bluuebunny/crossref_metadata_2025_split huggingface dataset:
MethylGenotyper: Accurate Estimation of SNP Genotypes and Genetic Relatedness from DNA Methylation Data
Authors: Jiang Yi , Qu Minghan , Jiang Minghui , Jiang Xuan , Fernandez Shane , Porter Tenielle , Laws Simon M , Masters Colin L , Guo Huan , Cheng Shanshan , Wang Chaolong 
Published: June 2024

Abstract
Epigenome-wide association studies (EWAS) are susceptible to widespread confounding caused by population structure and genetic relatedness. Nevertheless, kinship estimation is challenging in EWAS without genotyping data. Here, we proposed MethylGenotyper, a method that for the first time enables accurate genotyping at thousands of single nucleotide polymorphisms (SNPs) directly from commercial DNA methylation microarrays. We modeled the intensities of methylation probes near SNPs with a mixture of three beta distributions corresponding to different genotypes and estimated parameters with an expectation-maximization algorithm. We conducted extensive simulations to demonstrate the performance of the method. When applying MethylGenotyper to the Infinium EPIC array data of 4662 Chinese samples, we obtained genotypes at 4319 SNPs with a concordance rate of 98.26%, enabling the identification of 255 pairs of close relatedness. Furthermore, we showed that MethylGenotyper allows for the estimation of both population structure and cryptic relatedness among 702 Australians of diverse ancestry. We also implemented MethylGenotyper in a publicly available R package (https://github.com/Yi-Jiang/MethylGenotyper) to facilitate future large-scale EWAS.
Innovation Policy Beyond Patents: A Case Study on the Development of Climate-Friendly Fertilizers
Authors: Metzger Axel , Kusch Chiara 
Published: June 2024

Abstract
Nitrogen fertilizers have revolutionized agriculture since the early 20th century and made a decisive contribution to combating world hunger. Nevertheless, the technology is controversial today because production is energy-intensive and contributes significantly to climate change. In addition, conventional fertilizers pollute groundwater, rivers and coastal waters. Synthetic nitrogen fertilizer is made from ammonia (NH3) produced by the Haber-Bosch process, for which a patent was filed with the German Imperial Patent Office in 1908 (DE235421). For the urgently needed development of modern climate-friendly fertilizers, patent law seems to have played a minor role so far. The large and patent-active agrochemical corporations in the industrialized countries are focusing on other technologies, leaving fertilizer production to companies with direct access to energy below the global market price. Another reason is the very generous regulation of nitrogen fertilizers. For farmers, the use of less climate-damaging fertilizers is not worthwhile. However, the disruption of supply chains in the wake of Russia’s aggression in Ukraine and the aggravation of climate change could lead to a rethink. In the US, the first support programs for the development of climate-friendly, innovative ‘next-generation’ fertilizers have been launched. This paper examines the interplay of patent law in concert with regulatory law and government funding tools in the area of innovative fertilizers. It starts from the hypothesis that other legal frameworks have a stronger influence on innovation activity than patent law at the moment. But this could change if the regulatory framework were to impose stricter requirements for the use of fertilizers.
The impact of the Baby-Friendly Hospital Initiative on breastfeeding rates at maternity units in France
Authors: Guajardo-Villar Andrea , Pelat Camille , Blondel Beatrice , Lebreton Elodie , Demiguel Virginie , Salanave Benoit , Mitha Ayoub , Pilkington Hugo , Regnault Nolwenn ,   ENP2021 Study Group, Le Ray Camille , Lelong Nathalie , Cinelli Hélène , Blondel Béatrice , Regnault Nolwenn , Demiguel Virginie , Lebreton Elodie , Salanave Benoit , Fresson Jeanne , Vilain Annick , Deroyon Thomas , Raynaud Philippe , Rey Sylvie , Chemlal Khadoudja , Rabier-Thoreau Nathalie , Collombet-Migeon Frédérique 
Published: June 2024

Abstract

Background
The Baby-Friendly Hospital Initiative (BFHI) is associated with improved breastfeeding outcomes in many high-income countries including the UK and the USA, but its effectiveness has never been evaluated in France. We investigated the impact of the BFHI on breastfeeding rates in French maternity units in 2010, 2016 and 2021 to assess if the BFHI aids to reduce inequalities in breastfeeding.

