bluuebunny/crossref_metadata_2025_split huggingface dataset:
RetroRanker: leveraging reaction changes to improve retrosynthesis prediction through re-ranking
Authors: Li Junren , Fang Lei , Lou Jian-Guang 
Published: June 2023

AbstractRetrosynthesis is an important task in organic chemistry. Recently, numerous data-driven approaches have achieved promising results in this task. However, in practice, these data-driven methods might lead to sub-optimal outcomes by making predictions based on the training data distribution, a phenomenon we refer as frequency bias. For example, in template-based approaches, low-ranked predictions are typically generated by less common templates with low confidence scores which might be too low to be comparable, and it is observed that recorded reactants can be among these low-ranked predictions. In this work, we introduce RetroRanker, a ranking model built upon graph neural networks, designed to mitigate the frequency bias in predictions of existing retrosynthesis models through re-ranking. RetroRanker incorporates potential reaction changes of each set of predicted reactants in obtaining the given product to lower the rank of chemically unreasonable predictions. The predicted re-ranked results on publicly available retrosynthesis benchmarks demonstrate that we can achieve improvement on most state-of-the-art models with RetroRanker. Our preliminary studies also indicate that RetroRanker can enhance the performance of multi-step retrosynthesis.
Yeast diversity in pit mud and related volatile compounds in fermented grains of chinese strong-flavour liquor
Authors: Shoubao Yan , Jie Yang , TingTing Shen , Jiaquan Guang , Cuie Shi 
Published: June 2023

AbstractChinese strong-flavour liquor is produced via a traditional solid-state fermentation strategy facilitated by live microorganisms in pit mud-based cellars. For the present analysis, pit mud samples from different spatial locations within fermentation cellars were collected, and the yeast communities therein were assessed via culture-based and denaturing gradient gel electrophoresis (DGGE) approaches. These analyses revealed significant differences in the composition of yeast communities present in different layers of pit mud. In total, 29 different yeast species were detected, and principal component analyses revealed clear differences in microbial diversity in pit mud samples taken from different cellar locations. Culture-dependent strategies similarly detected 20 different yeast species in these samples. However, while Geotrichum silvicola, Torulaspora delbrueckii, Hanseniaspora uvarum, Saturnispora silvae, Issatchenkia orientalis, Candida mucifera, Kazachstania barnettii, Cyberlindnera jadinii, Hanseniaspora spp., Alternaria tenuissima, Cryptococcus laurentii, Metschnikowia spp., and Rhodotorula dairenensis were detected via a PCR-DGGE approach, they were not detectable in culture-dependent analyses. In contrast, culture-based approaches led to the identification of Schizosaccharomyces pombe and Debaryomyces hansenii in these pit mud samples, whereas they were not detected using DGGE fingerprints profiles. An additional HS-SPME-GC-MS-based analysis of the volatile compounds present in fermented grains samples led to the identification of 66 such compounds, with the highest levels of volatile acids, esters, and alcohols being detected in fermented grains from lower layer samples. A canonical correspondence analysis (CCA) suggested they were significant correlations between pit mud yeast communities and associated volatile compounds in fermented grains.
Guidance to best tools and practices for systematic reviews
Authors: Kolaski Kat , Logan Lynne Romeiser , Ioannidis John P. A. 
Published: June 2023

