bluuebunny/crossref_metadata_2025_split huggingface dataset:
Understanding the complex genetic architecture connecting rheumatoid arthritis, osteoporosis and inflammation: discovering causal pathways
Authors: Kasher Melody , Williams Frances M K , Freidin Maxim B , Malkin Ida , Cherny Stacey S ,   CHARGE Inflammation Working Group, Benjamin Emelia , Chasman Daniel I , Dehghan Abbas , Ahluwalia Tarunveer Singh , Meigs James , Tracy Russell , Alizadeh Behrooz Z , Ligthart Symen , Bis Josh , Eiriksdottir Gudny , Pankratz Nathan , Gross Myron , Rainer Alex , Snieder Harold , Wilson James G , Psaty Bruce M , Dupuis Josee , Prins Bram , Vaso Urmo , Stathopoulou Maria , Franke Lude , Lehtimaki Terho , Koenig Wolfgang , Jamshidi Yalda , Siest Sophie , Abbasi Ali , Uitterlinden Andre G , Abdollahi Mohammadreza , Schnabel Renate , Schick Ursula M , Nolte Ilja M , Kraja Aldi , Hsu Yi-Hsiang , Tylee Daniel S , Zwicker Alyson , Uher Rudolf , Davey-Smith George , Morrison Alanna C , Hicks Andrew , van Duijn Cornelia M , Ward-Caviness Cavin , Boerwinkle Eric , Rotter J , Rice Ken , Lange Leslie , Perola Markus , de Geus Eco , Morris Andrew P , Makela Kari Matti , Stacey David , Eriksson Johan , Frayling Tim M , Slagboom Eline P , Livshits Gregory 
Published: March 2022

AbstractRheumatoid arthritis (RA) and osteoporosis (OP) are two comorbid complex inflammatory conditions with evidence of shared genetic background and causal relationships. We aimed to clarify the genetic architecture underlying RA and various OP phenotypes while additionally considering an inflammatory component, C-reactive protein (CRP). Genome-wide association study summary statistics were acquired from the GEnetic Factors for OSteoporosis Consortium, Cohorts for Heart and Aging Research Consortium and UK Biobank. Mendelian randomization (MR) was used to detect the presence of causal relationships. Colocalization analysis was performed to determine shared genetic variants between CRP and OP phenotypes. Analysis of pleiotropy between traits owing to shared causal single nucleotide polymorphisms (SNPs) was performed using PL eiotropic A nalysis under CO mposite null hypothesis (PLACO). MR analysis was suggestive of horizontal pleiotropy between RA and OP traits. RA was a significant causal risk factor for CRP (β = 0.027, 95% confidence interval = 0.016–0.038). There was no evidence of CRP→OP causal relationship, but horizontal pleiotropy was apparent. Colocalization established shared genomic regions between CRP and OP, including GCKR and SERPINA1 genes. Pleiotropy arising from shared causal SNPs revealed through the colocalization analysis was all confirmed by PLACO. These genes were found to be involved in the same molecular function ‘protein binding’ (GO:0005515) associated with RA, OP and CRP. We identified three major components explaining the epidemiological relationship among RA, OP and inflammation: (1) Pleiotropy explains a portion of the shared genetic relationship between RA and OP, albeit polygenically; (2) RA contributes to CRP elevation and (3) CRP, which is influenced by RA, demonstrated pleiotropy with OP.
Contribution of marine zooplankton time series to the United Nations Decade of Ocean Science for Sustainable Development
Authors: Pitois Sophie , Yebra Lidia 
Published: March 2022

Abstract
Zooplankton play a central role in marine trophic webs, influencing both biogeochemistry and productivity of the oceans. Changes in their communities are important indicators of overall ecosystem health and global change impacts. With increasing exploitation and pressures on the marine environment, there is a growing need for high-resolution monitoring of marine zooplankton to provide detailed information about seasonal to decadal changes at local, regional, and global scales. This crucial knowledge is gathered mainly through long-term time series, which are key to characterizing and forecasting changes in marine zooplankton assemblages. In this Introduction, and through the articles included in this Themed Article Set, we bring together new insights, issuing from data time series, into zooplankton population dynamics. We also take up the application of such time series to the understanding of global change impacts on marine ecosystems and in providing advice on sustainable management of marine ecosystem resources and services. We highlight the importance of maintaining and supporting long-term marine zooplankton time series as key contributors to the development and advancement of the United Nations’ Decade of Ocean Science for Sustainable Development Goal 13-Climate action and Goal 14-Life below water.
Error estimates for DeepONets: a deep learning framework in infinite dimensions
Authors: Lanthaler Samuel , Mishra Siddhartha , Karniadakis George E 
Published: March 2022

