bluuebunny/crossref_metadata_2025_split huggingface dataset:
Affordable, accurate and unbiased RNA sequencing by manual library miniaturization: A case study in barley
Authors: Arlt Christopher , Wachtmeister Thorsten , Köhrer Karl , Stich Benjamin 
Published: August 2023

SummaryWe present an easy‐to‐reproduce manual miniaturized full‐length RNA sequencing (RNAseq) library preparation workflow that does not require the upfront investment in expensive lab equipment or long setup times. With minimal adjustments to an established commercial protocol, we were able to manually miniaturize the RNAseq library preparation by a factor of up to 1:8. This led to cost savings for miniaturized library preparation of up to 86.1% compared to the gold standard. The resulting data were the basis of a rigorous quality control analysis that inspected: sequencing quality metrics, gene body coverage, raw read duplications, alignment statistics, read pair duplications, detected transcripts and sequence variants. We also included a deep dive data analysis identifying rRNA contamination and suggested ways to circumvent these. In the end, we could not find any indication of biases or inaccuracies caused by the RNAseq library miniaturization. The variance in detected transcripts was minimal and not influenced by the miniaturization level. Our results suggest that the workflow is highly reproducible and the sequence data suitable for downstream analyses such as differential gene expression analysis or variant calling.
Activated Akt expression is associated with the recurrence of primary melanomas and further refines the prognostic and predictive values for relapse in acral melanomas
Authors: Nojima Kohei , Hayashi Masahiro , Tanemura Atsushi , Al‐Busani Hind , Saito Toru , Suzuki Tamio , Ishikawa Masashi , Mori Taisuke , Wada Shogo , Yamazaki Naoya , Katayama Ichiro , Mori Hiroki , Yokozeki Hiroo , Okiyama Naoko , Sasaki Yoshiyuki , Namiki Takeshi 
Published: August 2023

AbstractA PTEN deficiency leads to the activation of phospho‐Akt at serine 473 (p‐Akt) and promotes the tumorigenesis of melanomas by coupling with NUAK2 amplification. We tested the prognostic impact of p‐Akt and/or NUAK2 expression on the relapse‐free survival (RFS) and overall survival (OS) of melanoma patients. Primary tumors from patients with acral melanomas (112), Low‐cumulative sun damage (CSD) melanomas (38), and High‐CSD melanomas (18) were examined using immunohistochemistry and their prognostic significance was analyzed statistically. The expression of p‐Akt was found in 32.1%, 68.4%, and 55.6% of acral, Low‐CSD, and High‐CSD melanomas, while NUAK2 expression was found in 46.4%, 76.3%, and 50.0%, respectively. Either p‐Akt or NUAK2 expression was inversely correlated with the RFS of primary melanoma patients and acral melanoma patients (p‐Akt: p < .0001, p < .0001; NUAK2; p = .0005, p < .0001, respectively). Strikingly, multivariate analyses revealed that p‐Akt had a significant impact on RFS (Hazard ratio = 4.454; p < .0001), while NUAK2 did not. Further subset analyses revealed that p‐Akt expression had an inferior RFS of patients with acral melanomas (Hazard ratio = 4.036; p = .0005). We conclude that the expression of p‐Akt has a significant impact on RFS of patients with primary melanomas and can predict the relapse of patients with acral melanomas.
Contemporary outcomes of pediatric cardiac transplantation with a positive retrospective crossmatch
Authors: Lytrivi Irene D. , Koehl Devin , Esteso Paul , Frandsen Erik L. , Gibbons Meredith K. , Kirklin James K. , Cantor Ryan , Lamour Jacqueline M. , Putschoegl Adam , Shugh Svetlana , Williams Ryan J. , Pearce F. Bennett 
Published: August 2023

