bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature-Dependent Affinity Changes in Substrate Binding Affect the
Cleavage Activity of BthC2c1
Authors: Wu Dan , Liu Jieting , Liu Yong , Qiu Yufei , Cao Zhiqin , Pan Yu , Shi Jiayi , Yuan Xiaohuan 
Published: January 2023

Background:
The CRISPR-Cas system is an adaptive immune mechanism for bacteria and
archaea to resist foreign invasion. Currently, Cas9 and Cpf1 have been widely studied and applied in
gene editing. C2c1 is a newly discovered CRISPR-Cas system endonuclease. It has broad application
prospects due to its small molecular weight and high substrate recognition specificity.

Objectives:
Bacillus thermoamylovorans C2c1(BthC2c1) was expressed in E. coli C43 (DE3)
competent cells, purified, and the BthC2c1-sgRNA-dsDNA complex was assembled. The effect of
temperature on the cleavage ability of the BthC2c1 system was investigated.

Methods:
The cDNA of BthC2c1 was cloned into the vector pGEX-6P-1. BthC2c1 was expressed in E. coli C43(DE3) cells and purified using a GST affinity column and FPLC. The sgRNAs were transcribed and purified in vitro, and the complexes were assembled by gel filtration chromatography. The enzyme cleavage activity of BthC2c1 at different temperatures was investigated using an in vitro cleavage assay. Microscale Thermophoresis detected the affinity of the BthC2c1-sgRNA complexes to substrate DNA.

Method:
The cDNA of BthC2c1 was cloned into the vector pGEX-6P-1. BthC2c1 was expressed in
E. coli C43(DE3) cells and purified using a GST affinity column and FPLC. The sgRNAs were
transcribed and purified in vitro, and the complexes were assembled by gel filtration chromatography.
The enzyme cleavage activity of BthC2c1 at different temperatures was investigated using an in vitro
cleavage assay. Microscale Thermophoresis detected the affinity of the BthC2c1-sgRNA complexes
to substrate DNA.

Results:
BthC2c1 proteins were prokaryotically expressed and purified. The complex of BthC2c1
with sgRNA and dsDNA was assembled. In vitro cleavage assay results showed that BthC2c1
cleaved the target DNA at temperatures ranging from 37°C to 67°C. The cleavage ability of BthC2c1
at 42oC was stronger than that at 37oC. The results of affinity detection showed that the affinity
between the BthC2c1-sgRNA complex and ds36/36 at 42oC was stronger than that at 37oC.

Conclusion:
In this study, BthC2c1 was expressed, purified, and assembled into a complex with
sgRNA and dsDNA. BthC2c1 cleaved DNA within the temperature range of 37oC to 67oC. The
affinity of BthC2c1-sgRNA to DNA at 42°C was significantly enhanced than that at 37°C. It may be
related to its stringent substrate recognition pattern, which differs from Cas9 and Cpf1. The
temperature-dependent affinity changes of substrate binding may be part of the reason for the stronger
cleavage activity of BthC2c1 at 42oC. This study may provide an experimental basis for optimizing
and modifying the C2c1 gene editing system.
Perspectives on Agmatine Neurotransmission in Acute and Chronic Stressrelated
Conditions
Authors: Hassanshahi Amin , Soti Monavareh , Ranjbar Hoda , Razavinasab Moazamehosadat , Pirmoradi Zeynab , Kohlmeier Kristi Anne , Janahmadi Mahyar , Shabani Mohammad 
Published: January 2023

