bluuebunny/crossref_metadata_2025 huggingface dataset:
An all-atom protein generative model
Authors: Chu Alexander E. , Cheng Lucy , El Nesr Gina , Xu Minkai , Huang Po-Ssu
Published: May 2023

Abstract

Proteins mediate their functions through chemical interactions; modeling these interactions, which are typically through sidechains, is an important need in protein design. However, constructing an all-atom generative model requires an appropriate scheme for managing the jointly continuous and discrete nature of proteins encoded in the structure and sequence. We describe an all-atom diffusion model of protein structure, Protpardelle, which instantiates a “superposition” over the possible sidechain states, and collapses it to conduct reverse diffusion for sample generation. When combined with sequence design methods, our model is able to co-design all-atom protein structure and sequence. Generated proteins are of good quality under the typical quality, diversity, and novelty metrics, and sidechains reproduce the chemical features and behavior of natural proteins. Finally, we explore the potential of our model conduct all-atom protein design and scaffold functional motifs in a backbone- and rotamer-free way.
The T2T-CHM13 reference genome has more accurate sequences for immunoglobulin genes than GRCh38
Authors: Nie Junli , Tellier Julie , Tarasova Ilariya , Nutt Stephen L. , Smyth Gordon K.
Published: May 2023

Background

The production of antibody by members of the B-cell lineage is essential for protective immunity. The clonal selection theory posits that each mature B cell has a unique immunoglobulin receptor, generated through random gene recombination, and when stimulated to differentiate into an antibody-secreting cell has the capacity to produce only a single antibody specificity. Based on this classical, “one cell one antibody” dogma, analysis of single cell RNA sequencing data of antibody-secreting cells should reveal that each cell expresses only a single form of each of the immunoglobulin heavy and light chains. However, when using GRCh38 as the genome reference, many plasma cells appear to express multiple immunoglobulin isotypes.

Results

We show that this false mapping is caused by the inaccurate immunoglobulin sequences provided by GRCh38. The newly published human genome reference T2T-CHM13, due to its more accurate sequences, avoids this false mapping caveat. In addition, further reads mapped to GRCh38 with ambiguity also settle down perfectly.

Conclusions

These studies reveal that the sequences of the immunoglobulin genes within T2T-CHM13 are more accurate than GRCh38. Thus T2T-CHM13 is the reference genome of choice for accurate mapping and identification of the human immunoglobulin genes.
Low-dimensional neural manifolds for the control of constrained and unconstrained movements
Authors: Altan Ege , Ma Xuan , Miller Lee E. , Perreault Eric J. , Solla Sara A.
Published: May 2023

Across many brain areas, neural population activity appears to be constrained to a low-dimensional manifold within a neural state space of considerably higher dimension. Recent studies of the primary motor cortex (M1) suggest that the activity within the low-dimensional manifold, rather than the activity of individual neurons, underlies the computations required for planning and executing movements. To date, these studies have been limited to data obtained in constrained laboratory settings where monkeys executed repeated, stereotyped tasks. An open question is whether the observed low dimensionality of the neural manifolds is due to these constraints; the dimensionality of M1 activity during the execution of more natural and unconstrained movements, like walking and picking food, remains unknown. We have now found similarly low-dimensional manifolds associated with various unconstrained natural behaviors, with dimensionality only slightly higher than those associated with constrained laboratory behaviors. To quantify the extent to which these low-dimensional manifolds carry task-relevant information, we built task-specific linear decoders that predicted EMG activity from M1 manifold activity. In both settings, decoding performance based on activity within the estimated low-dimensional manifold was the same as decoding performance based on the activity of all recorded neurons. These results establish functional links between task-specific manifolds and motor behaviors, and highlight that both constrained and unconstrained behaviors are associated with low-dimensional M1 manifolds.
A comparative genomics approach reveals a local genetic signature ofLeishmania tropicain Morocco
Authors: Talimi Hasnaa , Daoui Othmane , Bussotti Giovanni , Mhaidi Idris , Boland Anne , Deleuze Jean-François , Fissoune Rachida , Späth Gerald F. , Lemrani Meryem
Published: May 2023

In Morocco, cutaneous leishmaniasis (CL) caused byLeishmania(L.)tropicais an important health problem. Despite its high incidence in the country, the genomic heterogeneity of these parasites is still incompletely understood. In this study, we sequenced the genomes of 14 Moroccan isolates ofL. tropicacollected from confirmed cases of CL to investigate their genomic heterogeneity. Comparative genomics analyses were conducted by applying the recently established Genome Instability Pipeline (GIP), which allowed us to conduct phylogenomic and PCA analyses, and to assess genomic variations at the levels of the karyotype, gene copy number, and single nucleotide polymorphisms (SNPs). The results identified a core group of 12 isolates that were genetically highly related but evolutionarily distant to the reference genome as judged by the presence of over 100,000 SNPs, 75% of which were shared inside this core group. In addition, we identified two highly divergent strains, M3015 and Ltr_16, that were phylogenetically distinct between each other as well as to the core group and the reference genome. Read-depth analysis revealed important karyotypic variations across all isolates and uncovered important differences in gene copy number between the isolates of the core group and theL. tropicareference genome, as well as between the core group and M3015. In conclusion, our NGS results suggest the presence of a local SNP signature that distinguishes MoroccanL. tropicafrom other endemic regions and from the reference genome. These results pave the way for future research with a larger number of strains that will allow to correlate diverse phenotypes (resistance to treatments, virulence) and origins (geography, host species, year of isolation) to defined genomic signals that may represent interesting biomarker candidates.
CRISPR/Cas9-based depletion of 16S ribosomal RNA improves library complexity of single-cell RNA-sequencing
Authors: Wang Kuang-Tse , Adler Carolyn E.
Published: May 2023

