bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular and Structural Basis of Oligopeptide Recognition and Transport by the Ami Transporter System in Pneumococci
Authors: Alcorlo Martín , Abdullah Mohammed R. , Steil Leif , Sotomayor Francisco , Oro Laura López-de , de Castro Sonia , Velázquez Sonsoles , Kohler Thomas P. , Jiménez Elisabet , Medina Ana , Usón Isabel , Keller Lance E. , Bradshaw Jessica L. , McDaniel Larry S. , Camarasa María-José , Völker Uwe , Hammerschmidt Sven , Hermoso Juan A. 
Published: December 2023

AbstractATP-binding cassette (ABC) transport systems are crucial for bacteria to ensure sufficient uptake of nutrients that are not produced de novo or improve the energy balance. The cell surface of the pathobiontStreptococcus pneumoniae(pneumococcus) is decorated with a substantial array of ABC transporters, critically influencing nasopharyngeal colonization and invasive infections. Given the auxotrophic nature of pneumococci for certain amino acids, the Ami ABC transporter system, orchestrating oligopeptide uptake, becomes indispensable in host compartments lacking amino acids. The system comprises five exposed Oligopeptide Binding Proteins (OBPs) and four proteins building the ABC transporter channel. Here, we present a structural analysis of all the OBPs in this system. Multiple crystallographic structures, capturing both open and closed conformations along with complexes involving chemically synthesized peptides, have been solved at high resolution providing insights into the molecular basis of their diverse peptide specificities. Mass spectrometry analysis of oligopeptides demonstrates the remarkable promiscuity of some of these proteins when expressed inEscherichia coli, displaying affinity for a wide range of peptides. Finally, a model is proposed for the complete Ami transport system in complex with its various OBPs. We further disclosed some essential structural changes facilitating oligopeptide transport into the cellular cytoplasm. Thus, the structural analysis of the Ami system provides valuable insights into the mechanism and specificity of oligopeptide binding by the different OBPs, shedding light on the intricacies of the uptake mechanism.Author SummaryThe uptake of diverse oligopeptides enables pneumococcal growth despite auxotrophies and functions as a critical sensor for assessing the composition of the local environment. The identification of additional OBPs in non-encapsulatedS. pneumoniaestrains suggests their involvement in sensing a broader spectrum of bacterial competitors coexisting with the highly commensal pneumococcus. This study presents a comprehensive analysis of the initial phase of peptide transport mediated by OBPs within the pneumococcal Ami permease system. We disclose a common mechanism for oligopeptide recognition that is modulated in each OBP to accommodate a diverse array of oligopeptides. Understanding how pneumococcus perceives external stimuli and responds to them is imperative for unraveling the transition from a commensal to a pathogenic state.
The effect of gravity on hand spatio-temporal kinematic features during functional movements
Authors: Bucchieri Anna , Tessari Federico , Buccelli Stefano , De Momi Elena , Laffranchi Matteo , De Michieli Lorenzo 
Published: December 2023

ABSTRACTExploring the impact of gravity on daily upper-limb movements is crucial for comprehending the complexities of upper-limb impairments. The present study delves into the relationship between the gravitational force and the functional aspects of upper-limb mobility. Starting from 9 pick-and-place tasks, hand trajectories of 24 healthy subjects were acquired using a motion capture system. Five in-use and two novel kinematic metrics were calculated by such trends and tested across conditions. Results suggest movements performed against and propelled by gravity lead to statistically significant changes in motor behaviour in terms of planning, smoothness, efficiency, and accuracy of the movement, underlining the need of differentiating the study of such movements in impaired subjects.
Algorithm for selecting potential SARS-CoV-2 dominant variants based on POS-NT frequency
Authors: Kang Eunhee , Ahn TaeJin , Park Taesung 
Published: December 2023