Abstract:
Adaptive responses to stressful stimuli in the environment are believed to restore homeostasis
after stressful events. Stress activates the hypothalamic-pituitary-adrenocortical (HPA) axis,
which releases glucocorticoids (GCs) into the bloodstream. Recently, agmatine, an endogenous
monoamine was discovered to have the potential as a pharmacotherapy for stress. Agmatine is released
in response to certain stress conditions, especially those involving GCs, and participates in
establishing homeostasis disturbed by stress following GC activation. The therapeutic potential of
agmatine for the management of psychological diseases involving stress and depression is promising
based on a significant amount of literature. When exogenously applied, agmatine leads to reductions
in levels of GCs and counteracts stress-related morphologic, synaptic, and molecular changes.
However, the exact mechanism of action by which agmatine modifies the effects resulting from
stress hormone secretion is not fully understood. This review aims to present the most possible
mechanisms by which agmatine reduces the harmful effects of chronic and acute stress. Several
studies suggest chronic stress exposure and repeated corticosteroid treatment lower agmatine levels,
contributing to stress-related symptoms. Agmatine acts as an antistress agent by activating mTOR
signaling, inhibiting NMDA receptors, suppressing iNOS, and maintaining bodyweight by activating
α-2adrenergic receptors. Exogenous administration that restores agmatine levels may provide
protection against stress-induced changes by reducing GCs release, stimulating anti-inflammatory
processes, and releasing neuroprotective factors, which are not found in all therapies currently being
used to treat stress-related disorders. The administration of exogenous agmatine should also be considered
a therapeutic element that is capable of triggering a neural protective response that counters
the effects of chronic stress. When combined with existing treatment strategies, this may have synergistic
beneficial effects.
Probing into the Flap-dimer Dynamics of the Mycobacterium tuberculosis Kasa Enzyme Binding Landscape Provides the Underlying Inhibitory Mechanisms of JSF-3285 and 5G
Authors: Adewumi Adeniyi T. , Oluyemi Wande M. , Adewumi Nonhlanhla , Adekunle Yemi A. , Alahmdi Mohamed Issa , Abo-Dya Nader E. , Soliman Mahmoud E.S. 
Published: January 2023

Background:
β-ketoacyl-ACP synthase I (KasA I) enzyme is crucial in mycolic acid synthesis via catalytic condensation reactions, hence implicated in M. tuberculosis’s virulence and drug resistance. Presently, there is no known potent KasA inhibitor; thiolactomycin lacks potency. Recently reported indazole compounds JSF-3285/tr1DG167 and 5G/tr2DG167 inhibit the KasA through binding to the substrate cavity. However, the molecular mechanism is still unclear, and the unknown resistance mechanisms raise concerns about JSF-3285's novelty.

Methods:
This study is the first to report the flap dimer opening and closing of the KasA pocket us-ing combined metrics to define the symmetry impact of the flap-dimer motions and investigate the underlying inhibitory mechanism of tr1DG167 and tr2DG167 using all-atom MD simulation.

Results:
The distance/d1 between the flap (PRO147) and dimer (LEU205) residues; TriC-α angle (θ1: PRO147-VAL83-LEU205 & θ2: PRO147-GLU199-LEU205); and the dihedral angle (ϕ) were applied to investigate the flap “twisting” and dimer shift closing due to concerted motion by adja-cent glycine-rich and glutamic acid-rich loops around the active site during the binding pocket’s opening. The full flap-dimer of the unbound opens at 230 ns (d1 = 21.51 Å), corresponding to the largest TriC-α angle θ1 44.5° as θ2 is unreliable to describe the flap-dimer motion. The overall av-erages θ1 and θ2 for the bounds were ~23.13° and ~23.31°, respectively. Thus, the degree of KasA flap dimer opening is best investigated by distance and θ1. BFE (Kcal/mol) of -44.05 (tr1DG167) showed a higher affinity for the pocket than tr2DG167-KasA (-32.16). Both tr1DG167 and tr2DG167 formed hydrophobic interactions with LEU116, GLY117, ALA119, and tr1DG167 formed strong H-bonds with GLU199. The average RMSD of 2.80 Å (Apo) and RoG of 20.97 Å showed that KasA is less stable and less tightly packed without the inhibitors.

