bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enabling interpretable machine learning for biological data with reliability scores
Authors: Ahlquist K. D. , Sugden Lauren , Ramachandran Sohini 
Published: February 2022

AbstractMachine learning has become an important tool across biological disciplines, allowing researchers to draw conclusions from large datasets, and opening up new opportunities for interpreting complex and heterogeneous biological data. Alongside the rapid growth of machine learning, there have also been growing pains: some models that appear to perform well have later been revealed to rely on features of the data that are artifactual or biased; this feeds into the general criticism that machine learning models are designed to optimize model performance over the creation of new biological insights. A natural question thus arises: how do we develop machine learning models that are inherently interpretable or explainable? In this manuscript, we describe reliability scores, a new concept for scientific machine learning studies that assesses the ability of a classifier to produce a reliable classification for a given instance. We develop a specific implementation of a reliability score, based on our work in Sugden et al. 2018 in which we introduced SWIF(r), a generative classifier for detecting selection in genomic data. We call our implementation the SWIF(r) Reliability Score (SRS), and demonstrate the utility of the SRS when faced with common challenges in machine learning including: 1) an unknown class present in testing data that was not present in training data, 2) systemic mismatch between training and testing data, and 3) instances of testing data that are missing values for some attributes. We explore these applications of the SRS using a range of biological datasets, from agricultural data on seed morphology, to 22 quantitative traits in the UK Biobank, and population genetic simulations and 1000 Genomes Project data. With each of these examples, we demonstrate how interpretability tools for machine learning like the SRS can allow researchers to interrogate their data thoroughly, and to pair their domain-specific knowledge with powerful machine-learning frameworks. We hope that this tool, and the surrounding discussion, will aid researchers in the biological machine learning space as they seek to harness the power of machine learning without sacrificing rigor and biological understanding.
Les déterminants d'accès à l'eau potable au Cameroun*
Authors: Dhin Etia Frank Charles , Mvogo Gregory , Honoré Bidiasse 
Published: February 2022

RésuméSur la base des données de la Cinquième Enquête Démographique de Santé réalisée auprès de 33 988 ménages au Cameroun, cet article identifie les déterminants d'accès à l'eau potable. De l'estimation d'une régression logistique multinomiale non ordonnée, les résultats montrent qu'il existe: une relation positive entre les ménages dirigés par les femmes et les probabilités d'accès à l'eau potable par robinet et par borne‐fontaine; une relation négative entre l'augmentation de la taille du ménage et ces probabilités d'accès. Une relation positive entre le quintile du bien‐être économique (catégorie la plus riche) et les probabilités d'accès à l'eau potable par robinet et forage; une relation positive entre le raccordement à l'électricité d'un ménage et la probabilité d'accès à l'eau potable par robinet. Enfin, une relation positive entre les ménages vivant en zones urbaines et les probabilités d'accès à ces trois catégories de sources d'eau potable améliorée que sont: l'eau par robinet, borne‐fontaine et forage. Sur ces déterminants, nous discutons les leçons pratiques de politiques publiques afin de favoriser l'accès à l'eau pour tous.
The effects of achievement goals and perceived reading instruction on Chinese student reading performance: Evidence from PISA 2018
Authors: Qian Quan , Lau Kit‐ling 
Published: February 2022

BackgroundResearch has shown that achievement goals and reading instruction play important roles in students' reading performance. However, little is known about the specific effects of different types of achievement goals and reading instructional practices on reading performance in mainland China.MethodsThis study used Programme of International Student Assessment (PISA) 2018 data to examine the effects of Chinese students' achievement goals and perceived reading instruction on reading performance. Four districts in mainland China, Beijing, Shanghai, Jiangsu, and Zhejiang (B–S–J–Z), participated in PISA 2018. A profile of B–S–J–Z students' achievement goals and perceived reading instruction compared with those in other East Asian societies is presented. The relative contributions of different achievement goals, instructional practices at the student and school levels, and their interactive effects on reading performance are then examined by using hierarchical linear modelling.ResultsThe results show that performance and avoidance goals are important for B–S–J–Z students' reading performance when classroom and school teaching environments are considered. The disciplinary climate, adaptative instruction and teachers' stimulation are positively related to reading performance at both the student and school levels. Some cross‐level interactions between personal achievement goals and school reading instruction are found.ConclusionsThe findings suggest that achievement goals and reading instructional practices at both the student and school levels contribute to Chinese students' reading performance. The relationships between school reading instruction practices and students' reading performance vary for different achievement goals.
Political socialization, political gender gaps and the intergenerational transmission of left‐right ideology
Authors: VAN DITMARS MATHILDE M. 
Published: February 2022

