bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sustained Weight Loss, Weight Cycling, and Weight Gain During Adulthood and Pancreatic Cancer Incidence in the Women’s Health Initiative
Authors: Schwalb Molly E , Smith-Warner Stephanie A , Hou Jianrui , Rohan Thomas E , Snetselaar Linda , Luo Juhua , Genkinger Jeanine M 
Published: January 2022

AbstractPancreatic cancer (PC) is the fourth leading cause of cancer mortality among women in the United States. Obesity is positively associated with PC risk. Current health recommendations focus on weight maintenance for healthy-weight individuals and weight loss for overweight/obese individuals; however, little research has assessed associations between PC risk and changes in weight throughout the life course. Using prospective cohort study data, we examined the relationship between baseline adulthood weight patterns self-reported between 1993 and 1998 and PC risk in 136,834 postmenopausal women with 873 incident PC cases through September 30, 2015, in the Women’s Health Initiative. Hazard ratios (HR) and 95% confidence intervals (CI) were estimated using Cox proportional hazards models, adjusting for age, smoking habits, heavy alcohol consumption, and body mass index. Compared with women with stable weight, no significant associations were found between steady weight gain (HR = 1.01, 95% CI: 0.83, 1.22), sustained weight loss (HR = 1.26, 95% CI: 0.85, 1.87), or weight cycling patterns (HR = 1.08, 95% CI: 0.89, 1.30) and PC. Results were similar when the outcome definition was restricted to pancreatic adenocarcinoma cases. Overall, we did not find evidence to suggest that weight changes in adulthood significantly impact PC risk among postmenopausal women.
Two-faced compliments
Authors: McDonald Lucy 
Published: January 2022

Abstract
Compliments have received only cursory attention from speech act theorists and are usually characterised as run-of-the-mill illocutionary acts. Yet both intentionalist and conventionalist theories of illocutionary force struggle to accommodate ordinary language uses of ‘compliment’. I argue that this is because there are in fact two kinds of compliment: illocutionary compliments and perlocutionary compliments. This account illuminates the practice of complimenting, as well as its converse, insulting, and illustrates the complex relationship between illocutionary force and perlocutionary effect.
Current structure predictors are not learning the physics of protein folding
Authors: Outeiral Carlos , Nissley Daniel A , Deane Charlotte M 
Published: January 2022

Abstract

Summary
Motivation. Predicting the native state of a protein has long been considered a gateway problem for understanding protein folding. Recent advances in structural modeling driven by deep learning have achieved unprecedented success at predicting a protein’s crystal structure, but it is not clear if these models are learning the physics of how proteins dynamically fold into their equilibrium structure or are just accurate knowledge-based predictors of the final state.
Results. In this work, we compare the pathways generated by state-of-the-art protein structure prediction methods to experimental data about protein folding pathways. The methods considered were AlphaFold 2, RoseTTAFold, trRosetta, RaptorX, DMPfold, EVfold, SAINT2 and Rosetta. We find evidence that their simulated dynamics capture some information about the folding pathway, but their predictive ability is worse than a trivial classifier using sequence-agnostic features like chain length. The folding trajectories produced are also uncorrelated with experimental observables such as intermediate structures and the folding rate constant. These results suggest that recent advances in structure prediction do not yet provide an enhanced understanding of protein folding.
Availability. The data underlying this article are available in GitHub at https://github.com/oxpig/structure-vs-folding/

Supplementary information
Supplementary data are available at Bioinformatics online.
Cancer diagnosis is associated with a lower burden of dementia and less Alzheimer’s-type neuropathology
Authors: Karanth Shama D , Katsumata Yuriko , Nelson Peter T , Fardo David W , McDowell Jaclyn K , Schmitt Frederick A , Kryscio Richard J , Browning Steven R , Braithwaite Dejana , Arnold Susanne M , Abner Erin L 
Published: January 2022