Abstract
DeepONets have recently been proposed as a framework for learning nonlinear operators mapping between infinite-dimensional Banach spaces. We analyze DeepONets and prove estimates on the resulting approximation and generalization errors. In particular, we extend the universal approximation property of DeepONets to include measurable mappings in non-compact spaces. By a decomposition of the error into encoding, approximation and reconstruction errors, we prove both lower and upper bounds on the total error, relating it to the spectral decay properties of the covariance operators, associated with the underlying measures. We derive almost optimal error bounds with very general affine reconstructors and with random sensor locations as well as bounds on the generalization error, using covering number arguments. We illustrate our general framework with four prototypical examples of nonlinear operators, namely those arising in a nonlinear forced ordinary differential equation, an elliptic partial differential equation (PDE) with variable coefficients and nonlinear parabolic and hyperbolic PDEs. While the approximation of arbitrary Lipschitz operators by DeepONets to accuracy $\epsilon $ is argued to suffer from a ‘curse of dimensionality’ (requiring a neural networks of exponential size in $1/\epsilon $), in contrast, for all the above concrete examples of interest, we rigorously prove that DeepONets can break this curse of dimensionality (achieving accuracy $\epsilon $ with neural networks of size that can grow algebraically in $1/\epsilon $).Thus, we demonstrate the efficient approximation of a potentially large class of operators with this machine learning framework.
Gestational trophoblastic disease and associated factors among women experiencing first trimester pregnancy loss at a regional referral hospital in central Tanzania: a cross-sectional study
Authors: Mdoe Mwajuma B , Mwakigonja Amos R , Mwampagatwa Ipyana 
Published: March 2022

Abstract

Background
Gestational trophoblastic diseases (GTDs) may follow any form of pregnancy or a pregnancy loss. Early detection of GTDs is important, as some benign forms of the disease may progress into a chemoresistant and metastatic disease. This study aimed at determining the frequency of GTDs among women experiencing first trimester pregnancy loss and the associated patients’ characteristics.

Methods
This was a cross-sectional study that included 200 conveniently sampled women who experienced first trimester pregnancy loss from January to December 2019 at a Regional Referral Hospital in central Tanzania. The specimen obtained from products of conception were collected, formalin-fixed and paraffin-embedded and submitted for histopathological evaluation, for which haematoxylin and eosin stain was used. Data were analysed using SPSS version 23.0. The χ2 test was used to determine the association between categorical variables. p-Values ˂0.05 were considered statistically significant.

Results
Among 200 study participants, the overall frequency of GTDs was 42 (21%). Among those with GTDs, the most common histopathological diagnosis was partial hydatidiform mole (18 [42.9%]), followed by complete hydatidiform mole (17 [40.5%]) and choriocarcinoma (7 [16.5%]). In the studied participants, only increased human chorionic gonadotropin hormone levels were found to be statistically significantly associated with GTDs (p=0.000).

Conclusions
Results from this study suggest that routine histopathological evaluation of the products of conception is recommended in order to allow early detection of GTDs, including choriocarcinoma, which usually carries a poor prognosis. The histopathological reporting of choriocarcinoma among first trimester products of conception from Tanzania is novel.
Rapid determination of ceftazidime/avibactam susceptibility of carbapenemase-producing Enterobacterales directly from blood cultures: a comparative evaluation of EUCAST disc diffusion RAST and direct Etest® RAST
Authors: Bianco Gabriele , Boattini Matteo , Comini Sara , Iannaccone Marco , Cavallo Rossana , Costa Cristina 
Published: March 2022

Abstract

Objectives
To evaluate the performance of two rapid antimicrobial susceptibility testing (RAST) methods to determine ceftazidime/avibactam susceptibility directly from blood cultures (BCs).

