bluuebunny/crossref_metadata_2025_split huggingface dataset:
Global Seasonal Influenza Mortality Estimates: A Comparison of 3 Different Approaches
Authors: Cozza Vanessa , Campbell Harry , Chang Howard H , Iuliano A Danielle , Paget John , Patel Neha N , Reiner Robert C , Troeger Chris , Viboud Cecile , Bresee Joseph S , Fitzner Julia 
Published: September 2020

Abstract
Prior to updating global influenza-associated mortality estimates, the World Health Organization convened a consultation in July 2017 to understand differences in methodology and implications for results of 3 influenza mortality projects from the US Centers for Disease Control and Prevention (CDC), the Netherlands Institute for Health Service Research’s Global Pandemic Mortality Project II (GLaMOR), and the Institute for Health Metrics and Evaluation (IHME). The expert panel reviewed estimates and discussed differences in data sources, analysis, and modeling assumptions. We performed a comparison analysis of the estimates. Influenza-associated respiratory death counts were comparable between CDC and GLaMOR; the IHME estimate was considerably lower. The greatest country-specific influenza-associated fold differences in mortality rate between CDC and IHME estimates and between GLaMOR and IHME estimates were among countries in Southeast Asia and the Eastern Mediterranean region. The data envelope used for the calculation was one of the major differences (CDC and GLaMOR: all respiratory deaths; IHME: lower-respiratory infection deaths). With the assumption that there is only one cause of death for each death, IHME estimates a fraction of the full influenza-associated respiratory mortality that is measured by the other 2 groups. Wide variability of parameters was observed. Continued coordination between groups could assist with better understanding of methodological differences and new approaches to estimating influenza deaths globally.
Genealogies Beyond Modernities
Authors: Ernest John 
Published: September 2020

AbstractThis essay is a response to six essays, and Derrick Spires’s introductory essay, gathered under the title “Genealogies of Black Modernity.” I argue against the usefulness of “modernity” as an organizing concept for the histories, global networks, publishing ventures, and scholarly initiatives explored in these essays, suggesting instead that we attend to the genealogies of a complex emergence for which we do not yet have an adequate descriptive framework. This is an emergence that challenges our usual approaches to historical periodization, our established concepts of collective achievement, or our habitual ways of framing a scholarly mission. The essays gathered here do not offer any simple vision of a coherent scholarly mission beyond the need to be attentive to a project of historical recovery that is always in danger of conceptual marginalizations. I explore the implications of archives that both reveal and obscure the operations of white supremacy, and I consider historical recovery projects that are overburdened by the racial politics they mean to address. Taking seriously the determined inclusiveness of the Black studies project, beyond class divisions and traditional markers of historical significance, I consider the ethical demands of a scholarly project devoted to recovering a history, and a historical process, that represents the imagined community these scholars are committed to serving.Accounting for the lower frequencies of the white supremacist project of modernity, it’s possible that we’ve underestimated the radicalism of the Black studies project as it pertains to those of us in literary and cultural studies.
Slippery flowers as a mechanism of defence against nectar-thieving ants
Authors: Takeda Kazuya , Kadokawa Tomoki , Kawakita Atsushi 
Published: September 2020

AbstractBackground and AimsThe great diversity of floral characteristics among animal-pollinated plants is commonly understood to be the result of coevolutionary interactions between plants and pollinators. Floral antagonists, such as nectar thieves, also have the potential to exert an influence upon the selection of floral characteristics, but adaptation against floral antagonists has attracted comparatively little attention. We found that the corollas of hornet-pollinated Codonopsis lanceolata (Campanulaceae) and the tepals of bee-pollinated Fritillaria koidzumiana (Liliaceae) are slippery to nectar-thieving ants living in the plant’s habitat; because the flowers of both species have exposed nectaries, slippery perianths may function as a defence against nectar-thieving ants.MethodsWe conducted a behavioural experiment and observed perianth surface microstructure by scanning electron microscopy to investigate the mechanism of slipperiness. Field experiments were conducted to test whether slippery perianths prevent floral entry by ants, and whether ant presence inside flowers affects pollination.Key ResultsScanning electron microscopy observations indicated that the slippery surfaces were coated with epicuticular wax crystals. The perianths lost their slipperiness when wiped with hexane. Artificial bridging of the slippery surfaces using non-slippery materials allowed ants to enter flowers more frequently. Experimental introduction of live ants to the Codonopsis flowers evicted hornet pollinators and shortened the duration of pollinator visits. However, no statistical differences were found in the fruit or seed sets of flowers with and without ants.ConclusionsSlippery perianths, most probably based on epicuticular wax crystals, prevent floral entry by ants that negatively affect pollinator behaviour. Experimental evidence of floral defence based on slippery surfaces is rare, but such a mode of defence may be widespread amongst flowering plants.
Bedtk: finding interval overlap with implicit interval tree
Authors: Li Heng , Rong Jiazhen 
Published: September 2020