Abstract
Cancer and Alzheimer’s disease are common diseases in ageing populations. Previous research has reported a lower incidence of Alzheimer’s disease-type (amnestic) dementia among individuals with a diagnosis of cancer. Both cancer and amnestic dementia are prevalent and potentially lethal clinical syndromes. The current study was conducted to investigate the association of cancer diagnosis with neuropathological and cognitive features of dementia.
Data were analysed from longitudinally evaluated participants in a community-based cohort study of brain ageing who came to autopsy at the University of Kentucky Alzheimer’s Disease Research Center. These data were linked to the Kentucky Cancer Registry, a population-based state cancer surveillance system, to obtain cancer-related data. We examined the relationship between cancer diagnosis, clinical dementia diagnosis, Mini-Mental State Examination scores and neuropathological features using inverse probability weighting to address bias due to confounding and missing data. To address bias due to inclusion of participants with dementia at cohort baseline, we repeated all analyses restricted to the participants who were cognitively normal at baseline.
Included participants (n = 785) had a mean ± standard deviation age of death of 83.8 ± 8.6 years; 60.1% were female. Cancer diagnosis was determined in 190 (24.2%) participants, and a diagnosis of mild cognitive impairment or dementia was determined in 539 (68.7%). APOE ɛ4 allele dosage was lower among participants with cancer diagnosis compared to cancer-free participants overall (P = 0.0072); however, this association was not observed among those who were cognitively normal at baseline. Participants with cancer diagnosis had lower odds of mild cognitive impairment or dementia, and higher cognitive test scores (e.g. Mini-Mental State Examination scores evaluated 6 and ≤2 years ante-mortem, P &lt; 0.001 for both comparisons). Cancer diagnosis also associated with lower odds of higher Braak neurofibrillary tangle stages (III/IV) or (V/VI), moderate/frequent neuritic plaques, moderate/frequent diffuse plaques and moderate/severe cerebral amyloid angiopathy (all P &lt; 0.05). By contrast, TDP-43, α-synuclein and cerebrovascular pathologies were not associated with cancer diagnosis.
Cancer diagnosis was associated with a lower burden of Alzheimer’s disease pathology and less cognitive impairment. These findings from a community-based cohort with neuropathological confirmation of substrates support the hypothesis that there is an inverse relationship between cancer and Alzheimer’s disease.
Endocarditis Caused by Nontypeable Streptococcus pneumoniae
Authors: Henriet Stefanie S V , Langereis Jeroen D , Lo Stephanie W , Bentley Stephen , Mesman Rob J , Fejzic Zina , van Niftrik Laura , van Sorge Nina M , Wertheim Heiman F L , de Jonge Marien I , Cremers Amelieke J H 
Published: January 2022

Abstract
The Streptococcus pneumoniae capsule is regarded as indispensable in bacteremia. We report an infant with a ventricular septal defect and infective endocarditis caused by nontypeable S. pneumoniae. In-depth investigation confirmed a deficient capsule yet favored pneumococcal fitness for causing infective endocarditis, rather than a host immune disorder, as the cause of infective endocarditis in this case.
More dissimilarities than affinities between DNAJB11-PKD and ADPKD
Authors: Pisani Isabella , Allinovi Marco , Palazzo Viviana , Zanelli Paola , Gentile Micaela , Farina Maria Teresa , Giuliotti Sara , Cravedi Paolo , Delsante Marco , Maggiore Umberto , Fiaccadori Enrico , Manenti Lucio 
Published: January 2022

ABSTRACT

Background
Polycystic kidney diseases (PKD) are an important cause of chronic kidney disease (CKD). Autosomal dominant polycystic kidney disease (ADPKD) due to PKD1 or PKD2 mutations is the most common form, but other genes can be responsible for ADPKD and its phenocopies. Among them, a form of atypical ADPKD caused by DNAJB11 mutations (DNAJB11-PKD) has been recently described.

Methods
We retrospectively recruited a cohort of 27 patients from six different families sharing common ancestries and harboring the same DNAJB11 mutation (c.100C&gt;T, p.Arg34*) and we compared it with a cohort of 42 typical ADPKD patients.

