bluuebunny/crossref_metadata_2025_split huggingface dataset:
Text mining for modeling of protein complexes enhanced by machine learning
Authors: Badal Varsha D , Kundrotas Petras J , Vakser Ilya A 
Published: September 2020

Abstract

Motivation
Procedures for structural modeling of protein–protein complexes (protein docking) produce a number of models which need to be further analyzed and scored. Scoring can be based on independently determined constraints on the structure of the complex, such as knowledge of amino acids essential for the protein interaction. Previously, we showed that text mining of residues in freely available PubMed abstracts of papers on studies of protein–protein interactions may generate such constraints. However, absence of post-processing of the spotted residues reduced usability of the constraints, as a significant number of the residues were not relevant for the binding of the specific proteins.

Results
We explored filtering of the irrelevant residues by two machine learning approaches, Deep Recursive Neural Network (DRNN) and Support Vector Machine (SVM) models with different training/testing schemes. The results showed that the DRNN model is superior to the SVM model when training is performed on the PMC-OA full-text articles and applied to classification (interface or non-interface) of the residues spotted in the PubMed abstracts. When both training and testing is performed on full-text articles or on abstracts, the performance of these models is similar. Thus, in such cases, there is no need to utilize computationally demanding DRNN approach, which is computationally expensive especially at the training stage. The reason is that SVM success is often determined by the similarity in data/text patterns in the training and the testing sets, whereas the sentence structures in the abstracts are, in general, different from those in the full text articles.

Availabilityand implementation
The code and the datasets generated in this study are available at https://gitlab.ku.edu/vakser-lab-public/text-mining/-/tree/2020-09-04.

Supplementary information
Supplementary data are available at Bioinformatics online.
ORP9 knockdown delays the maturation of junction-related endocytic structures in the testis and leads to impaired sperm release†
Authors: Adams Arlo , Vogl Wayne 
Published: September 2020

AbstractThe release of late spermatids from the seminiferous epithelium requires the internalization of intercellular junctions by Sertoli cell specific structures called “tubulobulbar complexes” (TBCs). These large, endocytic devices likely evolved from classic clathrin-mediated-endocytosis (CME) machinery, but have several important morphological differences to CME vesicles. Most notable among these differences is that extensive endoplasmic reticulum (ER) membrane contact sites (MCSs) occur with TBCs and not with clathrin-coated pits. One of the well-established functions of ER MCSs is lipid exchange. Previously, we have established that the ORP9 lipid exchange protein is localized to the TBC-ER MCS; however, the function of ORP9 and lipid exchange at the sites is not known. Here we use an in vivo knockdown approach to probe function. The testes of Sprague–Dawley rats were injected with ORP9 targeted siRNA or non-targeted reagents, and the tissues examined by bright field, super-resolution stimulated emission depletion, and electron microscopy. The knockdown of ORP9 was achieved and maintained with daily injections of siRNA for 2-3 day intervals. Compared to controls, sections from ORP9 siRNA-injected testes had longer TBC tubes and fewer fused TBC bulbs. Late spermatids were also abnormally retained in the epithelium of knockdown tissue. These results suggest that ORP9 is necessary for normal TBC bulb vesiculation and fusion, most likely by changing the plasma membrane lipid profile of the TBC. These data also further support the conclusion that TBCs are part of the normal mechanism of sperm release.
Fence Ecology: Frameworks for Understanding the Ecological Effects of Fences
Authors: McInturff Alex , Xu Wenjing , Wilkinson Christine E , Dejid Nandintsetseg , Brashares Justin S 
Published: September 2020

Abstract
Investigations of the links between human infrastructure and ecological change have provided eye-opening insights into humanity's environmental impacts and contributed to global environmental policies. Fences are globally ubiquitous, yet they are often omitted from discussions of anthropogenic impacts. In the present article, we address this gap through a systematic literature review on the ecological effects of fences. Our overview provides five major takeaways: 1) an operational definition of fencing to structure future research, 2) an estimate of fence densities in the western United States to emphasize the challenges of accounting for fences in human-footprint mapping, 3) a framework exhibiting the ecological winners and losers that fences produce, 4) a typology of fence effects across ecological scales to guide research, and 5) a summary of research trends and biases that suggest that fence effects have been underestimated. Through highlighting past research and offering frameworks for the future, we aim with this work to formalize the nascent field of fence ecology.
Perception and Conflict in Conservation: The Rashomon Effect
Authors: Levin Phillip S , Gray Steven A , Möllmann Christian , Stier Adrian C 
Published: September 2020

