bluuebunny/crossref_metadata_2025_split huggingface dataset:
BinderSpace: A Package for Sequence Space Analyses for Datasets of Affinity-Selected Oligonucleotides and Peptide-Based Molecules
Authors: Kelich Payam , Zhao Huanhuan , Vuković Lela 
Published: February 2023

AbstractDiscovery of target-binding molecules, such as aptamers and peptides, is usually performed with the use of high-throughput experimental screening methods. These methods typically generate large datasets of sequences of target-binding molecules, which can be enriched with high affinity binders. However, the identification of the highest affinity binders from these large datasets often requires additional low-throughput experiments or other approaches. Bioinformatics-based analyses could be helpful to better understand these large datasets and identify the parts of the sequence space enriched with high affinity binders. BinderSpace is an open-source Python package that performs motif analysis, sequence space visualization, clustering analyses, and sequence extraction from clusters of interest. The motif analysis, resulting in text-based and visual output of motifs, can also provide heat maps of previously measured user-defined functional properties for all the motif-containing molecules. Users can also run principal component analysis (PCA) and t-distributed stochastic neighbor embedding (t-SNE) analyses on whole datasets and on motif-related subsets of the data. Functionally important sequences can also be highlighted in the resulting PCA and t-SNE maps. If points (sequences) in two-dimensional maps in PCA or t-SNE space form clusters, users can perform clustering analyses on their data, and extract sequences from clusters of interest. We demonstrate the use of BinderSpace on a dataset of oligonucleotides binding to single-wall carbon nanotubes in the presence and absence of a bioanalyte, and on a dataset of cyclic peptidomimetics binding to bovine carbonic anhydrase protein.Abstract Figure
Visualizing H2O2and NO in endothelial cells: strategies and pitfalls
Authors: Altun Hamza Yusuf , Secilmis Melike , Caglar Tuba Akgul , Vatandaslar Emre , Öztürk Gürkan , Vilain Sven , Eroglu Emrah 
Published: February 2023

AbstractThe relationship between hydrogen peroxide (H2O2) and nitric oxide (NO) in the vasculature is multifaceted and remains controversial because the dynamic detection of these reactive molecules is challenging. Genetically encoded biosensors (GEBs) allow visualizing real-time dynamics in living cells and permit multiparametric detection of several analytes. Although robust, GEBs’ utility depends on several parameters that need fine-tuning for proper imaging and correct data analysis: i.e., camera binning, temperature, and the resolution power of the imaging instruments are some critical parameters that require optimization. We have generated a new double-stable transgenic endothelial cell line stably expressing the biosensors HyPer7 and O-geNOp and systematically tested different imaging modes and their impact on the performance of each biosensor. Ambient temperature and the type of imaging mode did not influence the results, while camera resolution settings significantly affected readouts of HyPer probes but not O-geNOp. Changing a single parameter in a co-imaging mode significantly altered the biosensor’s dynamic measurements, potentially causing misinterpretation. This study provides a general guide and the pitfalls of employing GEBs in a multispectral imaging mode.
Transcriptional read through interrupts boundary function in Drosophila
Authors: Kyrchanova Olga , Sokolov Vladimir , Tikhonov Maxim , Schedl Paul , Georgiev Pavel 
Published: February 2023