Results
DNAJB11-PKD patients show small/normal-sized kidneys, with significantly smaller cysts and a slower progression to end-stage kidney disease (ESKD) than ADPKD patients. In the DNAJB11-PKD cohort, the cystic phenotype could not be detected by ultrasound in about half of the patients, but all cases with available computed tomography/magnetic resonance scans displayed cysts. Clinically, DNAJB11-PKD patients displayed proteinuria (mostly albuminuria). Compared with ADPKD, DNAJB11-PKD patients were older and had a higher prevalence of type 2 diabetes mellitus (19% versus 0%; P = 0.007) and nephrolithiasis (62% versus 29%; P = 0.01), whereas the prevalence of cardiac valvular defects was lower (4% versus 51%; P &lt; 0.001).

Conclusions
Overall, clinical features of DNAJB11-PKD were more subtle compared with those of ADPKD. DNAJB11-PKD shows a unique renal and extrarenal phenotype, clinical presentation and natural history. Therefore our data support that this genetic disease is classified separately from ADPKD.
Multibranched endovascular repair using a modified endograft with hydrogel-reinforced fenestrations
Authors: Azuma Takashi , Yokoi Yoshihiko , Hayakawa Namiko , Domoto Satoru , Niinami Hiroshi 
Published: January 2022

Abstract

OBJECTIVES
We devised a novel physician-modified endograft (PMEG) with hydrogel-reinforced fenestrations to provide a more secure connection with the bridging graft than fenestrations alone. We applied this novel PMEG in a clinical setting and evaluated the clinical and technical results.

METHODS
In this study, patients with complex thoraco-abdominal aortic pathologies involving the renal, superior mesenteric or coeliac artery were included. However, patients with pararenal abdominal aneurysm were excluded. Regardless of anatomical suitability, all patients referred to our hospital were enrolled. All patients were treated via compassionate use of PMEG. All PMEGs were used following the same procedure using hydrogel-reinforced fenestrations. A retrospective analysis was conducted on consecutive patients who were treated between October 2018 and April 2021.

RESULTS
Out of 40 patients, 29 and 11 were men and women, respectively. The median patient age was 73.6 (range: 49–87) years. Among the patients, 36 (90%) had true aneurysms, whereas the others had false lumen aneurysms and penetrating atherosclerotic ulcer. Despite anatomical challenges, all branches were successfully reconstructed. The mean operative time was 333 (standard deviation 98) min. Postoperative computed tomography angiography did not reveal type I and IIIc endoleaks from the hydrogel-reinforced fenestrations. The 30-day survival rate was 97.5%. One patient died due to brain haemorrhage on postoperative day 5. During follow-up, computed tomography revealed no migration of any bridging graft.

CONCLUSIONS
We confirmed the effectiveness of the hydrogel as a sealing material and the secure connection between hydrogel-reinforced fenestrations and side branches in vivo.

Clinical trial registration number
5287.
Surgery for infective endocarditis following low-intermediate risk transcatheter aortic valve replacement—a multicentre experience
Authors: Saha Shekhar , Joskowiak Dominik , Marin-Cuartas Mateo , Diab Mahmoud , Schwaiger Benedikt M , Sandoval-Boburg Rodrigo , Popov Aron-Frederik , Weber Carolyn , Varghese Sam , Martens Andreas , Cebotari Serghei , Scherner Maximilian , Eichinger Walter , Holzhey David , Dohle Daniel-Sebastian , Wahlers Thorsten , Doenst Torsten , Misfeld Martin , Mehilli Julinda , Massberg Steffen , Hagl Christian 
Published: January 2022

Abstract

OBJECTIVES
With the expansion of transcatheter aortic valve replacement (TAVR) into intermediate and low risk, the number of TAVR procedures is bound to rise and along with it the number of cases of infective endocarditis following TAVR (TIE). The aim of this study was to review a multicentre experience of patients undergoing surgical intervention for TIE and to analyse the underlying indications and operative results.

METHODS
We retrospectively identified and analysed 69 patients who underwent cardiac surgery due to TIE at 9 cardiac surgical departments across Germany. The primary outcome was operative mortality, 6-month and 1-year survival.

