bluuebunny/crossref_metadata_2025_split huggingface dataset:
Best practices for single-cell histone modification analysis
Authors: Raimundo Félix , Prompsy Pacôme , Vert Jean-Philippe , Vallot Céline 
Published: September 2022

AbstractBackgroundSingle-cell histone post translation modification (scHPTM) assays such as scCUT&Tag or scChIP-seq allow single-cell mapping of diverse epigenomic landscapes within complex tissues, and are likely to unlock our understanding of various epigenetic mechanisms involved in development or diseases. Running an scHTPM experiment and analyzing the data produced remains, however, a challenging task since few consensus guidelines exist currently regarding good practices for experimental design and data analysis pipelines.MethodsWe perform a computational benchmark to assess the impact of experimental parameters and of the data analysis pipeline on the ability of the cell representation produced to recapitulate known biological similarities. We run more than ten thousands experiments to systematically study the impact of coverage and number of cells, of the count matrix construction method, of feature selection and normalization, and of the dimension reduction algorithm used.ResultsThe analysis of the benchmark results allows us to identify key experimental parameters and computational choices to obtain a good representation of single-cell HPTM data. We show in particular that the count matrix construction step has a strong influence on the quality of the representation, and that using fixed-size bin counts outperforms annotation-based binning; that dimension reduction methods based on latent semantic indexing outperform others; and that feature selection is detrimental, while keeping only high-quality cells has little influence on the final representation as long as enough cells are analyzed.
LINC02428, a liver-specific long noncoding RNA suppresses hepatocellular carcinoma progression
Authors: Zhang Qiangnu , Yan Lesen , Chen Jiaojuan , Liu Liping 
Published: September 2022

AbstractThere is growing evidence that lncRNAs play an important role in the progression of HCC, especially liver-specific expression of lncRNAs. LINC02428 is a liver-specific labeled lncRNA, but its role in HCC is unclear. We investigated the expression characteristics of LINC02428 in hepatocellular carcinoma tissues and analyzed its function in HCC. Using TCGA public data we found that the expression level of LINC02428 was significantly reduced in hepatocellular carcinoma tissues, compared to normal tissues. LINC02428 was also significantly reduced in hepatocellular carcinoma tissues in our cDNA microarray data from HCC patients. Survival analysis suggests that HCC patients with lower LINC02428 have a lower overall survival rate. In an in vitro analysis, overexpression of LINC02428 inhibited HCC cell proliferation, migration, and induced apoptosis. In conclusion, we report for the first time the expression profile of a liver-specific lncRNA, LINC02428, in HCC and confirmed its ability to inhibit the progression of HCC. LINC02428 may become a new target for the diagnosis and treatment of HCC.
Development of a Novel Air-Liquid Interface Airway Tissue Equivalent Model for In Vitro Respiratory Modeling Studies
Authors: Leach Timothy , Gandhi Uma , Reeves Kimberly D. , Stumpf Kristina , Okuda Kenichi , Marini Frank C. , Walker Steve , Chan Jeannie , Cox Laura A. , Atala Anthony , Murphy Sean V. 
Published: September 2022

AbstractThe human airways are complex structures with important interactions between cells, extracellular matrix (ECM) proteins and the biomechanical microenvironment. A robust, well-differentiated in vitro culture system that accurately models these interactions would provide a useful tool for studying normal and pathological airway biology. Here, we report the feasibility and analysis of a physiologically relevant air-liquid interface (ALI) 3D airway ‘organ tissue equivalent’ (OTE) model with three novel features: native pulmonary fibroblasts, solubilized lung ECM, and hydrogel substrate with tunable stiffness and porosity. We demonstrate the versatility of the OTE model by evaluating the impact of these features on human bronchial epithelial (HBE) cell phenotype. Variations of this model were analyzed during 28 days of ALI culture by evaluating epithelial confluence, trans-epithelial resistance, and epithelial phenotype via multispectral immuno-histochemistry and next-generation sequencing. Cultures that included both solubilized lung ECM and native pulmonary fibroblasts within the hydrogel substrate formed well-differentiated ALI cultures that maintained a barrier function and expressed mature epithelial markers relating to goblet, club and ciliated cells. Modulation of hydrogel stiffness did not negatively impact HBE differentiation and could be a valuable variable to alter epithelial phenotype. This study highlights the feasibility and versatility of a 3D airway OTE model to model the multiple components of the human airway 3D microenvironment.
Investigating the disclosure compliance of Basel III in emerging markets: a comparative study between UAE and Indian banks
Authors: Thomas Suja Sarah , Bansal Manish , Ahmed Ibrahim Elsiddig 
Published: September 2022