AbstractIn higher eukaryotes enhancer-promoter interactions are known to be restricted by the chromatin insulators/boundaries that delimit topologically associated domains (TADs); however, there are instances in which enhancer-promoter interactions span one or more boundary elements/TADs. At present, the mechanisms that enable cross-TAD regulatory interaction are not known. In the studies reported here we have taken advantage of the well characterizedDrosophilaBithorax complex (BX-C) to study one potential mechanism for controlling boundary function and TAD organization. The regulatory domains of BX-C are flanked by boundaries which function to block crosstalk with their neighboring domains and also to support long distance interactions between the regulatory domains and their target gene. As many lncRNAs have been found in BX-C, we asked whether transcriptional readthrough can impact boundary function. For this purpose, we took advantage of two BX-C boundary replacement platforms,Fab-7attP50andF2attP, in which theFab-7andFubboundaries, respectively, are deleted and replaced with anattPsite. We introduced boundary elements, promoters and polyadenylation signals arranged in different combinations and then assayed for boundary function. Our results show that transcriptional readthrough can interfere with boundary activity. Since lncRNAs represent a significant fraction of Pol II transcripts in multicellular eukaryotes, it is possible that many of them may function in the regulation of TAD organization.Author SummaryRecent studies have shown that much genome in higher eukaryotes is transcribed into non-protein coding lncRNAs. It is though that lncRNAs may preform important regulatory functions, including the formation of protein complexes, organization of functional interactions between enhancers and promoters and the maintenance of open chromatin. Here we examined how transcription from promoters inserted into theDrosophilaBithorax complex can impact the boundaries that are responsible for establishing independent regulatory domains. Surprisingly, we found that even a relatively low level of transcriptional readthrough can impair boundary function. Transcription also affects the activity of enhancers located in BX-C regulatory domains. Taken together, our results raise the possibility that transcriptional readthrough may be a widely used mechanism to alter chromosome structure and regulate gene expression.
Attention network for predicting T cell receptor-peptide binding can associate attention with interpretable protein structural properties
Authors: Koyama Kyohei , Hashimoto Kosuke , Nagao Chioko , Mizuguchi Kenji 
Published: February 2023

Understanding how a T cell receptor (TCR) recognizes its specific ligand peptide is crucial for gaining insight into biological functions and disease mechanisms. Despite its importance, experimentally determining TCR-peptide interactions is expensive and time-consuming. To address this challenge, computational methods have been proposed, but they are typically evaluated by internal retrospective validation only, and few have incorporated and tested an attention layer from language models into structural information.Therefore, in this study, we developed a machine learning model based on a modified version of the Transformer, a source-target-attention neural network, to predict TCR-peptide binding solely from the amino acid sequences of the TCR’s complementarity-determining region (CDR) 3 and the peptide. This model achieved competitive performance on a benchmark dataset of TCR-peptide binding, as well as on a truly new external dataset. Additionally, by analyzing the results of binding predictions, we associated the neural network weights with protein structural properties. By classifying the residues into large and small attention groups, we identified statistically significant properties associated with the largely attended residues, such as hydrogen bonds within the CDR3. The dataset that we have created and our model’s ability to provide an interpretable prediction of TCR-peptide binding should increase our knowledge of molecular recognition and pave the way to designing new therapeutics.
Identification of a new substrate for the ribosome associated endoribonuclease Rae1 reveals a link to theB. subtilisresponse and sensitivity to chloramphenicol
Authors: Deves Valentin , Trinquier Aude , Gilet Laetitia , Alharake Jawad , Leroy Magali , Condon Ciarán , Braun Frédérique 
Published: February 2023

ABSTRACTRae1 is a well-conserved endoribonuclease among Gram-positive bacteria, cyanobacteria and the chloroplasts of higher plants. We have previously shown that Rae1 cleaves theBacillus subtilis yrzIoperon mRNA in a translation-dependent manner, within a short open reading frame (ORF) called S1025, encoding a 17-amino acid (aa) peptide of unknown function. Here, we map a new Rae1 cleavage site in thebmrBCDoperon mRNA encoding a multidrug transporter, within a previously unannotated 26-aa short ORF that we have namedbmrX. Similar to S1025, Rae1 cleavage withinbmrXis both translation- and reading frame-dependent. Both mRNAs were previously shown to be induced by the presence of the protein synthesis inhibitor chloramphenicol (Cm). Strikingly, arae1deletion strain shows greater resistance to Cm than the wild-type strain, while its over-expression leads to increased Cm sensitivity, suggesting a link to translation quality control. Consistent with this, we show that cleavage by Rae1 promotes ribosome rescue by the tmRNA. Globally, our data point to a role of Rae1 in mRNA surveillance by eliminating mRNAs that encounter problems with translation.
Toxoplasma gondiiaspartic protease 5 (TgASP5): Understanding structural details and inhibition mechanism
Authors: Chakraborty Satadru , Deshmukh Anuradha , Kesari Pooja , Bhaumik Prasenjit 
Published: February 2023

