bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of size on middle-ear sound transmission in elephants, the largest terrestrial mammal
Authors: O’Connell-Rodwell Caitlin E. , Berezin Jodie L. , Dharmarajan Anbuselvan , Ravicz Michael E. , Hu Yihan , Guan Xiying , O’Connor Kevin N. , Puria Sunil 
Published: September 2023

AbstractElephants have a unique auditory system that is larger than any other terrestrial mammal. To quantify the impact of larger middle ear (ME) structures, we measured 3D ossicular motion and ME sound transmission in cadaveric temporal bones from both African and Asian elephants in response to air-conducted (AC) tonal pressure stimuli presented in the ear canal (PEC). Results were compared to similar measurements in humans. Velocities of the umbo (VU) and stapes (VST) were measured using a 3D laser Doppler vibrometer in the 7–13,000 Hz frequency range, stapes velocity serving as a measure of energy entering the cochlea—a proxy for hearing sensitivity. Below the elephant ME resonance frequency of about 300 Hz, the magnitude of VU/PECwas an order of magnitude greater than in human, and the magnitude of VST/PECwas 5x greater. Phase of VST/PECabove ME resonance indicated that the group delay in elephant was approximately double that of human, which may be related to the unexpectedly high magnitudes at high frequencies. A boost in sound transmission across the incus long process and stapes near 9 kHz was also observed. We discuss factors that contribute to differences in sound transmission between these two large mammals.
ProteinFlow: a Python Library to Pre-Process Protein Structure Data for Deep Learning Applications
Authors: Kozlova Elizaveta , Valentin Arthur , Khadhraoui Aous , Nakhaee-Zadeh Gutierrez Daniel 
Published: September 2023

ABSTRACTOver the past few years, deep learning tools for protein design have made significant advances in the field of bioengineering, opening up new opportunities for drug discovery, disease prevention or industrial biotechnology. However, despite the growing interest and excitement surrounding these tools, progress in the field is hindered by a lack of standardized datasets for benchmarking. Most models are trained on data from the Protein Data Bank (PDB), the largest repository of experimentally determined biological macromolecular structures. But filtering and processing this data involves many hyperparameter choices that are often not harmonized across the research community. Moreover, the task of splitting protein data into training and validation subsets with minimal data leakage is not trivial and often overlooked. Here we present ProteinFlow, a computational pipeline to pre-process protein sequence and structural data for deep learning applications. The pipeline is fully configurable and allows the extraction of all levels of protein organization (primary to quaternary), allowing end-users to cater the dataset for a multitude of downstream tasks, such as protein sequence design, protein folding modeling or protein-protein interaction prediction. In addition, we curate a feature-rich benchmarking dataset based on the latest annual release of the PDB and a selection of preprocessing parameters that are widely used across the research community. We showcase its utility by benchmarking a state-of-the-art (SOTA) deep learning model for protein sequence design. The open source code is packaged as a python library and can be accessed onhttps://github.com/adaptyvbio/ProteinFlow.
Calorimetric analysis using DNA thermal stability to determine protein concentration
Authors: Eskew Matthew W. , Reardon Patrick W. , Benight Albert S. 
Published: September 2023

ABSTRACTIt was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities,Cp,DNAandCp,PROfor equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm’s. For the molecules, in NaCl and CsCl buffer the evaluatedCp,PROandCp,DNAwere equivalent. Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. In all cases, evaluated protein concentrations determined from the DNA standard curve agreed with the UV-Vis concentration for monomeric proteins. For samples of multimeric proteins, streptavidin (tetramer), Herpes Simplex Virus glycoprotein D (trimer/dimer), and a 16 base pair DNA duplex (dimer), evaluated concentrations were greater than determined by UV-Vis by factors of 3.94, 2.65, and 2.15, respectively.
A rotational velocity estimate constructed through visuomotor competition updates the fly’s neural compass
Authors: Hulse Brad K. , Stanoev Angel , Turner-Evans Daniel B. , Seelig Johannes D. , Jayaraman Vivek 
Published: September 2023