AbstractWhile left and right are the main terms to distinguish political views in Western Europe, the family socialization of citizens has mainly been studied in terms of partisan preferences rather than identification with these ideological blocks. Therefore, this study investigates the intergenerational transmission of left‐right ideological positions in two European multiparty systems. To investigate expectations regarding gendered patterns in political socialization, ideological transmission between mothers, fathers, daughters and sons are analyzed, making use of German and Swiss household data. The results underline the relevance of the family in the transmission of political ideology in multiparty systems, showing high contemporary parent–child concordance in ideological positioning in line with classic work in political socialization. Moreover, the study demonstrates how the gender‐generation gap in political ideology is consequential for this process. Young women consistently place themselves on the left of men across all combinations of parental ideology, which indicates that the gender‐generation gap trumps other gendered patterns in intergenerational transmission. Consequently, daughters are less likely than sons to take over their parents’ rightist positions, while parent–son transmission is equally large on the left and the right. This also means that left‐leaning parents have a general advantage over right‐leaning parents in having their ideological identification reproduced by their daughters. The study highlights the importance of differentiating between the transmission of left‐ and right‐wing ideology in political socialization processes. Moreover, it demonstrates that the distinction by offspring gender is imperative when studying the intergenerational transmission of traits that display gender differences within and between parental and offspring generations. The findings point at the active role of especially female offspring in the political socialization process, as they seem to be more strongly impacted by influences outside the family that sustain generational processes of further gender realignment.
Can “race‐neutral” program eligibility requirements in criminal justice have disparate effects? An examination of race, ethnicity, and prison industry employment
Authors: Anderson Claudia N. , Wooldredge John , Cochran Joshua C. 
Published: February 2022

AbstractResearch SummaryThis study assesses whether racial and ethnic disparities exist in prison industry employment and whether seemingly race‐ and ethnicity‐neutral eligibility requirements contribute to any such disparities. We examine whether there are racial/ethnic disparities in industrial prison work, the extent to which disparities are explained by administrative policies, and the conditions under which disparities are most pronounced. Using 10 years of prison administrative data from Ohio, this study employs multilevel and mediation analyses to examine the effects of race and ethnicity on the odds of working an industrial prison job. Results suggest that Black and Hispanic incarcerated persons (IPs) are less likely to work industry jobs than White IPs. The majority of this disparity stems from program requirements; however, some disparities maintain even when accounting for requirements. Black IPs who do not meet program requirements are less likely to work than White IPs who do not meet program requirements. Racial disparities are smaller in facilities with greater racial heterogeneity among correctional staff.Policy ImplicationsIn our discussion, we underscore how prison policies can contribute to racially and ethnically disparate incarceration experiences. The results suggest the importance of evaluating prison and other correctional policies that utilize selection criteria that appear race neutral but are likely to be disparate in their consequences. Moreover, policies aimed at diversifying staff may contribute to more equitable prison experiences for non‐White incarcerated people, although doing so does not directly address underlying policy problems that lead to inequalities.
Clinicopathological characteristics and prognostic factors of patients with primary gallbladder neuroendocrine carcinomas
Authors: Wang Wei , Yang Chuan Xin , Yu Xin Zhe , Zhang Shi Lei , Wang Jie , Wang Jian 
Published: February 2022

ObjectivesPrimary gallbladder neuroendocrine carcinomas (GB‐NEC) are malignant neoplasms that remained to be studied. In this study we aimed to summarize their clinicopathological characteristics, effective treatment and prognostic factors for patients with GB‐NEC.MethodsPatients with GB‐NEC admitted to Shanghai Jiao Tong University Affiliated Sixth People's Hospital and Renji Hospital, School of Medicine, Shanghai Jiao Tong University from October 2012 to August 2020 were enrolled. Clinicopathological characteristics of our patients and those reported in previous studies were recorded. The Kaplan‐Meier method and univariate and multivariate Cox regression analyses were used for survival analysis.ResultsAltogether 15 patients from our hospitals and 47 patients from previous studies were included. A total of 55 patients who underwent surgical resection, including R0 and non‐R0 resection, had significantly longer overall survival compared with the other seven patients. A univariate analysis indicated that patients aged 60 years or older, with jaundice, carcinoid syndrome, non‐R0 resection, and advanced stage were associated with worse survival. A multivariate analysis showed that patients aged 60 years or older, carcinoid syndrome and non‐R0 resection, but not lymphadenectomy and adjuvant chemotherapy, were independently related to reduced survival.ConclusionsR0 resection should be the first‐line treatment for GB‐NEC. Older age, carcinoid syndrome and non‐R0 resection are independently associated with reduced survival after surgical resection.
Extensive sequence divergence between the reference genomes of two zebrafish strains, Tuebingen and AB
Authors: Deng Yu , Qian Yuting , Meng Minghui , Jiang Haifeng , Dong Yang , Fang Chengchi , He Shunping , Yang Liandong 
Published: February 2022