AbstractCOVID-19, currently prevalent worldwide, is caused by a novel coronavirus, SARS-CoV-2. Similar to other RNA viruses, SARS-CoV-2 continues to evolve through random mutations, creating numerous variants, such as Alpha, Beta, and Delta. It is, therefore, necessary to predict the mutations constituting the dominant variant before they are generated. This can be achieved by continuously monitoring the mutation trends and patterns. Hence, in the current study, we sought to design a dominant variant candidate (DVC) selection algorithm. To this end, we obtained COVID-19 sequence data from GISAID and extracted position-nucleotide (POS-NT) frequency ratio data by country and date through data preprocessing. We then defined the dominant dates for each variant in the USA and developed a frequency ratio prediction model for each POS-NT. Based on this model, we applied DVC criteria to develop the selection algorithm, verified for Delta and Omicron. Using Condition 3 as the DVC criterion, 69 and 102 DVC POS-NTs were identified for Delta and Omicron an average of 47 and 82 days before the dominant dates, respectively. Moreover, 13 and 44 Delta- and Omicron-defining POS-NTs were recognized 18 and 25 days before the dominant dates, respectively. We identified all DVC POS-NTs before the dominant dates, including soaring and gently increasing POS-NTs. Considering that we successfully defined all POS-NT mutations for Delta and Omicron, the DVC algorithm may represent a valuable tool for providing early predictions regarding future variants, helping improve global health.Author Summary
Kv4.2 regulates baseline synaptic strength by inhibiting R-type channel-mediated calcium signaling in the hippocampus
Authors: Lee Seung Yeon , Kwon Minjeong , Ho Won Kyung , Lee Suk-Ho 
Published: December 2023

AbstractKv4.2 channels, which mediate A-type K+current, exert significant influence on synaptic input signals and synaptic plasticity in the principal cells of the hippocampus. While their influence on activity-dependent regulation of synaptic response is well-established, the impact of Kv4.2 channels on baseline synaptic strength remains elusive. To investigate this, we selectively inhibited postsynaptic Kv4.2 by introducing Kv4.2 antibodies into the hippocampal granule cells and evaluated its impact on the baseline synaptic transmission. Our results demonstrated that Kv4.2 inhibitions led to notable increase in the amplitude of AMPA receptor (AMPAR)-mediated synaptic currents, and this effect was in parallel with the Kv4.2 expression level at dendritic regions. This Kv4.2-dependent synaptic potentiation was effectively abolished by intracellular 10 mM BAPTA or block of R-type calcium channels (RTCC) and downstream signaling molecules including protein kinase A (PKA) and protein kinase C (PKC). Importantly, Kv4.2 inhibitions did not occlude further synaptic strengthening high frequency stimulation, suggesting that synaptic strength regulation by Kv4.2 s distinct from the mechanism of long-term potentiation. Our study highlights the role of Kv4.2 in regulating the baseline synaptic strength, where Kv4.2-mediated inhibition of RTCC is crucial.
Dynamics of brainstem arousal systems and pupil size predict cortical interactions for flexible decision-making
Authors: van den Brink R.L. , Hagena K. , Wilming N. , Murphy P.R. , Calder-Travis J. , Finsterbusch J. , Büchel C. , Donner T.H. 
Published: December 2023

AbstractMost perceptual decisions entail a flexible mapping from sensory input to motor output. Flexible input-output mapping is reflected in correlated variability within the cortical network involved in perceptual decisions. Here, we tested the idea that brainstem arousal systems are involved in flexible input-output mapping and changes in cortical correlated variability. We combined brainstem fMRI, pupillometry, and time-resolved assessment of the intrinsic correlations between cortical population codes for stimulus and action. Human participants reported the orientation of visual stimuli by button presses, while the required stimulus-response mapping rule could undergo hidden and unpredictable changes. Rule switches evoked brainstem and pupil responses as well as changes in computational model-inferred, latent variables. These variables governed participants’ rule-switching behavior and pupil responses. Brainstem activity and pupil dilation preceded increases in the strength of correlations between cortical stimulus and action codes. Brainstem arousal systems may promote the reorganization of sensorimotor cortical pathways for flexible decisions.
Association between blood pressure and new onset of chronic kidney disease in non-diabetic Japanese adults: a population-based longitudinal study from 1998 to 2023
Authors: Okawa Yukari , Mitsuhashi Toshiharu 
Published: December 2023