Methods
We examined breastfeeding in maternity units (exclusive, mixed and any breastfeeding) in mothers of singleton full-term newborns using the 2010 (n = 13 075), 2016 (n = 10 919) and 2021 (n = 10 209) French National Perinatal Surveys. We used mixed-effect hierarchical multinomial regression models adjusting for neonatal, maternal, maternity unit and French administrative department characteristics, and tested certain interactions.

Results
The adjusted rate of exclusive breastfeeding was higher by +5.8 (3.4–8.1) points among mothers delivering in BFHI-accredited maternity units compared with those delivering in non-accredited units. When compared with average-weight newborns, this difference was sharper for infants with low birthweight: +14.9 (10.0–19.9) points when their birthweight was 2500 g. Mixed breastfeeding was lower by -1.7 points (-3.2–0) in BFHI-accredited hospitals, with no notable difference according to the neonatal or maternal characteristics.

Conclusion
Mothers delivering in BFHI-accredited maternity units had higher exclusive breastfeeding rates and lower mixed breastfeeding rates than those delivering in non-accredited maternity units. The positive impact of the BFHI was stronger among low-birthweight neonates, who are less often breastfed, helping reduce the gap for this vulnerable group while favouring mothers with higher education levels.
Effect of bone and analytical method on assessment of bone mineralization in response to dietary phosphorus, phytase, and vitamin D in finishing pigs
Authors: Williams Hadley R , Tokach Mike D , Woodworth Jason C , Goodband Robert D , DeRouchey Joel M , Bergstrom Jon R , Hastad Chad W , Post Zach B , Rahe Michael C , Siepker Christopher L , Sitthicharoenchai Panchan , Ensley Steve M , Radke Scott L , Gebhardt Jordan T 
Published: June 2024

AbstractA total of 882 pigs (PIC TR4 × [Fast LW × PIC L02]; initially 33.2 ± 0.31 kg) were used in a 112-d study to evaluate the effects of different bones and analytical methods on the assessment of bone mineralization response to changes in dietary P, phytase, and vitamin D in growing pigs. Pens of pigs (20 pigs per pen) were randomized to one of five dietary treatments with nine pens per treatment. Dietary treatments were designed to create differences in bone mineralization and included: 1) P at 80% of NRC (2012) standardized total tract digestible (STTD) P requirement, 2) NRC STTD P with no phytase, 3) NRC STTD P with phytase providing an assumed release of 0.14% STTD P from 2,000 FYT/kg, 4) high STTD P (128% of the NRC P) using monocalcium phosphate and phytase, and 5) diet 4 with additional vitamin D3 from 25(OH)D3. On day 112, one pig per pen was euthanized for bone, blood, and urine analysis. Additionally, 11 pigs identified as having poor body condition which indicated a history of low feed intake (unhealthy) were sampled. There were no differences between treatments for final body weight, average daily gain, average daily feed intake, gain to feed, or bone ash measurements (treatment × bone interaction) regardless of bone ash method. The response to treatment for bone density and bone mineral content was dependent upon the bone sampled (density interaction, P = 0.053; mineral interaction, P = 0.078). For 10th rib bone density, pigs fed high levels of P had increased (P &lt; 0.05) bone density compared with pigs fed NRC levels with phytase, with pigs fed deficient P, NRC levels of P with no phytase, and high STTD P with extra 25(OH)D3 intermediate, with no differences for metacarpals, fibulas, or 2nd ribs. Pigs fed extra vitamin D from 25(OH)D3 had increased (P &lt; 0.05) 10th rib bone mineral content compared with pigs fed deficient P and NRC levels of P with phytase, with pigs fed industry P and vitamin D, and NRC P with monocalcium intermediate. Healthy pigs had greater (P &lt; 0.05) serum Ca, P, vitamin D concentrations, and defatted bone ash than those unhealthy, with no difference between the two health statuses for non-defatted bone ash. In summary, differences between bone ash procedures were more apparent than differences between diets. Differences in bone density and mineral content in response to dietary P and vitamin D were most apparent with 10th ribs.
Factors Influencing Surgical Care and Outcome of Pediatric Burn Injuries and the Use of Synthetic Skin Substitutes
Authors: Wachenfeld-Teschner Victoria , Beier Justus P , Boos Anja M , Schäfer Benedikt 
Published: June 2024