Background

Single-cell RNA-sequencing (scRNA-seq) relies on PCR amplification to retrieve information from vanishingly small amounts of starting material. To selectively enrich mRNA from abundant non-polyadenylated transcripts, poly(A) selection is a key step during library preparation. However, some transcripts, such as mitochondrial genes, can escape this elimination and overwhelm libraries. Often, these transcripts are removedin silico, but whether physical depletion improves detection of rare transcripts in single cells is unclear.

Results

We find that a single 16S ribosomal RNA is widely enriched in planarian scRNA-seq datasets, independent of the library preparation method. To deplete this transcript from scRNA-seq libraries, we design 30 single-guide RNAs spanning its length. To evaluate the effects of depletion, we perform a side-by-side comparison of the effects of eliminating the 16S transcript and find a substantial increase in the number of genes detected per cell, coupled with virtually complete loss of the 16S RNA. Moreover, we systematically determine that library complexity increases with a limited number of PCR cycles following CRISPR treatment. When compared toin silicodepletion of 16S, physically removing it reduces dropout rates, retrieves more clusters, and reveals more differentially-expressed genes.

Conclusions

Our results show that abundant transcripts reduce the retrieval of informative transcripts in scRNA-seq and distort the analysis. Physical removal of these contaminants enables the detection of rare transcripts at lower sequencing depth, and also outperformsin silicodepletion. Importantly, this method can be easily customized to deplete any abundant transcript from scRNA-seq libraries.
Exploring the impact of incentive policy on the development of prefabricated buildings: a scenario-based system dynamics model
Authors: Han Yanhu , Fang Xiao , Zhao Xinyu , Wang Lufan
Published: May 2023

Purpose

The development of prefabricated buildings has become one of the primary solutions to transform the traditional construction industry around the world. Incentive policy is one of the important driving factors for the development of prefabricated building. The policy system in the field of prefabricated buildings needs to be improved urgently. However, there is still a dearth of research on how incentive policies exert impact on the development of prefabricated buildings. This paper aims to reveal the impact mechanisms of different types of policies on the development system of prefabricated buildings.

Design/methodology/approach

This study categorizes prefabricated building policies, constructs a system dynamics model of prefabricated building policies and conducts scenario simulations to examine the impact and sensitivity of different types of policies on the development system of prefabricated buildings.

Findings

The results show that compulsory policies play a greater role in the early stage of prefabricated building development and need to be withdrawn at the right time. Preferential and encouraging policies play an incentive role in the middle and later stages of prefabricated building development. Encouraging policies predominate in the later stage of prefabricated building development. Based on the research results, policy recommendations for prefabricated building development are put forward respectively from the government, developers and consumers.

Originality/value

The research results are expected to make up for the lack of clear policies paths in existing research and provide theoretical references for the formulation and optimization of future policies.
A contingency approach for time-cost trade-off in construction projects based on machine learning techniques
Authors: Wang Peipei , Wang Kun , Huang Yunhan , Fenn Peter
Published: May 2023

Purpose

Time-cost trade-off is normal conduct in construction projects when projects are expectedly late for delivery. Existing research on time-cost trade-off strategic management mostly focused on the technical calculation towards the optimal combination of activities to be accelerated, while the managerial aspects are mostly neglected. This paper aims to understand the managerial efforts necessary to prepare construction projects ready for an upcoming trade-off implementation.

Design/methodology/approach

A preliminary list of critical factors was first identified from the literature and verified by a Delphi survey. Quantitative data was then collected by a questionnaire survey to first shortlist the preliminary factors and quantify the predictive model with different machine learning algorithms, i.e. k-nearest neighbours (kNN), radial basis function (RBF), multiplayer perceptron (MLP), multinomial logistic regression (MLR), naïve Bayes classifier (NBC) and Bayesian belief networks (BBNs).

Findings

The model's independent variable importance ranking revealed that the top challenges faced were the realism of contractual obligation, contractor planning and control and client management and monitoring. Among the tested machine learning algorithms, multilayer perceptron was demonstrated to be the most suitable in this case. This model accuracy reached 96.5% with the training dataset and 95.6% with an independent test dataset and could be used as the contingency approach for time-cost trade-offs.