AbstractBackground and AimsHypertension is a risk factor for developing chronic kidney disease (CKD). Studies of adult participants in the USA reported that hypertension increased the risk of developing CKD even in the non-diabetic population. However, studies in non-diabetic populations are limited and additional studies in other races are required. This study aimed to examine the relationship between hypertension and the development of CKD in non-diabetic Asian adults.Methods and ResultsIn this longitudinal study, non-diabetic Japanese adults who took annual checkups from 1998 to 2023 were included. CKD was defined as <60 mL/min/1.73 m2, and hypertension was classified into four levels according to the guidelines of the American College of Cardiology/American Heart Association. The Weibull accelerated failure time model was selected because the proportional hazards assumption was violated. Of the 7 363 (men: 40.3%) people in the final cohort, 2 498 (men: 40.1%) developed CKD after a mean follow-up of 7.99 years. Elevated blood pressure (BP) and hypertension stage 2 had a 9% (95% confidence interval [CI]: 1%–16%) and 11% (95% CI: 5%–17%) shorter survival time to CKD onset, respectively, than normal BP. Hypertension stage 1 also had a shorter survival to CKD onset by point estimate, but all 95% CIs crossed 1 in all models.ConclusionsIn a relatively healthy Asian population without diabetes, controlling BP to an appropriate range reduces the risk of developing CKD.
Species-level classification provides new insights into the biogeographical patterns of microbial communities in shallow saline lakes
Authors: Len Polina , Meirkhanova Ayagoz , Nugumanova Galina , Cestaro Alessandro , Jeppesen Erik , Vorobjev Ivan A , Donati Claudio , Barteneva Natasha S 
Published: December 2023

AbstractSaline lakes are rapidly drying out across the globe, particularly in Central Asia, due to climate change and anthropogenic activities. We present the results of a long-read next generation sequencing analysis of the 16S rRNA-based taxonomic structure of bacteriomes of the Tengiz-Korgalzhyn lakes system. We found that the shallow endorheic, mostly saline lakes of the system show unusually low bacterioplankton dispersal rates at species-level taxonomic resolution. The major environmental factor structuring the lake’s microbial communities was salinity. The dominant bacterial phyla of the lakes with high salinity included a significant proportion of marine and halophilic species. In sum, these results, which can be applied to other lake systems of the semi-arid regions, improve our understanding of the factors influencing lake microbiomes undergoing salinization in response to climate change and other anthropogenic factors. Our results show that finer taxonomic classification can provide new insights and improve our understanding of the environmental factors influencing the microbiomes of lakes undergoing salinization in response to climate change and other anthropogenic factors.
Integration of rate and phase codes by hippocampal cell-assemblies supports flexible encoding of spatiotemporal context
Authors: Russo Eleonora , Becker Nadine , Domanski Aleks P. F. , Howe Timothy , Freud Kipp , Durstewitz Daniel , Jones Matthew W. 
Published: December 2023

AbstractSpatial information is encoded by location-dependent hippocampal place cell firing rates and sub-second, rhythmic entrainment of spike times. These ‘rate’ and ‘temporal’ codes have primarily been characterized in low-dimensional environments under limited cognitive demands; but how is coding configured in complex environments when individual place cells signal several locations, individual locations contribute to multiple routes and functional demands vary? Quantifying rat CA1 population dynamics during a decision-making task, we show that the phase of individual place cells’ spikes relative to the local theta rhythm shifts to differentiate activity in different place fields. Theta phase coding also disambiguates repeated visits to the same location during different routes, particularly preceding spatial decisions. Using unsupervised detection of cell assemblies alongside theoretical simulation, we show that integrating rate and phase coding mechanisms dynamically recruits units to different assemblies, generating spiking sequences that disambiguate episodes of experience and multiplexing spatial information with cognitive context.
Performance of Large Language Models on Pharmacy Exam: A Comparative Assessment Using the NAPLEX
Authors: Angel Mirana , Xing Haiyi , Patel Anuj , Alachkar Amal , Baldi Pierre 
Published: December 2023