Abstract
Burn trauma is one of the most common causes of inpatient treatment in children and is associated with severe physical and psychological consequences. Synthetic skin substitutes are designed to reduce the risk of infection, minimize wound pain, and reduce the frequency of dressing changes. However, data regarding premature detachment of these materials is scarce. The aim of this study was to identify factors associated with early detachment and subsequent consequences for surgical treatment. A retrospective analysis of 392 children with superficial and deep partial thickness burns undergoing inpatient treatment with the application of a skin substitute (Suprathel) was performed. Patient age, wound localization and progression, as well as burned total body surface area (TBSA%) were investigated as possible risk factors for early detachment of wound dressings and surgical intervention. Premature material detachment was significantly associated with burn localization (P &lt; .001) and correlated with burn depth progression (r = 0.23, &lt;0.001) and patient age (r = 0.22, &lt;0.001). Surgical revision after material detachment was required in 13% of patients. Patient age and burn localization seem to increase the risk of premature material detachment. In addition, we observed increased premature detachment of Suprathel® in areas that elicited higher wound progression rates. Identifying these areas might prove pivotal in the improvement of pediatric burn trauma management.
Prevalence and risk factors for atypical femoral fracture among Lebanese patients with hip and shaft fractures
Authors: Khalil Abir Bou , Yammine Ryan , Rameh Vanessa , Zadeh Catherina , Saad Randa , Mallah Hasan , Khoury Nabil J , El-Hajj Fuleihan Ghada 
Published: June 2024

Abstract
This retrospective study investigates the prevalence of atypical femoral fractures (AFFs) among patients admitted with hip and shaft fractures at a tertiary referral center in Beirut, Lebanon. We analyzed electronic medical records and radiology studies of patients aged above 40 admitted with hip and shaft fractures between January 2006 and December 2019. Fractures were confirmed by ICD9 or ICD10 codes. All cases were reviewed by radiologists, and AFFs were identified according to the 2013 revised ASBMR criteria. We identified 1366 hip and shaft fracture patients, of which 14 female patients had 19 AFFs. This represents a prevalence of 1.0% among all hip and shaft fractures patients and 1.7% among all female hip and shaft fracture patients. Bilateral AFFs were found in 5 of the 14 patients. Patients with AFF tended to be younger, with a mean age of 74.3 (±8.6) yr compared to 78.0 (±10.6) for patients with non-AFF fractures. A total of 36% of AFF patients had a prior history of non-traumatic fracture at first admission. A high percentage of patients with AFFs reported intake of proton pump inhibitors (42.9%) and glucocorticoids (21.4%). Bisphosphonate exposure was noted in 64.3% of AFF patients. None of the AFF patients were active smokers or consumed alcohol regularly. BMD assessments were available for 7 AFF patients, indicating osteoporosis in 4 and osteopenia in 3 cases. Hip axis length measurements showed no significant difference between AFF patients (N = 7) and sex and age-matched controls (N = 21). The study underlines the prevalence and characteristics of AFFs in Lebanon, which is consistent with the numbers reported in the literature (0.32%–5%). A larger prospective study that includes hospitals across the nation is needed to gain a more comprehensive view of the prevalence of AFFs in the Lebanese population.
Development of automated metabolite control using mid-infrared probe for bioprocesses and vaccine manufacturing
Authors: Reid Jennifer , Haer Manjit , Chen Airong , Adams Calvin , Lin Yu Chen , Cronin Jim , Yu Zhou , Kirkitadze Marina , Yuan Tao 
Published: June 2024

Abstract

Automation of metabolite control in fermenters is fundamental to develop vaccine manufacturing processes more quickly and robustly. We created an end-to-end process analytical technology and quality by design-focused process by replacing manual control of metabolites during the development of fed-batch bioprocesses with a system that is highly adaptable and automation-enabled. Mid-infrared spectroscopy with an attenuated total reflectance probe in-line, and simple linear regression using the Beer-Lambert Law, were developed to quantitate key metabolites (glucose and glutamate) from spectral data that measured complex media during fermentation. This data was digitally connected to a process information management system, to enable continuous control of feed pumps with proportional-integral-derivative controllers that maintained nutrient levels throughout fed-batch stirred-tank fermenter processes. Continuous metabolite data from mid-infrared spectra of cultures in stirred-tank reactors enabled feedback loops and control of the feed pumps in pharmaceutical development laboratories. This improved process control of nutrient levels by 20-fold and the drug substance yield by an order of magnitude. Furthermore, the method is adaptable to other systems and enables soft sensing, such as the consumption rate of metabolites. The ability to develop quantitative metabolite templates quickly and simply for changing bioprocesses was instrumental for project acceleration and heightened process control and automation.