AbstractData continue to accumulate indicating that many systematic reviews are methodologically flawed, biased, redundant, or uninformative. Some improvements have occurred in recent years based on empirical methods research and standardization of appraisal tools; however, many authors do not routinely or consistently apply these updated methods. In addition, guideline developers, peer reviewers, and journal editors often disregard current methodological standards. Although extensively acknowledged and explored in the methodological literature, most clinicians seem unaware of these issues and may automatically accept evidence syntheses (and clinical practice guidelines based on their conclusions) as trustworthy.A plethora of methods and tools are recommended for the development and evaluation of evidence syntheses. It is important to understand what these are intended to do (and cannot do) and how they can be utilized. Our objective is to distill this sprawling information into a format that is understandable and readily accessible to authors, peer reviewers, and editors. In doing so, we aim to promote appreciation and understanding of the demanding science of evidence synthesis among stakeholders. We focus on well-documented deficiencies in key components of evidence syntheses to elucidate the rationale for current standards. The constructs underlying the tools developed to assess reporting, risk of bias, and methodological quality of evidence syntheses are distinguished from those involved in determining overall certainty of a body of evidence. Another important distinction is made between those tools used by authors to develop their syntheses as opposed to those used to ultimately judge their work.Exemplar methods and research practices are described, complemented by novel pragmatic strategies to improve evidence syntheses. The latter include preferred terminology and a scheme to characterize types of research evidence. We organize best practice resources in a Concise Guide that can be widely adopted and adapted for routine implementation by authors and journals. Appropriate, informed use of these is encouraged, but we caution against their superficial application and emphasize their endorsement does not substitute for in-depth methodological training. By highlighting best practices with their rationale, we hope this guidance will inspire further evolution of methods and tools that can advance the field.
Existence results for the families of multi-mappings with applications to integral and functional equations
Authors: Rasham Tahair , Nazam Muhammad , Agarwal Praveen , Hussain Aftab , Al Sulmi Hamed H. 
Published: June 2023

AbstractThe aim of this manuscript is to prove some new fixed-point results for the two families of multivalued dominated-contractive maps defined on a closed ball in a complete multiplicative-metric space. The fixed-point theorems for multigraph-dominated maps are established. We also investigate the existence of fixed points of the two families of graphic contractions in a multiplicative-metric space. For illustration, an example is provided to clarify that the hypothesis of the obtained result is valid. Moreover, the applications of the obtained results to show the existence of solutions to the coupled systems of nonlinear Volterra-type integral equations and mappingal equations are presented as a confirmation of the novelty of our results.
Understanding agricultural land leasing in Ireland: a transaction cost approach
Authors: Onofri Laura , Trestini Samuele , Mamine Fateh , Loughrey Jason 
Published: June 2023

AbstractFormal written land leasing contracts offer an alternative to land purchase for those farmers wishing to expand their land area and provide greater security relative to informal short-term rental agreements and are particularly important for beginning farmers with resources insufficient to purchase land. Formal land leasing contracts vary in terms of their duration, but there is limited understanding about the determinants of contract duration in developed countries. In this research, we use econometric techniques and transaction level data to explore the determinants of duration for agricultural land lease contracts for two regions in Ireland. Under the transaction cost economics approach, the research explores the role of legal status, price and non-price conditions in influencing the contract duration. Results indicate that the legal status of the tenant is a significant factor in influencing the duration. Provisions such as break clauses appear positively related to duration and confirm the theoretical expectation that long-term contracts create a demand for processes that enable adaptation over the course of long-term exchange.
Patterns of pseudoprogression across different cancer entities treated with immune checkpoint inhibitors
Authors: Mönch Sebastian , Heimer Maurice M. , Winkelmann Michael , Guertler Anne , Schlaak Max , Tufman Amanda , Ben Khaled Najib , de Toni Enrico , Westphalen Christoph B. , von Bergwelt-Baildon Michael , Dinkel Julien , Kazmierczak Philipp M. , Ingrisch Michael , Mansour Nabeel , Unterrainer Marcus , Heinzerling Lucie , Ricke Jens , Kunz Wolfgang G. 
Published: June 2023

Abstract
Background
Pseudoprogression (PsPD) is a rare response pattern to immune checkpoint inhibitor (ICI) therapy in oncology. This study aims to reveal imaging features of PsPD, and their association to other relevant findings.

Methods
Patients with PsPD who had at least three consecutive cross-sectional imaging studies at our comprehensive cancer center were retrospectively analyzed. Treatment response was assessed according to immune Response Evaluation Criteria in Solid Tumors (iRECIST). PsPD was defined as the occurrence of immune unconfirmed progressive disease (iUPD) without follow-up confirmation. Target lesions (TL), non-target lesions (NTL), new lesions (NL) were analyzed over time. Tumor markers and immune-related adverse events (irAE) were correlated.

