bluuebunny/crossref_metadata_2025_split huggingface dataset:
Textbook Outcome and Survival in Patients With Gastric Cancer
Authors: Levy Jordan , Gupta Vaibhav , Amirazodi Elmira , Allen-Ayodabo Catherine , Jivraj Naheed , Jeong Yunni , Davis Laura E. , Mahar Alyson L. , De Mestral Charles , Saarela Olli , Coburn Natalie G. 
Published: March 2020

Objective:
To examine the association between Textbook Outcome (TO)—a new composite quality measurement—and long-term survival in gastric cancer surgery.

Background:
Single-quality indicators do not sufficiently reflect the complex and multifaceted nature of perioperative care in patients with gastric adenocarcinoma.

Methods:
All patients undergoing gastrectomy for nonmetastatic gastric adenocarcinoma registered in the Population Registry of Esophageal and Stomach Tumours of Ontario (PRESTO) between 2004 and 2015 were included. TO was defined according to negative margins; >15 lymph nodes sampled; no severe complications; no re-interventions; no unplanned ICU admission; length of stay ≤21 days; no 30-day readmission; and no 30-day mortality. Three-year survival was estimated using the Kaplan-Meier method. A marginal multivariable Cox proportional-hazards model was used to estimate the association between achieving TO metrics and long-term survival. E-value methodology was used to assess for risk of residual confounding.

Results:
Of the 1836 patients included in this study, 402 (22%) achieved all TO metrics. TO patients had a higher 3-year survival rate compared to non-TO patients (75% vs 55%, log-rank P < 0.001). After adjustments for covariates and clustering within hospitals, TO was associated with a 41% reduction in mortality (adjusted hazards ratio 0.59, 95% confidence interval 0.48, 0.72, P < 0.001). These results were robust to potential residual confounding.

Conclusions:
Achieving TO is strongly associated with improved long-term survival in gastric cancer patients and merits further focus in surgical quality improvement efforts.
Endoscopic Ampullectomy of Benign Ampullary Lesions: Outcomes From a Single Center Study
Authors: Ödemiş Bülent , Durak Muhammed B. , Cengiz Mustafa 
Published: March 2020

Background:
Endoscopic ampullectomy (EA) offers an insignificantly intrusive strategy for viably treating mucosal and occasionally submucosal lesions of the ampulla of Vater and encompassing periampullary area with high achievement and is more secure. The aim of this study was to present safety, efficacy, and outcomes of EA in the treatment of benign lesions of ampulla Vater performed by single experienced endoscopists in a high volume center.

Methods:
This retrospective study was conducted in patients referred to our hospital (Turkey High Speciality Training and Research Hospital, Turkey) for endoscopic evaluation of ampullary benign lesions over an 8-year period (between October 2011 and September 2019). Success rate was defined as complete resection of lesions.

Results:
Twenty-nine patients with a median age of 64 years were included. Twenty-five patients had lesions confined to the ampulla vateri (86.2%). Accordingly, 2 lesions had intraductal extension adenoma (IDA) (6.9%) and 2 were lateral spreading adenoma (6.9%). The median size of the lesion was 17.5 mm (10 to 36 mm). Nineteen lesions (65.5%) were resected en bloc and 10 lesions (34.5%) were resected in piecemeal manner. Complete resection was achieved in 21 of 23 patients with benign ampullary lesions. The procedure success rate was 91.3%. Complications occurred in 6 patients (20.6%) of these 3 had (10.3%) bleeding, 2 (6.8%) had pancreatitis, and 1 had (3.4%) perforation. Four patients (13.7%) had a recurrence.