Abstract

Summary
We present bedtk, a new toolkit for manipulating genomic intervals in the BED format. It supports sorting, merging, intersection, subtraction and the calculation of the breadth of coverage. Bedtk uses implicit interval tree, a data structure for fast interval overlap queries. It is several to tens of times faster than existing tools and tends to use less memory.

Availability and implementation
The source code is available at https://github.com/lh3/bedtk.
Transforming growth factor beta signaling and decidual integrity in mice†
Authors: Fang Xin , Ni Nan , Gao Yang , Lydon John P , Ivanov Ivan , Rijnkels Monique , Bayless Kayla J , Li Qinglei 
Published: September 2020

AbstractTransforming growth factor beta (TGFβ) signaling regulates multifaceted reproductive processes. It has been shown that the type 1 receptor of TGFβ (TGFBR1) is indispensable for female reproductive tract development, implantation, placental development, and fertility. However, the role of TGFβ signaling in decidual development and function remains poorly defined. Our objective is to determine the impact of uterine-specific deletion of Tgfbr1 on decidual integrity, with a focus on the cellular and molecular properties of the decidua during development. Our results show that the developmental dynamics of the decidua is altered in TGFBR1 conditionally depleted uteri from embryonic day (E) 5.5 to E8.5, substantiated by downregulation of genes associated with inflammatory responses and uterine natural killer cell abundance, reduced presence of nondecidualized fibroblasts in the antimesometrial region, and altered decidual cell development. Notably, conditional ablation of TGFBR1 results in the formation of decidua containing more abundant alpha smooth muscle actin (ACTA2)-positive cells at the peripheral region of the antimesometrial side versus controls at E6.5–E8.5. This finding is corroborated by upregulation of a subset of smooth muscle marker genes in Tgfbr1 conditionally deleted decidua at E6.5 and E8.5. Moreover, increased cell proliferation and enhanced decidual ERK1/2 signaling were found in Tgfbr1 conditional knockout mice upon decidual regression. In summary, conditional ablation of TGFBR1 in the uterus profoundly impacts the cellular and molecular properties of the decidua. Our results suggest that TGFBR1 in uterine epithelial and stromal compartments is important for the integrity of the decidua, a transient but crucial structure that supports embryo development.
Prostaglandin I2 mediates weak vasodilatation in human placental microvessels
Authors: Feng Xueqin , Zhang Yingying , Zhang Yumeng , Yang Xiaojun , Man Dongmei , Lu Likui , Xu Ting , Liu Yanping , Yang Chunli , Li Huan , Qi Linglu , Su Hongyu , Zhou Xiuwen , Xu Zhice 
Published: September 2020