Results
Thirty-two patients were included (mean age: 66.7 ± 13.6 years, 21.9% female) with mean baseline STL of 69.7 mm ± 55.6 mm. PsPD was observed in twenty-six patients (81.3%) at FU1, and no cases occurred after FU4. Patients with iUPD exhibited the following: TL increase in twelve patients, (37.5%), NTL increase in seven patients (21.9%), NL appearance in six patients (18.8%), and combinations thereof in four patients (12.5%). The mean and maximum increase for first iUPD in sum of TL was 19.8 and 96.8 mm (+ 700.8%). The mean and maximum decrease in sum of TL between iUPD and consecutive follow-up was − 19.1 mm and − 114.8 mm (-60.9%) respectively. The mean and maximum sum of new TL at first iUPD timepoint were 7.6 and 82.0 mm respectively. In two patients (10.5%), tumor-specific serologic markers were elevated at first iUPD, while the rest were stable or decreased among the other PsPD cases (89.5%). In fourteen patients (43.8%), irAE were observed.

Conclusions
PsPD occurred most frequently at FU1 after initiation of ICI treatment. The two most prevalent reasons for PsPD were TL und NTL progression, with an increase in TL diameter commonly below + 100%. In few cases, PsPD was observed even if tumor markers were rising compared to baseline. Our findings also suggest a correlation between PsPD and irAE. These findings may guide decision-making of ICI continuation in suspected PsPD.
Relationship between strain accumulation and release associated with recent slow slip events on the Japanese Islands
Authors: Kawabata Hiroki , Yoshioka Shoichi , Ortega-Culaciati Francisco 
Published: June 2023

AbstractIn this study, we investigated the relationship between the strain accumulation before a slow slip event (SSE) and the strain release during the SSE for three recent SSEs along the Suruga Trough, Sagami Trough, and Nankai Trough, which are subduction zones in central to southwest Japan. The three analysed SSEs were the 2013–2016 Tokai long-term SSE (L-SSE), the 2018 Boso-Oki short-term SSE (S-SSE), and the 2019–2021 Central Shikoku L-SSE. We applied exponential and logarithmic functions to remove the postseismic deformations caused by the Mw 9.0 2011 Tohoku-Oki earthquake. We discovered a strong negative correlation between strain accumulation and strain release in the dilatation of all three SSEs and in the maximum shear strain of the 2018 Boso-Oki S-SSE. A comparison of the amount of strain accumulation with that of strain release revealed that approximately 30% of the strain was released in the 2013–2016 Tokai L-SSE, that 40% of the strain was released in the 2019–2021 Central Shikoku L-SSE, and that approximately 60% of the strain was released in the 2018 Boso-Oki S-SSE. This finding suggests that all of the accumulated strains are not necessarily released by the SSEs.
Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa
Authors: Lamb Claire E. , Watts Joy E. M. 
Published: June 2023

AbstractBackgroundMarine sponges are diverse and functionally important members of marine benthic systems, well known to harbour complex and abundant symbiotic microorganisms as part of their species-specific microbiome. Changes in the sponge microbiome have previously been observed in relation to natural environmental changes, including nutrient availability, temperature and light. With global climate change altering seasonal temperatures, this study aims to better understand the potential effects of natural seasonal fluctuations on the composition and functions of the sponge microbiome.ResultsMetataxonomic sequencing of two marine sponge species native to the U.K. (Hymeniacidon perlevis and Suberites massa) was performed at two different seasonal temperatures from the same estuary. A host-specific microbiome was observed in each species between both seasons. Detected diversity withinS. massawas dominated by one family,Terasakiellaceae, with remaining dominant families also being detected in the associated seawater.H. perlevisdemonstrated sponge specific bacterial families including aforementionedTerasakiellaceaeas well asSphingomonadaceaeandLeptospiraceaewith further sponge enriched families present.ConclusionsTo our knowledge, these results describe for the first time the microbial diversity of the temperate marine sponge speciesH. perlevisandS. massausing next generation sequencing. This analysis detected the presence of core sponge taxa identified in each sponge species was not changed by seasonal temperature alterations, however, there were shifts observed in overall community composition due to fluctuations in less abundant taxa, demonstrating that microbiome stability across seasons is likely to be host species specific.
Fruit and vegetable consumption across population segments: evidence from a national household survey
Authors: Küçük Nihat , Urak Faruk , Bilgic Abdulbaki , Florkowski Wojciech J. , Kiani Adiqa K. , Özdemir Ferda Nur 
Published: June 2023

Abstract
Background
The 2002 World Health Report documented that low fruit and vegetable intake are among the top ten risk factors contributing to attributable mortality and up to three million lives could be saved each year by adequate consumption of F&V across the globe, leading an examination of behavioral preferences of the individual and family social, environmental, and behavioral factors that constitute perceived barriers to fruit and vegetable consumption.