Conclusion:
These findings provide a background for a new structure-based design of novel KasA inhibitors.
Efficient Preparation of Chloroquine Enantiomers via Crystallization Resolution and Palladium-Catalysed Coupling
Authors: Huang Shaohua , Sun Shanshan , Sha Xuming , Han Bowen , Guo Dandan 
Published: January 2023

Abstract:
Chloroquine (CQ) was found to exhibit antiviral activity against novel coronaviruses, which makes the preparation of CQ enantiomers particularly important. In this work, we developed an efficient method for the preparation of CQ enantiomers by crystallization resolution and palladium-catalyzed coupling. The obtained chiral CQ had been fully assigned by 1H-1H COSY, 1H-13C HSQC, and 1H-13C HMBC spectra. Moreover, the enantiomeric excess value of CQ was rapidly detected by binaphthol phosphate as a chiral NMR shift reagent.
Estimating Methods of the Undetected Infections in the COVID-19
Outbreak: A Systematic Review
Authors: Mehraeen Esmaeil , Pashaei Zahra , Akhtaran Fatemeh Khajeh , Dashti Mohsen , Afzalian Arian , Ghasemzadeh Afsaneh , Asili Pooria , Kahrizi Mohammad Saeed , Mirahmad Maryam , Rahimi Ensiyeh , Matini Parisa , Afsahi Amir Masoud , Dadras Omid , SeyedAlinaghi SeyedAhmad 
Published: January 2023

Introduction:
The accurate number of COVID-19 cases is essential knowledge to control an
epidemic. Currently, one of the most important obstacles in estimating the exact number of COVID-19
patients is the absence of typical clinical symptoms in a large number of people, called asymptomatic
infections. In this systematic review, we included and evaluated the studies mainly focusing on the
prediction of undetected COVID-19 incidence and mortality rates as well as the reproduction numbers,
utilizing various mathematical models.

Methods:
This systematic review aims to investigate the estimating methods of undetected infections
in the COVID-19 outbreak. Databases of PubMed, Web of Science, Scopus, Cochrane, and Embase,
were searched for a combination of keywords. Applying the inclusion/exclusion criteria, all retrieved
English literature by April 7, 2022, were reviewed for data extraction through a two-step screening
process; first, titles/abstracts, and then full-text. This study is consistent with the PRISMA checklist.

Results:
In this study, 61 documents were retrieved using a systematic search strategy. After an initial
review of retrieved articles, 6 articles were excluded and the remaining 55 articles met the inclusion
criteria and were included in the final review. Most of the studies used mathematical models to estimate
the number of underreported asymptomatic infected cases, assessing incidence and prevalence
rates more precisely. The spread of COVID-19 has been investigated using various mathematical models.
The output statistics were compared with official statistics obtained from different countries. Although
the number of reported patients was lower than the estimated numbers, it appeared that the
mathematical calculations could be a useful measure to predict pandemics and proper planning.

Conclusion:
In conclusion, our study demonstrates the effectiveness of mathematical models in unraveling
the true burden of the COVID-19 pandemic in terms of more precise, and accurate infection and
mortality rates, and reproduction numbers, thus, statistical mathematical modeling could be an effective
tool for measuring the detrimental global burden of pandemic infections. Additionally, they could
be a really useful method for future pandemics and would assist the healthcare and public health systems
with more accurate and valid information.
Evaluación de respuesta sísmica usando la teoría de vibraciones aleatorias en tres perfiles de suelo de Lima, Perú
Authors: Pastor Oliveros Brandon Omar , Calderón Cahuana Diana Lucía , Gonzales Trujillo Carlos Eduardo 
Published: January 2023

Seismic response analyses are performed using a minimum number of seismic records as input motions in order to achieve a statistically strong estimation. Unfortunately, the available information recorded from the current seismic networks is still scarce regarding events with considerable magnitude. In this context, the Random Vibration Theory (RVT) arises as an alternative tool for performing site response analyses without the need of seismic records, since it only requires adequate probabilistic seismic hazard assessment.
In this study, RVT was applied to three shear-wave velocity profiles in Lima city with distinct geomorphological origin. These profiles are characteristic for gravelly, sandy and fine deposits so the influence of each soil type in their corresponding transfer function was taken into account. In that sense, the three RVT-based normalized response spectra show good agreement with the design spectra specified in the Peruvian code, despite some amplification in the short (below 0.10 s) and long (above 0.80 s) period ranges related to noise or far-field effects. Furthermore, RVT-based response spectra for La Punta and Villa el Salvador show good agreement with the time-series based analyses from a previous study.
In addition, spectral acceleration values surpass those specified in the Peruvian code for a range beyond the corner period. This could suggest that the soil profile characterization based on the time-averaged shear wave velocity from the upper 30 m might be insufficient to evaluate the overall seismic behavior of a soil deposit. Therefore, additional parameters that account for the deeper soil substructure might be required.
Site dominant frequencies in Lima, Peru, by h/v spectral ratio of seismic records
Authors: Ccahua-Laqui Angel Leandro , Gonzales-Trujillo Carlos Eduardo , Moya-Huallpa Luis Angel , Lazares-La Rosa Luis Fernando , Yamazaki Fumio 
Published: January 2023