AbstractBackgroundA positive crossmatch (+ XM) has traditionally been associated with adverse outcomes following pediatric heart transplantation. However, more recent studies suggest that favorable intermediate‐term outcomes may be achieved despite a + XM. This study's hypothesis is that children with a + XM have similar long‐term survival, but higher rate of complications such as rejection, coronary allograft vasculopathy (CAV), and infection, compared to patients with a negative (−) XM.MethodsThe Pediatric Heart Transplant Society Registry (PHTS) database was queried from 2010–2021 for all patients <18 years of age with a known XM. Baseline demographics were compared between + XM and − XM groups using appropriate parametric and non‐parametric group comparisons. Cox Proportional Hazards Modeling was used to identify risk factors for post‐transplant graft loss, rejection, and CAV.ResultsOf 4599 pediatric heart transplants during the study period, XM results were available for 3914 (85%), of which 373 (9.5%) had a + XM. Univariate analysis showed lower 10‐year survival for patients with + XM (HR = 1.3, p = .04). Multivariate analyses revealed no significant difference in 10‐year survival in the 2 groups; however, time to first rejection (p = .0001) remained significantly shorter in the + XM group.ConclusionsPediatric patients transplanted across a + XM experience earlier rejection; however, after multivariate adjustment, + XM is not independently associated with intermediate‐term graft loss. The risk of heart transplantation against a + XM must be balanced with the ongoing risk of waitlist mortality.
Critical consciousness of public health nurses: A descriptive, comparative survey
Authors: Pirsch Anna M. , Austin Robin R. , Martin Lisa , Pieczkiewicz David , Monsen Karen A. 
Published: August 2023

AbstractBackgroundPublic Health Nurses (PHN) caring for vulnerable populations amid systemic inequality must navigate complex situations, and consequently they may experience serious moral distress known to be detrimental to PHN wellbeing.ObjectiveGiven PHN awareness of social inequities, the study aimed to determine if PHNs were motivated to enact social change and engage in social and political action to address inequality.Design and sampleA survey of 173 PHNs was conducted in fall 2022. The convenience sample was mainly female (96.5%), White (85%), had associate/bachelor's degrees (71.7%), and worked in governmental public health settings (70.7%).MeasureThe study employed the Short Critical Consciousness Scales’ subscales: Critical Reflection, Critical Motivation, and Critical Action.ResultsPHNs were highly motivated to address inequities (Critical Motivation = 20.83; SD = 3.16), with similarly high awareness (Critical Reflection = 17.89; SD = 5.18). However, social and political action scores were much lower (Critical Action = 7.13; SD = 2.63). A subgroup of PHNs with strong agreement regarding the impact of poverty were more likely to be younger (p = .039) and work in a community setting (p = .003); with higher scores across subscales (p < .001).ConclusionsHigh critical reflection and motivation among PHNs aligned with literature. Lower Critical Action scores warrant investigation into validity for PHNs, and possible role constraints.
The risk of weekend biopsy: Impact of specimen source and fixation status on HER2 assessment in the treatment of advanced gastric cancer (The HER_WEEKEND study)
Authors: Nakamura Michio , Watanabe Ayako , Yoshizawa Aki , Iwasaki Sari , Nomura Asako , Matsumura Mariko , Murai Taichi , Itaya Kazufumi , Koike Yuta , Izumi Takaaki , Endo Ayana , Kato Shin , Ono Yuji , Ohshima Takahiro , Okazaki Nanase , Nakagawa Shimpei , Ishii Yasushi , Fukasawa Yuichiro , Yokota Isao , Tsuji Takahiro , Nishikawa Shuji 
Published: August 2023

AbstractAccurate evaluation of human epidermal growth factor receptor type 2 (HER2) expression is crucial for determining chemotherapy regimens in gastric cancer. However, formalin fixation status has been identified as an important factor affecting HER2 assessment reliability. This retrospective cohort study aimed to investigate the correlation between sample collection day (weekday vs. weekend) and source (biopsy vs. surgical specimens) in assessing HER2 expression in patients with unresectable advanced/recurrent gastric cancer. Data were collected from gastric cancer patients who received chemotherapy at a single public hospital in Japan from 2008 to 2021. The analysis included 177 patients (109 men, 68 women) with a median age of 68.0 (21–88) years, and the primary outcome was the HER2 positivity rate. The overall HER2 positivity rate was 18.1%, with higher rates on weekdays (20.0%) compared to weekends (12.8%). Biopsies had higher positivity rates on weekdays (23.9%) but lower rates on weekends (11.1%) than surgical specimens. Significant differences were observed in formalin fixation times between weekdays and weekends for both biopsies and surgical samples. The study findings suggest that longer formalin fixation times on weekends may lead to underestimating HER2 expression, particularly in biopsies. Therefore, it is crucial to be cautious of excessive formalin fixation when collecting samples, especially during weekend biopsies.
Exploring Multiple Measures of Pregnancy Preferences and Their Relationship with Postpartum Contraceptive Uptake Using Longitudinal Data from PMA Ethiopia
Authors: Zimmerman Linnea A. , Karp Celia , Magalona Sophia , Shiferaw Solomon , Seme Assefa , Ahmed Saifuddin 
Published: August 2023