Objective
The study examines factors affecting the choice of eating fruits and vegetables by household members and calculates eating frequency probabilities of different population-origin associated with personal attributes and behavior.

Method
Turkish Health Survey (THS) 2019 data from the Turkish Statistical Institute (TSI) national representative household panel is applied. Estimating a random-effect bivariate probit model of fruit and vegetable choice, we calculated marginal probabilities of choosing fruits and vegetables, the joint probability of choosing both, and conditional probabilities between choosing to eat either, detecting consumption synergy.

Results
The role of uncontrolled variables in choosing to eat fruits and vegetable (F&V) differs between the decision of an average family and the decision of individual family members. The attitude is positive for an average family and contrasts with the negative attitude among some family members. Most individual and family attributes inversely affect fruit and vegetable choice across different groups, while a positive relationship exists between the likelihood of fruit and vegetable choice and attributes such as age, marital status, education, weight, having health insurance, income, and time and forms of physical activity.

Conclusion and recommendation
Instead of a general policy for the implementation of a healthy and balanced nutrition program to improve fruit and vegetable eating frequency, it appears more effective to adopt programs with distinct characteristics that segregate society into different cohorts. We suggest appropriate policies and offer suitable approaches to reach targeted groups.
Association between nutritional status and socio-economic status among school children aged 9–17 years in a semi-urban area of Nepal
Authors: Hamann Sophie Amalie , Thorup Lene , Patsche Cecilie Blenstrup , Hohwü Lena , Hjortdal Vibeke Elisabeth , Gyawali Bishal , Neupane Dinesh , Kallestrup Per 
Published: June 2023

Abstract
Background
In many low-and middle-income countries (LMICs), childhood overweight is increasing, while underweight remains a problem. This study aimed to investigate the association between socio-economic status (SES) and nutritional status among Nepalese school children.

Methods
This cross-sectional study used a multistage random cluster sampling method and included 868 students aged 9–17 years from both public and private schools located in a semi-urban area of Pokhara Metropolitan City, Nepal. SES was determined based on a self-reported questionnaire. Body weight and height were measured by health professionals and body mass index (BMI) was categorized based on the World Health Organization BMI-for-age cut-offs. The association between Lower and Upper SES and BMI was assessed using mixed-effects logistic regression model estimating the adjusted odds ratio (aOR) with a corresponding 95% confidence interval (CI) and compared to Middle SES.

Results
The proportion of obesity, overweight, underweight, and stunting among school children was 4%, 12%, 7%, and 17%, respectively. More girls were overweight/obese compared with boys (20% vs. 13%). The mixed-effects logistic regression model showed that both participants from Lower SES households and Upper SES households had a higher tendency to be overweight compared to participants from Middle SES; aOR = 1.4; 95% CI 0.7–3.1 and aOR = 1.1; 95% CI 0.6–2.1, respectively. Furthermore, stunting and overweight occurred simultaneously.

Conclusions
This study found that about one out of four children and adolescents in the study setting was malnourished. There was a tendency that both participants from Lower SES and Upper SES had higher odds of being overweight compared to participants from Middle SES. Furthermore, both stunting and overweight were present simultaneously in some individuals. This emphasizes the complexity and importance of awareness of childhood malnutrition in LMICs like Nepal.
Impact of federalization for health financing and workforce in Nepal
Authors: Chen Meifang , Thapa Dinesh , Ma Rongxiao , Weissglass Daniel , Li Hao , Karmachaya Biraj 
Published: June 2023