AbstractBackgroundThere has been considerable recent effort in integrating Large Language Models (LLMs) across different fields, including healthcare. However, the possibility of applying LLMs in pharmacy-related sciences is under-explored.ObjectivesThis study aims to evaluate the capabilities and limitations of six LLMs–GPT-3.5, GPT-4, Llama-2-7B, Llama-2-13B, Llama-2-70B, and Mistral-7B, in the field of pharmacy by assessing their reasoning abilities on a sample of the North American Pharmacist Licensure Examination (NAPLEX). Additionally, we explore the potential impacts of LLMs on pharmacy education and practice.MethodsTo evaluate the LLMs, we utilized the sample of the NAPLEX exam comprising 225 multiple-choice questions sourced from the APhA Complete Review for Pharmacy, 13th Edition | Pharmacy Library. These questions were presented to the Large Language Models through either local deployment or the Application programming interface (API), and the answers generated by the LLMs were subsequently compared with the answer key.ResultsThere is a notable disparity in the performance of the LLMs. GPT-4 emerged as the top performer, accurately answering 87.1% of the questions. Among the six LLMs evaluated, GPT-4 was the only model capable of passing the NAPLEX exam.ConclusionWe examined the performance of Large Language Models based on their model size, training methods, and fine-tuning algorithms. Given the continuous evolution of LLMs, it is reasonable to anticipate that future models will effortlessly excel in exams such as the NAPLEX. This highlights the significant potential of LLMs to influence the field of pharmacy. Hence, we must evaluate both the positive and negative implications associated with the integration of LLMs in pharmacy education and practice.
Female directors and firms’ financial performance: an empirical application of Kanter’s theory in the Indian context
Authors: Maji Santi Gopal , Saha Rupjyoti 
Published: December 2023

Purpose
Given the relevance of female directors in the governance of any firm, this paper aims to examine their effect on firms’ financial performance by investigating their general impact and segregating the same into different subgroups based on Kanter’s theory.

Design/methodology/approach
To achieve the purpose, this study selects a sample of the top 100 listed Indian firms for the period of 2014–2018 and gathers the data pertaining to the variables under consideration from the respective firms’ annual report and corporate database Capitaline Plus. For undertaking the investigation, the authors have segregated the sample into three groups, i.e. firms with boards having less than 10% of female directors are called skewed boards; firms with boards having female directors that range from 10% to 20% are called as tilted board; and firms with boards having sizable representation of female directors of above 20%. To examine the performance impact of overall female directors and their different subgroups, the authors have used a generalized estimating equation model. For the robustness test, the authors have used the fixed-effect model.

Findings
The authors find a significant positive impact of the overall percentage of female directors on the financial performance of firms. Additionally, the results indicate that boards with a titled group of female directors and boards with a sizable representation of female directors significantly positively impact firms’ performance. However, the authors fail to extricate any significant performance impact of boards with a skewed group of female directors.

Practical implications
First, the study reveals that despite prevailing nepotism in India, female directors, owing to their core characteristics, can create a favorable perception of firms in the market. Second, it also works as an eye-opener for regulators by revealing the minimum threshold for female directors that a board should have to exploit the benefits of a gender quota rather than mere compliance with the requirements of the Companies Act, 2013. Third, it implies that more gender-diverse boards can improve a firm’s financial performance only if female directors range between the thresholds of 10% to 20%. Finally, the finding is significant for changing the business culture in India, where institutions are traditionally less supportive of women than in other emerging countries.