Conclusions:
Deep resection of the benign ampullary lesions increases the complete resection rate, cannulation rate of the pancreatic duct, and stenting rate of the pancreatic duct. EA is a safe and successful procedure in patients with benign lesions of ampulla vater.
Transplant Outcomes in Older Patients With Nonalcoholic Steatohepatitis Compared to Alcohol-related Liver Disease and Hepatitis C
Authors: Henson Jacqueline B. , Wilder Julius M. , Kappus Matthew R. , Barbas Andrew S. , Moylan Cynthia A. , Niedzwiecki Donna , Muir Andrew J. , Berg Carl L. , Patel Yuval A. 
Published: March 2020

Background.
Patients with nonalcoholic steatohepatitis (NASH) are waitlisted at older ages than individuals with other liver diseases, but the effect of age on liver transplantation (LT) outcomes in this population and whether it differs from other etiologies is not known. We aimed to evaluate the impact of age on LT outcomes in NASH.

Methods.
The United Network for Organ Sharing database was used to identify adults with NASH, hepatitis C virus (HCV) infection, and alcohol-related liver disease (ALD) listed for LT during 2004–2017. Patients were split into age groups (18–49, 50–54, 55–59, 60–64, 65–69, ≥70), and their outcomes were compared.

Results.
From 2004 to 2017, 14 197 adults with NASH were waitlisted, and the proportion ≥65 increased from 15.8% to 28.9%. NASH patients ages 65–69 had an increased risk of waitlist and posttransplant mortality compared to younger groups, whereas the outcomes in ages 60–64 and 55–59 were similar. The outcomes of individuals with NASH were similar to patients of the same age group with ALD or HCV. Functional status and dialysis were predictors of posttransplant mortality in individuals ≥65 with NASH, and cardiovascular disease was the leading cause of death.

Conclusions.
Older NASH patients (≥65) have an increased risk of waitlist and posttransplant mortality compared to younger individuals, although outcomes were similar to patients with ALD or HCV of corresponding age. These individuals should be carefully evaluated prior to LT, considering their functional status, renal function, and cardiovascular risk. Further studies are needed to optimize outcomes in this growing population of transplant candidates.
The role of diet in preventing and reducing cognitive decline
Authors: Angeloni Cristina , Businaro Rita , Vauzour David 
Published: March 2020

Purpose of review
This review summarises the most recent evidence regarding the effects of diet in preventing and reducing age-related cognitive decline and neurodegenerative diseases.

Recent findings
Recent evidence indicates that nutraceuticals and whole diet approaches may protect against the development of age-related cognitive decline and pathological neurodegeneration. The neuroprotective effects are diverse depending on the nutrient employed and may involve a reduction of neuroinflammation, an activation of the endogenous antioxidant defence system and a modulation of the gut microbiota structure and function.

Summary
This review summarises the existing evidence in favour of diet as a viable alternative approach to directly impact cognitive decline and neurodegenerative diseases. The single nutrient (polyphenols, B vitamins, long-chain polyunsaturated fatty acids) versus whole diet approach (Mediterranean diet, Dietary Approaches to Stop Hypertension, MIND, Nordic, ketogenic) is presented and discussed. Potential mechanisms of action underlying the beneficial effects of these diets are also described. Implementation of large-scale preventive interventions based on dietary patterns identified as being beneficial to brain health should be a research and public health priority, ideally in conjunction with other health-promoting lifestyle factors.
Simple unity among the fundamental equations of science
Authors: Frank Steven A. 
Published: March 2020

The Price equation describes the change in populations. Change concerns some value, such as biological fitness, information or physical work. The Price equation reveals universal aspects for the nature of change, independently of the meaning ascribed to values. By understanding those universal aspects, we can see more clearly why fundamental mathematical results in different disciplines often share a common form. We can also interpret more clearly the meaning of key results within each discipline. For example, the mathematics of natural selection in biology has a form closely related to information theory and physical entropy. Does that mean that natural selection is about information or entropy? Or do natural selection, information and entropy arise as interpretations of a common underlying abstraction? The Price equation suggests the latter. The Price equation achieves its abstract generality by partitioning change into two terms. The first term naturally associates with the direct forces that cause change. The second term naturally associates with the changing frame of reference. In the Price equation’s canonical form, total change remains zero because the conservation of total probability requires that all probabilities invariantly sum to one. Much of the shared common form for the mathematics of different disciplines may arise from that seemingly trivial invariance of total probability, which leads to the partitioning of total change into equal and opposite components of the direct forces and the changing frame of reference.
This article is part of the theme issue ‘Fifty years of the Price equation’.
When science mirrors life: on the origins of the Price equation
Authors: Harman Oren 
Published: March 2020

