bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracking and Measuring Local Protein Synthesis In Vivo
Authors: Kays Ibrahim , Chen Brian E. 
Published: June 2021

AbstractDetecting when and how much a protein molecule is synthesized is important for understanding cell function, but current methods have poor cellular or temporal resolution or are destructive to cells (Dahm et al., 2008). Here, we developed a technique to detect and quantify subcellular protein synthesis events in real time in vivo. This Protein Translation Reporting (PTR) technique uses a genetic tag that produces a stoichiometric ratio of a small peptide portion of a split fluorescent protein and the protein of interest during protein synthesis. We show that the split fluorescent protein peptide can generate fluorescence within milliseconds upon binding the larger portion of the fluorescent protein, and that the fluorescence intensity is directly proportional to the number of molecules of the protein of interest synthesized. Using PTR, we tracked and measured protein synthesis events in single cells over time in vivo. We use split red fluorescent protein to detect multiple genes or alleles in single cells simultaneously. We also split a photoswitchable fluorescent protein to photoconvert the reconstituted fluorescent protein to a different channel and arbitrarily reset the time of detection of synthesis events, continually over time.
TLR4 regulation in human fetal membranes as an explicative mechanism of a pathological preterm case
Authors: Belville Corinne , Ponelle-Chachuat Flora , Rouzaire Marion , Gross Christelle , Pereira Bruno , Gallot Denis , Sapin Vincent , Blanchon Loïc 
Published: June 2021

ABSTRACTThe integrity of human fetal membranes is crucial for harmonious fetal development throughout pregnancy. Their premature rupture is often the consequence of a physiological phenomenon previously exacerbated. Beyond all biological processes implied, inflammation is of primary importance and is qualified as “sterile” at the end of pregnancy. Complementary methylomic and transcriptomic strategies on amnion and choriodecidua explants taken from the altered (cervix zone) and intact fetal membranes at term and before labor were used in this study. By cross-analyzing genome-wide studies strengthened byin vitroexperiments, we deciphered how the expression of Toll-like receptor 4 (TLR4), a well-known actor of pathological fetal membrane rupture, is controlled. Indeed, it is differentially regulated in the altered zone and between both layers by a dual mechanism: 1) the methylation of TLR4 and miRNA promoters and 2) targeting by miRNA (let-7a-2 and miR-125b-1) acting on the 3’-UTR of TLR4. Consequently, this study demonstrates that a fine regulation of TLR4 is required for sterile inflammation establishment at the end of pregnancy and that it may be dysregulated in the pathological premature rupture of membranes.
DeepMP: a deep learning tool to detect DNA base modifications on Nanopore sequencing data
Authors: Bonet Jose , Chen Mandi , Dabad Marc , Heath Simon , Gonzalez-Perez Abel , Lopez-Bigas Nuria , Lagergren Jens 
Published: June 2021

AbstractMotivationDNA Methylation plays a key role in a variety of biological processes. Recently, Nanopore long-read sequencing has enabled direct detection of these modifications. As a consequence, a range of computational methods have been developed to exploit Nanopore data for methylation detection. However, current approaches rely on a human-defined threshold to detect the methylation status of a genomic position and are not optimized to detect sites methylated at low frequency. Furthermore, most methods employ either the Nanopore signals or the basecalling errors as the model input and do not take advantage of their combination.ResultsHere we present DeepMP, a convolutional neural network (CNN)-based model that takes information from Nanopore signals and basecalling errors to detect whether a given motif in a read is methylated or not. Besides, DeepMP introduces a threshold-free position modification calling model sensitive to sites methylated at low frequency across cells. We comprehensively benchmarked DeepMP against state-of-the-art methods on E. coli, human and pUC19 datasets. DeepMP outperforms current approaches at read-based and position-based methylation detection across sites methylated at different frequencies in the three datasets.AvailabilityDeepMP is implemented and freely available under MIT license at github.com/pepebonet/DeepMPContactjose.bonet@irbbarcelona.org — mandiche@kth.se
Chemical unfolding of protein domains induces shape change in programmed
protein hydrogels
Authors: Khoury Luai R. , Popa Ionel 
Published: June 2021