Originality/value

The identified factor list contributed to the theoretical explanation of the failed implementation in general and practical managerial improvement to better avoid such failure. In addition, the established predictive model provided an ad-hoc early warning and diagnostic tool to better ensure time-cost implementation success.
Asymmetric information, capacity constraint and segmentation in credit markets
Authors: Chakraborty Pallabi , Mahanta Amarjyoti
Published: May 2023

Purpose

The purpose of this study is to propose a model of competition between a formal lender (bank) and an informal lender (moneylender) with informational asymmetry between these two lenders. Further, the authors introduce capacity constraint on the lending capacity of the moneylender and assume that borrowers differ in risk and wealth.

Design/methodology/approach

The solution concept of Nash equilibrium has been used to derive the optimal strategies of the lenders.

Findings

The equilibrium strategies in most of the results depend on the difference between the expected returns from risky and safe projects where the risky project has higher expected returns. The credit market is segmented in terms of risk and wealth levels. Rationing of poor safe borrowers from the credit market is inevitable when the moneylender's capacity is sufficiently small, suggesting a low-income trap for them. Further, when moneylender has capacity constraint of some form, a zero-profit outcome is never a Nash equilibrium outcome.

Research limitations/implications

There is a possibility of collusion between the lenders. However, the authors do not derive all possible outcomes under capacity constraint

Practical implications

When the informal lender has limited capacity, competition between formal and informal lenders may not alleviate credit rationing, instead aggravate the problem. Thus, the government should devise policies to ensure credit availability to resource poor households

Originality/value

While the literature models strategic interaction between lenders under the assumption of zero-profit (Bertrand Paradox) condition, this study shows that zero profit is not the only outcome under such a set-up. Also, in presence of capacity constraint of the moneylender, a zero-profit outcome is never a Nash equilibrium outcome for the lenders. There is an optimal contract at which the lenders differentiate in terms of repayment and collateral and earn positive profits under certain conditions.
The relationship between perception of well-being and depression among adolescents in Jordan: using PERMA model as a theoretical framework
Authors: Ghannam Bushra , Al Khatib Husam , Alzayyat Abeer , Hamdan Mansour Ayman
Published: May 2023

Purpose

Adolescence is a developmental stage of transition that is marked by multiple biopsychosocial changes that affect their well- and ill-being. This study aims to examine the multidimensional of well- and ill-being among adolescents, and to understand the relationship between well-being and depression using the PERMA model among school-age adolescents.

Design/methodology/approach

A descriptive, cross-sectional design was used to recruit 625 school-age adolescents (343 males and 282 females), using convenience sampling technique from the central district of Jordan. Self-administered questionnaire was used to collect data in relation to depression and well-being.

Findings

The analysis revealed that 32% had a well-being score below the median and 19% had severe depressive symptoms. Depression and well-being were moderately correlated, with the connectedness dimension being the most correlated to depression, whereas the engagement dimension was the least correlated. Females had higher scores on all subscales of depression and a significantly higher score on depression than males, whereas males had higher scores on all well-being dimensions and significantly higher scores on overall well-being than females.

Research limitations/implications

Adolescents’ mental health is compromised and affected by their perception of well-being, and a comprehensive psychoeducation for adolescents on how to enhance well-being might combat development of depressive symptoms.

Originality/value

This study used all PERMA model components to provide an in-depth description of adolescents’ well-being, which is a crucial initial phase in better understanding how this age group experiences well-being and how it connects to their ill-being, as indicated by their depressive symptoms. The in-depth description of adolescents’ well-being will aid in planning early intervention and prevention programs for mental illness.
Disable access compliance to university infrastructure: built environment students’ perceptions
Authors: Amoah Christopher , Bamfo-Agyei Emmanuel , Simpeh Fredrick
Published: May 2023

Purpose

Higher education institutions are the citadel of knowledge and are heavily involved in formulating building regulations and building infrastructure designs that must conform to the building regulations. The study aims to identify university infrastructures compliant with disabled access from the perspective of the built environment students in Ghanaian universities.

Design/methodology/approach

Questionnaire surveys were administered to 500 built environment students across ten technical universities in Ghana with a total population of 3066; 341 were expected based on the formula used. However, upon several reminders, 176 responded. Data collected were analysed using Statistical Package for the Social Sciences.

Findings

The findings show that all university facilities are not fully compliant with disabled access. Structures found to be least compliant are the laboratories, canteens, hall of residence, toilet facilities, football fields, places of worship and transport stations. The facilities with high compliance are the administration block, library, hospital building, lecture halls, department offices and ATM areas. The leading causes for this non-compliant are lack of enforcement of the building regulations, low level of disabled students’ enrolment, age of the building, lack of knowledge and poor building designs.

Practical implications

Compliance with disabled access makes universities world class and creates safe learning spaces for individuals with disabilities, enforcing the right to education for all individuals, particularly those with disabilities. Lack of compliance with disabled access will hamper the full utilisation of these facilities, thereby affecting quality education delivery to people with disabilities.