AbstractHuman placental vessels (HPVs) play important roles in the exchange of metabolites and oxygen in maternal-fetal circulation. Endothelial-derived prostacyclin (prostaglandin I2, PGI2) is a critical endothelial vasodilator in the body. However, the physiological and pharmacological functions of endothelial PGI2 in the human placenta are still unclear. Human, sheep, and rat blood vessels were used in this study. Unlike non-placental vessels (non-PVs), the PGI2 synthesis inhibitor tranylcypromine (TCP) did not modify 5-hydroxytryptamine (5-HT)-induced vascular contraction, indicating that endothelial-derived PGI2 was weak in PVs. Vascular responses to exogenous PGI2 showed slight relaxation followed by a significant contraction at a higher concentration in HPV, which was inhibited by the thromboxane-prostanoid (TP) receptors antagonist SQ-29,548. Testing PVs and non-PVs from sheep also showed similar functional results. More TP receptors than PGI2 (IP) receptors were observed in HPVs. The whole-cell K+ current density of HPVs was significantly weaker than that of non-PVs. This study demonstrated the specific characteristics of the placental endogenous endothelial PGI2 system and the patterns of placental vascular physiological/pharmacological response to exogenous PGI2, showing that placental endothelial PGI2 does not markedly contribute to vascular dilation in the human placenta, in notable contrast to non-PVs. The results provide crucial information for understanding the endothelial roles of HPVs, which may be helpful for further investigations of potential targets in the treatment of diseases such as preeclampsia.
Role of DNA damage and repair mechanisms in uterine fibroid/leiomyomas: a review
Authors: Toprani Sneh M , Kelkar Mane Varsha 
Published: September 2020

Abstract
There has been a significant annual increase in the number of cases of uterine leiomyomas or fibroids (UF) among women of all races and ages across the world. A fortune is usually spent by the healthcare sector for fibroid-related treatments and management. Molecular studies have established the higher mutational heterogeneity in UF as compared to normal myometrial cells. The contribution of DNA damage and defects in repair responses further increases the mutational burden on the cells. This in turn leads to genetic instability, associated with cancer risk and other adverse reproductive health outcomes. Such and many more growing bodies of literature have highlighted the genetic/molecular, biochemical and clinical aspects of UF; none the less there appear to be a lacuna bridging the bench to bed gap in addressing and preventing this disease. Presented here is an exhaustive review of not only the molecular mechanisms underlying the predisposition to the disease but also possible strategies to effectively diagnose, prevent, manage, and treat this disease.
Quasi-oracle estimation of heterogeneous treatment effects
Authors: Nie X , Wager S 
Published: September 2020

SummaryFlexible estimation of heterogeneous treatment effects lies at the heart of many statistical applications, such as personalized medicine and optimal resource allocation. In this article we develop a general class of two-step algorithms for heterogeneous treatment effect estimation in observational studies. First, we estimate marginal effects and treatment propensities to form an objective function that isolates the causal component of the signal. Then, we optimize this data-adaptive objective function. The proposed approach has several advantages over existing methods. From a practical perspective, our method is flexible and easy to use: in both steps, any loss-minimization method can be employed, such as penalized regression, deep neural networks, or boosting; moreover, these methods can be fine-tuned by cross-validation. Meanwhile, in the case of penalized kernel regression, we show that our method has a quasi-oracle property. Even when the pilot estimates for marginal effects and treatment propensities are not particularly accurate, we achieve the same error bounds as an oracle with prior knowledge of these two nuisance components. We implement variants of our approach based on penalized regression, kernel ridge regression, and boosting in a variety of simulation set-ups, and observe promising performance relative to existing baselines.
In Their Own Words: Marvalee Wake
Authors: Verdier James M 
Published: September 2020

Abstract
In Their Own Words chronicles the stories of scientists who have made great contributions to their fields. These short histories provide our readers a way to learn from and share their experiences. Each month, we will publish in the pages of BioScience and on our podcast, BioScience Talks (http://bioscienceaibs.libsyn.com), the results of these conversations. This history is with Marvalee Wake, professor of the Graduate School in the Department of Integrative Biology at the University of California, Berkeley. She is also a past president of AIBS.
Note: Both the text and audio versions have been edited for clarity and length.
Leaving ‘home?’ Belonging, break-up and becoming in the police family
Authors: Atkinson Colin , Murray Kath 
Published: September 2020

AbstractThis article considers the impact of police merger processes on officers and staff. The Railway Policing (Scotland) Act 2017 legislated that the Scottish functions and personnel of the British Transport Police (BTP) would be integrated into Scotland’s national police force. The journey towards this destination, however, has been protracted, problematic and now appears to be indefinitely postponed. Demonstrating the limits of the ‘police family’, our research provides important policy insights, demonstrating how a failure to account for distinct organizational cultures and occupational identities can damage the legitimacy of police mergers. Using data from a survey of BTP officers and staff in Scotland, we present our findings across three themes: belonging; break-up and becoming. We refract these findings through Bourdieusian theory.
Meningeal blood–brain barrier disruption in acute traumatic brain injury
Authors: Turtzo Lisa Christine , Jikaria Neekita , Cota Martin R , Williford Joshua P , Uche Victoria , Davis Tara , MacLaren Judy , Moses Anita D , Parikh Gunjan , Castro Marcelo A , Pham Dzung L , Butman John A , Latour Lawrence L 
Published: September 2020

