bluuebunny/crossref_metadata_2025_split huggingface dataset:
Yeast recombinational cloning for heterologous biosynthesis of polyketides: a molecular microbiology laboratory module for undergraduate students
Authors: Bejenari Mihaela , Nielsen Line , Spedtsberg Eva Mie Lang , Nielsen Mikkel Rank , Pedersen Tobias Bruun , Sørensen Jens Laurids 
Published: November 2023

ABSTRACT

Recombinant plasmids are essential tools in molecular biotechnology, and reliable plasmid assembly methods have, therefore, become a prerequisite for the successful cloning and transfer of genes. Among the multitude of available plasmid assembly strategies,
in vivo
homologous recombinational cloning in yeast has emerged as a cost-effective and relatively simple method. Since we use this method routinely in our group for assembling large plasmids with secondary metabolite gene clusters and for direct heterologous production of polyketides in
Saccharomyces cerevisiae
, we developed an exercise module for undergraduate students where they would get hands-on experience with these molecular practices. The exercises target several molecular techniques, including PCR, restriction enzyme digestion, and yeast recombinational cloning. The students will learn about plasmid assembly and yeast transformation methods by performing these experiments while inherently acquiring new skills valuable for their subsequent laboratory work or projects.
The role of lysosomes as intermediates in betacoronavirus PHEV egress from nerve cells
Authors: Wang Zhenzhen , He Wenqi , Li Caili , Chen Yuzhu , Li Zi , Jiao Yubo , Zhang Jing , Shi Junchao , Wang Gaili , Guan Jiyu , Zhao Kui , Song Deguang , Gao Feng , Lan Yungang 
Published: November 2023

ABSTRACT

The traditional view that betacoronaviruses exit occurs
via
the constitutive secretory route has recently been questioned by studies suggesting that this process involves lysosomal exocytosis. Here, we demonstrated that porcine hemagglutinating encephalomyelitis virus (PHEV), a neurotropic betacoronavirus, traffics to lysosomes prior to engaging in Arl8b-dependent lysosomal exocytosis. Notably, PHEV induces active or passive lysosomal acidification and activates lysosomal degradative enzymes. PHEV release depends on vacuolar H
+
-ATPase-mediated lysosomal acidification. In addition, PHEV transmission and PHEV-induced brain damage in the central nervous system can be blocked by the Rab7 GTPase competitive inhibitor CID1067700. Taken together, lysosome plays a critical role in PHEV egress
in vitro
and
in vivo
.

IMPORTANCE
Betacoronaviruses, including severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and mouse hepatitis virus (MHV), exploit the lysosomal exocytosis pathway for egress. However, whether all betacoronaviruses members use the same pathway to exit cells remains unknown. Here, we demonstrated that porcine hemagglutinating encephalomyelitis virus (PHEV) egress occurs by Arl8b-dependent lysosomal exocytosis, a cellular egress mechanism shared by SARS-CoV-2 and MHV. Notably, PHEV acidifies lysosomes and activates lysosomal degradative enzymes, while SARS-CoV-2 and MHV deacidify lysosomes and limit the activation of lysosomal degradative enzymes. In addition, PHEV release depends on V-ATPase-mediated lysosomal pH. Furthermore, this is the first study to evaluate βCoV using lysosome for spreading through the body, and we have found that lysosome played a critical role in PHEV neural transmission and brain damage caused by virus infection in the central nervous system. Taken together, different betacoronaviruses could disrupt lysosomal function differently to exit cells.
Effects of orbital decompression on duction, cyclotorsion and diplopia
Authors: Jellema Hinke Marijke , Althaus Martina , Merckel-Timmer Elly , Hartong Dyonne T , Kloos Roel , Saeed Peerooz 
Published: November 2023