AbstractConflict is a common feature in conservation and resource management. Environmental conflicts are frequently attributed to differences in values; however, variability in the perception of facts, rooted in social and cultural differences also underlies conflicts. Such differences in perception have been termed the Rashomon effect after the Kurosawa film. In the present article, we explore a conservation Rashomon effect—a phenomenon that results from a combination of differences in perspective, plausible alternative perspectives of a conservation issue, and the absence of evidence to elevate one perspective above others. As a remedy to the Rashomon effect, policy-makers have turned to scientists as honest brokers who share a common environmental reality. We evaluate this supposition and suggest that scientists, themselves, display Rashomon effects. We suggest that Rashomon effects can be reduced by acknowledging the plurality of reality, embracing epistemic pluralism, and prioritizing an inclusive process of resource management.
A Comparison of Quantitative R1 and Cortical Thickness in Identifying Age, Lifespan Dynamics, and Disease States of the Human Cortex
Authors: Erramuzpe A , Schurr R , Yeatman J D , Gotlib I H , Sacchet M D , Travis K E , Feldman H M , Mezer A A 
Published: September 2020

Abstract
Brain development and aging are complex processes that unfold in multiple brain regions simultaneously. Recently, models of brain age prediction have aroused great interest, as these models can potentially help to understand neurological diseases and elucidate basic neurobiological mechanisms. We test whether quantitative magnetic resonance imaging can contribute to such age prediction models. Using R1, the longitudinal rate of relaxation, we explore lifespan dynamics in cortical gray matter. We compare R1 with cortical thickness, a well-established biomarker of brain development and aging. Using 160 healthy individuals (6–81 years old), we found that R1 and cortical thickness predicted age similarly, but the regions contributing to the prediction differed. Next, we characterized R1 development and aging dynamics. Compared with anterior regions, in posterior regions we found an earlier R1 peak but a steeper postpeak decline. We replicate these findings: firstly, we tested a subset (N = 10) of the original dataset for whom we had additional scans at a lower resolution; and second, we verified the results on an independent dataset (N = 34). Finally, we compared the age prediction models on a subset of 10 patients with multiple sclerosis. The patients are predicted older than their chronological age using R1 but not with cortical thickness.
All-cause Mortality Due to Bacteremia during a 60-Day Non-Physician Healthcare Worker Strike
Authors: Jansåker Filip , Holm Mona Katrine Alberthe , Gradel Kim Oren , Knudsen Jenny Dahl , Boel Jonas Bredtoft ,   Danish Collaborative Bacteraemia Network (DACOBAN), Østergaard J D , Knudsen U S , Jensen M , Arpi M , Pinholt S Thønnings , Schønheyder H C , Søgaard M , Koch K , Smit J , Gradel K O 
Published: September 2020

Abstract
This study explored all-cause mortality of bacteremia diagnosed during a 60-day non-physician healthcare worker strike in 2008. A significant change, with 5.0% (95% confidence interval [CI] 1.2–8.7%, P &lt; .01) absolute risk increase, was seen in 90-day mortality during the strike (n = 598) compared with the rest of the study period 2000–2015 (n = 75 647).
Carvedilol induces biased β1 adrenergic receptor-nitric oxide synthase 3-cyclic guanylyl monophosphate signalling to promote cardiac contractility
Authors: Wang Qingtong , Wang Ying , West Toni M , Liu Yongming , Reddy Gopireddy R , Barbagallo Federica , Xu Bing , Shi Qian , Deng Bingqing , Wei Wei , Xiang Yang K 
Published: September 2020

Abstract

Aims
β-blockers are widely used in therapy for heart failure and hypertension. β-blockers are also known to evoke additional diversified pharmacological and physiological effects in patients. We aim to characterize the underlying molecular signalling and effects on cardiac inotropy induced by β-blockers in animal hearts.