Abstract
The meninges serve as a functional barrier surrounding the brain, critical to the immune response, and can be compromised following head trauma. Meningeal enhancement can be detected on contrast-enhanced MRI in patients presenting with acute traumatic brain injury, even when head CT is negative. Following head trauma, gadolinium-based contrast appears to extravasate from the vasculature, enhancing the dura within minutes, and later permeates the subarachnoid space. The aims of this study were to characterize the initial kinetics of the uptake of contrast agent after injury and the delayed redistribution of contrast enhancement in the subarachnoid space in hyperacute patients. Neuroimaging was obtained prospectively in two large ongoing observational studies of patients aged 18 years or older presenting to the emergency department with suspected acute head injury. Dynamic contrast-enhanced MRI studies in a cohort of consecutively enrolling patients with mild traumatic brain injury (n = 36) determined that the kinetic half-life of dural-related meningeal enhancement was 1.3 ± 0.6 min (95% enhancement within 6 min). The extravasation of contrast into the subarachnoid space was investigated in a cohort of CT negative mild traumatic brain injury patients initially imaged within 6 h of injury (hyperacute) who subsequently underwent a delayed MRI, with no additional contrast administration, several hours after the initial MRI. Of the 32 patients with delayed post-contrast imaging, 18 (56%) had conspicuous expansion of the contrast enhancement into the subarachnoid space, predominantly along the falx and superior sagittal sinus. Patients negative for traumatic meningeal enhancement on initial hyperacute MRI continued to have no evidence of meningeal enhancement on the delayed MRI. These studies demonstrate that (i) the initial enhancement of the traumatically injured meninges occurs within minutes of contrast injection, suggesting highly permeable meningeal vasculature, and that (ii) contrast in the meninges redistributes within the subarachnoid space over the period of hours, suggesting a compromise in the blood–brain and/or blood-cerebrospinal barriers. Data from the parent study indicate that up to one in two patients with mild traumatic brain injury have traumatic brain injury on acute (&lt;48 h) MRI, with a higher prevalence seen in patients with moderate or severe traumatic brain injury. The current study’s findings of traumatic meningeal enhancement and the subsequent delayed extravasation of contrast into the subarachnoid spaces indicate that a substantial percentage of patients with even mild traumatic brain injury may have a transient disruption in barriers separating the vasculature from the brain.
Dentate Gyrus Somatostatin Cells are Required for Contextual Discrimination During Episodic Memory Encoding
Authors: Morales Cristian , Morici Juan Facundo , Espinosa Nelson , Sacson Agostina , Lara-Vasquez Ariel , García-Pérez M A , Bekinschtein Pedro , Weisstaub Noelia V , Fuentealba Pablo 
Published: September 2020

Abstract
Memory systems ought to store and discriminate representations of similar experiences in order to efficiently guide future decisions. This problem is solved by pattern separation, implemented in the dentate gyrus (DG) by granule cells to support episodic memory formation. Pattern separation is enabled by tonic inhibitory bombardment generated by multiple GABAergic cell populations that strictly maintain low activity levels in granule cells. Somatostatin-expressing cells are one of those interneuron populations, selectively targeting the distal dendrites of granule cells, where cortical multimodal information reaches the DG. Nonetheless, somatostatin cells have very low connection probability and synaptic efficacy with both granule cells and other interneuron types. Hence, the role of somatostatin cells in DG circuitry, particularly in the context of pattern separation, remains uncertain. Here, by using optogenetic stimulation and behavioral tasks in mice, we demonstrate that somatostatin cells are required for the acquisition of both contextual and spatial overlapping memories.
SARS-CoV-2 infects and induces cytotoxic effects in human cardiomyocytes
Authors: Bojkova Denisa , Wagner Julian U G , Shumliakivska Mariana , Aslan Galip S , Saleem Umber , Hansen Arne , Luxán Guillermo , Günther Stefan , Pham Minh Duc , Krishnan Jaya , Harter Patrick N , Ermel Utz H , Frangakis Achilleas S , Milting Hendrik , Zeiher Andreas M , Klingel Karin , Cinatl Jindrich , Dendorfer Andreas , Eschenhagen Thomas , Tschöpe Carsten , Ciesek Sandra , Dimmeler Stefanie 
Published: September 2020