Abstract
Programmable behavior combined with tailored stiffness and tunable
biomechanical response are key requirements for developing successful materials.
However, these properties are still an elusive goal for protein-based
biomaterials. Here, we present a new method based on protein-polymer
interactions, to manipulate the stiffness of protein-based hydrogels made from
bovine serum albumin (BSA) by using polyelectrolytes such as poly(Ethelene)imine
(PEI) and poly-L-lysine (PLL) at various concentrations. This approach confers
protein-hydrogels tunable wide-range stiffness, from ~ 10 - 60 kPa when treated
with PEI, without affecting the protein mechanics and nanostructure. We ascribe
the increase in stiffness to the synergistic effect of the non-covalent
electrostatic polymer-protein interaction, as well as the polymer-shell that
stabilizes the protein domains nanomechanics. We use the 6-fold increase in
stiffness induced by PEI to program BSA-hydrogels in various shapes. By
utilizing the characteristic protein unfolding we can induce reversible
shape-memory behavior of these composite materials using chemical denaturing
solutions. We anticipate this novel approach based on protein engineering and
polymer reinforcing will enable the development and investigation of new smart
biomaterials and extend protein hydrogel capabilities beyond their conventional
applications.
A systematic literature review of lean manufacturing implementation in manufacturing-based sectors of the developing and developed countries
Authors: Maware Catherine , Okwu Modestus Okechukwu , Adetunji Olufemi 
Published: June 2021

Purpose
This study aims to comparatively discuss the effect of lean manufacturing (LM) implementation in the manufacturing sectors of developing and developed countries.

Design/methodology/approach
An in-depth literature review focused on previous research published between 2015 and March 2020. The papers published by the databases such as Google Scholar, Scopus, ProQuest and Web of Science were used in the study. A total of 63 studies that focused on LM application in manufacturing industries in developing and developed countries were used in the research.

Findings
It was observed that LM improves operational performance for manufacturing organizations in developing and developed countries. Small and medium-sized enterprises in both developed and developing countries have difficulties transforming their organizations into lean organizations compared to large enterprises. Furthermore, the review also found that there seems to have been no paper had reported the negative impact of implementing LM in manufacturing industries in developing and developed countries from 2015 to March 2020.

Research limitations/implications
The study used research papers written between January 2015 and March 2020 and only considered manufacturing organizations from developed and developing nations.

Practical implications
The study provides more insight into LM implementation in developing and developed countries. It gives the LM practices and the implications of applying these practices in manufacturing organizations for developing and developed countries.

Originality/value
A preliminary review of papers indicated that this seems to be the first paper that comparatively studies how LM implementation has affected manufacturing organizations in developed and developing countries. The study also assessed the LM practices commonly used by the manufacturing industries in developing and developed countries.
Industry 4.0: technology spillover impact on digital manufacturing industry
Authors: Miao Zeyi 
Published: June 2021

PurposeUnder the guidance of the concept of openness and development, the paper grasps the mechanism of technology spillover in developed countries and analyzes how to better absorb advanced manufacturing technology based on empirical analysis so as to point out the path for the transformation and development of China’s digital manufacturing industry.Design/methodology/approachThe paper constructs the panel data model and further analyzes the impact of international technology spillovers on the transformation and development of the digital manufacturing industry.FindingsThis paper measures the level of technology spillover in the Yangtze River Delta region and finds that foreign direct investment (FDI) technology spillover and import trade technology spillover among four provinces and cities show a growth trend from 2010 to 2017. But after 2017, there is a certain degree of decline.Originality/valueWith the advent of industry 4.0, the digital manufacturing industry of all countries in the world is developing with a new attitude, the global technology spillover methods are diverse and the spillover channels have changed greatly, which will affect the transformation and upgrading of China's digital manufacturing industry.
Modeling the enablers of sourcing risks faced by startups in COVID-19 era
Authors: Sreenivasan Aswathy , Suresh M. 
Published: June 2021

Purpose
Startups across all sectors are affected by the COVID-19 pandemic and are facing a formidable challenge in terms of marketing and operations. Most of the startups have experienced a downturn in demand and supply due to COVID-19 led disturbances in sourcing networks. This paper aims to identify, analyze and categorize the significant risks influencing sourcing operations in startups during the COVID-19 era in India, using the total interpretive structural modeling (TISM) approach.

Design/methodology/approach
Eight enablers were identified through literature review and expert opinions from various startups in India. This study adopted the TISM approach to analyze the inter-relationships between the enablers. Multiplication Applied to Classification (MICMAC) analysis was used to rank the sourcing risk enablers and classify them as autonomous, independent, linkage and dependent enablers.

Findings
The results indicate “insufficient fund” as the most critical enabler. Network issues and employee flexibility risk were among the other critical enablers that have a high driving power. Supplier risk, quality risk and demand risk were found to have highly dependent on other enablers for implementation.

Research limitations/implications
This study mainly focuses on the sourcing risks in startup operations in India. This study can be extended to many other countries.

Practical implications
This study will help startup industry managers and practitioners understand the interactions of enablers and identify critical enablers to mitigate risks in startup sourcing operations in the COVID-19 era.