Methods and results
Wild-type mice fed high-fat diet (HFD) were treated with carvedilol, metoprolol, or vehicle and echocardiogram analysis was performed. Heart tissues were used for biochemical and histological analyses. Cardiomyocytes were isolated from normal and HFD mice and rats for analysis of adrenergic signalling, calcium handling, contraction, and western blot. Biosensors were used to measure β-blocker-induced cyclic guanosine monophosphate (cGMP) signal and protein kinase A activity in myocytes. Acute stimulation of myocytes with carvedilol promotes β1 adrenergic receptor (β1AR)- and protein kinase G (PKG)-dependent inotropic cardiac contractility with minimal increases in calcium amplitude. Carvedilol acts as a biased ligand to promote β1AR coupling to a Gi-PI3K-Akt-nitric oxide synthase 3 (NOS3) cascade and induces robust β1AR-cGMP-PKG signal. Deletion of NOS3 selectively blocks carvedilol, but not isoproterenol-induced β1AR-dependent cGMP signal and inotropic contractility. Moreover, therapy with carvedilol restores inotropic contractility and sensitizes cardiac adrenergic reserves in diabetic mice with minimal impact in calcium signal, as well as reduced cell apoptosis and hypertrophy in diabetic hearts.

Conclusion
These observations present a novel β1AR-NOS3 signalling pathway to promote cardiac inotropy in the heart, indicating that this signalling paradigm may be targeted in therapy of heart diseases with reduced ejection fraction.
Oestrogen inhibits salt-dependent hypertension by suppressing GABAergic excitation in magnocellular AVP neurons
Authors: Jin Xiangyan , Kim Woong Bin , Kim Mi-Na , Jung Won Woo , Kang Hyung Kyung , Hong Eun-Hwa , Kim Yoon Sik , Shim Wan Joo , Han Hee Chul , Colwell Christopher S , Kim Young-Beom , Kim Yang In 
Published: September 2020

Abstract

Aims
Abundant evidence indicates that oestrogen (E2) plays a protective role against hypertension. Yet, the mechanism underlying the antihypertensive effect of E2 is poorly understood. In this study, we sought to determine the mechanism through which E2 inhibits salt-dependent hypertension.

Methods and results
To this end, we performed a series of in vivo and in vitro experiments employing a rat model of hypertension that is produced by deoxycorticosterone acetate (DOCA)-salt treatment after uninephrectomy. We found that E2 prevented DOCA-salt treatment from inducing hypertension, raising plasma arginine-vasopressin (AVP) level, enhancing the depressor effect of the V1a receptor antagonist (Phenylac1,D-Tyr(Et)2,Lys6,Arg8,des-Gly9)-vasopressin, and converting GABAergic inhibition to excitation in hypothalamic magnocellular AVP neurons. Moreover, we obtained results indicating that the E2 modulation of the activity and/or expression of NKCC1 (Cl− importer) and KCC2 (Cl− extruder) underpins the effect of E2 on the transition of GABAergic transmission in AVP neurons. Lastly, we discovered that, in DOCA-salt-treated hypertensive ovariectomized rats, CLP290 (prodrug of the KCC2 activator CLP257, intraperitoneal injections) lowered blood pressure, and plasma AVP level and hyperpolarized GABA equilibrium potential to prevent GABAergic excitation from emerging in the AVP neurons of these animals.

Conclusion
Based on these results, we conclude that E2 inhibits salt-dependent hypertension by suppressing GABAergic excitation to decrease the hormonal output of AVP neurons.
The JAK Inhibitor Tofacitinib Rescues Intestinal Barrier Defects Caused by Disrupted Epithelial-macrophage Interactions
Authors: Spalinger Marianne R , Sayoc-Becerra Anica , Ordookhanian Christ , Canale Vinicius , Santos Alina N , King Stephanie J , Krishnan Moorthy , Nair Meera G , Scharl Michael , McCole Declan F 
Published: September 2020