Originality/value

The findings are essential to the Ghanaian built environment, the lives of disabled individuals and universities. The results provide knowledge on areas of improvement for complete access to structures and facilities by disabled individuals.
Preparation of cool composite pigment by the layer-by-layer assembling of phthalocyanine green on the surface of rutile TiO2
Authors: Cao Lingyun , Ren Shuaibin , Zhou ZhengHao , Fei Xuening , Huang Changliang
Published: May 2023

Purpose

This study aims to fabricate a cool phthalocyanine green/TiO2 composite pigment (PGT) with high near-infrared (NIR) reflectance, good color performance and good heat-shielding performance under sunlight and infrared irradiation.

Design/methodology/approach

With the help of anionic and cationic polyelectrolytes, the PGT composite pigment was prepared using a layer-by-layer assembly method under wet ball milling. Based on the light reflectance properties and color performance tested by ultraviolet-visible-NIR spectrophotometer and colorimeter, the preparation conditions were optimized and the properties of PGT pigment with different assembly layers (PGT-1, PGT-3, PGT-5 and PGT-7) were compared. In addition, their heat-shielding performance was evaluated and compared by temperature rise value for their coating under sunlight and infrared irradiation.

Findings

The PGT pigment had a core/shell structure, and the PG thickness increased with the self-assembly layers, which made the PGT-3 and PGT-7 pigment show higher color purity and saturation than PGT-1 pigment. In addition, the PGT-3 and PGT-7 pigment showed 11%–16% lower light reflectance in the visible region. However, their light reflectance in the NIR region was similar. Under infrared irradiation the PGT-5 and PGT-7 pigment coating showed 1.1°C–3.4°C and 1.3°C–4.7°C lower temperature rise value than PGT-1 pigment coating and physical mixture pigment coating, respectively. And under sunlight the PGT-3 pigment coating showed 1.5–2.6°C lower temperature rise value than the physical mixture pigment coating.

Originality/value

The layer-by-layer assembling makes the core/shell PGT composite pigment possess low visible light reflectance, high NIR reflectance and good heat-shielding performance.
The role of resin in optimizing the performance and printing properties of water-based inkjet inks for food packaging
Authors: Kusber Aniela , Gaida Rafał Józef , Dziubek Katarzyna , Wit Marian
Published: May 2023

Purpose

This study aims to investigate the influence of commercially available resins in water-based magenta pigment inkjet ink formulations on the properties of ink printability and the characteristics of ink application in food packaging. The impact of the resin on the jettability of the existing printability phase diagrams was also assessed.

Design/methodology/approach

Inks with different resin loadings were tested for selected properties, such as viscosity, particle size and surface tension. Stability was determined using a Turbiscan AGS turbidimeter and LumiFuge photocentrifuge analyzer. The ink layer fastness against abrasion and foodstuffs was evaluated using an Ugra device and according to PN-EN 646, respectively. JetXpert was used to assess Ricoh printhead jetting performance.

Findings

Printability diagrams successfully characterized the jettability of polyurethane inkjet inks on a multi-nozzle printhead and the binder improved droplet formation and printing precision.

Originality/value

Magenta water-based inkjet inks with commercial resins have been developed for printing on paper substrates. To the best of the authors’ knowledge, for the first time, inkjet ink stability was evaluated using the Turbiscan AGS and LumiFuge analyzers, and jettability models were verified using an industrial multi-nozzle printhead.
PLOD2 promotes colorectal cancer progression by stabilizing USP15 to activate the AKT/mTOR signaling pathway
Authors: Lan Jiawen , Zhang Sijing , Zheng Lin , Long Xiaoli , Chen Jianxiong , Liu Xunhua , Zhou Miao , Zhou Jun
Published: May 2023

Procollagen‐lysine, 2‐oxoglutarate 5‐dioxygenase 2 (PLOD2) has been reported as an oncogenic gene, affecting various malignant tumors, including endometrial carcinoma, osteosarcoma, and gastric cancer. These effects are mostly due to the enhanced deposition of collagen precursors. However, more studies need to be conducted on how its lysyl hydroxylase function affects cancers like colorectal carcinoma (CRC). Our present results showed that PLOD2 expression was elevated in CRC, and its higher expression was associated with poorer survival. Overexpression of PLOD2 also facilitated CRC proliferation, invasion, and metastasis in vitro and in vivo. In addition, PLOD2 interacted with USP15 by stabilizing it in the cytoplasm and then activated the phosphorylation of AKT/mTOR, thereby promoting CRC progression. Meanwhile, minoxidil was demonstrated to downregulate the expression of PLOD2 and suppress USP15, and the phosphorylation of AKT/mTOR. Our study reveals that PLOD2 plays an oncogenic role in colorectal carcinoma, upregulating USP15 and subsequently activating the AKT/mTOR pathway.
Risk factors for the development of sepsis in patients with cirrhosis in intensive care units
Authors: Kou Yan‐qi , Yang Yu‐ping , Du Shen‐shen , Liu Xiongxiu , He Kun , Yuan Wei‐nan , Nie Biao
Published: May 2023

