filter provides low-pass, high-pass, band-pass, band-reject and all-pass responses in voltage-mode (VM), current-mode (CM), trans-impedance-mode (TIM) and trans-admittance-mode (TAM).

Design/methodology/approach

The proposed filter uses two VD-DVCCs, three resistors and two capacitors. All the capacitors used are grounded, which is advantageous from the monolithic integration point of view. The VD-DVCC is designed and validated in Cadence software using CMOS 0.18 µm process design kit from Silterra Malaysia at a supply voltage of ±1 V.

Findings

The proposed novel filter enjoys many attractive features including as follows: the ability to operate in all four modes, no requirement of capacitive matching, tunability of quality factor (Q) independent of pole frequency, availability of both inverting and non-inverting outputs for VM and TIM mode, high output impedance explicit current output for CM and TAM, no requirement for double/negative input signals (voltage/current) for response realization and low active and passive sensitivities. The filter is designed for a pole frequency of 5.305 MHz. The obtained results bear a close resemblance with the theoretical findings.

Originality/value

The proposed novel filter structure requires a minimum number of active and passive components and provides operation in all four operating modes. The filter will find application in structures of mixed-mode systems.
Local 5G services on campus premises: scenarios for a make 5G or buy 5G decision
Authors: Kulkarni Venkatesh , Walia Jaspreet , Hämmäinen Heikki , Yrjölä Seppo , Matinmikko-Blue Marja , Jurva Risto
Published: August 2021

Purpose

The purpose of this paper is to build possible future scenarios for indoor connectivity in a venue such as a university campus and build alternative value network configurations (VNCs) defining different local network deployment options, focused on the Finnish telecom market.

Design/methodology/approach

In this paper, Schoemaker’s scenario planning method (Schoemaker, 1995) is used to construct future scenarios and the VNC method of Casey et al. (2010) is used to build alternative VNCs. The paper studies the Aalto University campus network for current end-user data usage demand and the existing technology used in meeting the end-user needs and forecasts the demand for the next five years to understand the need for 5G.

Findings

This research concludes that with the provision of local spectrum licenses, there is an opportunity for venue owners to take the role of 5G local operator on the venue premises. Furthermore, it enables venue owners to collaborate with the incumbent mobile network operators (MNOs) in a neutral host model and provide venue-specific connectivity services.

Research limitations/implications

A detailed economic assessment for the network deployment in the campus is considered for future study.

Originality/value

Considering the provision for local spectrum licenses, this paper has taken a unique attempt in identifying the future scenarios for local 5G network operations. It provides a strategic direction for the venue owners in adopting 5G technology and whether to make 5G or buy 5G from MNOs.
An implicit-explicit local method for parabolic partial differential equations
Authors: Tunc Huseyin , Sari Murat
Published: August 2021

Purpose

The purpose of this article is to derive an implicit-explicit local differential transform method (IELDTM) in dealing with the spatial approximation of the stiff advection-diffusion-reaction (ADR) equations.

Design/methodology/approach

A direction-free numerical approach based on local Taylor series representations is designed for the ADR equations. The differential equations are directly used for determining the local Taylor coefficients and the required degrees of freedom is minimized. The complete system of algebraic equations is constructed with explicit/implicit continuity relations with respect to direction parameter. Time integration of the ADR equations is continuously utilized with the Chebyshev spectral collocation method.

Findings

The IELDTM is proven to be a robust, high order, stability preserved and versatile numerical technique for spatial discretization of the stiff partial differential equations (PDEs). It is here theoretically and numerically shown that the order refinement (p-refinement) procedure of the IELDTM does not affect the degrees of freedom, and thus the IELDTM is an optimum numerical method. A priori error analysis of the proposed algorithm is done, and the order conditions are determined with respect to the direction parameter.

Originality/value

The IELDTM overcomes the known disadvantages of the differential transform-based methods by providing reliable convergence properties. The IELDTM is not only improving the existing Taylor series-based formulations but also provides several advantages over the finite element method (FEM) and finite difference method (FDM). The IELDTM offers better accuracy, even when using far less degrees of freedom, than the FEM and FDM. It is proven that the IELDTM produces solutions for the advection-dominated cases with the optimum degrees of freedom without producing an undesirable oscillation.
Three decades of interventions for the unemployed – review of practices between 1990 and 2020 and their effects on (re) employment competencies
Authors: Celume Macarena-Paz , Korda Helene
Published: August 2021

Purpose

This paper provides evidence of the outcomes proposed by the reviewed programmes and their level of effectiveness.

Design/methodology/approach

Articles were screened by title and abstract to ensure correspondence with exclusion/inclusion criteria. Themes were analysed through collective coding and scoring. Size effects were calculated.

Findings

Three expected outcomes: psychological, technical and (re) employment. The most frequent and significant results are found in psychological. The review could not find consistent results in effectiveness of the type of training, because of the diversity of propositions and socio-cultural origins of interventions.

Research limitations/implications

Socio-cultural context acts as variable; thus, deep interdisciplinary analysis on context where trainings were developed is suggested in order to understand the impact of trainings according to their population defining effectiveness.

Originality/value

There is no previous review of type of interventions for the unemployed focusing on last 30 years.
A bibliometric review on the development in e-tourism research
Authors: Singh Shalini , Bashar Abu
Published: August 2021

Purpose

E-tourism is instilling in the tourism industry with the advancement in the technological infrastructure all over the world and fetching tremendous tourists’ attention. The dynamic changes in the technological aspects unveil varied developments in the tourism industry. This paper attempts to reveal the developments in the field of e-tourism by a systematic review of the literature using bibliometric analysis.