AbstractThe zebrafish (Danio rerio) is one of the most widely used model organisms for studying vertebrate gene function and human disease, given the 70% conserved protein‐coding genes between zebrafish and human. Two of the most common laboratory zebrafish strains are Tuebingen and AB. Despite the fact that the zebrafish reference genome is derived from the Tuebingen strain, the AB strain is still widely used although a high‐quality genome comparable to Tuebingen is lacking. Here, we report a 1.40‐Gb representative de novo genome assembly of the AB strain (DrAB1), with contig N50 length of 21 Mb, by integrating Illumina short‐read sequencing, Nanopore long‐read sequencing and HiC‐based chromatin mapping. Compared with the published zebrafish Zv11 reference genome (GRCz11), this genome assembly shows considerable improvements in both contiguity and completeness. In addition, substantial structural differences and extensive sequence divergence of unprecedented resolution have been uncovered, especially with respect to 9,029,929 single nucleotide polymorphisms, 2,376,812 InDels, 32,623 insertions, 22,089 deletions and 220 inversions, which constitute ~2.6% of the DrAB1 genome. Many of these variants may have potential functional effects on phenotype, which should be considered in further experimental designs. Consequently, our study provides additional genomic resources and a high‐resolution structural variation map based on whole‐genome alignment for the zebrafish community, which could also be an indispensable reference genome from a model species in future research on fish phylogenetic genomics, comparative genomics and adaptive evolution.
The effectiveness of psychosocial interventions at reducing the frequency of alcohol and drug use in parents: findings of a Cochrane Review and meta‐analyses
Authors: McGovern Ruth , Newham James , Addison Michelle , Hickman Matt , Kaner Eileen 
Published: February 2022

AbstractBackground and aimParental substance use is a major public health and safeguarding concern. There have been a number of trials examining interventions targeting this risk factor. We aimed to estimate the effectiveness of psychosocial interventions at reducing parental substance use.DesignWe used systematic methods to identify trials; pooling data using a random‐effects model. Moderator analyses examined influence of parent gender, presence of child in treatment and intervention type.SettingNo restrictions on setting.ParticipantsSubstance using parents of children below the age of 21 years.InterventionsPsychosocial interventions including those that targeted drug and alcohol use only, and drug and alcohol use in combination with associated issues.MeasurementsFrequency of alcohol use and frequency of drug use.FindingsWe included eight unique studies with a total of 703 participants. Psychosocial interventions were more effective at reducing the frequency of parental alcohol use than comparison conditions at 6‐month [standardized mean difference (SMD) = – 0.32, 95% confidence interval (CI) = –0.51 to −0.13, P = 0.001] and 12‐month follow‐up (SMD = –0.25, 95% CI = –0.47 to −0.03, P = 0.02) and frequency of parental drug use at 12 months only (SMD = –0.21, 95% CI = –0.41 to −0.01, P = 0.04). Integrated interventions which combined both parenting and substance use targeted components were effective at reducing the frequency of alcohol use (6 months: SMD = –0.56, 95% CI = –0.96 to −0.016, P = 0.006; 12 months: SMD = –0.42, 95% CI = –0.82 to −0.03, P = 0.04) and drug use (6 months: SMD = –0.39, 95% CI = –0.75 to −0.03, P = 0.04; 12 months: SMD = –0.43, 95% CI = –0.80 to −0.07, P = 0.02). Interventions targeting only substance use or parenting skills were not effective at reducing frequency of alcohol or drug use at either time‐point.ConclusionPsychosocial interventions should target both parenting and substance use in an integrated intervention.
Quantity versus quality: A balance between egg and clutch size among Australian amphibians in relation to other life‐history variables
Authors: Gould John , Beranek Chad , Valdez Jose , Mahony Michael 
Published: February 2022

AbstractDue to resource limitations and physical constraints of the reproducing female, a trade‐off must be made between the number of eggs she produces and their size per clutch. This generally results in an inverse relationship between egg and clutch size, which has been found repeatedly across animal groups. Few studies have investigated this relationship with respect to selection pressures, environmental variables and other life‐history traits. We aimed to test current hypotheses regarding the trade‐off between egg and clutch size among the three Australian Anuran families (Hylidae, Myobatrachidae and Microhylidae). Specifically, we used a comparative phylogenetic approach to look at the influence of environmental selection pressures (egg‐laying location, environment persistence and bioregion) and life‐history traits (female body size, egg development type, parental care level, breeding period and temporal breeding pattern) on this trade‐off. As expected, a strong inverse relationship was found between egg and clutch size. Smaller clutches of larger eggs tended to be produced by species with smaller female sizes that (i) oviposit terrestrially and arboreally compared with aquatically, (ii) have prolonged compared with explosive breeding periods, (iii) directly develop compared with having a feeding tadpole stage and (iv) exhibit high compared with low levels of parental care. These findings show that the shift towards producing larger eggs in smaller clutches is associated with the transition away from the ancestral amphibian reproductive pattern. We highlight how the balance made when provisioning finite resources to egg within a clutch differs between species that have evolved diverse life histories, providing a framework for future examinations of the trade‐off between egg and clutch sizes among anurans.
The enigma: Decision‐making to transfer residents to the emergency department; communication and care delivery between emergency department staff and residential aged care facilities' nurses
Authors: Gurung Apil , Romeo Michele , Clark Sean , Hocking Julia , Dhollande Shannon , Broadbent Marc 
Published: February 2022