Sepsis is a serious complication of liver cirrhosis. This study aimed to develop a risk prediction model for sepsis among patients with liver cirrhosis. A total of 3130 patients with liver cirrhosis were enrolled from the Medical Information Mart for Intensive Care IV database, and randomly assigned into training and validation cohorts in a 7:3 ratio. The least absolute shrinkage and selection operator (LASSO) regression was used to filter variables and select predictor variables. Multivariate logistic regression was used to establish the prediction model. Based on LASSO and multivariate logistic regression, gender, base excess, bicarbonate, white blood cells, potassium, fibrinogen, systolic blood pressure, mechanical ventilation, and vasopressor use were identified as independent risk variables, and then a nomogram was constructed and validated. The consistency index (C‐index), receiver operating characteristic curve, calibration curve, and decision curve analysis (DCA) were used to measure the predictive performance of the nomogram. As a result of the nomogram, good discrimination was achieved, with C‐indexes of 0.814 and 0.828 for the training and validation cohorts, respectively, and an area under the curve of 0.849 in the training cohort and 0.821 in the validation cohort. The calibration curves demonstrated good agreement between the predictions and observations. The DCA curves showed the nomogram had significant clinical value. We developed and validated a risk‐prediction model for sepsis in patients with liver cirrhosis. This model can assist clinicians in the early detection and prevention of sepsis in patients with liver cirrhosis.
Evidence of policy learning in emergency declarations as communication tools in Australia
Authors: Beccari Ben
Published: May 2023

Emergency declarations are important legal tools for the state to protect itself and its citizens during times of crisis. Such declarations permit the exercise of extraordinary powers to address an emergency or disaster. They present an opportunity to explore policy learning in crises, through the ability to examine emergency declaration instruments and the detail of post‐emergency inquiries and reviews. This paper briefly assesses Australian law that provides for emergency declarations and places it in the context of theories of policy learning and change. Two case studies reveal evidence of policy learning in emergency declaration practice in Australia. There is an emerging practice of using declarations primarily or purely as tools to communicate the seriousness of an emergency. This policy learning has occurred both within and between jurisdictions, including the federal government. This paper also probes opportunities for future research on policy learning and emergency legislation, especially in relation to the COVID‐19 pandemic.
Normal range of intraoperative three‐dimensionally derived right ventricular free‐wall strain in coronary artery bypass surgery patients
Authors: Labus Jakob , Winata Johan , Schmidt Torsten , Nicolai Joachim , Zwaag Stanislaw Vander , Sveric Kunislav , Wilbring Manuel , Scholz Markus , Fassl Jens
Published: May 2023

Background

Data on intraoperative three‐dimensionally derived right ventricular free‐wall strain (3D‐RV FWS) is sparse.

Objectives

We sought to evaluate the normal range of intraoperative 3D‐RV FWS in patients scheduled for coronary artery bypass graft (CABG) surgery and compared to conventional echocardiographic parameters. Prospective observational study.

Methods

A total of 150 patients with preserved left and right ventricular (RV) function and sinus rhythm, without significant heart valve disease or pulmonary hypertension undergoing isolated on‐pump CABG surgery, with an uneventful, complication‐free intraoperative course. 3D‐RV FWS analysis and conventional echocardiographic assessment of RV function were performed intraoperatively in anesthetized and ventilated patients using transesophageal echocardiography (TEE). TomTec 4D RV‐Function 2.0 software for assessment of 3D‐RV FWS and three‐dimensional right ventricular ejection fraction (3D‐RV EF). Philips QLAB 10.8 was used to evaluate tissue velocity of the tricuspid annulus (RV S´), tricuspid annular systolic excursion (TAPSE), and RV fractional area change (FAC). All echocardiographic measurements were performed under stable hemodynamic conditions and predefined fluid management without any vasoactive support or pacing. The prospective observational study was performed in a single university hospital setting.

Results

Assessment of 3D‐RV FWS was feasible in 95% of patients. No included patient experienced any serious perioperative complication. In our group of patients, median values with interquartile range (IQR) for 3D‐RV FWS and 3D‐RV EF were ‒25.2 (IQR ‒29.9 to ‒21.8) and 46.3% (IQR 41.0%‒50.1%), respectively. RV FAC, RV S´, and TAPSE accounted for 39.7% (IQR 34.5%‒44.4%), 14.8 cm/s (IQR 11.8‒19.0 cm/s), and 22 mm (IQR 20‒25 mm). The normal range (2.5% to 97.5% percentile) for 3D‐RV FWS was ‒37.1 to ‒12.8. There was no relevant correlation of 3D‐RV FWS to postoperative outcome in this group of CABG patients.

Conclusion

We present distribution values for intraoperative 3D‐RV FWS and conventional parameters of RV function assessment in a healthy on‐pump CABG patient population without serious perioperative complications. We observed no correlations of these parameters with any of the outcome parameters considered. Therefore, we consider these values to be intraoperative TEE‐assessed normal values, which can be expected in on‐pump CABG patients.
A qualitative analysis of adolescent motherhood within the broader family context in Peru
Authors: Levey Elizabeth J. , Morfín Rodriguez Alejandra E. , Chang Andrew R. , Rondon Marta B. , Jimenez Sanchez Maria Luisa , Harrison Alexandra M. , Gelaye Bizu , Becker Anne E.
Published: May 2023

Objective

The purpose of this study was to characterize the impact of adolescent pregnancy on families and describe the needs of adolescent mothers and their infants in order to assess the need for intervention and identify potential intervention targets.