Strong motion records are important for improving seismic design, damage assessment and analysis of earthquake effects. Despite the relevance of having strong motion networks, their implementation in Peru has been performed in the very recent years. For instance, only five strong motion stations in Lima recorded the 2007 Mw 7.9 Pisco earthquake, whereas 55 stations recorded the 2021 Mw 6.0 Mala earthquake. The current number of instrumentations in Lima city provides an opportunity to improve soil characterization. This study aims to determine the dominant frequency (fd) of the seismic stations located in Metropolitan Lima. The procedure we adopted, first considered collecting, for an arbitrary station, all the available events recorded from 2011-2021, including the 2007 Mw 7.9 Pisco earthquake. Then, the pseudo spectral acceleration, using 5% damping, for each component were computed, and the horizontal-to-vertical (H/V) spectral ratios were calculated. Finally, the average H/V spectral ratio was used to adequately characterize the values of fd . In total, we evaluated 51 stations throughout Lima city. Values of fd lower than 1 Hz were observed for the coastal areas in which the underlying soil consist of clayey/sandy deposits and regions with an important impedance contrast in the deeper part of the substructure. These values increment towards the center of the city coinciding with surficial gravel deposits.
Seismic analysis of underground structures: Influence of the soil type, the relative stiffness and seismic intensity
Authors: Garcia Velasquez Jhonatan Smith , Scaletti Farina Hugo Victor 
Published: January 2023

Las estructuras subterráneas se desempeñan como medios para llevar a cabo actividades esenciales en una sociedad moderna. Por lo tanto, su apropiado desempeño sísmico es importante para la reducción del riesgo de desastres. El presente trabajo trata sobre los efectos sísmicos sobre las estructuras subterráneas ubicadas en zonas altamente sísmicas, como la costa del Perú. Se empleó el programa de cómputo FLAC para realizar varios análisis dinámicos de estructuras subterráneas de sección rectangular, considerando condiciones de borde de tipo campo libre y el comportamiento no lineal e inelástico del suelo ante siete sismos ajustados a un mismo espectro objetivo. Dichos análisis se llevaron a cabo variando factores como el tipo de suelo (homogéneo o estratificado), la geometría y espesores de la estructura y el periodo de retorno del sismo. Se ha encontrado que cuando la estructura está implantada en suelo homogéneo las fuerzas y desplazamientos presentas poca variación. Sin embargo, cuando la estructura está en suelo heterogéneo los resultados muestran variaciones importantes. De manera que el ajuste a un mismo espectro elástico no implica uniformizar la demanda sísmica. La geometría de la estructura y el espesor de los muros tienen considerable influencia. En suelos heterogéneos las estructuras muy flexibles pueden tener grandes deformaciones que implicarían niveles de daño importante.
Toward Diabetes Device Development That Is Mindful to the Needs of Young People Living With Type 1 Diabetes: A Data- and Theory-Driven Qualitative Study
Authors: Brew-Sam Nicola , Parkinson Anne , Chhabra Madhur , Henschke Adam , Brown Ellen , Pedley Lachlan , Pedley Elizabeth , Hannan Kristal , Brown Karen , Wright Kristine , Phillips Christine , Tricoli Antonio , Nolan Christopher J , Suominen Hanna , Desborough Jane 
Published: January 2023

Background
An important strategy to understand young people’s needs regarding technologies for type 1 diabetes mellitus (T1DM) management is to examine their day-to-day experiences with these technologies.

Objective
This study aimed to examine young people’s and their caregivers’ experiences with diabetes technologies in an exploratory way and relate the findings to the existing technology acceptance and technology design theories. On the basis of this procedure, we aimed to develop device characteristics that meet young people’s needs.