Originality/value
Departing from existing studies, which provide evidence on the performance impact of the overall percentage of female directors, the study unveils the differential impact of female directors on firms’ financial performance depending on their level of representation on the board. To the best of the authors’ knowledge, this is the first study in the context of an emerging market to test Kanter’s theory.
Understanding the determinants of innovation across European member states: a fuzzy-set approach
Authors: Fabri Stephanie , Pace Lisa A. , Cassar Vincent , Bezzina Frank 
Published: December 2023

Purpose
The European Innovation Scoreboard is an important indicator of innovation performance across European Member States. Despite its wide application, the indicator fails to highlight the interlinkages that exist among innovation measures and focuses primarily on the linear relationship between the individual measures and the predicted outcome. This study aims to address this gap by applying a novel technique, the fuzzy-set qualitative comparative analysis (fsQCA), to shed light on these interlinkages and highlight the complexity of the determinants underlying innovation performance.

Design/methodology/approach
The authors adopted a configurational approach based on fsQCA that is implemented on innovation performance data from European Member States for the period 2011–2018. The approach is based on non-linearity and allows for the analysis of interlinkages based on equifinality, that is, the model recognises that there are different potential paths of high and low innovation performance. In addition, the approach allows for asymmetric relations, where a low innovation outcome is not the exact inverse of that which leads to high innovation outcome.

Findings
The results clearly indicate that innovation outcomes are not based on simple linear relations. Thus, to reap the desired effects from investments in innovation inputs, the complex set of indicators on which innovation performance is based should be taken into consideration. The results clearly indicate the elements of equifinality and asymmetric relations. Different paths lead to high innovation performance and low innovation performance.

Originality/value
The method applied to investigate the determinants of innovation performance is the prime original factor of this study. Thus, the study contributes to literature by highlighting the complexity involved in understanding innovation. By recognising and attempting to detangle this complexity, this study will assist not just academics but also policymakers in designing the necessary measures required to reach this important outcome for a country’s competitive edge.
The impact of environmental terrorism on land degradation: legal comparative studies between Indonesia and Malaysia
Authors: Trihastuti Nanik , Hananto Pulung Widhi H. , Prabandari Adya Paramita , Basir Salawati Mat , Pratama Aditya Agung , Puteri Efrema Ardratya Prakasita 
Published: December 2023

Purpose
The purpose of this paper is to explore the problem of land degradation as a category of environmental terrorism, which has been increasing along with the rise of open pit mining and oil palm plantation activities.

Design/methodology/approach
This study uses a doctrinal approach that aims to find the best solution to address the problem of land degradation and environmental terrorism activities in Indonesia through a comparative legal study conducted with the handling of similar cases in Malaysia, which has almost the same character as Indonesia.

Findings
This paper finds that both Indonesia and Malaysia have enacted laws and regulations to address environmental concerns. However, it turns out that relying only on law enforcement is not an optimal solution. Addressing the problem of land degradation would also require the implementation of sustainable development practices, public awareness and cooperative dialogue.

Originality/value
This paper provides a new approach to answer the inclusion of environmental degradation as environmental terrorism, which should also be considered a crime against humanity.
Dyeing of some Egyptian cotton varieties using agricultural wastes (peanut outer skin)
Authors: Bahlool Shereen Omar , Kenawy Zeinab M. 
Published: December 2023

Purpose
Peanut skins are an agro-waste product with no commercial value. The purpose of this paper is to evaluate peanut skin as a natural dyestuff and to determine if this natural dye could be used in the dyeing of some Egyptian cotton cultivars.

Design/methodology/approach
The methodology consists of several steps; dye extraction procedure from peanut skin through aqueous extraction, then dyeing optimized using simultaneous mordanting using alum. Finally, dyed cotton has been subjected to different textile laboratory tests, for example, color measurements and mechanical properties. Color-fastness was determined on Egyptian cotton fabric. The peanut skin as a source of natural dye and the dyed cotton sample were characterized by fourier transform infrared spectroscopy (FTIR) analysis.

Findings
It was found that the natural dye extracted from peanut skin has an affinity for cotton samples and showed high dyeability with a unique color shade, good color strength and very good fastness.

Originality/value
The novelty of this paper is the extraction of color from the peanut's outer skin which is discarded as waste such as agro-waste of the agricultural process which can be used as a natural dye in the textile industry and applied to dyeing some Egyptian cotton fibers from different genotypes.