Purpose
This study aims at investigating banks’ compliance with the disclosure requirements of Basel III in two emerging market economies, namely, the United Arab Emirates (UAE) and India. This study also examines the impact of economic factors on the extent of disclosures.

Design/methodology/approach
The authors compare the Basel disclosure practices between UAE and Indian listed banks and have used panel data regression models to investigate the compliance and level of reporting based on three market variables, namely, size, leverage and profitability of listed banks.

Findings
After examining Basel reporting for each of three categories of independent factors, size was found to be the predominant factor influencing the Basel disclosures, followed by profitability and degree of financial leverage. It is prudent for all the banks irrespective of size to capitalize on themselves with an intent to tide over the frequent economic crises and prevent every economic crisis from becoming a full-blown financial crisis.

Practical implications
The findings suggest that there is an urgent need for a high level of concerted action in the context of listed banks in the selected emerging market nations to direct more resources to ensure full compliance with Basel III. The findings inform practitioners in emerging countries of compliance and plan expanded future applications. Investors should consider the BASEL compliance level of Banks before parking their funds in the bank’s stocks. The banks having a higher degree of compliance are expected to be safer than their counterparts having lower Basel compliance.

Originality/value
Many previous studies have examined the implementation of Basel III in general. This study is specific in assessing the compliance with disclosure requirements as prescribed by Pillar III of the Basel norms. To the best of the authors’ knowledge, this is the first research to compare market discipline in emerging markets. Existing studies have either assessed the level of compliance in one individual or similar types of markets. However, this study made a pioneering attempt to compare two different countries in the same category (emerging markets).
Differential impact of work-based learning on employee agility, ambidexterity and proactive goal generation
Authors: Hanu Charles , Amegbe Hayford , Yawson Monica Dede Tekyi Ansah , Mensah Philip 
Published: September 2022

Purpose
This study aims to examine the moderating effect of supportive organisational culture (SOC) on the differential impact of work-based learning (WBL) on employee agility, ambidexterity and proactive goal generation.

Design/methodology/approach
A cross-sectional survey was conducted using an online structured questionnaire with 443 respondents in Ghana. The data set was analysed using structural equation modelling.

Findings
The outcomes of the study show that WBL has a significant and positive impact on employee agility, ambidexterity and proactive goal generation. However, the effect on employee agility was higher, followed by proactive goal generation and employee ambidexterity. The moderating effect of SOC on H1, H3a and H3b was found to have a decreasing effect.

Originality/value
This study augments knowledge by examining how different approaches to WBL collectively affect proactive goal generation, agility and ambidexterity. To the best of the authors’ knowledge, this is the first attempt to examine the differential impact of summative WBL approaches on employee outcomes.
Consumer understanding of sugar types predicts food label use
Authors: Clarke Chantelle , Abel Kate , Best Talitha 
Published: September 2022

Purpose
There is growing awareness internationally of the need to reduce intake of added sugars. The purpose of this study was to examine consumer sugar knowledge and food label use.

Design/methodology/approach
This cross-sectional online survey included 229 adult participants (85% female and 15% male). Participants completed measures of demographics, sugar knowledge, interest in food and nutrition, food choice motivations and beliefs and food label use. The sample of convenience showed that participants were from Australasia (n = 90), the USA (n = 90) and other Western (Europe and Canada, n = 49) countries.