The Price equation was a piece of abstract mathematics. What kind of a connection could it possibly have had to George Price's personal life and biography? Here, I will argue that the initial impetus for Price's foray into mathematical population genetics stemmed from a preoccupation with the origins of family, one that was born following a divorce from his wife and the abandonment of their two young girls. What is special about the Price equation is the way in which it associates statistically between two groups, a ‘mother’ and ‘daughter’ population. The association need not mean genetic relatedness in the narrow sense of direct descent, and it allows us to see selection working at different levels simultaneously, a fact that was not lost on William Hamilton. Hamilton was one of the few friends who desperately tried to save Price from falling into the abyss of depression and homelessness in the period following the publication of ‘Selection and covariance’ (Price 1928Nature227, 520–521 (doi:10.1038/227520a0)). Viewed in this light, the Price equation assumes new meaning.This article is part of the theme issue ‘Fifty years of the Price equation’.
The Price equation and reproductive value
Authors: Grafen Alan 
Published: March 2020

The Price equation is widely recognized as capturing conceptually important properties of natural selection, and is often used to derive versions of Fisher’s fundamental theorem of natural selection, the secondary theorems of natural selection and other significant results. However, class structure is not usually incorporated into these arguments. From the starting point of Fisher’s original connection between fitness and reproductive value, a principled way of incorporating reproductive value and structured populations into the Price equation is explained, with its implications for precise meanings of (two distinct kinds of) reproductive value and of fitness. Once the Price equation applies to structured populations, then the other equations follow. The fundamental theorem itself has a special place among these equations, not only because it always incorporated class structure (and its method is followed for general class structures), but also because that is the result that justifies the important idea that these equations identify the effect of natural selection. The precise definitions of reproductive value and fitness have striking and unexpected features. However, a theoretical challenge emerges from the articulation of Fisher’s structure: is it possible to retain the ecological properties of fitness as well as its evolutionary out-of-equilibrium properties?This article is part of the theme issue ‘Fifty years of the Price equation’.
The Price equation as a bridge between animal breeding and evolutionary biology
Authors: Bijma P. 
Published: March 2020

The genetic response to selection is central to both evolutionary biology and animal and plant breeding. While Price's theorem (PT) is well-known in evolutionary biology, most breeders are unaware of it. Rather than using PT, breeders express response to selection as the product of the intensity of selection (i), the accuracy of selection (ρ) and the additive genetic standard deviation (σA);R=iρσA. In contrast to the univariate ‘breeder's equation’, this expression holds for multivariate selection on Gaussian traits. Here, I relateR=iρσAto PT, and present a generalized version,R=iwρA,wσA, valid irrespective of the trait distribution. Next, I consider genotype–environment covariance in relation to the breeder's equation and PT, showing that the breeder's equation may remain valid depending on whether the genotype–environment covariance works across generations. Finally, I consider the response to selection in the prevalence of an endemic infectious disease, as an example of an emergent trait. The result shows that disease prevalence has much greater heritable variation than currently believed. The example also illustrates that the indirect genetic effect approach moves elements of response to selection from the second to the first term of PT, so that changes acting via the social environment come within the reach of quantitative genetics.This article is part of the theme issue ‘Fifty years of the Price equation’.
The Price equation and the causal analysis of evolutionary change
Authors: Okasha Samir , Otsuka Jun 
Published: March 2020