Originality/value
The present study identifies the sourcing risk enablers in the COVID-19 era. It is the first attempt to analyze the interrelationship among sourcing risks in startups using the TISM approach.
A meta-analysis of the variables related to turnover intention among IT personnel
Authors: Özkan Ahmet Hakan 
Published: June 2021

PurposeThis study aims to investigate the relationships between job satisfaction, organizational commitment and turnover intention of information technology (IT) personnel.Design/methodology/approach3,844 studies which are published between 1998 and 2019 are screened on ScienceDirect, Scopus and ProQuest databases. 10,523 subjects formed the first data set regarding the relationship between job satisfaction and turnover intention, 7,903 subjects formed the second data set regarding the relationship between organizational commitment and turnover intention, 843 subjects formed the third data set regarding the relationship between empowerment and turnover intention, and 3,430 subjects formed the fourth data set regarding the relationship between job satisfaction and organizational commitment.FindingsResults showed that the effect size of the relationship between job satisfaction and organizational commitment is the strongest (r = 0.59). The effect size of the relationship between job satisfaction and turnover intention (r = −0.50), and the effect size of the relationship between organizational commitment and turnover intentionr = −0.51) were also large. But the effect size of the relationship between empowerment and turnover intention was medium (r = −0.34).Originality/valueThis study is rare, and it can be used by the managers working in the IT industry.
The confluence approach – a theoretical proposition for effective structuring of architecture studio pedagogy in e-learning mode
Authors: Khan Asif R. , Thilagam N. Lakshmi 
Published: June 2021

Purpose
The Covid-19 crisis has inflicted a disruptive impact on the conventional institutional format of architecture studio pedagogy. As a result, there is a critical suddenness for an alternative approach to ensure continuity. The research pursues is to pursue a multidisciplinary study with a focus on the following domains: architecture, the science of learning and e-learning architecture. Inference from the study would become the basis for a theoretical proposition for improvement of the existing pedagogical framework. Moreover, the literature would add valuable insights to the knowledge base.

Design/methodology/approach
An exploratory research approach is used for this study. The inquiry-based approach enlightens on the role of the architect in society. Also, the nature of architectural design education that existed prior to the Covid-19 outbreak is examined. Further, the paper explores the impact of the paradigm shift from institutional mode to e-learning mode overnight. Purposefully multi-disciplinary studies are pursued to develop a broad understanding of the associated domains. This could effectively contribute to developing an effective pedagogical framework. This would facilitate the conduct of architecture studio discourse in a structured manner during the current scenario.

Findings
The confluence approach – a theoretical proposition for effective structuring of architecture studio pedagogy has evolved as part of the research. Further, the proposed virtual learning pyramid enlightens on the drive to continue on with augmentation of students existing creative acumen. Which is one of the universally sought-after goals of studio pedagogy even during times of uncertainties.

Research limitations/implications
Pedagogues would find the study very meaningful for the conduct of architecture design studio in e-learning mode. They would also acquire a broad understanding of factors to be considered. The research would pave way for future studies in this area from a multi-disciplinary perspective.

Social implications
The current Covid-19 crisis deters architecture studio discourse from being conducted in an accustomed institutional format. Therefore, it becomes important for institutions to ensure continuity of architectural education with the help of new measures. In concurrence, the research envisions an alternative approach: virtual design studio using e-learning mode. This would ensure continuity of architectural education even when the instructor and students are separated in either time or place.

Originality/value
The study presents a unique contribution to the limited literature available on architecture studio pedagogy during the e-learning scenario.
Supply chain sustainability learning: the COVID-19 impact on emerging economy suppliers
Authors: Pereira Michele Morais Oliveira , Silva Minelle E. , Hendry Linda C. 
Published: June 2021

Purpose
This paper aims to investigate the impact of the COVID-19 pandemic on supply chain (SC) sustainability learning. In particular, it focuses on the learning associated with changes in the sustainability initiatives of emerging economy suppliers.

Design/methodology/approach
Through studying three scenarios (pre-outbreak, buyer-centred peak and supplier-centred peak) over a nine-month period, a multi-case study strategy was used to gain an understanding of the learning of export-oriented Brazilian coffee producers, using both exploitation and exploration capabilities. Content analysis was developed after each data collection phase to investigate how sustainability initiatives had changed.

Findings
Social sustainability was observed to be the main priority by suppliers facing this unprecedented outbreak, in ways that go beyond expected sustainability certification requirements. For instance, there was evidence of outstanding contributions to the local community. Suppliers initially developed their sustainability initiatives during the outbreak without any support from global buyers, certification bodies or government. In spite of this, stronger relationships with buyers ultimately emerged facilitating greater SC sustainability. Consequently, by using both exploitation and exploration learning capabilities, multiple levels of learning were observed (i.e. individual, organisational and SC) as related to planning, new procedures and social awareness.

Practical implications
A greater awareness of supplier learning processes will aid buyers in developing recovery plans that are appropriate for their global SC partners.

