bluuebunny/crossref_metadata_2025_split huggingface dataset:
Measurement of biomechanical behavior of dentin hard tissue in response to unbound water loss using stereo-digital image correlation
Authors: Chen Zhenning , Shao Xinxing 
Published: May 2020

Abstract
Understanding the biomechanical behavior of dentin hard tissue with fluid-filled dentin tubules and hydrated matrices is essential for studying this functionally graded biological composite. The stereo-digital image correlation technique with an adaptive high-magnification field of view (FOV) for fully hydrated biological tissue measurement was investigated. The adaptive magnification is controlled by the length of extension tubes. To determine both the unbound water loss induced and load-induced three-dimensional (3D) deformation of dentin hard tissue from a fully hydrated state to a non-hydrated condition, samples of dentin blocks and half teeth in sagittal sections were studied for a period of 2 h in situ over varied speckle patterns. The effects of speckles on water evaporation, camera pre-heating, and measurement accuracy in the wet, curved and long-term measurement were analyzed. The elastic modulus and Poisson’s ratio of both dentin and pulp in response to unbound water evaporation were measured. With the unbound water loss, the mean values of the elastic modulus generally increased from ∼8 GPa to ∼10 GPa in pulp region and from ∼10 GPa to ∼12 GPa in dentin region. The mean values of the Poisson’s ratio increased both in pulp and in dentin. Poisson’s ratio in the dentin regions (∼0.3) were generally smaller than those in the pulp regions (even can reach 0.6), irrespective of the partial dehydration time. Further analysis of the full-field deformation results provided insight into the unbound water-induced regional deformations and mechanical changes in human dentin. It’s found that the unbound water loss induced deformations were more prominent when compared to load induced deformations.
Gravito-electromagnetic approach for the space-time of a plane gravitational wave
Authors: Ruggiero Matteo Luca , Ortolan Antonello 
Published: May 2020

Abstract
We build the Fermi frame associated to the world-line of a reference observer, arbitrary moving in a given space-time, and we show that local measurements can be described in terms of a gravito-electromagnetic analogy, where the gravito-electric and gravito-magnetic fields are related to the non inertial features of the observer’s motion and to the curvature of space-time. We apply this formalism to the space-time of a plane gravitational wave and show that the interaction of the wave with antennas can be explained in terms of gravito-electromagnetic forces acting on test masses. Moreover, we show that, besides the known gravito-electric effects, on which present gravitational waves antennas are based, gravito-magnetic effects could in principle lead to other kinds of detectors.
Polyethylene glycol functionalized cerium oxide nanoparticle confer protection against UV- induced oxidative damage in skin: evidences for a new class of UV filter
Authors: Arya Aditya , Gangwar Anamika , Singh Sushil Kumar , Bhargava Kalpana 
Published: May 2020

AbstractAcute exposure to high dose of ultraviolet (UV) radiations is known to cause significant harm to skin, primarily due to the generation of free radicals and damage to DNA, which often culminate in rapid aging of the skin, or cancers. Keratinocytes being the most abundant skin’s cells are affected most by UV. Although a degree of endogenous protection is present, the vulnerability of UV-induced damaged can be minimized using protective agents. A few UV filters (organic and inorganic) have been successfully commercialized, yet, due to prevailing disadvantages such as low solubility, photostability, and aesthetic sense, suitable and more efficient UV filters continue to be explored as potential ingredients of cosmaceutical agents. A recently studied antioxidant enzyme mimetic cerium oxide nanoparticles showed emerging piece of evidence on benefits under environmental stress. However, its protective abilities as potential UV filter and therefore applicability in cosmaceutical has not yet been completely explored. This study provides a piece of evidence in support of beneficial effects of this new class of UV filters, polyethyleneglycol functionalized nanoceria (PEG-CNP) against UV - induced damagein vitroandin vivo. The nanomolar concentration of PEG-CNPs in the cell culture showed significant protection from UV exposure, by direct ROS scavenging, the rescue of cells from cell cycle arrest and DNA damage. Further, a proof of the concept study in dehaired rat skin showed that the topical application of 50μM PEG-CNPs prevented the initial signs of UV induced damage. Unlike conventional UV filters, PEG-CNPs confer protection by internalizing the cells, and scavenging the radicals.
Endovascular Hyaluronidase Application Through Superselective Angiography to Rescue Blindness Caused by Hyaluronic Acid Injection
Authors: Zhang Lei , Luo Zuyan , Li Jian , Liu Zhe , Xu Hong , Wu Miaoqin , Wu Sufan 
Published: May 2020

Abstract

Background
Blindness is a rare but catastrophic complication of facial hyaluronic acid (HA) injection. Although various means to rescue visual impairment have been employed, no consensus regarding effective treatment has yet been reached. We organized a multidisciplinary team to address this emergency situation by means of endovascular hyaluronidase application.

