bluuebunny/crossref_metadata_2025_split huggingface dataset:
T cell receptor repertoire sequencing reveals chemotherapy-driven clonal expansion in colorectal liver metastases
Authors: Høye Eirik , Dagenborg Vegar J , Torgunrud Annette , Lund-Andersen Christin , Fretland Åsmund A , Lorenz Susanne , Edwin Bjørn , Hovig Eivind , Fromm Bastian , Inderberg Else M , Greiff Victor , Ree Anne H , Flatmark Kjersti 
Published: May 2023

Abstract

Background
Colorectal liver metastasis (CLM) is a leading cause of colorectal cancer mortality, and the response to immune checkpoint inhibition (ICI) in microsatellite-stable CRC has been disappointing. Administration of cytotoxic chemotherapy may cause increased density of tumor-infiltrating T cells, which has been associated with improved response to ICI. This study aimed to quantify and characterize T-cell infiltration in CLM using T-cell receptor (TCR) repertoire sequencing. Eighty-five resected CLMs from patients included in the Oslo CoMet study were subjected to TCR repertoire sequencing. Thirty-five and 15 patients had received neoadjuvant chemotherapy (NACT) within a short or long interval, respectively, prior to resection, while 35 patients had not been exposed to NACT. T-cell fractions were calculated, repertoire clonality was analyzed based on Hill evenness curves, and TCR sequence convergence was assessed using network analysis.

Results
Increased T-cell fractions (10.6% vs. 6.3%) were detected in CLMs exposed to NACT within a short interval prior to resection, while modestly increased clonality was observed in NACT-exposed tumors independently of the timing of NACT administration and surgery. While private clones made up &gt;90% of detected clones, network connectivity analysis revealed that public clones contributed the majority of TCR sequence convergence.

Conclusions
TCR repertoire sequencing can be used to quantify T-cell infiltration and clonality in clinical samples. This study provides evidence to support chemotherapy-driven T-cell clonal expansion in CLM in a clinical context.
An Animal Model of Neonatal Intensive Care Unit Exposure to Light and Sound in the Preterm Infant
Authors: Gay Jennifer D , Dangcil Evelynne , Nacipucha Jacqueline , Botrous Jonathon E , Suresh Nikhil , Tucker Aaron , Carayannopoulos Nicolas L , Khan Muhammad R , Meng Raphael , Yao Justin D , Wackym P Ashley , Mowery Todd M 
Published: May 2023

SynopsisAccording to the World Health Organization, ∼15 million children are born prematurely each year. Many of these infants end up spending days to weeks in a neonatal intensive care unit (NICU). Infants who are born prematurely are often exposed to noise and light levels that affect their auditory and visual development. Children often have long-term impairments in cognition, visuospatial processing, hearing, and language. We have developed a rodent model of NICU exposure to light and sound using the Mongolian gerbil (Meriones unguiculatus), which has a low-frequency human-like audiogram and is altricial. To simulate preterm infancy, the eyes and ears were opened prematurely, and animals were exposed to the NICU-like sensory environment throughout the gerbil’s cortical critical period of auditory development. After the animals matured into adults, auditory perceptual testing was carried out followed by auditory brainstem response recordings and then histology to assess the white matter morphology of various brain regions. Compared to normal hearing control animals, NICU sensory-exposed animals had significant impairments in learning at later stages of training, increased auditory thresholds reflecting hearing loss, and smaller cerebellar white matter volumes. These have all been reported in longitudinal studies of preterm infants. These preliminary results suggest that this animal model could provide researchers with an ethical way to explore the effects of the sensory environment in the NICU on the preterm infant’s brain development.
Child marriage as a risk factor for non-communicable diseases among women in India
Authors: Vikram Kriti , Visaria Abhijit , Ganguly Dibyasree 
Published: May 2023

Abstract

Background
Child marriage, defined as marriage under the age of 18 years, remains pervasive in India. Global evidence documents a negative association between child marriage and women's reproductive and sexual health outcomes; however, its relationship with non-communicable diseases (NCDs) remains underexplored.

Methods
We utilize biomarkers and self-reported data from the nationally representative National Family and Health Survey 4 (2015–2016) to examine the associations between child marriage and hypertension, diabetes, heart disease, asthma and thyroid disorder among currently married women (N = 421 107). We use regression models adjusted for a range of demographic and socio-economic controls to assess the association between child marriage and NCDs among women in India. We further assess whether and to what extent these relationships are mediated by early motherhood using the Karlson, Holm and Breen method of decomposition.