Originality/value
This paper provides an understanding of how emerging economy suppliers of global SCs are coping with this unprecedented outbreak in regard to sustainability management. Moving the spotlight from buyers to suppliers, the research demonstrates that supplier learning is central to global SC sustainability.
Brexit, Covid‐19, and Possible Frameworks for Future UK/EU Financial Governance Cooperation
Authors: Howell Elizabeth 
Published: June 2021

AbstractThe EU project is at an inflection point. Intra‐EU alliances are altering following the UK's departure, the EU's financial markets remain segmented, and there is limited appetite for completing the Banking Union. The second stage of Brexit negotiations also collided with the Covid‐19 pandemic, which has strained economies around the world. These issues amount to a ‘polycrisis’ for the EU, raising existential questions about its future. This article focuses on one strand of the debates generated within this polycrisis: future UK/EU policy cooperation with respect to financial governance. The article discusses the importance of the financial services sector to the UK and the EU, and examines potential institutional options for future cooperation. In particular, it advocates harnessing dexterous aspects evident within precedents, including existing EU/third country association agreements, to develop a functional arrangement for future financial governance cooperation, which could also lead to closer UK/EU cooperation than currently appears likely.
A hierarchy of expert performance as applied to forensic anthropology
Authors: Hartley Stephanie , Winburn Allysha Powanda 
Published: June 2021

AbstractDue to their medicolegal repercussions, forensic anthropology conclusions must be reliable, consistent, and minimally compromised by bias. Yet, a synthetic analysis of the reliability and biasability of the discipline's methods has not yet been conducted. To do so, this study utilized Dror's (2016) hierarchy of expert performance (HEP), an eight‐level model aimed at examining intra‐ and inter‐expert reliability and biasability (the potential for cognitive bias) within the literature of forensic science disciplines. A systematic review of the forensic anthropology literature was conducted (1972‐present), including papers published in the American Journal of Physical Anthropology, Forensic Anthropology, Forensic Science International, and the Journal of Forensic Sciences and Anthropology Section abstracts published in the Proceedings of the Annual Meeting of the AAFS which matched keywords such as “forensic anthropology,” “bias,” “reliability,” “cognition,” “cognitive,” or “error.” The resulting forensic anthropology HEP showcases areas that have ample research and areas where more research can be conducted. Specifically, statistically significant increases in reliability (p < 0.001) and biasability (p < 0.001) publications were found since 2009 (publication of the NAS report). Extensive research examined the reliability of forensic anthropological observations and conclusions (n = 744 publications). However, minimal research investigated the biasability of forensic anthropological observations and conclusions (n = 20 publications). Notably, while several studies demonstrated the biasing effect of extraneous information on anthropological morphological assessments, there was no research into these effects on anthropological metric assessments. The findings revealed by the forensic anthropology HEP can help to guide future research, ultimately informing the development and refinement of best‐practice standards for the discipline.
Magnetic Resonance Imaging evidence of Inflammation at Interphalangeal joint of Thumb — A distinct entity in psoriatic arthritis
Authors: Mathew Ashish J , Ganapati Arvind , Panwar Jyoti , Koshy Varghese , Desai Anu , Danda Debashish 
Published: June 2021

AbstractBackgroundThis study aimed to compare inflammation at the interphalangeal (IP) joint of thumb in patients with psoriatic arthritis (PsA), rheumatoid arthritis (RA), undifferentiated inflammatory arthritis (UIA), and in psoriasis patients without clinical arthritis (PsO) using low‐field magnetic resonance imaging (MRI).MethodsAge‐matched and disease duration‐matched patients with inflammatory arthritis (RA, PsA, and UIA) and psoriasis patients without clinical arthritis (PsO), who had undergone MRI of hands were included in this study. The presence or absence of MRI inflammatory lesions including synovitis, tenosynovitis, and bone marrow edema was assessed by three independent readers. Agreement between the readers was assessed using the intraclass correlation coefficient. Risk ratio of MRI global inflammation around thumb IP joints among patients with PsA was compared with the other groups.ResultsClinical parameters and MRI inflammation were studied in 161 patients (42 PsA, 28 RA, 29 UIA, and 62 PsO). Global MRI inflammation at the IP joint of the thumb was observed in 33.3% of PsA patients compared with 14.3% in RA, and 10.3% in UIA. Subclinical MRI inflammation was observed in 8.1% of patients with PsO. The risk ratios of MRI global inflammation at the IP joint of the thumb in PsA patients were 2.3 (95% confidence interval [CI] 0.86‐6.36) and 3.2 (95% CI 1.02‐10.21) compared with RA and UIA patients, respectively.ConclusionGlobal MRI inflammation around the IP joint of the thumb is significantly more common in patients with PsA as compared to individuals with UIA.