Methods
A total of 246 Escherichia coli or Klebsiella pneumoniae isolates were tested for ceftazidime/avibactam susceptibility directly from BC bottles using EUCAST RAST and Etest® RAST. Results obtained after 4, 6 and 8 h of incubation were compared with those obtained by reference broth microdilution on pure overnight subcultures.

Results
In total, the proportion of readable zones after 4 h of incubation was 96.7% and reached 100% after 6 and 8 h of incubation. EUCAST RAST yielded &gt;98% of categorical agreement (CA) with all reading times. Major error (ME) and very major error (VME) rates were inferior to 3%, for each of the reading times. The proportion of results in the area of technical uncertainty (ATU) was almost similar (3.8%–4.1%) at the different reading times. DET-RAST yielded 97.5%, 98% and 99.6% of CA with readings at 4, 6 and 8 h, respectively. One (0.6%) ME was observed at each reading time, whereas five (5.9%) and four (4.5%) VMEs were observed analysing readings at 4 and 6 h, respectively. No VME was observed with readings at 8 h.

Conclusions
EUCAST RAST was accurate to determine ceftazidime/avibactam susceptibility of carbapenemase-producing K. pneumoniae and E. coli directly from BC bottles. DET-RAST has the advantage of determining MIC values and avoiding ATU results but showed to be an accurate method only with reading at 8 h.
The Future of Burn Care From a Complexity Science Perspective
Authors: van Zuijlen Paul P M , Korkmaz Halil Ibrahim , Sheraton Vivek M , Haanstra Tsjitske M , Pijpe Anouk , de Vries Annebeth , van der Vlies Cornelis H , Bosma Eelke , de Jong Evelien , Middelkoop Esther , Vermolen Fred J , Sloot Peter M A 
Published: March 2022

AbstractHealth care is undergoing a profound technological and digital transformation and has become increasingly complex. It is important for burns professionals and researchers to adapt to these developments which may require new ways of thinking and subsequent new strategies. As Einstein has put it: “We must learn to see the world anew.” The relatively new scientific discipline “Complexity science” can give more direction to this and is the metaphorical open door that should not go unnoticed in view of the burn care of the future. Complexity science studies “why the whole is more than the sum of the parts.” It studies how multiple separate components interact with each other and their environment and how these interactions lead to “behavior of the system.” Biological systems are always part of smaller and larger systems and exhibit the behavior of adaptivity, hence the name complex adaptive systems. From the perspective of complexity science, a severe burn injury is an extreme disruption of the “human body system.” But this disruption also applies to the systems at the organ and cellular levels. All these systems follow the principles of complex systems. Awareness of the scaling process at multilevel helps to understand and manage the complex situation when dealing with severe burn cases. This paper aims to create awareness of the concept of complexity and to demonstrate the value and possibilities of complexity science methods and tools for the future of burn care through examples from preclinical, clinical, and organizational perspectives in burn care.
Learning About One’s Self
Authors: Le Yaouanq Yves , Schwardmann Peter 
Published: March 2022

Abstract
To understand why naiveté about present-biased behavior is so prevalent and persistent, our experiment investigates how well participants learn from their past behavior in a real-effort task. While participants display naive present-biased behavior initially, our novel methodology allows us to establish that their updating is unbiased and would eliminate naiveté in the long run. Moreover, learning is unencumbered by a change in the environment. Our results suggest that persistent naiveté does not result from a fundamental inferential bias. However, participants underestimate their future learning—a bias that may lead to underinvestment in experimentation and a failure to activate self-regulation mechanisms.
High expression of HHLA2 predicts poor prognosis in medullary thyroid carcinoma
Authors: Niu Yongzhi , Wang Wei , Jiang Xiaodan , Huang Yichuan , Yan Shu , Jiang Yan 
Published: March 2022

Abstract

Background
Human endogenous retrovirus-H long terminal repeat-associating protein 2 is a newly identified immune checkpoint molecule that was aberrantly expressed in many malignant tumors. However, its expression in medullary thyroid carcinoma is still unclear. This study aimed to investigate the human endogenous retrovirus-H long terminal repeat-associating protein 2 expression in medullary thyroid carcinoma tissues and to evaluate the relationships between its expression and clinicopathologic together with prognostic relevance.