RESULTS
Median age was 78 years (72–81) and 48(69.6%) were male. The median time to surgical aortic valve replacement was 14 months (5–24) after TAVR, with 32 patients (46.4%) being diagnosed with early TIE. Cardiac reoperations were performed in 17% of patients and 33% underwent concomitant mitral valve surgery. The main causative organisms were: Enterococcus faecalis (31.9%), coagulase-negative Staphylococcus spp. (26.1%), Methicillin-sensitive Staphylococcus aureus (15.9%) and viridians group streptococci (14.5%). Extracorporeal life support was required in 2 patients (2.9%) for a median duration of 3 days. Postoperative adverse cerebrovascular events were observed in 13 patients (18.9%). Postoperatively, 9 patients (13.0%) required a pacemaker and 33 patients (47.8%) needed temporary renal replacement therapy. Survival to discharge was 88.4% and survival at 6 months and 1 year was found to be 68% and 53%, respectively.

CONCLUSIONS
Our results suggest that TIE can be treated according to the guidelines for prosthetic valve endocarditis, namely with early surgery. Surgery for TIE is associated with acceptable morbidity and mortality rates. Surgery should be discussed liberally as a treatment option in patients with TIE by the ‘endocarditis team’ in referral centres.
Not Just Sea Turtles, Let’s Protect Women Too: Invoking Public Morality Exception or Negotiating a New Gender Exception in Trade Agreements?
Authors: Bahri Amrita , Boklan Daria 
Published: January 2022

Abstract
The most common provisions we find in almost all multilateral, regional and bilateral trade agreements are the exception clauses that allow countries to protect public morals, humans, animals or plant health and life and conserve exhaustible natural resources. If countries can allow trade-restrictive measures that aim to protect these non-economic interests, is it possible to negotiate a specific exception to justify measures that are aimed at protecting women’s economic interests as well? Is the removal of barriers that impede women’s participation in trade any less important than the conservation of exhaustible natural resources such as sea turtles or dolphins? In that context, this article prepares a case for the inclusion of a specific exception that can allow countries to leverage women’s economic empowerment through international trade agreements. This is done after carrying out an objective assessment of whether a respondent could seek protection under the existing public morality exception to justify a measure that is taken to protect women’s economic interests.
Multiresidue pesticide analysis in tomato using GC-MS/MS using modified QuEChERS method with titanium-coated graphite with CNT-ABS nanocomposite as dispersive solid-phase extraction materials
Authors: Khetagoudar Mahadev C , Deepa G T , Goroji P T , Chetti Mahadev B , Praveen Kumar Avvaru , Bilehal Dinesh C 
Published: January 2022

Abstract
The presence of pesticide residues in food and vegetables is a growing concern for consumers. To monitor these residues reliably, a selective and sensitive multiresidue system has been developed and validated in tomato by gas chromatography–tandem mass spectrometry (GC-MS/MS). Titanium-coated graphite with carbon nanotube (CNT) in acrylonitrile–butadiene–styrene (ABS) used as reversed-dispersive solid-phase (extraction materials with modified QuEChERS (Quick, Easy, Cheap, Effective, Rugged, and Safe) method. Titanium-coated graphite with CNT-ABS is synthesized, characterized by X-ray diffraction and scanning electron microscopy. The clean-up performance of titanium-coated graphite with CNT-ABS was demonstrated to be better to primary secondary amine and graphitized carbon black cartridges. The processing of two multiple reaction monitoring transformations for each analyte is done using GC-MS/MS in electron impact mode. Satisfactory purification and recovery effects (74%–100%) of 35 pesticides were achieved in tomato matrices when using 5 mg of titanium-coated graphite ABS-CNT nanocomposite. It was observed that quinolphos and deltamethrin are present above the maximum residue limit. The technique proved to be reliable and sensitive in tomato samples for the routine testing of 35 pesticides.
Migration of bisphenol A and its related compounds in canned seafood and dietary exposure estimation
Authors: Lin Na , Ma Derong , Liu Zhidong , Wang Xichang , Ma Liyan 
Published: January 2022