Findings
Overall, participant sugar knowledge predicted nutrition label use over and above individual demographic and psychological characteristics (interest in food and nutrition, health beliefs and food choice motivations) (p < 0.001). Country comparisons revealed that those in Australasia reported lower sugar knowledge compared to the USA (p =< 0.001) and other Western countries (p = 0.028).

Research limitations/implications
Overall, participant sugar knowledge predicted nutrition label use over and above individual demographic and psychological characteristics (interest in food and nutrition, health beliefs and food choice motivations) (p < 001). Country comparisons revealed that those in Australasia reported lower sugar knowledge compared to the USA (p =< 0.001) and other Western countries (p = 0.028).

Originality/value
This study explored sugar knowledge as a unique predictor of food label use, taking into account individual characteristics in demographics, food choice motivations and health beliefs.
Dysphagia in nursing home residents: a cross-sectional study
Authors: Oliveira Isabel de Jesus , Ferreira Flávio Filipe Sousa , Fernandes Licínia Vanessa Rodrigues 
Published: September 2022

Purpose
This paper aims to disseminate the results of research aiming to identify the prevalence of dysphagia and related clinical factors in nursing home residents.

Design/methodology/approach
A cross-sectional descriptive study was developed, including 99 residents in five nursing homes. A sociodemographic questionnaire and the Gugging Swallowing Screen for dysphagia screening were used for data collection.

Findings
The prevalence of dysphagia was 59.59%. A significant correlation was found between dysphagia and worse scores for fall risk, pressure ulcer, level of independence for activities of daily living and cognitive functioning.

Research limitations/implications
Results should be interpreted carefully due to sample size and specific country context. A larger sample must be achieved in further research.

Practical implications
Nurses must receive proper training to perform systematic dysphagia screening, and it should be considered, given the high prevalence, the inclusion of professionals specially trained for rehabilitating dysphagic residents in nursing home teams.

Social implications
The social and economic burden of dysphagia, in addition to all the implications on the person’s quality of life, requires a differentiated focus on this issue by nursing home managers.

Originality/value
Nursing homes have nurses providing health care; however, trained professionals for dysphagia treatment commonly are not. These results highlight the importance of systematic screening for dysphagia in all residents, thus promoting timely intervention to prevent respiratory and nutritional complications.
Global drivers of variation in cup nest size in passerine birds
Authors: Vanadzina Karina , Street Sally E. , Healy Susan D. , Laland Kevin N. , Sheard Catherine 
Published: September 2022

Abstract

The size of a bird's nest can play a key role in ensuring reproductive success and is determined by a variety of factors. The primary function of the nest is to protect offspring from the environment and predators. Field studies in a number of passerine species have indicated that higher‐latitude populations in colder habitats build larger nests with thicker walls compared to lower‐latitude populations, but that these larger nests are more vulnerable to predation. Increases in nest size can also be driven by sexual selection, as nest size can act as a signal of parental quality and prompt differential investment in other aspects of care. It is unknown, however, how these microevolutionary patterns translate to a macroevolutionary scale.

Here, we investigate potential drivers of variation in the outer and inner volume of open cup nests using a large dataset of nest measurements from 1117 species of passerines breeding in a diverse range of environments. Our dataset is sourced primarily from the nest specimens at the Natural History Museum (UK), complemented with information from ornithological handbooks and online databases.

We use phylogenetic comparative methods to test long‐standing hypotheses about potential macroevolutionary correlates of nest size, namely nest location, clutch size and variables relating to parental care, together with environmental and geographical factors such as temperature, rainfall, latitude and insularity.

After controlling for phylogeny and parental body size, we demonstrate that the outer volume of the nest is greater in colder climates, in island‐dwelling species and in species that nest on cliffs or rocks. By contrast, the inner cup volume is associated solely with average clutch size, increasing with the number of chicks raised in the nest. We do not find evidence that nest size is related to the length of parental care for nestlings.