Objectives
The aim of this study was to investigate the direct delivery of hyaluronidase to ophthalmic artery occlusion through endovascular cannulation to resolve HA-induced blindness.

Methods
Four patients with visual impairments caused by HA filler embolization were subjected to sequential treatments. Through superselective angiography, a microcatheter was introduced along a guidewire from the femoral artery to the ophthalmic artery to directly deliver hyaluronidase to the HA embolism. The safety and efficiency of this treatment were systematically analyzed.

Results
Selective cerebral angiography demonstrated that the endovascular application of hyaluronidase significantly alleviated occlusion in 3 patients. One patient showed slight visual improvement, whereas the other patients showed no improvement in their visual function during a follow-up period of more than 3 months. One patient suffered from cerebral infarction in the left middle cerebral artery during the intervention surgery. Moreover, 2 patients showed multiple lacunar cerebral infarctions after the operation, whereas none exhibited symptoms of hemiplegia during follow-up.

Conclusions
Although the endovascular application of hyaluronidase could partially recanalize the occluded branches of the ophthalmic artery, it had limited effects on restoring vision. Considering the risks of vascular intervention surgery, this approach should be considered with caution.

Level of Evidence: 5
Identification of population-level differentially expressed genes in one-phenotype data
Authors: Xie Jiajing , Xu Yang , Chen Haifeng , Chi Meirong , He Jun , Li Meifeng , Liu Hui , Xia Jie , Guan Qingzhou , Guo Zheng , Yan Haidan 
Published: May 2020

Abstract

Motivation
For some specific tissues, such as the heart and brain, normal controls are difficult to obtain. Thus, studies with only a particular type of disease samples (one phenotype) cannot be analyzed using common methods, such as significance analysis of microarrays, edgeR and limma. The RankComp algorithm, which was mainly developed to identify individual-level differentially expressed genes (DEGs), can be applied to identify population-level DEGs for the one-phenotype data but cannot identify the dysregulation directions of DEGs.

Results
Here, we optimized the RankComp algorithm, termed PhenoComp. Compared with RankComp, PhenoComp provided the dysregulation directions of DEGs and had more robust detection power in both simulated and real one-phenotype data. Moreover, using the DEGs detected by common methods as the ‘gold standard’, the results showed that the DEGs detected by PhenoComp using only one-phenotype data were comparable to those identified by common methods using case-control samples, independent of the measurement platform. PhenoComp also exhibited good performance for weakly differential expression signal data.

Availability and implementation
The PhenoComp algorithm is available on the web at https://github.com/XJJ-student/PhenoComp.

Supplementary information
Supplementary data are available at Bioinformatics online.
TransformerCPI: improving compound–protein interaction prediction by sequence-based deep learning with self-attention mechanism and label reversal experiments
Authors: Chen Lifan , Tan Xiaoqin , Wang Dingyan , Zhong Feisheng , Liu Xiaohong , Yang Tianbiao , Luo Xiaomin , Chen Kaixian , Jiang Hualiang , Zheng Mingyue 
Published: May 2020

Abstract

Motivation
Identifying compound–protein interaction (CPI) is a crucial task in drug discovery and chemogenomics studies, and proteins without three-dimensional structure account for a large part of potential biological targets, which requires developing methods using only protein sequence information to predict CPI. However, sequence-based CPI models may face some specific pitfalls, including using inappropriate datasets, hidden ligand bias and splitting datasets inappropriately, resulting in overestimation of their prediction performance.

Results
To address these issues, we here constructed new datasets specific for CPI prediction, proposed a novel transformer neural network named TransformerCPI, and introduced a more rigorous label reversal experiment to test whether a model learns true interaction features. TransformerCPI achieved much improved performance on the new experiments, and it can be deconvolved to highlight important interacting regions of protein sequences and compound atoms, which may contribute chemical biology studies with useful guidance for further ligand structural optimization.