Results
Child marriage was associated with hypertension [adjusted odds ratio 1.20 (95% CI: 1.17–1.24)], diabetes [1.29 (1.22–1.37)], heart disease [1.27 (1.18–1.36)], asthma [1.19 (1.11–1.28)] and thyroid disorder [1.10 (1.02–1.18)]. Early motherhood also increased the risk of NCDs among women. Furthermore, it emerged as a pathway linking child marriage with hypertension, diabetes and heart disease; however, it provided a partial explanation for the disadvantage associated with child marriages.

Conclusions
Child marriage emerges as a risk factor for NCDs among women in India. Health systems need to recognize the enduring influence of child marriages on women’s health and ensure early detection and effective treatment of NCDs for this vulnerable group.
Influence of liquid column impact wall on liquid film thickness fluctuation outside the horizontal tube
Authors: Chen Lele , Qiu Qinggang , Zhang Xiaocui , Zhang Kun 
Published: May 2023

Abstract
A 3D falling film flow model outside the horizontal tube is established to study the influence of the liquid column impact the wall on the liquid film thickness distribution. It is found that the liquid film thickness fluctuates significantly at 0°–60° in single liquid column, and the minimum thickness appears. In the jet flow, there is a critical value of 70° due to the liquid film fluctuation. The liquid film thickness change before 70° was negatively correlated with Reynolds number and positively correlated after 70°. And the fluctuation amplitude negatively correlates with the Reynolds number.
Decoupling analysis of economic growth, energy consumption and CO2 emissions in the industrial sector of Guangdong Province
Authors: Guo Qing , You Wenlan 
Published: May 2023

Abstract
Industrial carbon emissions are the main part of China’s carbon emissions, so industrial carbon emission reduction is an important tool to achieve the ‘double carbon’ target. This paper constructs a Tapio model to decompose the total decoupling indicators into energy-saving decoupling indicators and emission-reduction decoupling indicators, with a view to revealing more deeply the reasons and mechanisms for the changes in the decoupling indicators between economic growth and CO2 emissions in the industrial sector of each prefecture-level city in Guangdong Province, as well as using cluster analysis to further explore the changes in the effect of energy saving and emission reduction in the industrial sector over the three five-year plans. The conclusions showed that: ( 1) the overall efficiency of energy saving and emission reduction in the industrial sector of Guangdong Province has improved, but there are large differences in efficiency between different cities and ( 2) the energy structure of the industrial sector in Guangdong Province has changed little due to immature technology. Based on the aforementioned findings, this paper puts forward corresponding policy recommendations.
Forum: Russia's Invasion of Ukraine: What Did We Miss?
Authors: Mahon Anastassiya , Pearce James C , Korobkov Andrei , Gabdulhakov Rashid , Gozalishvili Nino , Topuria Revaz , Stercul Natalia , Vacarelu Marius 
Published: May 2023

Abstract
This forum focuses on the overlooked areas of the moment surrounding the nature and progression of Russia's invasion of Ukraine in 2022. It brings together scholars of different disciplines, backgrounds, and locations to provide analyses of the Russian aggression from varying perspectives such as history, law, military studies, politics, and media and communications, to name a few, encouraging the authors to focus on intricacies to deliver a deeper analysis of the invasion. Each author offers a unique take on the analyses of the past and present. The forum has two aims. First, the collection raises the question “What did we miss?” and it aims to highlight the lack of attention by Western scholars to Russian perceptions of Western threats and the concerns of former Soviet countries regarding Russia's aggressive foreign policy. Second, the forum intends to start a conversation on different non-Western perspectives of thinking about the Russian invasion. The forum covers the events of the period from the beginning of the invasion up to July 2022, with some post-revision comments in the introduction and conclusion mentioning the events up to February 2023.
Knowledgebase strategies to aid interpretation of clinical correlation research
Authors: Stead William W , Lewis Adam , Giuse Nunzia B , Koonce Taneya Y , Bastarache Lisa 
Published: May 2023

Abstract

Objective
Knowledgebases are needed to clarify correlations observed in real-world electronic health record (EHR) data. We posit design principles, present a unifying framework, and report a test of concept.