BackgroundOrbital decompression is commonly performed to correct proptosis in patients with Graves’ orbitopathy (GO). In literature, the incidence of new-onset constant diplopia after orbital decompression varies. Few studies have evaluated changes in duction and cyclodeviation after orbital decompression. We evaluated the changes in duction, cyclodeviation, eye position and degree of diplopia after orbital decompression.MethodsWe retrospectively analysed data from patients who underwent orbital decompression at our hospital between January 2016 and July 2020. Data regarding the type of decompression, eye position, duction, cyclodeviation and level of diplopia according to the Gorman score were recorded.ResultsData from 281 eyes/orbits of 156 patients were analysed. Proptosis decreased from 23.8±2.5 to 20.9±2.5 mm. Horizontal and vertical duction range decreased (horizontal d=0.40 and vertical 0.30; p=0.000) after surgery; however, the change was not clinically significant (≤5°). Horizontal deviation changed towards esodeviation (d=−0.45; p=0.000), whereas vertical deviation remained stable (d=0.15; p=0.161). Preoperative cyclotorsion in the primary and downgaze positions changed towards incyclodeviation (primary: d=0.30, p=0.021; downgaze d=0.30, p=0.039). Diplopia improved in 22% (18 patients), whereas new-onset constant diplopia developed in 11% (12 patients). Elevation has an excellent predictive value of causing new-onset constant diplopia when measured preoperatively as <19°, sensitivity 88.0%, specificity 41.7% (area under the curve 0.812 (95% CI 0.660 to 0.963); p=0.000).ConclusionAfter orbital decompression, incidence of new-onset constant diplopia was 11% and 22% of the patients had partial or complete improvement of their diplopia. The changes in duction, cyclodeviation and horizontal deviation showed a statistical but not clinical difference. Patients with GO and a preoperatively restricted elevation of <19° are at risk of developing new-onset constant diplopia. In addition, preoperative incyclodeviation may worsen after decompression surgery.
Use of loop diuretics in patients with chronic heart failure: an observational overview
Authors: Scholte Niels TB , Aydin Dilan , Linssen Gerard CM , Koudstaal Stefan , Rademaker Philip C , Geerlings Peter R , van Gent Marco WF , Aksoy Ismail , Oosterom Liane , Boersma Eric , Brunner-La Rocca Hans-Peter , Brugts Jasper J 
Published: November 2023

IntroductionThis study aimed to evaluate the use and dose of loop diuretics (LDs) across the entire ejection fraction (EF) spectrum in a large, ‘real-world’ cohort of chronic heart failure (HF) patients.MethodsA total of 10 366 patients with chronic HF from 34 Dutch outpatient HF clinics were analysed regarding diuretic use and diuretic dose. Data regarding daily diuretic dose were stratified by furosemide dose equivalent (FDE)>80 mg or ≤80 mg. Multivariable logistic regression models were used to assess the association between diuretic dose and clinical features.ResultsIn this cohort, 8512 (82.1%) patients used diuretics, of which 8179 (96.1%) used LDs. LD use was highest among HF with reduced EF (HFrEF) patients (81.1%) followed by HF with mild-reduced EF (76.1%) and HF with preserved ejection fraction EF (73.8%, p<0.001). Among all LDs users, the median FDE was 40 mg (IQR: 40–80). The results of the multivariable analysis showed that New York Heart Association classes III and IV and diabetes mellitus were one of the strongest determinants of an FDE >80 mg, across all HF categories. Renal impairment was associated with a higher FDE across the entire EF spectrum.ConclusionIn this large registry of real-world HF patients, LD use was highest among HFrEF patients. Advanced symptoms, diabetes mellitus and worse renal function were significantly associated with a higher diuretic dose regardless of left ventricular ejection fraction.
Connecting community-based monitoring to Arctic environmental decision-making and governance: A systematic scoping review of the literature
Authors: Wilson Nicole J. , Worden Elizabeth , O'Hanlon Grace 
Published: November 2023