One-Sentence Summary
Intelligent digital control systems using continuous in-line metabolite data enabled end-to-end automation of fed-batch processes in stirred-tank reactors.
RET overexpression leads to increased brain metastatic competency in luminal breast cancer
Authors: Jagust Petra , Powell Aoibhin M , Ola Mihaela , Watson Louise , de Pablos-Aragoneses Ana , García- Gómez Pedro , Fallon Ramón , Bane Fiona , Heiland Mona , Morris Gareth , Cavanagh Brenton , McGrath Jason , Ottaviani Daniela , Hegarty Aisling , Cocchiglia Sinéad , Sweeney Kieron J , MacNally Stephen , Brett Francesca M , Cryan Jane , Beausang Alan , Morris Patrick , Valiente Manuel , Hill Arnold D K , Varešlija Damir , Young Leonie S 
Published: June 2024

Abstract

Background
Breast cancer brain metastasis is a rising occurrence, necessitating a better understanding of the mechanisms involved for effective management. Breast cancer brain metastases diverge notably from the primary tumor, with gains in kinase and concomitant losses of steroid signaling observed. In this study, we explored the role of the kinase receptor RET in promoting breast cancer brain metastases and provide a rationale for targeting this receptor.

Methods
RET expression was characterized in a cohort of patients with primary and brain metastatic tumors. RET functionality was assessed using pharmacological inhibition and gene silencing in patient-derived brain metastatic tumor explants and in vivo models, organoid models, and brain organotypic cultures. RNA sequencing was used to uncover novel brain metastatic relevant RET mechanisms of action.

Results
A statistically significant enrichment of RET in brain metastases was observed in estrogen receptor–positive breast cancer, where it played a role in promoting cancer cell adhesion, survival, and outgrowth in the brain. In vivo, RET overexpression enhanced brain metastatic competency in patient-derived models. At a mechanistic level, RET overexpression was found to enhance the activation of gene programs involved in cell adhesion, requiring EGFR cooperation to deliver a pro–brain metastatic phenotype.

Conclusion
Our results illustrate, for the first time, the role of RET in regulating colonization and outgrowth of breast cancer brain metastasis and provide data to support the use of RET inhibitors in the management strategy for patients with breast cancer brain metastases.
Perceived acceptability and appropriateness of a web-based program targeting risk for anxiety in young children and their parents
Authors: Mirzadegan Isaac A , Lewis Ericka M , Cole Sally L , Meyer Alexandria 
Published: June 2024

Abstract

Objective
This mixed-methods study examined perceived acceptability and appropriateness of a novel digital mental health program targeting anxiety risk (i.e., perfectionism or error sensitivity) in 5-to-7-year-old children and their parents.

Methods
Parent–child dyads participated in a modular, web-based cognitive-behavioral program targeting negative overreactions to making mistakes. The program, “Making Mistakes”, consisted of a 6-month series of short video clips, journaling activities, and weekly reminders, and modules were delivered to caregivers and children separately. 86 dyads completed self-report measures, 18 of whom participated in semi-structured interviews, following completion of the primary program module. A standard thematic analysis was used to elucidate themes from the parent and child interview content.

Results
Our quantitative and qualitative results were generally aligned. Children and parents viewed the novel digital mental health program as acceptable and appropriate, favoring the cognitive behavioral strategies such as modeling positive reactions to mistakes, responding positively to child mistakes, and emphasizing effort over outcome. Participants also provided helpful feedback related to program content, delivery, and engagement, as well as suggestions to enhance the program.