AbstractThere are significant gaps in our understanding of how the experience of an unintended pregnancy affects subsequent contraceptive behavior. Our objective was to explore how three measures of pregnancy preferences—measuring timing‐based intentions, emotional orientation, and planning status—were related to the uptake of postpartum family planning within one year after birth. Additionally, we tested whether the relationship between each measure and postpartum family planning uptake differs by parity, a key determinant of fertility preference. Adjusted hazards regression results show that the timing‐based measure, specifically having a mistimed pregnancy, and the emotional response measure, specifically being unhappy, were associated with contraceptive uptake in the extended postpartum period, while those related to pregnancy planning, as measured by an adapted London Measure of Unplanned Pregnancy, were not. This effect differed by parity; high parity women were consistently the least likely to use contraception in the postpartum period, but the effect of experiencing an unwanted pregnancy or having a mixed reaction to a pregnancy was significantly stronger among high parity compared to low parity women. Greater attention to the entirety of women's responses to unanticipated pregnancies is needed to fully understand the influence of unintended pregnancy on health behaviors and outcomes for women and their children.
Decomposing gender wage gaps: a family economics perspective
Authors: Averkamp Dorothée , Bredemeier Christian , Juessen Falko 
Published: August 2023

AbstractWe propose a simple way to embed family‐economics arguments for pay differences between genders into standard decomposition techniques. To account appropriately for the role of the family in the determination of wages, one has to compare men and women with similar own characteristics – and with similar partners. In US survey data, we find that our extended decomposition explains considerably more of the wage gap than a standard approach, in line with our theory that highlights the role of career prioritization in dual‐earner couples.
Asymmetric market power and wage suppression
Authors: Blumkin Tomer , Lagziel David 
Published: August 2023

AbstractWe study a labor market in which two identical firms compete over a pool of homogeneous workers. Firms pre‐commit to their outreach to potential employees, either through their informative advertising choices, or through their screening processes, before engaging in a wage (Bertrand) competition. Although firms are homogeneous, the unique pure‐strategy equilibrium is asymmetric: one firm maximizes its outreach whereas the other compromises on a significantly smaller market share. The features of the asymmetric equilibrium extend to a general oligopsony with any finite number of firms.
Conspiracy theories explained by a cheating detection mechanism
Authors: Aubert‐Teillaud Benjamin , Vaidis David C. 
Published: August 2023

AbstractResearch on conspiracy theories sometimes tends to pathologise this phenomenon with a focus on the impact of (sub)pathological predictors. However, socio‐political factors also play a significant role in predicting belief in specific conspiracy theories. The aim of this article is to bridge these two perspectives through a unified cognitive mechanism. Based on an overlap between cheating and conspiracy concepts, we assume a cheating detection mechanism likely to underlie belief in conspiracy theories. Starting from the adaptive challenges of cheating detection, we explore the workings of this mechanism using signal detection theory and error management theory. The probability of cheating and decision bias according to the asymmetry of error costs in cheating detection could lead individuals to infer conspiracy theories. This functional mechanism not only explains the links between socio‐political predictors and adherence to conspiracy theories but also helps us deduce alterations that may foster a stable inclination towards believing in conspiracy theories. These alterations, in turn, offer an explanation for the links between (sub)pathological predictors and conspiracy mentality. By integrating existing literature, our proposed model sheds light on the mechanisms underlying belief in conspiracy theories and presents new predictions to guide future research.
Exploring the increasing need for plasma collection: Perspectives of voluntary nonremunerated donors on payment for plasma in Canada
Authors: Holloway Kelly 
Published: August 2023