AbstractBackground and AimsLoss-of-function variants in protein tyrosine phosphatase non-receptor type-2 [PTPN2] promote susceptibility to inflammatory bowel diseases [IBD]. PTPN2 regulates Janus-kinase [JAK] and signal transducer and activator of transcription [STAT] signalling, while protecting the intestinal epithelium from inflammation-induced barrier disruption. The pan-JAK inhibitor tofacitinib is approved to treat ulcerative colitis, but its effects on intestinal epithelial cell-macrophage interactions and on barrier properties are unknown. We aimed to determine if tofacitinib can rescue disrupted epithelial-macrophage interaction and barrier function upon loss of PTPN2.MethodsHuman Caco-2BBe intestinal epithelial cells [IECs] and THP-1 macrophages expressing control or PTPN2-specific shRNA were co-cultured with tofacitinib or vehicle. Transepithelial electrical resistance and 4 kDa fluorescein-dextran flux were measured to assess barrier function. Ptpn2fl/fl and Ptpn2-LysMCre mice, which lack Ptpn2 in myeloid cells, were treated orally with tofacitinib citrate twice daily to assess the in vivo effect on the intestinal epithelial barrier. Colitis was induced via administration of 1.5% dextran sulphate sodium [DSS] in drinking water.ResultsTofacitinib corrected compromised barrier function upon PTPN2 loss in macrophages and/or IECs via normalisation of: [i] tight junction protein expression; [ii] excessive STAT3 signalling; and [iii] IL-6 and IL-22 secretion. In Ptpn2-LysMCre mice, tofacitinib reduced colonic pro-inflammatory macrophages, corrected underlying permeability defects, and prevented the increased susceptibility to DSS colitis.ConclusionsPTPN2 loss in IECs or macrophages compromises IEC-macrophage interactions and reduces epithelial barrier integrity. Both of these events were corrected by tofacitinib in vitro and in vivo. Tofacitinib may have greater therapeutic efficacy in IBD patients harbouring PTPN2 loss-of-function mutations.
Changes in the Summer Wild Bee Community Following a Bark Beetle Outbreak in a Douglas-fir Forest
Authors: Foote Gabriel G , Foote Nathaniel E , Runyon Justin B , Ross Darrell W , Fettig Christopher J 
Published: September 2020

AbstractThe status of wild bees has received increased interest following recent estimates of large-scale declines in their abundances across the United States. However, basic information is limited regarding the factors affecting wild bee communities in temperate coniferous forest ecosystems. To assess the early responses of bees to bark beetle disturbance, we sampled the bee community of a Douglas-fir, Pseudotsuga menziesii (Mirb.), forest in western Idaho, United States during a Douglas-fir beetle, Dendroctonus pseudotsugae Hopkins (Coleoptera: Curculionidae), outbreak beginning in summer 2016. We resampled the area in summer 2018 following reductions in forest canopy cover resulting from mortality of dominant and codominant Douglas-fir. Overall, results from rarefaction analyses indicated significant increases in bee diversity (Shannon’s H) in 2018 compared to 2016. Results from ANOVA also showed significant increases in bee abundance and diversity in 2018 compared to 2016. Poisson regression analyses revealed percent tree mortality from Douglas-fir beetle was positively correlated with increases in total bee abundance and species richness, where community response variables displayed a cubic trend with percent tree mortality. Percent reduction in canopy cover from 2016 to 2018 was also correlated with bee species richness and diversity. These findings suggest that wild bee communities may benefit from changes in forest structure following bark beetle outbreaks.
Percutaneous coronary intervention for delayed coronary obstruction due to endothelialization of self-expandable transcatheter heart valve: a case report
Authors: Takiguchi Hiroshi , Yamaji Kyohei , Shirai Shinichi , Ando Kenji 
Published: September 2020

Abstract

Background
Coronary obstruction is one of the serious complications associated with transcatheter aortic valve implantation (TAVI). Delayed coronary obstruction (DCO) is a rare manifestation of coronary obstruction.

Case summary
A 91-year-old woman was diagnosed with severe aortic stenosis. She underwent TAVI with a self-expandable valve, without any complications. After 8 months, she was readmitted to our hospital for effort angina. Transthoracic echocardiogram and myocardial scintigraphy suggested left coronary artery ischaemia. Computed tomography revealed that the transcatheter heart valve (THV) frame was covered with a low-density mass that occluded the left coronary sinus (LCS). Transoesophageal echocardiogram showed a Doppler signal flowing from the non-coronary sinus to the LCS through the roundabout route between the aortic wall and the THV. Percutaneous coronary intervention was performed for the roundabout route. Although intravascular ultrasound after the implantation of one drug-eluting stent showed the underexpansion of the stent, another stent deployment improved the expansion. After the procedure, her symptom improved.