Materials and Methods
We structured a knowledge framework along 3 axes: condition of interest, knowledge source, and taxonomy. In our test of concept, we used hypertension as our condition of interest, literature and VanderbiltDDx knowledgebase as sources, and phecodes as our taxonomy. In a cohort of 832 566 deidentified EHRs, we modeled blood pressure and heart rate by sex and age, classified individuals by hypertensive status, and ran a Phenome-wide Association Study (PheWAS) for hypertension. We compared the correlations from PheWAS to the associations in our knowledgebase.

Results
We produced PhecodeKbHtn: a knowledgebase comprising 167 hypertension-associated diseases, 15 of which were also negatively associated with blood pressure (pos+neg). Our hypertension PheWAS included 1914 phecodes, 129 of which were in the PhecodeKbHtn. Among the PheWAS association results, phecodes that were in PhecodeKbHtn had larger effect sizes compared with those phecodes not in the knowledgebase.

Discussion
Each source contributed unique and additive associations. Models of blood pressure and heart rate by age and sex were consistent with prior cohort studies. All but 4 PheWAS positive and negative correlations for phecodes in PhecodeKbHtn may be explained by knowledgebase associations, hypertensive cardiac complications, or causes of hypertension independently associated with hypotension.

Conclusion
It is feasible to assemble a knowledgebase that is compatible with EHR data to aid interpretation of clinical correlation research.
Developing, pilot testing, and refining requirements for 3 EHR-integrated interventions to improve diagnostic safety in acute care: a user-centered approach
Authors: Garber Alison , Garabedian Pamela , Wu Lindsey , Lam Alyssa , Malik Maria , Fraser Hannah , Bersani Kerrin , Piniella Nicholas , Motta-Calderon Daniel , Rozenblum Ronen , Schnock Kumiko , Griffin Jacqueline , Schnipper Jeffrey L , Bates David W , Dalal Anuj K 
Published: May 2023

Abstract

Objective
To describe a user-centered approach to develop, pilot test, and refine requirements for 3 electronic health record (EHR)-integrated interventions that target key diagnostic process failures in hospitalized patients.

Materials and Methods
Three interventions were prioritized for development: a Diagnostic Safety Column (DSC) within an EHR-integrated dashboard to identify at-risk patients; a Diagnostic Time-Out (DTO) for clinicians to reassess the working diagnosis; and a Patient Diagnosis Questionnaire (PDQ) to gather patient concerns about the diagnostic process. Initial requirements were refined from analysis of test cases with elevated risk predicted by DSC logic compared to risk perceived by a clinician working group; DTO testing sessions with clinicians; PDQ responses from patients; and focus groups with clinicians and patient advisors using storyboarding to model the integrated interventions. Mixed methods analysis of participant responses was used to identify final requirements and potential implementation barriers.

Results
Final requirements from analysis of 10 test cases predicted by the DSC, 18 clinician DTO participants, and 39 PDQ responses included the following: DSC configurable parameters (variables, weights) to adjust baseline risk estimates in real-time based on new clinical data collected during hospitalization; more concise DTO wording and flexibility for clinicians to conduct the DTO with or without the patient present; and integration of PDQ responses into the DSC to ensure closed-looped communication with clinicians. Analysis of focus groups confirmed that tight integration of the interventions with the EHR would be necessary to prompt clinicians to reconsider the working diagnosis in cases with elevated diagnostic error (DE) risk or uncertainty. Potential implementation barriers included alert fatigue and distrust of the risk algorithm (DSC); time constraints, redundancies, and concerns about disclosing uncertainty to patients (DTO); and patient disagreement with the care team’s diagnosis (PDQ).

Discussion
A user-centered approach led to evolution of requirements for 3 interventions targeting key diagnostic process failures in hospitalized patients at risk for DE.