Abstract

Aims
Coronavirus disease 2019 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and has emerged as a global pandemic. SARS-CoV-2 infection can lead to elevated markers of cardiac injury associated with higher risk of mortality. It is unclear whether cardiac injury is caused by direct infection of cardiomyocytes or is mainly secondary to lung injury and inflammation. Here, we investigate whether cardiomyocytes are permissive for SARS-CoV-2 infection.

Methods and results
Two strains of SARS-CoV-2 infected human induced pluripotent stem cell-derived cardiomyocytes as demonstrated by detection of intracellular double-stranded viral RNA and viral spike glycoprotein expression. Increasing concentrations of viral RNA are detected in supernatants of infected cardiomyocytes, which induced infections in Caco-2 cell lines, documenting productive infections. SARS-CoV-2 infection and induced cytotoxic and proapoptotic effects associated with it abolished cardiomyocyte beating. RNA sequencing confirmed a transcriptional response to viral infection as demonstrated by the up-regulation of genes associated with pathways related to viral response and interferon signalling, apoptosis, and reactive oxygen stress. SARS-CoV-2 infection and cardiotoxicity was confirmed in a 3D cardiosphere tissue model. Importantly, viral spike protein and viral particles were detected in living human heart slices after infection with SARS-CoV-2. Coronavirus particles were further observed in cardiomyocytes of a patient with coronavirus disease 2019. Infection of induced pluripotent stem cell-derived cardiomyocytes was dependent on cathepsins and angiotensin-converting enzyme 2, and was blocked by remdesivir.

Conclusion
This study demonstrates that SARS-CoV-2 infects cardiomyocytes in vitro in an angiotensin-converting enzyme 2- and cathepsin-dependent manner. SARS-CoV-2 infection of cardiomyocytes is inhibited by the antiviral drug remdesivir.
Effect of anastomotic leaks on long-term survival after oesophagectomy for oesophageal cancer: systematic review and meta-analysis
Authors: Gujjuri Rohan R , Kamarajah Sivesh K , Markar Sheraz R 
Published: September 2020

Summary

Introduction
Long-term survival after curative surgery for oesophageal cancer surgery remains poor, and the prognostic impact of anastomotic leak (AL) remains unknown. A meta-analysis was conducted to investigate the impact of AL on long-term survival.

Methods
A systematic electronic search for articles was performed for studies published between 2001 and 2020 evaluating the long-term oncological impact of AL. Meta-analysis was performed using the DerSimonian-Laird random-effects model to compute hazard ratios and 95% confidence intervals.

Results
Nineteen studies met the inclusion criteria, yielding a total of 9885 patients. Long-term survival was significantly reduced after AL (HR: 1.79, 95% CI: 1.33–2.43). AL was associated with significantly reduced overall survival in studies within hospital volume Quintile 1 (HR: 1.35, 95% CI: 1.12–1.63) and Quintile 2 (HR: 1.83, 95% CI: 1.35–2.47). However, no significant association was found for studies within Quintile 3 (HR: 2.24, 95% CI: 0.85–5.88), Quintile 4 (HR: 2.59, 95% CI: 0.67–10.07), and Quintile 5 (HR: 1.29, 95% CI: 0.92–1.81). AL was significantly associated with poor long-term survival in patients with associated overall Clavien Dindo Grades 1–5 (HR: 2.17, 95% CI: 1.31–3.59) and severe Clavien Dindo Grades 3–5 (HR: 1.42, 95% CI: 1.14–1.78) complications.

Conclusions
AL has a negative prognostic impact on long-term survival after restorative resection of oesophageal cancers, particularly in low-volume centers. Future efforts must be focused on strategies to minimize the septic and immunological response to AL with early recognition and treatment thus reducing the impact on long-term survival.