Methods
Overall, 16 in-person and web-based face-to-face interviews were conducted with 7 female and 9 male young people with T1DM (aged between 12 and 17 years) and their parents between December 2019 and July 2020. The participants were recruited through a pediatric diabetes clinic based at Canberra Hospital. Data-driven thematic analysis was performed before theory-driven analysis to incorporate empirical data results into the unified theory of acceptance and use of technology (UTAUT) and value-sensitive design (VSD). We used the COREQ (Consolidated Criteria for Reporting Qualitative Research) checklist for reporting our research procedure and findings. In this paper, we summarize the key device characteristics that meet young people’s needs.

Results
Summarized interview themes from the data-driven analysis included aspects of self-management, device use, technological characteristics, and feelings associated with device types. In the subsequent theory-driven analysis, the interview themes aligned with all UTAUT and VSD factors except for one (privacy). Privacy concerns or related aspects were not reported throughout the interviews, and none of the participants made any mention of data privacy. Discussions around ideal device characteristics focused on reliability, flexibility, and automated closed loop systems that enable young people with T1DM to lead an independent life and alleviate parental anxiety. However, in line with a previous systematic review by Brew-Sam et al, the analysis showed that reality deviated from these expectations, with inaccuracy problems reported in continuous glucose monitoring devices and technical failures occurring in both continuous glucose monitoring devices and insulin pumps.

Conclusions
Our research highlights the benefits of the transdisciplinary use of exploratory and theory-informed methods for designing improved technologies. Technologies for diabetes self-management require continual advancement to meet the needs and expectations of young people with T1DM and their caregivers. The UTAUT and VSD approaches were found useful as a combined foundation for structuring the findings of our study.
Linking Activity Theory Within User-Centered Design: Novel Framework to Inform Design and Evaluation of Adverse Drug Reaction Reporting Systems in Pharmacy
Authors: Fossouo Tagne Joel , Yakob Reginald Amin , Mcdonald Rachael , Wickramasinghe Nilmini 
Published: January 2023

Background
Adverse drug reactions (ADRs) may cause serious injuries including death. Timely reporting of ADRs may play a significant role in patient safety; however, underreporting exists. Enhancing the electronic communication of ADR information to regulators and between health care providers has the potential to reduce recurrent ADRs and improve patient safety.

Objective
The main objectives were to explore the low rate of ADR reporting by community pharmacists (CPs) in Australia, evaluate the usability of an existing reporting system, and how this knowledge may influence the design of subsequent electronic ADR reporting systems.

Methods
The study was carried out in 2 stages. Stage 1 involved qualitative semistructured interviews to identify CPs’ perceived barriers and facilitators to ADR reporting. Data were analyzed by thematic analysis, and identified themes were subsequently aligned to the task-technology fit (TTF) framework. The second stage involved a usability evaluation of a commercial web-based ADR reporting system. A structured interview protocol that combined virtual observation, think-aloud moderating techniques, retrospective questioning of the overall user experience, and a System Usability Scale (SUS). The field notes from the interviews were subjected to thematic analysis.

Results
In total, 12 CPs were interviewed in stage 1, and 7 CPs participated in stage 2. The interview findings show that CPs are willing to report ADRs but face barriers from environmental, organizational, and IT infrastructures. Increasing ADR awareness, improving workplace practices, and implementing user-focused electronic reporting systems were seen as facilitators of ADR reporting. User testing of an existing system resulted in above average usability (SUS 68.57); however, functional and user interpretation issues were identified. Design elements such as a drop-down menu, free-text entry, checkbox, and prefilled data fields were perceived to be extremely useful for navigating the system and facilitating ADR reporting.

Conclusions
Existing reporting systems are not suited to report ADRs, or adapted to workflow, and are rarely used by CPs. Our study uncovered important contextual information for the design of future ADR reporting interventions. Based on our study, a multifaceted, theory-guided, user-centered, and best practice approach to design, implementation, and evaluation may be critical for the successful adoption of ADR reporting electronic interventions and patient safety. Future studies are needed to evaluate the effectiveness of theory-driven frameworks used in the design and implementation of ADR reporting systems.