Design/methodology/approach

In total,146 research articles were retrieved from the Web of Science data during the period of 2004 – 2020, for further analysis using VOSviewer and Biblioshiny package of R Studio.

Findings

Useful insights resulted in the form of most cited papers, contribution in e-tourism research by different authors, countries, institutions, journals and so on, co-occurrence analysis and cluster analysis for major trends or themes of e-tourism. This study solicits an elaborated review of e-tourism research and unveils the future directions for the researchers.

Originality/value

This study adds substantial value to the research of e-tourism by analysing the bibliometric data of the last 16 years, that is, from 2004 – 2020, procured from the Scopus by analysing the significant trends developed in the e-tourism research. It also adds value by indicating the emerging areas of e-tourism.
Enablers of knowledge management: practical research-based in the construction industry
Authors: Boamah Fredrick Ahenkora , Zhang Jianhua , Wen Dandan , Sherani Mrs , Hayat Adil , Horbanenko Oleksandra
Published: August 2021

Purpose

To effectively implement knowledge management, one prerequisite is to understand and implement the knowledge management enablers in the sense of optimal institutional efficiency. This paper aims to analyze and measure the significant enablers in overseeing knowledge management in the construction sector.

Design/methodology/approach

The mixed-method technique was used to achieve the objective of this study and involved the application of detailed questions to project engineers and project managers within leading construction engineering companies, provided by the Institution of Engineering and Technology Ghana. In total, 150 questionnaires were collected and analyzed using the Statistical Package for Social Sciences v. 26.

Findings

The study confirms that the knowledge management enablers such as employees knowledge, motivations, effective decisions and strategic planning are some of the important ways in which construction professionals can achieve different strategic goals in many processes and concluded that the progress of the next generation knowledge management strategy will be based on content sharing, decision-making and by promoting the free flow of ideas.

Originality/value

The study offers perspectives into knowledge management enablers and recommends key performance factors, championed by Ghanaian construction contractors for institutional knowledge capture.
Insights gained from early modelling of COVID-19 to inform the management of outbreaks in UK prisons
Authors: Bays Declan , Williams Hannah , Pellis Lorenzo , Curran-Sebastian Jacob , O'Mara Oscar , Team PHE Joint Modelling , Finnie Thomas
Published: August 2021

Purpose

In this work, the authors present some of the key results found during early efforts to model the COVID-19 outbreak inside a UK prison. In particular, this study describes outputs from an idealised disease model that simulates the dynamics of a COVID-19 outbreak in a prison setting when varying levels of social interventions are in place, and a Monte Carlo-based model that assesses the reduction in risk of case importation, resulting from a process that requires incoming prisoners to undergo a period of self-isolation prior to admission into the general prison population.

Design/methodology/approach

Prisons, typically containing large populations confined in a small space with high degrees of mixing, have long been known to be especially susceptible to disease outbreaks. In an attempt to meet rising pressures from the emerging COVID-19 situation in early 2020, modellers for Public Health England’s Joint Modelling Cell were asked to produce some rapid response work that sought to inform the approaches that Her Majesty’s Prison and Probation Service (HMPPS) might take to reduce the risk of case importation and sustained transmission in prison environments.

Findings

Key results show that deploying social interventions has the potential to considerably reduce the total number of infections, while such actions could also reduce the probability that an initial infection will propagate into a prison-wide outbreak. For example, modelling showed that a 50% reduction in the risk of transmission (compared to an unmitigated outbreak) could deliver a 98% decrease in total number of cases, while this reduction could also result in 86.8% of outbreaks subsiding before more than five persons have become infected. Furthermore, this study also found that requiring new arrivals to self-isolate for 10 and 14 days prior to admission could detect up to 98% and 99% of incoming infections, respectively.

Research limitations/implications

In this paper we have presented models which allow for the studying of COVID-19 in a prison scenario, while also allowing for the assessment of proposed social interventions. By publishing these works, the authors hope these methods might aid in the management of prisoners across additional scenarios and even during subsequent disease outbreaks. Such methods as described may also be readily applied use in other closed community settings.

Originality/value

These works went towards informing HMPPS on the impacts that the described strategies might have during COVID-19 outbreaks inside UK prisons. The works described herein are readily amendable to the study of a range of addition outbreak scenarios. There is also room for these methods to be further developed and built upon which the timeliness of the original project did not permit.
Comprehensive evaluation of Iranian regional innovation system (RIS) performance using analytic hierarchy process (AHP)
Authors: Sadabadi Ali Asghar , Rahimi Rad Zohreh , Fartash Kiarash
Published: August 2021

Purpose

This study aims to to provide a model based on the context and conditions of the regions in Iran for monitoring regional innovation systems (RISs).

Design/methodology/approach

In the first stage, after reviewing the literature, interviewing the experts, and then thematic analyzing the content of the obtained data, initial Dimensions and indicators were identified. Then, a fuzzy Delphi technique and a seven-scale questionnaire were used to test the results and expert opinion. Finally, after the extraction and correction of the indicators to evaluate the RISs, a comprehensive model was identified in 5 dimensions, 16 indicators and 176 sub-indicators. In the next step, the importance weights of the main 16 indicators were determined using the analytic hierarchy process method.

Findings

The proposed RIS assessment model consists of firms’ behavior and regional interactions, economy, human capital, innovative outputs, locational features, that each dimension has its own indicators and sub-indicators, each one is discussed in the paper.

Originality/value

The research contribution is that the proposed RIS model of this research is the first model that is appropriate to the context of Iran.