Our study reveals that the average temperature in the breeding range, along with several key life‐history traits and proxies of predation threat, shapes the global interspecific variation in passerine cup nest size. We also showcase the utility of museum nest collections—a historically underused resource—for large‐scale studies of trait evolution.
Manifestation of TASER drive stun burn marks on fabrics
Authors: Ruffo Hannah Elizabeth , Liscio Eugene , Cao Wanying , Zhou Yu Ran , Doucette Corrin 
Published: September 2022

AbstractThe TASER® is a type of conducted energy weapon (CEW) used with increasing frequency by law enforcement to subdue subjects in circumstances where compliance is necessary. When operated in the drive stun method of deployment, the electrodes at the head of this CEW are intended to make direct contact with a surface, generating heat and light which may result in burn marks as a by‐product of the electrical discharge that occurs. This research aims to tackle a crucial gap in CEW research that fails to address the appearance of burn marks on fabrics. A drive stun duration (DSD) of 1, 3, and 5 s was used with three TASER models (X26P, X2, & TASER 7) on three fabrics (white 100% cotton, 100% polyester, 35:65 cotton‐polyester blend) with an underlying backing of pork hock. Using a Keyence VHX‐6000 confocal microscope, high magnification images were taken to observe any qualitative changes to the fabric. On polyester fabric, with increasing DSD, darker brown discoloration occurred. Additionally, on polyester fabric, the spatial orientation of the burn marks corresponded with that of the electrodes at the muzzle of each TASER model. These features enabled the correct identification of the TASER model and DSD on polyester fabric in the blind tests performed. Evidence of burn marks on cotton and blend fabrics were both limited and inconsistent such that no features were sufficiently unique to link them to any TASER model or DSD. Despite this, overall features such as discoloration and the formation of holes on these fabric types may be sufficiently unique to suggest the use of a CEW.
A Middle Pleistocene Glaciation Record from Lacustrine Sediments in the Western Tibetan Plateau and Discussion on Climate Change
Authors: ZHAO Zhenming , JI Wenhua , FU Chaofeng 
Published: September 2022

AbstractThe Tibetan Plateau is an important area for studying global climate change, but the answers to many scientific problems remain unknown. Here, we present new information from the lacustrine sedimentary record in the western Tibetan Plateau, related to the third most‐recent glaciations. Continuous sediment data, including sporopollen, particle size, total organic carbon, mass susceptibility, CaCO3, CaSO4, BaSO4 contents and chronological data, were reconstructed and revealed that climate and environmental conditions obviously and distinctly changed between 600 and 700 thousand years ago. In comparison, the data obtained from the Guliya ice core in this area also corresponds to the global glacial climatic characteristics recorded in basin sediments in the eastern and southeastern regions of the plateau and to the information obtained from ice cores in the Antarctic and Arctic regions. In this study, we conclude that the main reason for the glaciations and new tectonic movement must be a geomagnetic polarity reversal 774 thousand years ago (from Matuyama to Brunhes). Indeed, the results of this study suggest that the described reversal event might have influenced the current global climate pattern and will continue to impact climatic changes in the future.
A Comparison Study of Synkinematic Illite Isolation, Quantitative X‐ray Powder Diffraction, and K‐Ar Dating for Direct Fault Gouge Analyses
Authors: ZHENG Yong , LI Haibing , LI Junjie , ZHANG Guohe , SI Jialiang 
Published: September 2022