AbstractObjectivesThe aim of this paper is to understand how voluntary nonremunerated plasma donors in Canada view payment for plasma and the emerging commercial sector.BackgroundThere is a growing global demand for plasma, to produce plasma‐derived medical products. Source plasma for these products is collected through voluntary nonremunerated donation, sometimes by a national blood service, or by a commercial plasma collector, remunerating donors.Methods/MaterialsThis paper presents findings from qualitative semi‐structured interviews with source plasma donors in three new source plasma centres in Canada. Interview data were analysed using abductive analysis, an interpretivist approach that builds on grounded theory.ResultsThis study indicates that there are a range of perspectives on payment for plasma and the emerging commercial sector, from disinterest in payment, to opposition to payment based on the belief that it could undermine donating to help others, and risk public health and safety. One fifth of participants are open to CBS paying donors if it is necessary to increase national sufficiency of plasma. Almost two thirds of participants are opposed to commercial plasma collection in Canada, claiming that it could undermine Canada's public healthcare system, raising questions about transparency and accountability of the commercial plasma industry.ConclusionFindings point to important areas for future study, on publicly collected source plasma, the emerging commercial plasma sector, and the role of the donor as a social actor in a complex political system.
DOSIMETRY ANALYSIS OF BORON NEUTRON CAPTURE THERAPY (BNCT) ON THYROID CANCER USING PHITS CODE WITH NEUTRON FROM 30 MeV CYCLOTRON
Authors: Bilalodin Bilalodin , Wihantoro Wihantoro , Haryadi Aris , Abdullatif Farzand 
Published: August 2023

The dosimetry analysis of Boron Neutron Capture Therapy (BNCT) on thyroid cancer using the Particle and Heavy Ion Transport Code System (PHITS) has been carried out. The purpose of research was to determine the received dose rate and the irradiation time required for thyroid cancer therapy using the BNCT method. The geometry of thyroid model is based on MIRD phantom with cancer cells located in the center of the thyroid. The phantom was irradiated using a neutron source from DLBSA based 30 MeV cyclotron. Simulations were carried out at boron concentrations of (10, 20, 30, 40, 50, 60, and 70) mg/g tissue. Simulation results show that the boron concentration increases with dose rate. The highest dose rate was obtained in the Gross Target Volume (GTV) of 1.590 x 10-2 Gy/s using a boron concentration of 70 mg/g tissue. The effective time for cancer therapy was calculated based on the highest dose rate obtained at 57 minutes.
Derived categories of hearts on Kuznetsov components
Authors: Li Chunyi , Pertusi Laura , Zhao Xiaolei 
Published: August 2023

AbstractWe prove a general criterion that guarantees that an admissible subcategory of the derived category of an abelian category is equivalent to the bounded derived category of the heart of a bounded t‐structure. As a consequence, we show that has a strongly unique dg enhancement, applying the recent results of Canonaco, Neeman, and Stellari. We apply this criterion to the Kuznetsov component when is a cubic fourfold, a GM variety, or a quartic double solid. In particular, we obtain that these Kuznetsov components have strongly unique dg enhancement and that exact equivalences of the form are of Fourier–Mukai type when , belong to these classes of varieties, as predicted by a conjecture of Kuznetsov.
Age-Related Reference Intervals for Physical Performance Test Outcomes Relevant to Male Youth Middle Eastern Football Players
Authors: Lolli Lorenzo , Gregson Warren , Bonanno Daniele , Kuitunen Sami , Di Salvo Valter 
Published: August 2023

Purpose: To develop age-specific reference intervals for physical performance test outcomes relevant to male youth Middle Eastern football players. Methods: We analyzed mixed-longitudinal data (observations range: 1751–1943 assessments) from a sample of 441 male youth outfield football players (chronological age range: 11.7–18.4 y) as part of the Qatar Football Association and Aspire Academy development program over 14 competitive seasons. Semiparametric generalized additive models for location, scale, and shape estimated age-specific reference centiles for 10-m sprinting, 40-m sprinting, countermovement jump height, and maximal aerobic speed variables. Results: The estimated reference intervals indicated that the distribution of the physical performance test scores increased monotonically and nonlinearly with advancing chronological age for sprinting and countermovement jump outcome measures, reaching a plateau after 16 years common to each of these performance variables. The maximal aerobic speed median score increased substantially until ∼14.5 years, with the nonlinear trend flattening off toward relatively older chronological ages. Conclusions: We developed age-related reference intervals for physical performance test outcomes relevant to youth Qatari football players. Country-wide age-specific reference intervals can assist in the longitudinal tracking of the individual players’ progress over time against benchmark values derived from the reference population.
Ten-Year Changes in the Physical Activity and Sedentary Behaviors of Adults: An Analysis of the 2 Cross-Sectional Observation of Cardiovascular Risk Factors in Luxembourg Studies
Authors: Christofoletti Marina , Collings Paul , Tharrey Marion , Perchoux Camille , Malisoux Laurent 
Published: August 2023