AbstractNavigating animals continuously integrate velocity signals to update internal representations of their directional heading and spatial location in the environment. How neural circuits combine sensory and motor information to construct these velocity estimates and how these self-motion signals, in turn, update internal representations that support navigational computations are not well understood. Recent work inDrosophilahas identified a neural circuit that performs angular path integration to compute the fly’s head direction, but the nature of the velocity signal is unknown. Here we identify a pair of neurons necessary for angular path integration that encode the fly’s rotational velocity with high accuracy using both visual optic flow and motor information. This estimate of rotational velocity does not rely on a moment-to-moment integration of sensory and motor information. Rather, when visual and motor signals are congruent, these neurons prioritize motor information over visual information, and when the two signals are in conflict, reciprocal inhibition selects either the motor or visual signal. Together, our results suggest that flies update their head direction representation by constructing an estimate of rotational velocity that relies primarily on motor information and only incorporates optic flow signals in specific sensorimotor contexts, such as when the motor signal is absent.
Design of an effective sgRNA for CRISPR/Cas9 knock-ins in polyploidSynechocystis sp. PCC 6803
Authors: Nares-Rodriguez María Isabel , Karunakaran Esther 
Published: September 2023

AbstractSynechocystis sp. PCC 6803 (Synechocystis) is a highly promising organism for the production of diverse recombinant chemicals, including biofuels. However, conventional genetic engineering inSynechocystisis challenging due to its highly polyploid genome which not only leads to low product yields but also makes the recombinant organism less reliable for use in biomanufacturing. Due to its precision, effectiveness and reliability in a vast array of chassis, CRISPR/Cas9 has the potential of overcoming the drawbacks effected by a polyploid genome. Here we identified and developed an effective sgRNA for the knock-in of nucleotide sequences of varying lengths in the neutral siteslr0168 of polyploidSynechocystisusing CRISPR/Cas9. The gene encoding digeranylgeranylglycerophospholipid reductase fromSulfolobus acidocaldariusand the methyl ketone operon fromSolanum habrochaiteswere chosen as the exemplar nucleotide sequences for incorporation into the chromosome ofSynechocystis. It is demonstrated here that our sgRNA design was effective for both knock-ins and that CRISPR/Cas9 achieves complete mutant segregation after a single step of selection and induction.
Modifications to gene body methylation does not alter gene expression plasticity in a reef-building coral
Authors: Abbott Evelyn , Loockerman Coral , Matz Mikhail 
Published: September 2023

AbstractAs coral reefs continue to decline due to climate change, the role of coral epigenetics (specifically, gene body methylation, GBM) in coral acclimatization warrants investigation. The evidence is currently conflicting. In diverse animal phyla the baseline GBM level is associated with gene function: continuously expressed “housekeeping” genes are typically highly methylated, while inducible context-dependent genes have low or no methylation at all. Some authors report association between GBM and the environment, and interpret this observation as evidence of GBM’s role in acclimatization. Yet, others argue that correlation between GBM change and gene expression change is typically absent or negligible. Here, we used the reef- building coral,Acropora millepora,to test whether environmentally driven changes in GBM are associated with a gene’s ability to respond to environmental changes (plasticity) rather than expression level. We analyzed two cases of modified gene expression plasticity observed in a three-week-long heat acclimatization experiment. The first one was a group of heat-induced genes that failed to revert their expression after the coral was translocated back to the control tank. The second case involved genes that changed the magnitude of their response to the daily temperature fluctuations over the course of the experiment. In both cases we found negligible or no association with GBM change. We conclude that although both gene expression plasticity and GBM can change during acclimatization, there is no direct association between the two. This adds to the increasing volume of evidence that the function of GBM in invertebrates is unrelated to acclimatization on physiological timescales.
Enhancers associated with unstable RNAs are rare in plants
Authors: Mcdonald Bayley R. , Picard Colette , Brabb Ian M. , Savenkova Marina I. , Schmitz Robert J. , Jacobsen Steven E. , Duttke Sascha H. 
Published: September 2023

AbstractUnstable transcripts have emerged as markers of active enhancers in vertebrates and shown to be involved in many cellular processes and medical disorders. However, their prevalence and role in plants is largely unexplored. Here, we comprehensively captured all actively initiating (“nascent”) transcripts across diverse crops and other plants using capped small (cs)RNA-seq. We discovered that unstable transcripts are rare, unlike in vertebrates, and often originate from promoters. Additionally, many “distal” elements in plants initiate tissue-specific stable transcripts and are likelybone fidepromoters of yet-unannotated genes or non-coding RNAs, cautioning against using genome annotations to infer “enhancers” or transcript stability. To investigate enhancer function, we integrated STARR-seq data. We found that annotated promoters, and other regions that initiate stable transcripts rather than unstable transcripts, function as stronger enhancers in plants. Our findings underscore the blurred line between promoters and enhancers and suggest that cis-regulatory elements encompass diverse structures and mechanisms in eukaryotes.
Matrix selection for the visualization of small molecules and lipids in brain tumors using untargeted MALDI-TOF mass spectrometry imaging
Authors: Lu Tianyao , Freytag Lutz , Narayana Vinod K. , Moore Zachery , Oliver Shannon J. , Valkovic Adam , Nijagal Brunda , Peterson Amanda , de Souza David P. , McConville Malcolm J. , Whittle James R. , Best Sarah A. , Freytag Saskia 
Published: September 2023