AbstractK‐Ar dating of synkinematic illite is increasingly recognized as a central method to constrain the timing of shallow crustal faulting. Methods of efficient sample preparation and quantitative identification of illite polytypes are critical to acquiring K‐Ar isotope data for authigenic clays. In this respect, we compared the commonly used clay size separation method through centrifugation with vacuum filtration technology, showing that the former is prone to extract fractions with finer particle sizes under similar conditions, thus improving the error in the authigenic end‐member age. Additionally, we demonstrated that the side‐packed mounting method for X‐ray diffraction analysis can significantly enhance the randomness in powder samples, thus improving the quantification accuracy compared with the front‐packed and back‐packed methods. The validity of our quantification method was confirmed by comparing Profex® modeling patterns with a suite of synthetic mixtures of known compositions, yielding an average analytical error of 3%. Dating results of these artificial mixtures and the reference materials indicated that a large range in percentages of detrital illite and a sufficient amount of age data will produce reliable results for ages of both extrapolated end‐members. However, if the range is limited, the extrapolated age close to those of datasets is still reliable.
Pazopanib for treating rhabdomyosarcoma in adult patients with poor performance status: A case report
Authors: Nishii Yuuya , Sasaki Jun , Sudou Misa , Yano Ryo , Tokisawa Saeko , Takaki Reiko , Tokito Takaaki , Hoshino Tomoaki 
Published: September 2022

AbstractRhabdomyosarcoma (RMS) is a common soft tissue sarcoma usually observed in children. However, RMS rarely occurs in adults. The prognosis of adult RMS is poor and a standard chemotherapy regimen has not yet been established. Herein, we report the case of a 60‐year‐old Japanese woman with primary anterior mediastinal alveolar RMS (T3N0M0, stage III). The tumor increased aggressively despite first‐line treatment with doxorubicin (60 mg/m2 every 3 weeks for 1 cycle) and second‐line treatment with eribulin (1.4 mg/m2 every 3 weeks for 2 cycles). Although her shortness of breath and chest tightness worsened as the tumor compressed her heart and left main bronchus, and her performance status (PS) decreased to 3, third‐line treatment with pazopanib (800 mg once daily) was commenced. The treatment led to suppression of tumor growth and resulted in 4‐month progression‐free survival. Therefore, in cases of adult RMS, considering pazopanib treatment as an option may be beneficial, even with previous ineffective treatments or poor PS.
Bioavailability and cardiovascular effects of adrenaline administered by Anapen 500 μg auto‐injector in healthy volunteers
Authors: Duvauchelle Thierry , Robert Philippe , Donazzolo Yves , Loyau Sabrina , Orlandini Bernard , Lehert Philippe , Lecomte Jeanne‐Marie , Schwartz Jean‐Charles 
Published: September 2022

AimsAnaphylaxis guidelines recommend intramuscular adrenaline, commonly 300 μg administered using an auto‐injector device. However, overweight/obese patients may require a higher adrenaline dose for adequate cardiovascular (CV) response. This study evaluated the pharmacokinetics (PK) and pharmacodynamic (PD) CV profiles after a single 500 μg adrenaline injection via Anapen auto‐injector in healthy normal weight males and otherwise healthy, overweight or obese females.MethodsIn this exploratory open‐label, single‐centre study, 54 healthy volunteers aged 18‐50 years received a single 500 μg adrenaline injection (Anapen auto‐injector) in the thigh (antero‐lateral middle third [18 males] or antero‐inferior third [36 females]). Assessments included depot depth (ultrasonography), plasma adrenaline levels (liquid chromatography‐tandem mass spectrometry) and heart rate (HR; ECG Holter monitor).ResultsUltrasonography showed that 82.4% of normal weight males received intramuscular injections; all overweight and obese females received subcutaneous injections. Anapen injection produced rapid increases in circulating adrenaline levels and significant increases in systolic blood pressure (SBP) and HR. Second peak plasma adrenaline concentrations (Cmax2) were reduced, and time to Cmax2 increased in overweight and obese females compared with males with normal body mass index; area under the curve (0–240 min) (AUC(0‐240)) was increased in overweight and obese females. Obese females had reduced maximal SBP values compared with normal weight males or overweight females; overweight and obese females had markedly different HR time courses compared with normal weight males.ConclusionA 500 μg adrenaline injection via Anapen produced rapid PK/PD changes in normal weight, overweight and obese subjects, irrespective of intramuscular or subcutaneous injection, and was well tolerated.