Background: Monitoring population physical activity (PA) and sedentary behavior over time is important to guide public health actions. The objective of this study was to investigate the changes in PA and sedentary behavior of adult residents in Luxembourg over 10 years. We also investigated variations in change over time across sociodemographic subgroups. Methods: Two population-based cross-sectional studies of adults living in Luxembourg (Observation of Cardiovascular Risk Factors in Luxembourg [ORISCAV-LUX] [2007–2008] and ORISCAV-LUX 2 [2016–2018]) were considered. Multilevel mixed-effects models were used to investigate changes over time between the studies with regard to self-reported total PA (metabolic equivalent of task-min/week), PA levels (inactive/sufficiently active/highly active), total sitting time, recreational television viewing, and personal computer (PC) use outside of work (in minutes per day). Results: The ORISCAV-LUX study included 1318 participants and the ORISCAV-LUX 2 study involved 1477 participants; 573 adults took part in both studies. The proportion of participants categorized as highly active increased over time by 6.9%. Total PA (761 metabolic equivalent of task-min/wk), television viewing (12 min/d), and PC use outside of work (13 min/d) also increased, whereas the total sitting time decreased by 25 minutes per day. Variations in change over time were observed by sex, country of birth, education, employment status, and perceived financial difficulty. Conclusions: Over a 10-year period, PA increased and total sitting time decreased in adults living in Luxembourg. With regard to specific sedentary behaviors, television viewing, and PC use outside of work increased. Specific population subgroups will benefit the most from targeted efforts to increase PA and minimize sedentary behavior.
The African swine fever virus I10L protein inhibits the NF-
κ
B signaling pathway by targeting IKK
β
Authors: Chen Xing , Li Lian-Feng , Yang Zhong-Yuan , Li Meilin , Fan Shuai , Shi Lan-Fang , Ren Zi-Yu , Cao Xue-Jing , Zhang Yuhang , Han Shichong , Wan Bo , Qiu Hua-Ji , Zhang Gaiping , He Wen-Rui 
Published: August 2023

ABSTRACT

Proinflammatory factors play important roles in the pathogenesis of African swine fever virus (ASFV), which is the causative agent of African swine fever (ASF), a highly contagious and severe hemorrhagic disease. Efforts in the prevention and treatment of ASF have been severely hindered by knowledge gaps in viral proteins responsible for modulating host antiviral responses. In this study, we identified the I10L protein (pI10L) of ASFV as a potential inhibitor of the TNF-
α
- and IL-1
β
-triggered NF-
κ
B signaling pathway, the most canonical and important part of host inflammatory responses. The ectopically expressed pI10L remarkably suppressed the activation of NF-
κ
B signaling in HEK293T and PK-15 cells. The ASFV mutant lacking the
I10L
gene (ASFV
ΔI10L
) induced higher levels of proinflammatory cytokines production in primary porcine alveolar macrophages (PAMs) compared with its parental ASFV HLJ/2018 strain (ASFV
WT
). Mechanistic studies suggest that pI10L inhibits IKK
β
phosphorylation by reducing the K63-linked ubiquitination of NEMO, which is necessary for the activation of IKK
β
. Morever, pI10L interacts with the kinase domain of IKK
β
through its N-terminus, and consequently blocks the association of IKK
β
with its substrates I
κ
B
α
and p65, leading to reduced phosphorylation. In addition, the nuclear translocation efficiency of p65 was also altered by pI10L. Further biochemical evidence supported that the amino acids 1–102 on pI10L were essential for the pI10L-mediated suppression of the NF-
κ
B signaling pathway. The present study clarifies the immunosuppressive activity of pI10L, and provides novel insights into the understanding of ASFV pathobiology and the development of vaccines against ASF.

IMPORTANCE

African swine fever (ASF), caused by the African swine fever virus (ASFV), is now widespread in many countries and severely affects the commercial rearing of swine. To date, few safe and effective vaccines or antiviral strategies have been marketed due to large gaps in knowledge regarding ASFV pathobiology and immune evasion mechanisms. In this study, we deciphered the important role of the ASFV-encoded I10L protein in the TNF-
α
-/IL-1
β
-triggered NF-
κ
B signaling pathway. This study provides novel insights into the pathogenesis of ASFV and thus contributes to the development of vaccines against ASF.