AbstractObjectiveTo investigate the experience of nurses involved in decision‐making to transfer residents from a residential aged care facility (RACF) to their local hospital emergency department. This paper reports on the findings of the second phase of a two‐phase study.MethodsQualitative semi‐structured interviews with 19 aged care nurses were conducted. Interviews were audio‐taped and transcribed verbatim, and a thematic analysis was carried out.ResultsThe analysis revealed five major themes that influenced decision‐making in relation to the transfer of a resident from the residential aged care facility to the emergency department: conflict with key stakeholders; knowledge and experience; policy and process; stakeholder perception; and recognition and support.ConclusionsRobust outreach programs, support from other health‐care professionals, and improving interdisciplinary understanding and communication between aged care nurses, paramedics and the emergency department would be advantageous to ensure effective care delivery and decision‐making.
Survey of Raspberry Leaf Tea in pregnancy
Authors: Farnaghi Soheil , Braniff Kathleen 
Published: February 2022

BackgroundRaspberry leaf tea (RLT) is a traditional herb purported to help with many pregnancy‐related outcomes including reducing the duration of labour. No experimental data exist to support these claims.AimsThis study aims to determine how common use and knowledge of RLT are during pregnancy. It also aims to explore whether it would be possible to recruit women for a trial of raspberry leaf in the future.Materials and MethodsPostnatal women were asked to fill in a survey about their use of RLT during pregnancy, and their knowledge of its purported benefits. They were asked whether they would consider being part of a randomised controlled trial of raspberry leaf in the future.ResultsOne hundred and twenty‐one women completed the survey. Of these, 88 (73%) were aware of herbal tea use in pregnancy and 46 (38%) reported using raspberry leaf during pregnancy. Of all women surveyed, 79% indicated they would be happy to participate in a trial of RLT in pregnancy if they were asked.ConclusionsDespite no scientific evidence of the efficacy of RLT in pregnancy, 38% of women surveyed used it during pregnancy. Further studies are required to determine whether the claims made about RLT are correct. Clinicians should base their advice on available evidence.
Preserved renal function during long‐term follow‐up in children with chronic liver disease
Authors: Berg Ulla B. , Häbel Henrike , Németh Antal 
Published: February 2022

AbstractAimWe have previously found well‐maintained renal function in children with new‐onset chronic liver disease. In this study, we investigated their renal function during long‐term follow‐up of the disease.MethodsIn a study of 289 children with chronic liver disease, renal function was investigated as glomerular filtration rate (GFR) measured as clearance of inulin or iohexol. Yearly change in GFR was calculated based on a linear mixed model. The data were analysed with regard to different subgroups of liver disease and with regard to the outcome.ResultsThe initially well‐preserved renal function remained so in most patients during the observation period, even in children with progressive liver disease leading to decompensation. The greatest fall in GFR occurred in patients with initial hyperfiltration. Cholestasis seemed to have a nephroprotective effect.ConclusionChronic liver disease in childhood seems to have less impact on renal function than believed earlier, at least as long as the liver function remains compensated. Regular renal check‐ups remain an essential tool for optimal patient care. Hyperfiltration seems to predict decline in renal function. Otherwise no further reliable prognostic markers were found in patients whose liver disease was not decompensated.
Market structure and exchange rate pass‐through in the Turkish manufacturing industry: Evidence from sectoral data
Authors: Kal Süleyman Hilmi , Çiftçi Muhsin 
Published: February 2022

ABSTRACTIn this paper, we study the impact of market share on exchange rate pass‐through to Turkish manufacturing sector prices using four‐digit industry level disaggregate data. Our findings provide evidence that exchange rate pass‐through in the manufacturing sector has an asymmetric U‐shape with respect to market share, implying that highly competitive and concentrated industries pass‐through exchange rate movements in both directions (appreciation and depreciation) to local producer prices more than moderately concentrated sectors. However, when directional asymmetries of exchange rate movements are added to the models, results become more revealing, that is, highly monopolized industries pass‐through exchange rate depreciation at higher rates than highly competitive industries. We also find that the size of the exchange rate movement has an impact on the asymmetry and the curvature of the U‐shaped Exchange Rate Pass‐Through (ERPT) curve with respect to the market share.