AbstractMatrix-assisted laser desorption/ionization mass spectrometry imaging allows the study of metabolic activity in the tumor microenvironment of brain cancers. The detectable metabolites within these tumors are contingent upon the choice of matrix, deposition technique, and polarity setting. In this study, we compared the performance of three different matrices, two deposition techniques, and use of positive and negative polarity in two different brain cancer types and across two species. Optimal combinations were confirmed by comparative analysis of lipid and small molecule abundance using liquid chromatography–mass spectrometry and RNA-sequencing assessing differential metabolites between normal and tumor regions. Our findings indicate that the recrystallized α cyano-4-hydroxycinnamic acid matrix in positive polarity offered superior performance for both detected metabolites and consistency with other techniques. Beyond these implications for brain cancer, our work establishes a workflow to identify optimal matrices for spatial metabolomics studies.
Mobile applications to reduce food waste in supply chains: a systematic literature review
Authors: Hong Jiequan , Jaegler Anicia , Gergaud Olivier 
Published: September 2023

PurposeWith the launch of mobile applications to reduce food waste, this study reviews scholarly articles to answer the questions: (1) What research topics are extensively discussed in relation to food waste mobile applications (FWMA)? (2) How do these applications impact food waste and food poverty? (3) At which stage of the supply chain are digital applications employed?Design/methodology/approachThis paper conducts a systematic literature review of scholarly articles on the topic of mobile applications and food waste to answer three research questions.FindingsThe article provides a definition of mobile applications to reduce food waste. Most published studies on mobile applications are from developed countries. Over half of the applications address procurement and consumption along the supply chain. The applications are categorized by food saving method and used in studies on innovation management, platform relations and performance, the supply chain activities impacted and platform acceptance.Research limitations/implicationsThe articles and applications analyzed suggest more quantitative studies. A wider range of cases in diverse cultural settings is needed, as well as analyses of the factors influencing the development, performance and market acceptance of platforms.Originality/valueThis study is the first study to systematically review the relevant scholarly contributions related to mobile applications, an innovative practice that helps reduce food waste. It allows making an initial progress report on the research carried out.
Leader's desire for promotion, workplace anxiety and exploitative leadership: the moderating effect of Machiavellianism
Authors: Huang Jie , Li Yali , Tang Chunyong 
Published: September 2023

PurposeDrawing on the conservation of resources theory, the present research paper examines the moderating role of leaders' Machiavellianism in the relationships between the desire for promotion, workplace anxiety and exploitative leadership.Design/methodology/approachThe authors collected matched time-lagged data from part-time MBA students and their subordinates. The subordinate questionnaires were paired and coded by the researchers and then directly distributed and instructed to be filled out, which would not be known to the MBA students. The final sample size came to 370 leader-subordinate dyads. The data were analyzed using SPSS 24 and Mplus 7.0.FindingsLeaders' desire for promotion is positively related to exploitative leadership via workplace anxiety. Furthermore, this mediating effect is significant when Machiavellianism is high, but not when Machiavellianism is low.Originality/valueFor business ethics scholars and practitioners, this study points out that leaders with a desire for promotion can produce workplace anxiety, lead to subordinates' perception of exploitative leadership and how this process varies by key personality trait—Machiavellianism.
Drinking to cope and college grade point average
Authors: Douglass Morgan A. , Colley Madison L. , Tyskiewicz Alexander J. , Prince Mark A. 
Published: September 2023

Purpose
College students report high levels of stress, with academic performance serving as a major contributor. The purpose of this study was to examine how drinking to cope with stressors related to student grade point average (i.e., GPA), while testing academic achievement orientations (i.e. mastery or performance) as possible moderators for this relationship.

Design/methodology/approach
In total, 325 undergraduate college students from a university in the Mountain West of the USA reported on GPA, daily drinking, coping and academic achievement orientations.

Findings
Drinking to cope negatively predicted GPA. Holding a mastery academic achievement orientation was related to higher GPA, whereas a performance academic achievement orientation was related to a more deleterious relationship between drinking to cope and GPA. However, neither orientation (i.e. mastery or performance) moderated the relationship between drinking to cope and GPA.