Methods
Using 51 surgical specimens obtained from medullary thyroid carcinoma patients, the expression levels of the human endogenous retrovirus-H long terminal repeat-associating protein 2 protein in medullary thyroid carcinoma tumor tissues and adjacent noncancerous tissues were measured by immunohistochemistry, and its correlations with clinicopathologic and prognostic features were analyzed. Status of CD8+ tumor infiltrating lymphocytes was also investigated.

Results
The results showed that human endogenous retrovirus-H long terminal repeat-associating protein 2 was only detected in tumor tissues, and 31.4% of the medullary thyroid carcinoma patients had high expression of human endogenous retrovirus-H long terminal repeat-associating protein 2. High human endogenous retrovirus-H long terminal repeat-associating protein 2 expression was significantly associated with lymph node metastasis and advanced American Joint Committee on Cancer stages (P = 0.005). There existed an inverse trend between human endogenous retrovirus-H long terminal repeat-associating protein 2 expression and CD8+ tumor infiltrating lymphocytes infiltration in medullary thyroid carcinoma tumor samples (P = 0.042). The log-rank test showed a shorter disease-free survival in patients with high human endogenous retrovirus-H long terminal repeat-associating protein 2 expression (P = 0.002). The disease-free survival rates were also significantly low in cases of medullary thyroid carcinoma with lymph node metastasis, American Joint Committee on Cancer stages III–IV and multifocality. Multivariate Cox analysis confirmed that human endogenous retrovirus-H long terminal repeat-associating protein 2 acted as an independent predictive factor in the disease-free survival of medullary thyroid carcinoma patients (hazard ratio = 4.138, 95% confidence interval: 1.027–16.667, P = 0.046).

Conclusions
Taken together, human endogenous retrovirus-H long terminal repeat-associating protein 2 is highly expressed in medullary thyroid carcinoma patients and is a poor prognostic biomarker of disease-free survival of medullary thyroid carcinoma patients.
Lower Exome Sequencing Coverage of Ancestrally African Patients in The Cancer Genome Atlas
Authors: Wickland Daniel P , Sherman Mark E , Radisky Derek C , Mansfield Aaron S , Asmann Yan W 
Published: March 2022

AbstractBackgroundIn the United States, cancer disproportionately impacts Black and African American individuals. Identifying genetic factors underlying cancer disparities has been an important research focus and requires data that are equitable in both quantity and quality across racial groups. It is widely recognized that DNA databases quantitatively underrepresent minorities. However, the differences in data quality between racial groups have not been well studied.MethodsWe compared the qualities of germline and tumor exomes between ancestrally African and European patients in The Cancer Genome Atlas of 7 cancers with at least 50 self-reported Black patients in the context of sequencing depth, tumor purity, and qualities of germline variants and somatic mutations.ResultsGermline and tumor exomes from ancestrally African patients were sequenced at statistically significantly lower depth in 6 out of the 7 cancers. For 3 cancers, most ancestrally European exomes were sequenced in early sample batches at higher depth, whereas ancestrally African exomes were concentrated in later batches and sequenced at much lower depth. For the other 3 cancers, the reasons of lower sequencing coverage of ancestrally African exomes remain unknown. Furthermore, even when the sequencing depths were comparable, African exomes had disproportionally higher percentages of positions with insufficient coverage, likely because of the known European bias in the human reference genome that impacted exome capture kit design.ConclusionsOverall and positional lower sequencing depths of ancestrally African exomes in The Cancer Genome Atlas led to underdetection and lower quality of variants, highlighting the need to consider epidemiological factors for future genomics studies.
Health Economics Research in Cancer Screening: Research Opportunities, Challenges, and Future Directions
Authors: Shih Ya-Chen Tina , Sabik Lindsay M , Stout Natasha K , Halpern Michael T , Lipscomb Joseph , Ramsey Scott , Ritzwoller Debra P 
Published: March 2022