AbstractToxoplasma gondii, a worldwide prevalent parasite, is responsible for causing toxoplasmosis by infecting almost all warm-blooded animals, including humans. To establish a successful infection, the parasite exports a series of effector proteins which modulates the host immune system; Golgi-residentT. gondiiaspartyl protease 5 (TgASP5) plays an essential role in the maturation and export of these effector proteins. This is the first report of the detailed structural investigation of theTgASP5 mature enzyme. Molecular modeling and all-atom simulation provided in-depth knowledge of the active site architecture ofTgASP5. The analysis of the binding mode of TEXEL substrate highlighted the importance of the active site residues forming the pocket; the Ser505, Ala776 and Tyr689 in the S2 binding pocket provide the specificity towards Arg at the P2 position. Our study also provides insights into the binding mode of the known inhibitor RRLStatine.Screening the known aspartic protease inhibitors againstTgASP5 active site and performing 100 ns all-atom molecular dynamic simulations, MM-PBSA binding energy calculations provided the best nine inhibitor protein complexes. Besides that, Principal Component Analysis (PCA) was employed to identify the change in protein dynamics with respect to the substrate and ligand binding.TgASP5 is essential for the fitness and virulence of the parasite; inhibiting this enzyme can be a possible therapeutic strategy against toxoplasmosis. Our study put forth the inhibitors which can act as initial scaffolds for developing potent mechanistic inhibitors againstTgASP5.
The effects of dihedral angle on hover rigidity and planar maneuvers in rotary-wing UAVs
Authors: Kayatas Erol , Celik Murat 
Published: February 2023

Purpose
Any consensus about the effects of dihedral angle on hover rigidity of rotary-wing unmanned aerial vehicles (RW-UAVs) does not exist in the literature. There are researchers who state that the dihedral angle has an effect on flight stability and researchers who claim the opposite. The discord stems from the different approaches of these groups to the concept of “stability,” the fact that they conduct experiments whose measurements are largely influenced by environmental conditions, and the physical assumptions are not similar. On the other hand, there is no study examining the effect of dihedral angle on the maneuverability of drones either. This study aims to analytically reveal the consequences of dihedral angles in RW-UAVs in terms of flight agility and maneuverability.

Design/methodology/approach
Dihedral angle examinations on both hover rigidity and maneuverability are carried out analytically. Equations of motions for a multicopter’s rigid body with a dihedral angle under two different conditions (zero and nonzero dihedral angles) are derived. Numerical simulations are conducted by defining the simulation parameters, and then displacement graphics for the center of mass are interpreted.

Findings
The presence of a dihedral angle makes the multicopter platforms behave like a pendulum, and this pendulum motion affects the disturbance rejection and the planar maneuver capabilities of multicopters. Since deflections can be spread to the orthonormal axes thanks to rotation about a pivot, net deflections of the geometric center may be diminished. Besides, pendulum motion eases the maneuvers with yaw rotations since the required rotation might occur without rotors’ revolution per minute changes.

Practical implications
Proposed dihedral angle implementation may enhance the hover stiffness and maneuverability capabilities of multicopters which, in turn, raise the performance of the drones.