Originality/value
Regardless of academic achievement orientation, drinking to cope was negatively associated with GPA. The negative relationship between drinking to cope and GPA for those with a performance orientation may suggest that these students drink to cope with academic stressors. Importantly, students who choose to drink alcohol to cope with academic stress may paradoxically experience poorer academic performance. Future research should examine whether teaching a mastery orientation to college students can protect against the deleterious effects of drinking to cope on GPA.
A research for the effectiveness of stitch type and stitch direction on dynamic drape behaviors
Authors: Demir Murat , Balci Kilic Gonca 
Published: September 2023

PurposeThe purpose of this study is to explore the effect of stitch type and stitch direction on the dynamic drape behavior of the woven fabric.Design/methodology/approachIn this paper, the effectiveness of stitch type and stitch directions on dynamic drape behaviors were investigated. Fabric parts were sewn together with two types of the stitch (lockstitch and overlock stitch) on three different stitch directions (warp, weft and bias (45°)). The static drape coefficients (SDC) of unsewn and sewn fabrics were measured according to the image process method. Dynamic drape coefficients (DDC) of fabrics were also measured using the same method at six different (25, 50, 75, 100, 125, 150 rpms) rotation speeds. Additionally, bending length and bending rigidity were measured using the Cantilever test method.FindingsExperimental results showed that stitch type and stitch directions are effective on the dynamic drape behaviors of the fabric. Overlock stitch resulted in greater DDC than the lock stitch. For both of the stitch type, DDC for the stitch on the warp direction are greater than the stitch on the weft and bias direction for all speeds. In addition, bending length, hence the bending rigidity, are greater for overlock stitch type and always weft direction resulted in greater than the warp and bias direction.Originality/valueFabric drape is vital for garment appearance and is gaining popularity with the advancement of virtual technology, enabling virtual visualization of garments. While previous studies have predominantly examined either the static or dynamic drape behavior of individual fabric panels, or solely focused on the static drape behavior of sewn fabrics, this study acknowledges the significance of incorporating the influence of stitch type and direction on dynamic drape behaviors. Considering that fabrics are sewn together to create garments and that DDC provides a more accurate representation of real-time fabric behavior compared to SDC, this research makes a valuable contribution to the existing literature by investigating the impact of stitch type and direction specifically on DDC.
An exploration of perceptions and experiences of Australian paramedics following the introduction of professional regulation
Authors: Reed Buck , Cowin Leanne , O'Meara Peter , Metusela Christine , Wilson Ian 
Published: September 2023

PurposeSince 2018, Australian paramedics have been regulated under the National Registration and Accreditation Scheme (NRAS) for health practitioners. Established professions have been regulated in Australia for some time, so there is limited knowledge of their entry to regulation. However, as paramedicine has not been previously centrally regulated, this provides a unique case study to explore the transition to regulated practice.Design/methodology/approachAustralian paramedics undertook two surveys: pre- and post-introduction of registration. The first survey was in the month leading up to the commencement of registration (N = 419), and the second survey took place 31 months after registration (N = 407). This paper presents the results of statistical analyses of the post-registration survey including comparisons to the pre-registration survey.FindingsAlthough support for regulation has increased over time, there remains strong dissent consistent with 2018 levels. After 31 months of regulation, respondents reported increasing knowledge of the scheme and greater ease of navigation. The impacts of regulation are more nuanced and less polarised than in the first survey. Identity is again canvassed, and results suggest a shift from employment status and qualifications as key elements of identity to a community of practice and registration.Originality/valueParamedics' experiences and understanding of the rationale for registration are developing. Further support is needed to assist with the emerging professional identity and behaviours. Regulation is one of many occupational factors influencing professional identity and professionalism. Exploring the experience of regulation potentially assists regulators in better supporting practitioners and helps better understand professional evolution.
Responsible leadership and organisational citizenship behaviour for the environment: mediated by environmental corporate social responsibility
Authors: Sahar Noor e , Zawawi Dahlia , Jaharuddin Nor Siah , Abbasi Munir A. 
Published: September 2023

Purpose
This study aims to use stewardship theory to investigate the effect of responsible leadership (RL) on organisational citizenship behaviour for the environment (OCBE) through the mediatory role of environmental corporate social responsibility (ECSR).

Design/methodology/approach
Data was collected from a sample of 224 individuals employed in the manufacturing sector of Pakistan. The study used partial least squares structural equation modelling to estimate the relationships within the model.

Findings
The findings indicate that RL positively impacts OCBE, and ECSR is a partial mediator that mediates the relationship between RL and OCBE.

Practical implications
This research offers novel perspectives for organisational leaders, highlighting the significance of RL quality for instilling OCBE among the employees of manufacturing sectors. Organisational leaders must prioritise ECSR in their CSR initiatives.

Originality/value
This study’s novelty lies in confirming the mediating role of ECSR to drive the positive impact of RL on OCBE through stewardship theory.