Arctic community-based monitoring (CBM) programs have proliferated in recent decades. While the desire to influence decision-making is frequently listed as a motivation for CBM, there is a dearth of literature examining whether and how this goal is achieved in the Arctic. We draw on a systematic scoping literature review to examine the current state of the literature on Arctic CBM and environmental decision-making. Relevant articles ( n = 27) were identified through inclusion/exclusion criteria (i.e., English language, peer reviewed, published between 1991 and 2021, and based on primary research) and analyzed using a data extraction questionnaire. We find that there is a growing focus on the relationship between Arctic CBM and decision-making in a range of decision contexts, most notably including co-management institutions. We note that less attention was paid to the potential effects of the often unequal, settler-colonial politics within the broader environmental governance system on the relationship between CBM and decision-making. Indigenous peoples and Indigenous Knowledge systems play a significant role within the included references, but less than half of the included references incorporated Indigenous governance concepts to a major extent. Based on our findings, we recommend future studies engage critical analysis of the influence of the governance and politics in the Arctic (1) on environmental decision-making; (2) the politics of knowledge; and (3) the use of digital technologies in the collection, storage, and mobilization of CBM data.
The Effects of Age and Reading Experience on the Lifespan Neurodevelopment for Reading Comprehension
Authors: Liu Xinyang , Zhang Lihuan , Yu Saiwen , Bai Zilin , Qi Ting , Mao Hengyu , Zhen Zonglei , Dong Qi , Liu Li 
Published: November 2023

Abstract
Reading comprehension is a vital cognitive skill that individuals use throughout their lives. The neurodevelopment of reading comprehension across the lifespan, however, remains underresearched. Furthermore, factors such as maturation and experience significantly influence functional brain development. Given the complexity of reading comprehension, which incorporates lower-level word reading process and higher-level semantic integration process, our study aims to investigate how age and reading experience influence the neurobiology underpinning these two processes across the lifespan. fMRI data of 158 participants aged from 7 to 77 years were collected during a passive word viewing task and a sentence comprehension task to engage the lower- and higher-level processes, respectively. We found that the neurodevelopment of the lower-level process was primarily influenced by age, showing increased activation and connectivity with age in parieto-occipital and middle/inferior frontal lobes related to morphological-semantic mapping while decreased activation in the temporoparietal regions linked to phonological processing. However, the brain function of the higher-level process was primarily influenced by reading experience, exhibiting a greater reliance on the frontotemporal semantic network with enhanced sentence-level reading performance. Furthermore, reading experience did not significantly affect the brain function of children, but had a positive effect on young adults in the lower-level process and on middle-aged and older adults in the higher-level process. These findings indicate that the brain function for lower- and higher-level processes of reading comprehension is differently affected by maturation and reading experience, and the experience effect is contingent on age regarding the two processes.
Superior Attentional Efficiency of Auditory Cue via the Ventral Auditory-thalamic Pathway
Authors: Wang Ke , Fang Ying , Guo Qiang , Shen Lu , Chen Qi 
Published: November 2023

Abstract
Auditory commands are often executed more efficiently than visual commands. However, empirical evidence on the underlying behavioral and neural mechanisms remains scarce. In two experiments, we manipulated the delivery modality of informative cues and the prediction violation effect and found consistently enhanced RT benefits for the matched auditory cues compared with the matched visual cues. At the neural level, when the bottom–up perceptual input matched the prior prediction induced by the auditory cue, the auditory-thalamic pathway was significantly activated. Moreover, the stronger the auditory-thalamic connectivity, the higher the behavioral benefits of the matched auditory cue. When the bottom–up input violated the prior prediction induced by the auditory cue, the ventral auditory pathway was specifically involved. Moreover, the stronger the ventral auditory-prefrontal connectivity, the larger the behavioral costs caused by the violation of the auditory cue. In addition, the dorsal frontoparietal network showed a supramodal function in reacting to the violation of informative cues irrespective of the delivery modality of the cue. Taken together, the results reveal novel behavioral and neural evidence that the superior efficiency of the auditory cue is twofold: The auditory-thalamic pathway is associated with improvements in task performance when the bottom–up input matches the auditory cue, whereas the ventral auditory-prefrontal pathway is involved when the auditory cue is violated.
Multi
3
WOZ: A Multilingual, Multi-Domain, Multi-Parallel Dataset for Training and Evaluating Culturally Adapted Task-Oriented Dialog Systems
Authors: Hu Songbo , Zhou Han , Hergul Mete , Gritta Milan , Zhang Guchun , Iacobacci Ignacio , Vulić Ivan , Korhonen Anna 
Published: November 2023