Abstract
Cancer screening has long been considered a worthy public health investment. Health economics offers the theoretical foundation and research methodology to understand the demand- and supply-side factors associated with screening and evaluate screening-related policies and interventions. This article provides an overview of health economic theories and methods related to cancer screening and discusses opportunities for future research. We review 2 academic disciplines most relevant to health economics research in cancer screening: applied microeconomics and decision science. We consider 3 emerging topics: cancer screening policies in national as well as local contexts, “choosing wisely” screening practices, and targeted screening efforts for vulnerable subpopulations. We also discuss the strengths and weaknesses of available data sources and opportunities for methodological research and training. Recommendations to strengthen research infrastructure include developing novel data linkage strategies, increasing access to electronic health records, establishing curriculum and training programs, promoting multidisciplinary collaborations, and enhancing research funding opportunities.
Cefazolin sodium pentahydrate cause urolithiasis: a case report and literature review
Authors: Wang Fujun , Nie Wen , Wang Zongjun , Tian Sujian , Dong Junqiang 
Published: March 2022

Abstract
We report a rare case of urolithiasis induced by cefazolin sodium pentahydrate and review the relevant literature. A 12-year-old girl with right kidney injury was admitted to our hospital, a computed tomography scan revealed that no signs of disease in her left kidney but her right kidney was traumatized severely. After receiving cefazolin sodium pentahydrate, 2.0 g by intravenous infusion daily for 10 days, urolithiasis was found in the left urinary tract by computed tomography scan. Later, the patient complained of left back pain, nausea and vomiting, and a further computed tomography scan showed calculi persisted in the left urinary tract, and some of which had caused left hydronephrosis. A double-J catheter was placed in the left ureter, but no calculi were seen to drain with urine in the next 2 weeks, those calculi were removed by a flexible ureteroscope.
Kernel weight contribution to yield genetic gain of maize: a global review and US case studies
Authors: Fernández Javier A , Messina Carlos D , Salinas Andrea , Prasad P V Vara , Nippert Jesse B , Ciampitti Ignacio A 
Published: March 2022

AbstractOver the past century of maize (Zea mays L.) breeding, grain yield progress has been the result of improvements in several other intrinsic physiological and morphological traits. In this study, we describe (i) the contribution of kernel weight (KW) to yield genetic gain across multiple agronomic settings and breeding programs, and (ii) the physiological bases for improvements in KW for US hybrids. A global-scale literature review concludes that rates of KW improvement in US hybrids were similar to those of other commercial breeding programs but extended over a longer period of time. There is room for a continued increase of kernel size in maize for most of the genetic materials analysed, but the trade-off between kernel number and KW poses a challenge for future yield progress. Through phenotypic characterization of Pioneer Hi-Bred ERA hybrids in the USA, we determine that improvements in KW have been predominantly related to an extended kernel-filling duration. Likewise, crop improvement has conferred on modern hybrids greater KW plasticity, expressed as a better ability to respond to changes in assimilate availability. Our analysis of past trends and current state of development helps to identify candidate targets for future improvements in maize.
Consistent equivalence principle tests with fast radio bursts
Authors: Reischke Robert , Hagstotz Steffen , Lilow Robert 
Published: March 2022

ABSTRACT
Fast radio bursts (FRBs) are astrophysical transients of still debated origin. So far several hundred events have been detected, mostly at extragalactic distances, and this number is expected to grow significantly over the next years. The radio signals from the burst experience dispersion as they travel through the free electrons along the line-of-sight characterised by the dispersion measure (DM) of the radio pulse. In addition, each photon also experiences a gravitational Shapiro time delay while travelling through the potentials generated by the large-scale structure. If the weak equivalence principle (WEP) holds, the Shapiro delay is the same for photons of all frequencies. In case the WEP is broken, one would expect an additional dispersion to occur which could be either positive or negative for individual sources. Here, we suggest to use angular statistics of the DM fluctuations to put constraints on the WEP parametrized by the post-Newtonian parameter γ. Previous studies suffer from the problem that the gravitational potential responsible for the delay diverges in a cosmological setting, which our approach avoids. We carry out a forecast for a population of FRBs observable within the next years and show that any significant detection of the DM angular power spectrum will place the tightest constraints on the WEP to date, Δγ &lt; 10−15.