AbstractThe adoption of its 2015 constitution has converted Nepal to a federal government while simultaneously resulted in significant reforms of the health system in Nepal in terms of both structure and commitment. In this commentary, we review evidence ranging from health financing to health workforce development to show that the impact of federalization on Nepal’s health system and its efforts to achieve equitable and affordable universal health care have been mixed. On the one hand, careful efforts of the federal government to support subnational governments during the transition appears to have avoided serious disruption, subnational governments have successfully taken on the financial burden of the health system, and increase subnational control has allowed more flexible adaptation to changing needs than might have otherwise been possible. On the other hand, financing resource and ability disparities across subnational governments contributes to significant disparities in workforce development, and subnational authorities appear to have underestimated significant health issues (e.g. NCDs) in their budgets. We then provide three recommendations to improve the success of the Nepalese system: (1) to assess whether the services covered by health financing and insurance schemes like the National Health Insurance Program adequately address the needs of the rising burden of NCDs in Nepal, (2) to set clear minimum requirements on key metrics for subnational health systems, and (3) to extend grant programs to address resource disparities.
Post-acute COVID-19 in three doses vaccinated autoimmune rheumatic diseases patients: frequency and pattern of this condition
Authors: Silva Clovis Artur , de Vinci Kanda Kupa Leonard , Medeiros-Ribeiro Ana Cristina , Pasoto Sandra Gofinet , Saad Carla Gonçalves Schahin , Yuki Emily Figueiredo Neves , Landim Joaquim Ivo Vasques Dantas , Léda Victor Hugo Ferreira e , de Camargo Correia Luisa Sacchi , Sartori Artur Fonseca , Martins Carolina Campagnoli Machado Freire , Ribeiro Carolina Torres , Waridel Filipe , de Oliveira Martins Victor Adriano , Shinjo Samuel Katsuyuki , Andrade Danieli Castro Oliveira , Sampaio-Barros Percival Degrava , Neto Eduardo Ferreira Borba , Aikawa Nadia Emi , Bonfa Eloisa 
Published: June 2023

Abstract
Background
Data on post-acute COVID-19 in autoimmune rheumatic diseases (ARD) are scarce, focusing on a single disease, with variable definitions of this condition and time of vaccination. The aim of this study was to evaluate the frequency and pattern of post-acute COVID-19 in vaccinated patients with ARD using established diagnosis criteria.

Methods
Retrospective evaluation of a prospective cohort of 108 ARD patients and 32 non-ARD controls, diagnosed with SARS-CoV-2 infection (RT-PCR/antigen test) after the third dose of the CoronaVac vaccine. Post-acute COVID-19 (≥ 4 weeks and > 12 weeks of SARS-CoV-2 symptoms) were registered according to the established international criteria.

Results
ARD patients and non-ARD controls, balanced for age and sex, had high and comparable frequencies of ≥ 4 weeks post-acute COVID-19 (58.3% vs. 53.1%, p = 0.6854) and > 12 weeks post-acute COVID-19 (39.8% vs. 46.9%, p = 0.5419). Regarding ≥ 4 weeks post-acute COVID-19, frequencies of ≥ 3 symptoms were similar in ARD and non-ARD controls (54% vs. 41.2%, p = 0.7886), and this was also similar in > 12 weeks post-acute COVID-19 (68.3% vs. 88.2%, p = 0.1322). Further analysis of the risk factors for ≥ 4 weeks post-acute COVID-19 in ARD patients revealed that age, sex, clinical severity of COVID-19, reinfection, and autoimmune diseases were not associated with this condition (p > 0.05). The clinical manifestations of post-acute COVID-19 were similar in both groups (p > 0.05), with fatigue and memory loss being the most frequent manifestations.

Conclusion
We provide novel data demonstrating that immune/inflammatory ARD disturbances after third dose vaccination do not seem to be a major determinant of post-acute COVID-19 since its pattern is very similar to that of the general population. Clinical Trials platform (NCT04754698).
Myofibrillar myopathy: a rare but important differential diagnosis of camptocormia in a patient with Parkinson’s Disease
Authors: Petry-Schmelzer Jan Niklas , Abicht Angela , Barbe Michael T. , Wunderlich Gilbert 
Published: June 2023

AbstractHere we report on a patient with Parkinson's Disease and camptocormia due to Myofibrillar Myopathy Type 3. By leading the reader through the clinical reasoning process and highlighting the respective red flags we aim to increase the readers’ awareness for the differential diagnosis of camptocormia.