Though the Price equation in itself is simply a statistical identity, biologists have often adopted a ‘causal interpretation’ of the equation, in the sense that its component terms have been supposed to correspond to distinct causal processes in evolution, such as natural selection and transmission bias. In this paper, we bring the issue of causal interpretation to the fore, by studying the conditions under which it is legitimate to read causal meaning into the Price equation. We argue that only if substantive assumptions about causal structure are made, which can be represented in the form of a causal model, can the component terms of the Price equation be interpreted as causally meaningful. We conclude with a reflection on the epistemic uses of the Price equation, emphasizing the difference between the description, explanation and prediction of evolutionary change.
This article is part of the theme issue ‘Fifty years of the Price equation’.
AI-aided design of novel targeted covalent inhibitors against SARS-CoV-2
Authors: Tang Bowen , He Fengming , Liu Dongpeng , Fang Meijuan , Wu Zhen , Xu Dong 
Published: March 2020

AbstractThe focused drug repurposing of known approved drugs (such as lopinavir/ritonavir) has been reported failed for curing SARS-CoV-2 infected patients. It is urgent to generate new chemical entities against this virus. As a key enzyme in the life-cycle of coronavirus, the 3C-like main protease (3CLproor Mpro) is the most attractive for antiviral drug design. Based on a recently solved structure (PDB ID: 6LU7), we developed a novel advanced deep Q-learning network with the fragment-based drug design (ADQN-FBDD) for generating potential lead compounds targeting SARS-CoV-2 3CLpro. We obtained a series of derivatives from those lead compounds by our structure-based optimization policy (SBOP). All the 47 lead compounds directly from our AI-model and related derivatives based on SBOP are accessible in our molecular library athttps://github.com/tbwxmu/2019-nCov. These compounds can be used as potential candidates for researchers in their development of drugs against SARS-CoV-2.
Loss of α2-6 sialylation promotes the transformation of synovial fibroblasts into a pro-inflammatory phenotype in Rheumatoid Arthritis
Authors: Wang Yilin , Khan Aneesah , Antonopoulos Aristotelis , Bouché Laura , Buckley Christopher D , Filer Andrew , Raza Karim , Ping-Li Kun , Tolusso Barbara , Gremese Elisa , Kurowska-Stolarska Mariola , Alivernini Stefano , Dell Anne , Haslam Stuart M. , Pineda Miguel A. 
Published: March 2020

AbstractIn healthy joints, synovial fibroblasts (SFs) provide the microenvironment required to mediate homeostasis but are recognized to adopt a pathological role in rheumatoid arthritis (RA), promoting the infiltration and activation of immune cells to perpetuate local inflammation, pain and joint destruction. Carbohydrates (glycans) attached to cell surface proteins are fundamental regulators of cellular interactions between stromal and immune cells, but very little is known about the glycome of SFs or how glycosylation regulates their biology. Here we fill these gaps in our understanding of stromal guided pathophysiology by systematically mapping glycosylation pathways in healthy and arthritic SFs. We used a combination of transcriptomic and glycomic analysis to show that transformation of fibroblasts into pro-inflammatory cells in RA is associated with profound glycan remodeling, a process that involves reduction of α2-6 terminal sialylation that is mostly mediated by TNFα-dependent inhibition of the glycosyltransferase ST6Gal1. We also show that sialylation of SFs correlates with distinct disease stages and SFs functional subsets in both human RA and models of mouse arthritis. We propose that pro-inflammatory cytokines in the joint remodel the SF-glycome, transforming a regulatory tissue intended to preserve local homeostasis, into an under-sialylated and highly pro-inflammatory microenvironment that contributes to an amplificatory inflammatory network that perpetuates chronic inflammation. These results highlight the importance of cell glycosylation in stromal immunology.
Computer vision for pattern detection in chromosome contact maps
Authors: Matthey-Doret Cyril , Baudry Lyam , Breuer Axel , Montagne Rémi , Guiglielmoni Nadège , Scolari Vittore , Jean Etienne , Campeas Arnaud , Henri Chanut Philippe , Oriol Edgar , Meot Adrien , Politis Laurent , Vigouroux Antoine , Moreau Pierrick , Koszul Romain , Cournac Axel 
Published: March 2020