Originality/value
This paper presents the analytical basis for the dihedral angle's effects on flight stability and agility.
Impact of COVID-19 on education in India: stakeholders' voice
Authors: Kalia Prateek , Behal Bhavana , Kaur Kulvinder , Mehta Deepa 
Published: February 2023

PurposeThis exploratory study aims to discover the different forms of challenges encountered by school stakeholders, including students, teachers, parents and management due to the coronavirus disease 2019 (COVID-19) pandemic.Design/methodology/approachQualitative methodology was deployed for the study. A purposive sampling technique was used to select the respondents for a semi-structured interview. Data were examined using interpretative phenomenological analysis (IPA).FindingsIt was found that each stakeholder faced four different challenges: mental distress, physical immobility, financial crunches and technological concerns. Findings suggest that teachers are experiencing higher financial, technological and physical challenges as compared to other stakeholders followed by parents.Originality/valueThis paper discusses the major challenges faced by each stakeholder along with the opportunities. These findings will be useful for educationists, regulatory authorities, policymakers and management of educational institutions in developing countries to revisit their policy frameworks to develop new strategies and processes for the smooth implementation of remote learning during a period of uncertainty.
The effects of power imbalance on supply chain sustainability adoption: evidence from the artisanal fishing industry
Authors: Rivera-Valle Sylvia , Silva Minelle E. 
Published: February 2023

PurposeGrounded on resource dependence theory, the authors explored how power and dependence affect sustainability adoption in an artisanal fishing supply chain (AFSC) in Mexico.Design/methodology/approachAn in-depth longitudinal case study was conducted to identify relationships among fishers, a cooperative and intermediaries using a content analysis of data gathered from a combination of interviews, focus groups, observations, participatory workshops and secondary data.FindingsAs a result of the existing power imbalance among AFSC members, mediated forces (e.g. rewards for intermediary–fishers relationship) were the most prominent observed. In addition, a close and high dependence on resources affecting supply chain sustainability (SCS) adoption was identified. For example, within intermediary–cooperative relationships, a power imbalance caused mostly by financial resource dependence generated a negative impact on economic sustainability related to unfair prices and unfair trade. The results, thus, showed the detrimental influence of intermediaries among AFSC members on SCS adoption.Practical implicationsA greater understanding of power imbalance and dependence can help AFSC members to identify their weaknesses and develop actions to adopt sustainability.Originality/valueUnlike previous research, the authors go beyond the often positive research focus of SCS studies and provide, through the resource dependence theory, a longitudinal view on how power imbalance negatively affects SCS adoption.
The influence of membership fluidity on the coevolution of the social and knowledge systems in online knowledge communities
Authors: Qiu Jiangnan , Gu Wenjing , Ma Zhongming , You Yue , Cai Chengjie , Zhang Meihui 
Published: February 2023

PurposeIn the extant research on online knowledge communities (OKCs), little attention has been paid to the influence of membership fluidity on the coevolution of the social and knowledge systems. This article aims to fill this gap.Design/methodology/approachBased on the attraction-selection-attrition (ASA) framework, this paper constructs a simulation model to study the coevolution of these two systems under different levels of membership fluidity.FindingsBy analyzing the evolution of these systems with the vector autoregression (VAR) method, we find that social and knowledge systems become more orderly as the coevolution progresses. Furthermore, in communities with low membership fluidity, the microlevel of the social system (i.e. users) drives the coevolution, whereas in communities with high membership fluidity, the microlevel of the knowledge system (i.e. users' views) drives the coevolution.Originality/valueThis paper extends the application of the ASA framework and enriches the literature on membership fluidity of online communities and the literature on driving factors for coevolution of the social and knowledge systems in OKCs. On a practical level, our work suggests that community administrators should adopt different strategies for different membership fluidity to efficiently promote the coevolution of the social and knowledge systems in OKCs.
“We adapted because we had to”: how domestic violence perpetrator programmes adapted to work under COVID-19 in the UK, the USA and Australia
Authors: Bellini Rosanna , Westmarland Nicole 
Published: February 2023

Purpose
This study explores responses by domestic violence perpetrator programme (DVPP) providers of three Western countries (UK, USA and Australia) to the COVID-19 pandemic and population movement control measures on their practice. The purpose of this paper was to offer an evidence base for changes to programme and intervention delivery around domestic violence to sustain integrity of safe, effective working practices with perpetrators, survivors and staff.