Abstract
The present study sought to investigate the migration of target bisphenols, such as bisphenol-A (BPA), bisphenol-F (BPA), bisphenol-A diglycidyl ether (BADGE), bisphenol-A (2,3-dihydroxypropyl) glycidyl ether (BADGE·H2O), bisphenol-A bis(2,3-dihydroxypropyl) ether (BADGE·2H2O), and bisphenol F diglycidyl ether (BFDGE) in 102 samples of several canned seafood, namely canned Antarctic krill, scallop, oysters, mussel, clam, and mantis shrimp stored for months at different temperatures through a high-performance liquid chromatographic-fluorescence detector combined with a microwave-assisted extraction method. Except for BFDGE, the other five bisphenols were observed in most of the analyzed samples. The canned shrimp showed the highest migration of BPA (0.089 mg/kg), exceeding the specific migration limit (SML) of BPA (0.05 mg/kg) specified by the European Union, while the migration levels of BADGE and its derivatives were within their SMLs. The migration behavior of bisphenols in the canned seafood was majorly affected by the analytes, storage conditions, and food types. BPA, BADGE·H2O, and BADGE·2H2O were characterized by a rapid migration during the first half of the shelf life, which increased with the increase of temperature, followed by a stabilization or decline of their concentrations for prolonged durations. Besides, the migration of target bisphenols was significantly influenced by the storage temperature in some seafood species. Notably, higher migration level of BPA was found in samples with higher fat content. The average dietary exposure of Chinese adults to BPA, BPF, BADGE·2H2O, BADGE·H2O, and BADGE of canned seafood was estimated at 11.69, 1.21, 6.47, 8.74, and 4.71 ng/(kg·d), respectively. The target hazard quotient values of all the analyzed bisphenols were below 1 for the Chinese adults, suggesting an insignificant exposure to these bisphenols through canned seafood consumption.
A Broad Survey of Gene Body and Repeat Methylation in Cnidaria Reveals a Complex Evolutionary History
Authors: Zhang Xinhui , Jacobs David 
Published: January 2022

Abstract
DNA methylation, an important component of eukaryotic epigenetics, varies in pattern and function across Metazoa. Notably, bilaterian vertebrates and invertebrates differ dramatically in gene body methylation (GbM). Using the frequency of cytosine-phospho-guanines (CpGs), which are lost through mutation when methylated, we report the first broad survey of DNA methylation in Cnidaria, the ancient sister group to Bilateria. We find that: 1) GbM differentially relates to expression categories as it does in most bilaterian invertebrates, but distributions of GbM are less discretely bimodal. 2) Cnidarians generally have lower CpG frequencies on gene bodies than bilaterian invertebrates potentially suggesting a compensatory mechanism to replace CpG lost to mutation in Bilateria that is lacking in Cnidaria. 3) GbM patterns show some consistency within taxonomic groups such as the Scleractinian corals; however, GbM patterns variation across a range of taxonomic ranks in Cnidaria suggests active evolutionary change in GbM within Cnidaria. 4) Some but not all GbM variation is associated with life history change and genome expansion, whereas GbM loss is evident in endoparasitic cnidarians. 5) Cnidarian repetitive elements are less methylated than gene bodies, and methylation of both correlate with genome repeat content. 6) These observations reinforce claims that GbM evolved in stem Metazoa. Thus, this work supports overlap between DNA methylation processes in Cnidaria and Bilateria, provides a framework to compare methylation within and between Cnidaria and Bilateria, and demonstrates the previously unknown rapid evolution of cnidarian methylation.
Whole-Genome Sequences of Two Kazachstania barnettii Strains Isolated from Anthropic Environments
Authors: Devillers Hugo , Sarilar Véronique , Grondin Cécile , Sterck Lieven , Segond Diego , Jacques Noémie , Sicard Delphine , Casaregola Serge , Tinsley Colin 
Published: January 2022

Abstract
Recent studies have suggested that species of the Kazachstania genus may be interesting models of yeast domestication. Among these, Kazachstania barnettii has been isolated from various microbially transformed foodstuffs such as sourdough bread and kefir. In the present work, we sequence, assemble, and annotate the complete genomes of two K. barnettii strains: CLIB 433, being one of the two reference strains for K. barnettii that was isolated as a spoilage organism in soft drink, and CLIB 1767, recently isolated from artisan bread-making sourdough. Both assemblies are of high quality with N50 statistics greater than 1.3 Mb and BUSCO score greater than 99%. An extensive comparison of the two obtained genomes revealed very few differences between the two K. barnettii strains, considering both genome structure and gene content. The proposed genome assemblies will constitute valuable references for future comparative genomic, population genomic, or transcriptomic studies of the K. barnettii species.