AbstractChromosomes of all species studied so far display a variety of higher order organizational features such as domains or loops often associated to biological functions and visible on Hi-C contact maps. We developedChromosight, an algorithm inspired from computer vision that can detect patterns in Hi-C maps.Chromosighthas greater sensitivity than existing methods, while being faster and applicable to any type of genomes, including bacteria, viruses, yeasts and mammals. Code and documentation:https://github.com/koszullab/chromosight
Hippocampal cells integrate past memory and present perception for the future
Authors: Yang Cen , Naya Yuji 
Published: March 2020

AbstractThe ability to use stored information in a highly flexible manner is a defining feature of the declarative memory system. However, the neuronal mechanisms underlying this flexibility are poorly understood. To address this question, we recorded single-unit activity from the hippocampus of two non-human primates performing a newly devised task requiring the monkeys to retrieve long-term item-location association memory and then use it flexibly in different circumstances. We found that hippocampal neurons signaled both mnemonic information representing the retrieved location and perceptual information representing the external circumstance. The two signals were combined at a single-neuron level to construct goal-directed information by three sequentially occurring neuronal operations (e.g., convergence, transference, targeting) in the hippocampus. Thus, flexible use of knowledge may be supported by the hippocampal constructive process linking memory and perception, which may fit the mnemonic information into the current situation to present manageable information for a subsequent action.
The coupled dual-oscillator model of wing and haltere motion in flies
Authors: Deora Tanvi , Sane Sanjay P. 
Published: March 2020

AbstractThe mechanics of Dipteran thorax is dictated by a network of exoskeletal linkages which, when deformed by flight muscles, generate coordinated wing movements. In Diptera, forewings power flight, whereas hindwings have evolved into specialized halteres which provide rapid mechanosensory feedback for flight stabilization. Although actuated by independent muscles, wing-haltere motion is precisely phase-coordinated at high frequencies. Because wingbeat frequency is a product of wing-thorax resonance, wear-and-tear of wings or thorax should impair flight ability. Here, we show that wings and halteres are independently-driven, linked, coupled oscillators. We systematically reduced wing length in flies and observed how wing-haltere synchronization was affected. The wing-wing system is a strongly-coupled oscillator, whereas wing-haltere system is weakly-coupled through mechanical linkages which synchronize phase and frequency. Wing-haltere link is unidirectional; altering wingbeat frequency affects haltere frequency, but not vice-versa. Exoskeletal linkages are thus key morphological features of Dipteran thorax, ensuring robust wing-haltere synchrony despite wing damage.
Tests of hybridisation inTetragonulastingless bees using multiple genetic markers
Authors: Hereward James P. , Smith Tobias J. , Gloag Ros , Brookes Dean R. , Walter Gimme H. 
Published: March 2020

AbstractDiscrepancies in mitochondrial and nuclear genetic data are often interpreted as evidence of hybridisation. We re-examined reports of hybridisation in three cryptic stingless bee species in the genusTetragonulain South East Queensland, Australia (T. carbonaria, T. davenporti, andT. hockingsi). Previous studies on this group using microsatellite markers proposed that occasional hybrids are found. In contrast, we find that allele frequencies at neutral regions of the nuclear genome, both microsatellites and randomsnps, reliably separated the three species, and thus do not support hybridisation. We found no inter-species variation in PCR amplicons of the nuclear geneEF1alpha, but low and moderate species-specific polymorphisms in the nuclear geneOpsinand the mitochondrial16Srespectively, with no cases of mito-nuclear discordance at these genes. We confirm that nuclear divergence between these species is low, based on 10-26kb of non-coding sequence flankingEF1alphaandOpsin(0.7-1% pairwise difference between species). However, we find mitogenomes to be far more diverged than nuclear genomes (21.6-23.6% pairwise difference between species). Based on these comprehensive analyses of multiple marker types, we conclude that there is no ongoing gene flow in theTetragonulaspecies of South East Queensland, despite their high morphological similarity to one another and the low nuclear divergence among them. The mitogenomes and draft nuclear genomes provided for these species will be a resource for further molecular studies on this group, which are important pollinators in Australian natural and agroecosystems.