Background

Adolescent mothers and their offspring face an increased risk of mental health problems. Adolescent mothers and their families also face significant resource constraints; 95% live in low‐ and middle‐income countries (LMICs). Cost‐effective interventions are needed to improve outcomes for this vulnerable group.

Method

This qualitative study conducted in Lima, Peru, consisted of four clinician focus groups and 18 in‐depth interviews with adolescent mothers and their family members. Data were coded thematically, and direct content analysis was employed.

Results

The study identified the following issues facing adolescent parents: the transition to parenthood, the need for family support, difficulty accessing support, the difficulty for family members of providing support, and ideas about responsibility and adolescent autonomy.

Conclusion

Overall, these findings demonstrate the need for interventions that engage families and address barriers to accessing support, including relationship conflict and differing beliefs about responsibility and autonomy.

Implications

Interventions are needed for adolescent mothers in LMICs that mobilize family support. Clinicians who care for these patients need to be aware of the family context and the resources available where they practice.
Using values in cognitive and behavioral therapy: A bridge back to philosophy
Authors: Martin Sylvia
Published: May 2023

Ancient therapeutic practices have influenced the development of cognitive behavioral therapy (CBT) theories such as Albert Ellis's rational emotive behavior therapy and Aaron Beck's cognitive therapy. By drawing inspiration from Socratic questioning, the importance of philosophy in evidence‐based practices in human mental health can be acknowledged. Stoicism has also informed CBT, notably its emphasis on establishing psychological distance from emotions. Cognition and emotion are two aspects of mental processes, and irrational demands are processed through rational deliberation. Using mental imaging techniques and acceptance strategies (to accept oneself and the world as imperfect), avoiding catastrophic interpretations and acknowledging emotions are also included among such practices.

Methods

We will explore the use of values across CBT, acceptance and commitment therapy (ACT), and radically open dialectical behavioral therapy (RO DBT) to clarify their use of values.

Results

In this framework, values are conceptualized as life‐orienting principles and are now widely used across CBTs, such as acceptance and commitment therapy and radically open dialectical behavioral therapy. In recent years, the development of CBT has involved a renewed relationship with philosophy through the use of values, interest in dialectics and development of self‐questioning practices reminiscent of classical Socratic principles. This movement from applied clinical psychology toward philosophical skills has also encouraged the recent emergence of philosophical health considerations. The opposition between psychological and philosophical health can be questioned, and the fundamental issue of philosophical skills implemented in psychiatric treatment (and not solely as practices of enhancement for the sane) needs to be considered.
Multi‐omics profiling of primary hepatic stellate cells from advanced liver fibrosis patients reveals distinctive molecular signatures
Authors: Dong Yutong , Liu Yuwei , Liu Xu , Ma Heming , Liu Yahui , Lv Guoyue , Niu Junqi
Published: May 2023

Background and Aim

Hepatic fibrosis is a common pathogenic outcome of almost all chronic liver diseases and a growing public health problem globally. However, the key genes or proteins driving liver fibrosis and cirrhosis are not well understood. We aimed to identify novel hepatic fibrosis genes of human primary hepatic stellate cells (HSCs).

Methods

Human primary HSCs were isolated from surgically resected advanced fibrosis liver tissues (n = 6) and surgical resection of normal liver tissue around hemangioma (n = 5). Differences in the expression levels of mRNA and proteins from HSCs in advanced fibrosis group and the control group were analyzed using RNA sequencing and mass spectrometry as transcriptomic and proteomic approaches. The obtained biomarkers were further validated through real‐time quantitative polymerase chain reaction (RT‐qPCR), immunofluorescence, and Western blot.

Results

A total of 2156 transcripts and 711 proteins were found to be differently expressed between the advanced fibrosis group and the control group patients. The Venn diagram shows that a total of 96 upregulated molecules are overlapped in both the transcriptomic and proteomic datasets. Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes analysis indicated that those overlapped genes were mainly involved in wound healing, cell adhesion regulation, and actin binding, which reflects the major biological conversions in liver cirrhosis process. Pyruvate kinase M2 and EH domain‐containing 2 were identified as potential new markers for advanced liver cirrhosis, which have been validated in primary human HSCs and in vitro cellular hepatic fibrosis model Lieming Xu‐2 (LX‐2) cells.