Conclusions
We identify challenges and offer lessons from our user-centered design process.
A metadata framework for computational phenotypes
Authors: Spotnitz Matthew , Acharya Nripendra , Cimino James J , Murphy Shawn , Namjou Bahram , Crimmins Nancy , Walunas Theresa , Liu Cong , Crosslin David , Benoit Barbara , Rosenthal Elisabeth , Pacheco Jennifer A , Ostropolets Anna , Reyes Nieva Harry , Patterson Jason S , Richter Lauren R , Callahan Tiffany J , Elhussein Ahmed , Pang Chao , Kiryluk Krzysztof , Nestor Jordan , Khan Atlas , Mohan Sumit , Minty Evan , Chung Wendy , Wei Wei-Qi , Natarajan Karthik , Weng Chunhua 
Published: May 2023

Abstract
With the burgeoning development of computational phenotypes, it is increasingly difficult to identify the right phenotype for the right tasks. This study uses a mixed-methods approach to develop and evaluate a novel metadata framework for retrieval of and reusing computational phenotypes. Twenty active phenotyping researchers from 2 large research networks, Electronic Medical Records and Genomics and Observational Health Data Sciences and Informatics, were recruited to suggest metadata elements. Once consensus was reached on 39 metadata elements, 47 new researchers were surveyed to evaluate the utility of the metadata framework. The survey consisted of 5-Likert multiple-choice questions and open-ended questions. Two more researchers were asked to use the metadata framework to annotate 8 type-2 diabetes mellitus phenotypes. More than 90% of the survey respondents rated metadata elements regarding phenotype definition and validation methods and metrics positively with a score of 4 or 5. Both researchers completed annotation of each phenotype within 60 min. Our thematic analysis of the narrative feedback indicates that the metadata framework was effective in capturing rich and explicit descriptions and enabling the search for phenotypes, compliance with data standards, and comprehensive validation metrics. Current limitations were its complexity for data collection and the entailed human costs.
Validation of a Rapid Microbiological Method for the Detection and Quantification of the Burkholderia cepacia Complex in an Antacid Oral Suspension
Authors: Prada-Ramírez Harold A , Celeita Sandra , Fonseca Juan Camilo 
Published: May 2023

Abstract

Background
Despite the broad adoption of Soleris® technology in the food industry as semiquantitative method, it is almost completely unexplored in the pharmaceutical industry as a quantitative method for quantification of Burkholderia cepacia complex (Bcc).

Objective
The efficacy of an automated growth-based system for a quantitative determination of the Bcc in an antacid oral suspension was studied. The main purpose of this validation study was to prove that the alternative method’s entire performance is not inferior to the conventional method for a quantitative determination of Bcc.

Method
The antacid oral suspension’s preservatives were neutralized, leading to the Burkholderia complex’s recovery by means of the alternative method and the reference method. A calibration curve was generated for each strain by plotting DTs relative to the corresponding log CFU values. An equivalence of results was done through the construction of calibration curves that allowed the establishment of numerically equivalent results between the enumeration data from the reference method and the alternative method.

Results
Thus following the guidelines of USP, essential validation parameters were shown, such as equivalence of results (CC &gt;0.95), linearity (R2 &gt;0.9025), accuracy (% recovery &gt;70%), operating range, precision and ruggedness (DS &lt;5 and CV &lt;35%), specificity (inclusivity and exclusivity), limit of detection (LOD), and limit of quantification (LOQ).

Conclusions
It was shown that all the test results obtained from the alternative method were in statistical agreement with the standard method. Thus this new technology was found to meet all the validation criteria needed to be considered as an alternative method for the quantification of the Burkholderia complex in the antacid oral suspension tested.

Highlights
As outlined in USP chapter &lt;1223&gt; and demonstrated in this research the implementation of alternative methods can offer benefits in execution and automation while improving accuracy, sensitivity, and precision and can reduce the microbiological process time compared to the traditional ones.
Endocrine changes during the peripartal period related to colostrogenesis in mammalian species
Authors: Bigler Naomi A , Gross Josef J , Baumrucker Craig R , Bruckmaier Rupert M 
Published: May 2023