Design/methodology/approach
Based on 36 semi-structured qualitative interviews conducted from July to September 2020, the authors mapped the experiences of changes in service with frontline staff, managers and sector-wide representatives.

Findings
The findings focus on how providers of DVPPs adapted to the increase in referrals and workload that had a positive impact on service delivery innovation but an adverse impact on staff wellbeing. Digital services were reported to be adopted into mainstream approaches but introduced new barriers to service access and group dynamics. Integrated safety support for survivors, if not adequately connected to programmes pre-pandemic, risked being disconnected from DVPP that may undermine positive programme outcomes.

Originality/value
The paper provides a documentation of changes in DVPPs, and a cross-comparison of services across three Western countries during the first wave of COVID-19. The work offers implications of the development of digital modes of service delivery for DVPPs and highlights the need for focus on resource management and integration of safety services for survivors in DVPP services.
Can salespeople use social media to enhance brand awareness and sales performance? The role of manager empowerment and creativity
Authors: Kalra Ashish , Itani Omar S. , Rostami Amin 
Published: February 2023

Purpose
Although research analyzing the consequences of salesperson social media use in driving sales behaviors and performance outcomes has proliferated in the recent past, there are significant research gaps in the domain. Grounded in task-technology fit theory, this paper aims to propose a conceptual framework that integrates between previously disjointed areas of research and analyzes the relationships between salesperson social media use, brand awareness, creativity, manager empowerment and company performance.

Design/methodology/approach
Survey responses were collected from a multi-industry sample of 158 business-to-business salespeople. Structural relationships were tested using partial least squares structural equation modeling.

Findings
The analysis shows that salesperson social media use positively affects brand awareness. The relationship between social media and brand awareness is magnified with the increase in salesperson creativity. Findings also show that manager empowerment increases salesperson creativity. Finally, brand awareness positively affects company performance.

Practical implications
Sales organizations should focus on developing digital strategies, especially focusing on salesperson social media use to enhance company’s brand awareness, which in turn increases company performance. Moreover, sales managers should also follow empowering leader behaviors to enhance creativity.

Originality/value
The authors amalgamate salesperson social media use literature and branding literature by proposing salesperson social media use’s positive effects on brand awareness. This study also expands the knowledge by exploring the moderating effect of individual-level variables such as salesperson creativity on driving the effects of salesperson social media use.
Thinking of how you think of me: working cancer survivors' metaperceptions of competence and why they matter
Authors: Zheng Dianhan , Marbut Alexander R. , Zhang Jing , Britt Avery , Nwadike David 
Published: February 2023

PurposeCancer-related stigma is a troubling challenge faced by working cancer survivors and organizations aiming to promote inclusive work environments. Research suggests that a harmful stereotype faced by cancer survivors is that the cancer survivors are low in competence. Leveraging the concept of the looking glass self and social cognitive theory, the authors develop a theoretical model about psychological processes through which cancer survivors' competence metaperceptions are related to work outcomes.Design/methodology/approachThe authors recruited 200 working cancer survivors from online research panels and empirically test a theoretical model on how cancer survivors' metaperceptions of competence are related to the survivors' turnover intention and vigor at work. The authors additionally conducted an experimental vignette study among a sample of 133 students to examine confounds concerning causal order.FindingsThe authors found that favorable competence metaperceptions were related to decreased turnover intentions and increased vigor through cancer survivors' enhanced self-efficacy, especially for survivors high in need for emotional support.Practical implicationsThis study suggests that inclusive organizations should pay attention to employees with cancer histories as a hidden disadvantaged group. To protect and motivate working cancer survivors, managers need to create a positive socio-cognitive working environment where cancer survivors are respected and valued.Originality/valueBy examining cancer survivors' metaperceptions and showing that survivors may internalize others' stereotype about individuals with a history of cancer, the authors advance the understanding about cancer survivors' return-to-work challenges.