Abstract
Creating high-quality annotated data for task-oriented dialog (ToD) is known to be notoriously difficult, and the challenges are amplified when the goal is to create equitable, culturally adapted, and large-scale ToD datasets for multiple languages. Therefore, the current datasets are still very scarce and suffer from limitations such as translation-based non-native dialogs with translation artefacts, small scale, or lack of cultural adaptation, among others. In this work, we first take stock of the current landscape of multilingual ToD datasets, offering a systematic overview of their properties and limitations. Aiming to reduce all the detected limitations, we then introduce Multi3WOZ, a novel multilingual, multi-domain, multi-parallel ToD dataset. It is large-scale and offers culturally adapted dialogs in 4 languages to enable training and evaluation of multilingual and cross-lingual ToD systems. We describe a complex bottom–up data collection process that yielded the final dataset, and offer the first sets of baseline scores across different ToD-related tasks for future reference, also highlighting its challenging nature.
Statistical characterization of microcellular polyurethane foams microstructure based on 2D and 3D image analysis
Authors: Le Saux Matthieu , Le Bail Jean-Baptiste , Becker Justin , Caër Célia , Charrier Pierre , Le Saux Vincent , Maheo Laurent , Marco Yann 
Published: November 2023

This paper presents protocols developed to quantitatively characterize the cellular microstructure of microcellular polyurethane foams, from scanning electron microscopy (2D) and X-ray micro-computed tomography (2D and 3D) data. The objectives are to provide, for both techniques: (i) a detailed description of the analysis steps based on open source Python algorithms; (ii) a method for automatic, robust and objective detection of the cells to limit user’s biases; (iii) a statistical description of fraction, size, shape and spatial distribution of cells. The study considers 12 samples with densities ranging from about 400 to 600 kg m−3and pore sizes from a few micrometers to several hundred micrometers. In addition, the database obtained is used to investigate the reliability of 2D measurements to describe the cellular microstructure statistics.
Funerary Objects and an Intact Secondary Burial in the Early Ramesside Tomb of Iurokhy at Saqqara
Authors: Hassan Khaled 
Published: November 2023

The area of the North Saqqara plateau south of the causeway of King Unas became one of the most prominent necropolis sites of Memphis during the New Kingdom. It is where the archaeological expedition of the Faculty of Archaeology, Cairo University discovered dozens of temple-shaped tombs dating to the Ramesside Period. Recently, the expedition led by Ola El-Aguizy uncovered the tomb of Iurokhy (Urhiya), an army general during the early reign of Ramesses II. This paper focuses on the unusual finds discovered in one of the tomb’s chapels. These comprise an intact secondary burial in a wooden coffin along with wooden shabtis. This paper proposes to identify the individual buried in the chapel as a member of the personnel that serviced the mortuary cult of Iurokhy. Further objects deposited in the chapel shed light on the continued use of the chapel as a space of burial and commemoration. [Formula: see text]
Early versus delayed ureterolithotripsy following obstructive acute pyelonephritis treatment
Authors: Kazan Huseyin Ozgur , Cicek Muhammet , Caskurlu Hulya , Atis Ramazan Gokhan , Yildirim Asif 
Published: November 2023