AbstractThis review discusses endocrine and functional changes during the transition from late gestation to lactation that are related to the production of colostrum in different mammalian species. Species covered in this article include ungulate species (cattle, sheep, goats, pigs, horses), rodents (rat, mouse), rabbits, and carnivores (cats, dogs), as well as humans. An immediate availability of high quality colostrum for the newborn after birth is crucial in species where a transfer of immunoglobulins (Ig) does not or only partially occur via the placenta during pregnancy. Declining activity of gestagens, in most species progesterone (P4), is crucial at the end of pregnancy to allow for the characteristic endocrine changes to initiate parturition and lactation, but the endocrine regulation of colostrogenesis is negligible. Both, the functional pathways and the timing of gestagen withdrawal differ considerably among mammalian species. In species with a sustaining corpus luteum throughout the entire pregnancy (cattle, goat, pig, cat, dog, rabbit, mouse, and rat), a prostaglandin F2α (PGF2α)-induced luteolysis shortly before parturition is assumed to be the key event to initiate parturition as well as lactogenesis. In species where the gestagen production is taken over by the placenta during the course of gestation (e.g., sheep, horse, and human), the reduction of gestagen activity is more complex, as PGF2α does not affect placental gestagen production. In sheep the steroid hormone synthesis is directed away from P4 towards estradiol-17β (E2) to achieve a low gestagen activity at high E2 concentrations. In humans the uterus becomes insensitive to P4, as parturition occurs despite still high P4 concentrations. However, lactogenesis is not completed as long as P4 concentration is high. Early colostrum and thus Ig intake for immune protection is not needed for the human newborn which allows a delayed onset of copious milk secretion for days until the placenta expulsion causes the P4 drop. Like humans, horses do not need low gestagen concentrations for successful parturition. However, newborn foals need immediate immune protection through Ig intake with colostrum. This requires the start of lactogenesis before parturition which is not fully clarified. The knowledge of the endocrine changes and related pathways to control the key events integrating the processes of colostrogenesis, parturition, and start of lactation are incomplete in many species.
Genetic parameters for mouth size and their influence on growth traits in pasture-raised Nelore cattle
Authors: Dominguez-Castaño Pablo , Marchi Maiorano Amanda , Silva Lopes Jose Eduardo , Vargas de Oliveira Matheus Henrique , Michel Castilhos Andre , Vasconcelos Silva Josineudson Augusto Ii 
Published: May 2023

Abstract
Evaluating traits that allow breeders to increase production efficiency in beef production systems is important. The mouth size (MS) score is a trait easily measured and implemented by breeders. Bite size is related to MS in beef cattle and is a determinant of daily feed intake of pasture-raised animals, influencing their growth. The aim of this study was to estimate genetic parameters for MS, weaning weight (WW) and postweaning weight gain (PWG) of Nelore cattle and to evaluate the influence of the interaction between MS and WW on PWG. Phenotypic records of 134,282 Nelore animals born between 1995 and 2019 were used. Variance components were estimated using multitrait animal model with the Bayesian method. The model included the contemporary group as fixed effect, age at measurement of the trait as linear covariate, and direct additive genetic and residual effects as random effects. For WW, random maternal and maternal permanent environmental effects were added to the model. A Bayesian approach was used to analyze the interaction between WW clusters and MS. The heritability estimates were 0.24, 0.15, and 0.23 for MS, WW, and PWG, respectively. The genetic correlation between variables studied ranged from 0.24 to 0.46. The results suggest that animals with a larger mouth tend to have greater PWG, demonstrating the positive influence of MS score on the postweaning performance of cattle. The direct heritability estimates confirm the possibility of selecting animals for the traits studied.
Lone star ticks (Acari: Ixodidae) infected with Bourbon virus in New Jersey, USA
Authors: Egizi Andrea , Wagner Nicole E , Jordan Robert A , Price Dana C 
Published: May 2023

Abstract
Lone star ticks (Amblyomma americanum L.) are expanding within the northeast United States, a region historically focused on Ixodes scapularis-transmitted diseases. In Monmouth County, NJ, the shift has been dramatic, and lone star ticks now vastly outnumber blacklegged ticks. As a result, there is an enhanced need to focus on the potential health risks of A. americanum-transmitted pathogens, such as the emerging Heartland (HRTV) and Bourbon (BRBV) viruses. We screened 1,205 nymphal lone star ticks for HRTV and BRBV using RT-qPCR assays and detected BRBV in 3 ticks collected in Monmouth County, NJ, in 2021. Additionally, we sequenced a complete BRBV genome from a single infected specimen, finding 99.4% identity with human pathogenic isolates from the eastern-central United States. Our results have important public health implications for a region only recently becoming aware of public health risks posed by lone star ticks. Of note, we report successful detection of viral RNA in samples that were stored and intended for DNA preservation, for example, kept in ethanol at room temperature, which may reduce barriers for public health agencies seeking to expand their tick testing to include viruses.