Discussion
Reportedly, the mechanism of DCO occurring months or years after TAVI is thought to be thrombus formation or THV endothelialization. In our case, the low-density mass was considered to be endothelium which developed along the THV frame. Low sinotubular junction height and higher THV position could be the underlying mechanisms of DCO. Percutaneous coronary intervention is a possible treatment option for DCO caused by THV endothelialization.
Surgical management of a giant right coronary artery aneurysm with coronary arteriovenous fistula: case report
Authors: Guerrero Becerra Albert Franz , Palacio Andres Mauricio , Camacho Jaime , Sandoval Nestor 
Published: September 2020

Abstract

Background
Coronary artery aneurysms (CAAs) are uncommon, and giant aneurysms (&gt;2 cm) are even more unusual. Coronary atherosclerosis and Kawasaki disease are the leading causes for this pathology. The treatment for this condition is controversial because the evidence is based on case report series.

Case summary
We describe the case of a 77-year-old female patient who presented with heart failure symptoms. She was diagnosed with a giant saccular aneurysm arising from the right coronary artery (RCA) ostium and a fistula between the RC and the left anterior descending artery (LAD) to the coronary sinus. And an atrial septal defect (ASD) and severe tricuspid regurgitation were also found. The patient underwent surgery through a medium sternotomy, the aneurysm was opened and resected under cardiopulmonary bypass. The RCA was ligated at the distal end of the aneurysm, and a saphenous vein graft bypass was performed. A coronary arteriovenous fistula from the distal portion of RC and LAD artery to a severely enlarged coronary sinus was found and corrected with an autologous pericardial patch. Closure of the ASD was performed with a pericardial patch and a tricuspid ring annuloplasty was done. Post-operative course was uneventful.

Discussion
There are few cases of giant coronary aneurysms associated with fistulas reported in the literature. Despite the endovascular percutaneous techniques available to treat these patients, we believe that surgical treatment was the best option for this particular case. We consider that surgical treatment is a very good option for giant CAAs associated with AV fistulas that are not susceptible for current endovascular available devices. The literature lacks evidence regarding the best approach for these cases, and we think that invasive treatment should be tailored according to the heart’s anatomy and patient risk.
Fashioning an enduring musical identity in image, sound and stone
Authors: Hatter Jane 
Published: September 2020

Abstract
Death and commemoration were central to the devotions that filled the side chapels and adorned the votive altars of 15th-century churches with exquisite sounds, forms and colours. Musicians participated in this outpouring of innovative memorials as both contributors to the ceremonies, providing the sacred harmonies that permeated these spaces on behalf of the deceased, and also as donors who funded their own visual and aural commemorations. How can this dual role help us understand the importance of musical identity for 15th-century professional singers and composers? Du Fay’s complex of commemorations—his will, personalized compositions and wall-mounted memorial—provides the most comprehensive specimen of this fascinating overlap between commemorator and commemorated, but there also remain many fragments from other musicians. Using Du Fay’s example, we can find connections between the visual and musical artefacts created or funded by other musicians, and infer that being remembered after death was an important impetus for the recognition of a distinct musical identity and the development of the professional composer.
Trade, price and quality upgrading effects of agri-food standards
Authors: Fiankor Dela-Dem Doe , Curzi Daniele , Olper Alessandro 
Published: September 2020

Abstract
This paper assesses how cross-country differences in public mandatory food standards affect trade, prices and product quality upgrading in the agri-food sector. We estimate different gravity-type models that exploit the bilateral difference in maximum residue limits (MRLs) over the period from 2005 to 2014 for 145 products across 59 countries. Our findings show that cross-country differences in MRLs restrict trade. However, conditional on trading, they increase product prices—even when we adjust prices for quality—with null effects on estimated product quality. These effects are pronounced for South–North trade but not for exports to the South.