Conclusions
Findings have implications for design and content features of parent-based and dyad-based programs, as well as digital mental health programs focused on reducing anxiety risk.
Trajectories of illness uncertainty among parents of children with atypical genital appearance due to differences of sex development
Authors: Traino Katherine A , Ciciolla Lucia M , Perez Megan N , Chaney John M , Welch Ginger , Baskin Laurence S , Buchanan Cindy L , Chan Yee-Ming , Cheng Earl Y , Coplen Douglas E , Wisniewski Amy B , Mullins Larry L 
Published: June 2024

Abstract

Objective
The present study aimed to identify distinct trajectories of parental illness uncertainty among parents of children born with atypical genital appearance due to a difference of sex development over the first year following diagnosis. It was hypothesized that four trajectory classes would emerge, including “low stable,” “high stable,” “decreasing,” and “increasing” classes, and that select demographic, familial, and medical factors would predict these classes.

Methods
Participants included 56 mothers and 43 fathers of 57 children born with moderate to severe genital atypia. Participants were recruited from eleven specialty clinics across the U.S. Growth mixture modeling (GMM) approaches, controlling for parent dyad clustering, were conducted to examine classes of parental illness uncertainty ratings over time.

Results
A three-class GMM was identified as the best-fitting model. The three classes were interpreted as “moderate stable” (56.8%), “low stable” (33.0%), and “declining” (10.3%). Findings suggest possible diagnostic differences across trajectories.

Conclusions
Findings highlight the nature of parents’ perceptions of ambiguity and uncertainty about their child’s diagnosis and treatment the year following their child’s birth/diagnosis. Future research is needed to better understand how these trajectories might shift over the course of the child’s development. Results support the development of tailored, evidence-based interventions to address coping with uncertainty among families raising a child with chronic health needs.
Large bronchial artery-pulmonary artery fistula due to cavitating tuberculosis
Authors: Morrow Joseph , Garvey Christopher , McEniff Niall , Kavanagh John 
Published: June 2024

Abstract
Bronchial artery-pulmonary artery fistulae are rare vascular malformations most commonly caused by infection. Our case presents a 57-year-old male who presented to the Emergency Department with a symptomatic bronchial artery-pulmonary artery fistula due to cavitating pulmonary tuberculosis (TB). The diagnosis was made with multiphase CT angiography of the thorax (including pulmonary and systemic arterial phases). The patient was brought to interventional radiology for further investigation and management. The left upper lobe bronchial artery-pulmonary artery fistula was successfully identified and treated with endovascular embolization. Bronchial artery-pulmonary artery fistulae can pose a diagnostic and therapeutic challenge. Our case demonstrates endovascular embolization as an effective method of treating symptomatic bronchial artery-pulmonary artery fistulae.
Introduction and Overview
Authors: Anderson Robert D , Jones Alison , Kovacic William E 
Published: June 2024

Abstract
This chapter introduces the problem of corruption and supplier collusion (or bid rigging) in public procurement and its harm to a nation and to democratic governance. It sets out broad definitions of both corruption and supplier collusion and highlights how, in the public procurement context, their pernicious effects often overlap and are mutually reinforcing. The chapter outlines the structure and the purpose of this book, which is to consider why corruption and collusion persist and to identify and advocate for reforms and improvements that will help countries to defend the integrity of their public procurement systems from these two practices. In particular, the book proposes that distinct policies—especially public procurement, anti-corruption, and competition law and policy—are more closely united around a ‘joined-up’ public procurement strategy, and seeks to make proposals that will help enable countries to achieve significant improvements in public purchasing with ensuing benefits for their economic and social welfare.
Basic Elements for Combatting Corruption and Collusion in Public Procurement: Well-Constructed Procurement, Competition, and Anti-Corruption Regimes
Authors: Anderson Robert D , Jones Alison , Kovacic William E 
Published: June 2024

Abstract
This chapter seeks to set out the basic elements of a system capable of successfully combatting corruption and collusion in public procurement. Such a system—guided by international best practices—should involve a well-constructed public procurement regime; robust competition and anti-corruption laws outlawing anti-competitive and corrupt practices; proactive and independent public agencies to administer the public procurement regime and to enforce the competition and anti-corruption statutes working together with citizens and business to prevent corruption and collusion and to root it out when it does occur; effective investigatory powers and techniques; and effective adjudication of the law and related sanctions, both to punish infringers appropriately and to deter future violations. The chapter recognizes, nonetheless, that any system will need to be tailored to reflect the particular needs and circumstances of an individual jurisdiction.