Background and objectives: There is no recommendation on the timing of ureterolithotripsy after the treatment of obstructive acute pyelonephritis (APN). The effect of early and delayed ureterolithotripsy on postoperative urinary tract infection (UTI) and other complications was investigated. Methods: Patients who underwent ureterolithotripsy after obstructive APN treatment between February 2017 and August 2021 were divided into two groups, those operated during hospitalization and those operated within 3 months after discharge. Two groups were compared in terms of stone-free status, postoperative complications, postoperative UTI, and urosepsis rates. Results: Of the 91 patients included in the study, 68 were in the early ureterolithotripsy group, while 23 patients were in the delayed ureterolithotripsy group. The postoperative UTI rate was significantly higher in patients who underwent early ureterolithotripsy (29.4% vs 8.7%, p = 0.045). Patients with postoperative UTI had a higher moderate/severe perinephric fat stranding (PFS) on non-contrast CT at hospital admission (52.2% vs 29.4%, p = 0.048). Among the laboratory parameters, white blood cells were significantly higher in the group with postoperative UTI (21604.5 vs 14728.9, p = 0.042). In the multivariate analysis, early ureterolithotripsy and moderate/severe PFS were independent predictors for postoperative UTI. In the created model, the probability of postoperative UTI after ureterolitripsy after obstructive APN treatment was 3.5% in patients without risk factors, while this rate was 51.9% in patients with both risk factors. Conclusion: There is no consensus on the timing of stone removal after treatment of obstructive APN. Early ureterolithoripsy and moderate/severe perinephric fat stranding on non-contrast CT are risk factors for postoperative UTI.
A survey and biomechanical analysis of the feasibility of the thumb test for determining the cancellous bone quality for stemless shoulder prosthesis
Authors: Hatta Taku , Shinagawa Kiyotsugu , Kawakami Jun , Kanazawa Kenji , Hayakawa Takashi , Yamamoto Nobuyuki , Yamakado Kotaro 
Published: November 2023

Background The effect of the thumb test for assessing the cancellous bone quality at the resection plane of the proximal humerus on determining the application of a stemless shoulder prosthesis remains unclear. This study was conducted to survey the current utilization of the thumb test among surgeons and to investigate biomechanical features of the thumb test. Method A survey among shoulder surgeons who had experience with stemless prostheses was conducted to investigate the current utilization of preoperative assessments and intraoperative thumb test when applying stemless prosthesis. Biomechanical experiments for the thumb test using artificial bone models were performed to assess the compression force, contact pressure and area. According to the preliminary survey, three compression techniques were assessed: compression perpendicular to the surface with thumb pad (P-pad technique) or tip of the thumb (P-tip technique), or compression in the vertical direction simulating compression along the longitudinal axis of the humeral shaft with tip-pad of the thumb (H-axis technique). The contact area was separated into three subregions (proximal, middle and distal) to assess the distribution of contact pressure. Results Among 38 surgeons, 66% utilized the thumb test intraoperatively. The P-pad technique was more frequently applied than the P-tip or H-axis techniques (80%, 4% and 16%, respectively). Although with wide variation among the examiners, biomechanical assessments revealed the P-pad technique showed larger contact area and less compression force than the P-tip technique. The P-pad technique provided no significant localized differences in the mean contact pressure on the compressed plane, whereas the P-tip and H-axis techniques showed significant differences among subregions. Conclusion This survey demonstrated relatively frequent application of the thumb test on applying the stemless shoulder prosthesis. Biomechanical assessment revealed the thumb test can hinder objective reproducibility among examiners; therefore, further investigations to identify feasible assessments of the bone quality is required.
Effects of TLD on suppressing the dynamic responses of a multilayer structure
Authors: Dou Peng , Xu Xiaosen , Wang Zhidong , Xing Yihan 
Published: November 2023

Two different Tuned liquid dampers (TLDs) were installed on the floors of a three-floor structure. The TLD natural frequencies were tuned to the first two resonance frequencies of the structure, and its base was subjected to harmonic excitation. The excitation frequency of the sweep tests ranged from 0.8 to 3.2 Hz, and the mass ratio for all the simulations was constant and equalled 2%. The FVM/FEM method was used to solve the fluid-structure coupling, and the maximum displacement of the three floors were obtained. The dissipated energy by damping force was used to study the coupling mechanism of TLD and multilayer structure. Findings indicated that the scheme of the multiple-TLD design was stable and effective, which ensured that the structure-TLD system under the same mass ratio had no local adverse effects. The proportion of positive work time of tank hydrodynamic force is the intuitive embodiment of TLD damping performance. The frequency doubling effect generated by the sloshing nonlinearity in TLD has been confirmed for use in the vibration control of higher-order modes of structures. On the premise of constant mass ratio, it is suggested to adopt a multi-TLD damping system, in which each damper is installed at the height of the maximum displacement of each structural mode.