Conclusions

Our results revealed the major transcriptomic and proteomic changes during liver cirrhosis process and identified new biomarkers and potential therapeutic targets for advanced liver fibrosis.
Reusing Natural Experiments
Authors: HEATH DAVIDSON , RINGGENBERG MATTHEW C. , SAMADI MEHRDAD , WERNER INGRID M.
Published: May 2023

After a natural experiment is first used, other researchers often reuse the setting, examining different outcome variables. We use simulations based on real data to illustrate the multiple hypothesis testing problem that arises when researchers reuse natural experiments. We then provide guidance for future inference based on popular empirical settings including difference‐in‐differences, instrumental variables, and regression discontinuity designs. When we apply our guidance to two extensively studied natural experiments, business combination laws and the Regulation SHO pilot, we find that many results that were statistically significant using single hypothesis testing do not survive corrections for multiple hypothesis testing.
Association of intra‐shift nap duration with heart rate variability in medical night shift workers
Authors: Deng Saiyue , Wang Quan , Fan Jingjing , Lu Jiajia , Liu Wenhua , Wang Wei , Yang Yuan , Ding Fengfei , Mei Junhua , Ba Li
Published: May 2023

Napping during night shifts effectively reduces disease risk and improves work performance, but few studies have investigated the association between napping and physiological changes, particularly in off‐duty daily lives. Changes in the autonomic nervous system precede diseases like cardiovascular disease, diabetes, and obesity. Heart rate variability is a good indicator of autonomic nervous system. This study aimed to investigate the link between night shift nap durations and heart rate variability indices in the daily lives of medical workers. As indicators of chronic and long‐term alterations, the circadian patterns of heart rate variability indices were evaluated. We recruited 146 medical workers with regular night shifts and divided them into four groups based on their self‐reported nap durations. Heart rate variability circadian parameters (midline‐estimating statistic of rhythm, amplitude, and acrophase) were obtained by obtaining 24‐h electrocardiogram on a day without night shifts, plotting the data of the heart rate variability indices as a function of time, and fitting them into periodic cosine curves. Using clinical scales, depression, anxiety, stress, fatigue, and sleepiness were assessed. Linear regression analysis revealed a positive relationship between 61–120‐min naps and 24‐h, daytime, and night‐time heart rate variability indices, and the parasympathetic activity oscillation amplitude (indexed by high‐frequency power, the square root of the mean of the sum of squares of differences between adjacent normal intervals, standard deviation of short‐term R‐R‐interval variability) within one circadian cycle. This study indicated that napping for 61–120 min during night shifts could benefit medical workers’ health, providing physiological evidence to promote nap management.
External validity of the reduced Morningness–Eveningness Questionnaire for Children and Adolescents: an actigraphic study
Authors: Tonetti Lorenzo , Andreose Alice , Bacaro Valeria , Giovagnoli Sara , Grimaldi Martina , Natale Vincenzo , Crocetti Elisabetta
Published: May 2023

The aim of this study was to examine the external validity of the reduced Morningness–Eveningness Questionnaires for Children and Adolescents, using circadian motor activity, assessed through actigraphy, as an external criterion. Overall, 458 participants (269 females), with a mean (standard deviation) age of 15.75 (1.16) years, took part in this study. Each adolescent was requested to wear the actigraph Micro Motionlogger Watch actigraph (Ambulatory Monitoring, Inc., Ardlsey, NY, USA) around the non‐dominant wrist for 1 week. At the end of the actigraphic recording, participants completed the reduced Morningness–Eveningness Questionnaires for Children and Adolescents. We extracted the motor activity counts, minute‐by‐minute over the 24 h, to depict the 24‐h motor activity pattern, and we adopted the statistical framework of functional linear modelling to examine its changes according to chronotype. According to the reduced Morningness–Eveningness Questionnaires for Children and Adolescents cut‐off scores, 13.97% of participants (n = 64) belonged to the evening‐types category, 9.39% (n = 43) to morning‐types, while the remaining (76.64%, n = 351) to the intermediate‐types category. Evening types moved significantly more than the intermediate and morning types from around 10:00 p.m. to 2:00 a.m., while the opposite pattern of results was observed around 4:00 a.m. The results highlighted a significant difference in the 24‐h motor activity pattern between chronotypes, in line with the expectations based on their well‐known behaviour. Therefore, this study shows that the external validity of the reduced Morningness–Eveningness Questionnaire for Children and Adolescents, established by considering motor activity (recorded through actigraphy) as an external criterion, is satisfactory.
Eggonomics: Vitrification and bioeconomies of egg donation in the United States and Spain
Authors: Tober Diane , Pavone Vincenzo , Lafuente‐Funes Sara , Konvalinka Nancy
Published: May 2023

Regulations governing assisted reproduction control the degree to which gamete donation is legal and how people providing genetic material are selected and compensated. The United States and Spain are both global leaders in fertility treatment with donor oocytes. Yet both countries take different approaches to how egg donation is regulated. The US model reveals a hierarchically organized form of gendered eugenics. In Spain, the eugenic aspects of donor selection are more subtle. Drawing upon fieldwork in the United States and Spain, this article examines (1) how compensated egg donation operates under two regulatory settings, (2) the implications for egg donors as providers of bioproducts, and (3) how advances in oocyte vitrification enhances the commodity quality of human eggs. By comparing these two reproductive bioeconomies we gain insight into how different cultural, medical, and ethical frameworks intersect with egg donor embodied experiences.
‘First in family’ experiences in a Canadian medical school: A critically reflexive study
Authors: Wright Sarah R. , Boyd Victoria A. , Okafor Ike , Sharma Malika , Giroux Ryan , Richardson Lisa , Brosnan Caragh
Published: May 2023

Background

Medical students from affluent and highly educated backgrounds remain overrepresented in Canadian medical schools despite widespread efforts to improve diversity. Little is known of the medical school experiences of students who are first in their family (FiF) to attend university. Drawing on Bourdieu and a critically reflexive lens, this study explored the experiences of FiF students in a Canadian medical school to better understand the ways in which the medical school environment can be exclusive and inequitable to underrepresented students.

Methods

We interviewed 17 medical students who self‐identified as being FiF to attend university. Utilising theoretical sampling, we also interviewed five students who identified as being from medical families to test our emerging theoretical framework. Participants were asked to discuss what ‘first in family’ meant to them, their journey into medical school and their experiences at medical school. Bourdieu's theories and concepts were used as sensitising concepts to explore the data.

Results

FiF students discussed the implicit messages they received about who belongs in medical school, challenges in shifting from their pre‐medical lives to a medical identity and competing with peers for residency programmes. They reflected on the advantages they perceived they had over their fellow students due to their less ‘typical’ social backgrounds.

Conclusion

While medical schools continue to make strides when it comes to increasing diversity, inclusivity and equity require increased attention. Our findings highlight the ongoing need for structural and cultural change at admissions and beyond—change that recognises the much‐needed presence and perspectives that underrepresented medical students, including those who are FiF, bring to medical education and healthcare. Engaging in critical reflexivity represents a key way that medical schools can continue to address issues of equity, diversity and inclusion.
Arctic rooting depth distribution influences modelled carbon emissions but cannot be inferred from aboveground vegetation type
Authors: Blume‐Werry Gesche , Dorrepaal Ellen , Keuper Frida , Kummu Matti , Wild Birgit , Weedon James T.
Published: May 2023

The distribution of roots throughout the soil drives depth‐dependent plant–soil interactions and ecosystem processes, particularly in arctic tundra where plant biomass, is predominantly belowground. Vegetation is usually classified from aboveground, but it is unclear whether such classifications are suitable to estimate belowground attributes and their consequences, such as rooting depth distribution and its influence on carbon cycling.

We performed a meta‐analysis of 55 published arctic rooting depth profiles, testing for differences both between distributions based on aboveground vegetation types (Graminoid, Wetland, Erect‐shrub, and Prostrate‐shrub tundra) and between ‘Root Profile Types’ for which we defined three representative and contrasting clusters. We further analyzed potential impacts of these different rooting depth distributions on rhizosphere priming‐induced carbon losses from tundra soils.

Rooting depth distribution hardly differed between aboveground vegetation types but varied between Root Profile Types. Accordingly, modelled priming‐induced carbon emissions were similar between aboveground vegetation types when they were applied to the entire tundra, but ranged from 7.2 to 17.6 Pg C cumulative emissions until 2100 between individual Root Profile Types.

Variations in rooting depth distribution are important for the circumpolar tundra carbon‐climate feedback but can currently not be inferred adequately from aboveground vegetation type classifications.
Diagnostic and prognostic biomarkers for tubulointerstitial fibrosis
Authors: Rende Umut , Guller Anna , Goldys Ewa M. , Pollock Carol , Saad Sonia
Published: May 2023

Renal fibrosis is the final common pathophysiological pathway in chronic kidney disease (CKD) regardless of the underlying cause of kidney injury. Tubulointerstitial fibrosis (TIF) is considered to be the key pathological predictor of CKD progression. Currently, the gold‐standard tool to identify TIF is kidney biopsy, an invasive method that carries risks. Non‐invasive diagnostics rely on an estimation of glomerular filtration rate and albuminuria to assess kidney function, but these fail to diagnose early CKD accurately or to predict progressive decline in kidney function. In this review, we summarize the current and emerging molecular biomarkers that have been studied in various clinical settings and in animal models of kidney disease and that are correlated with the degree of TIF. We examine the potential of these biomarkers to diagnose TIF non‐invasively and to predict disease progression. We also examine the potential of new technologies and non‐invasive diagnostic approaches in assessing TIF. Limitations of current and potential biomarkers are discussed and knowledge gaps identified.

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Torus-Shaped Wave Energy Converter Attached to a Hinged Arm
Authors: Kamarlouei Mojtaba , Hallak Thiago S. , Gaspar José F. , Calvário Miguel , Soares C. Guedes
Published: May 2023

This study presents the adaptation of a torus-shaped prime mover of a wave energy converter to an onshore or nearshore fixed platform by a hinged arm, with the objective of providing more favorable conditions for device survivability at extreme sea state. An optimization code is developed to obtain the best prime mover and arm geometries, as well as the power take-off parameters, with the objective to maximize the total absorbed power. In this paper, the power take-off system is modeled as a simplified damper and spring system, where the parameters are optimized for the power absorption of the wave energy converter in each sea state, whereas the optimization process is performed with a genetic algorithm. The results indicate that better survivability performance may be achieved with the torus-shaped prime mover in comparison to a conventional one without a moonpool, despite a relatively lower wave-absorbed power.
Emerging frontiers in regenerative medicine
Authors: McKinley Kara L. , Longaker Michael T. , Naik Shruti
Published: May 2023

Bridging knowledge gaps could enable regenerative therapy