Availability and implementation
https://github.com/lifanchen-simm/transformerCPI.
ESTIpop: a computational tool to simulate and estimate parameters for continuous-time Markov branching processes
Authors: Roney James P , Ferlic Jeremy , Michor Franziska , McDonald Thomas O 
Published: May 2020

Abstract

Summary
ESTIpop is an R package designed to simulate and estimate parameters for continuous-time Markov branching processes with constant or time-dependent rates, a common model for asexually reproducing cell populations. Analytical approaches to parameter estimation quickly become intractable in complex branching processes. In ESTIpop, parameter estimation is based on a likelihood function with respect to a time series of cell counts, approximated by the Central Limit Theorem for multitype branching processes. Additionally, simulation in ESTIpop via approximation can be performed many times faster than exact simulation methods with similar results.

Availability and implementation
ESTIpop is available as an R package on Github (https://github.com/michorlab/estipop).

Supplementary information
Supplementary data are available at Bioinformatics online.
Experimentally Induced Endometritis Impairs the Developmental Capacity of Bovine Oocytes†
Authors: Dickson Mackenzie J , Piersanti Rachel L , Ramirez-Hernandez Rosabel , de Oliveira Eduardo Barros , Bishop Jeanette V , Hansen Thomas R , Ma Zhengxin , Jeong Kwang Cheol C , Santos Jose E P , Sheldon Martin I , Block Jeremy , Bromfield John J 
Published: May 2020

Abstract
Uterine infection is associated with infertility in women and dairy cows, even after the resolution of infection. However, the mechanisms causing this persistent infertility are unclear. Here, we hypothesized that induced endometritis in non-lactating dairy cows would reduce the developmental competence of oocytes. Non-lactating Holstein cows received an intrauterine infusion of endometrial pathogenic bacteria (Escherichia coli and Trueperella pyogenes; n = 12) or vehicle control (n = 11) on day 2 of the estrous cycle. Bacterial infusion increased expression of endometrial inflammatory mediators, and a mucopurulent discharge in the vagina confirmed the establishment of endometritis. Oocytes were collected by transvaginal ultrasound-guided ovum pickup on days 2, 24, 45, and 66 following infusion and subjected to in vitro fertilization and embryo culture. Bacterial infusion resulted in fewer cleaved oocytes developing to morulae compared to vehicle-infused controls (30.7 versus 45.0%), with the greatest effect observed in oocytes collected on day 24. Development to morula was inversely correlated with endometrial expression of IL6 on day 6. The expression of genes associated with embryo quality did not differ significantly between morulae from bacteria-infused and control cows. Artificial insemination 130 days after intrauterine infusion resulted in normal, filamentous embryos that produced interferon tau 16 days after conception in both infusion groups. This model of experimentally induced uterine infection successfully resulted in endometritis and a reduction in the proportion of oocytes that developed to morulae following in vitro fertilization. In conclusion, endometritis reduced the capacity of oocytes to develop to morulae.
In vitro ovarian follicle growth: a comprehensive analysis of key protocol variables†
Authors: Simon Leah E , Kumar T Rajendra , Duncan Francesca E 
Published: May 2020

Abstract
Folliculogenesis is a complex process that requires integration of autocrine, paracrine, and endocrine factors together with tightly regulated interactions between granulosa cells and oocytes for the growth and survival of healthy follicles. Culture of ovarian follicles is a powerful approach for investigating folliculogenesis and oogenesis in a tightly controlled environment. This method has not only enabled unprecedented insight into the fundamental biology of follicle development but also has far-reaching translational applications, including in fertility preservation for women whose ovarian follicles may be damaged by disease or its treatment or in wildlife conservation. Two- and three-dimensional follicle culture systems have been developed and are rapidly evolving. It is clear from a review of the literature on isolated follicle culture methods published over the past two decades (1980–2018) that protocols vary with respect to species examined, follicle isolation methods, culture techniques, culture media and nutrient and hormone supplementation, and experimental endpoints. Here we review the heterogeneity among these major variables of follicle culture protocols.
Significant Regional Differences in Antibiotic Use Across 576 US Hospitals and 11 701 326 Adult Admissions, 2016–2017
Authors: Goodman Katherine E , Cosgrove Sara E , Pineles Lisa , Magder Laurence S , Anderson Deverick J , Dodds Ashley Elizabeth , Polk Ronald E , Quan Hude , Trick William E , Woeltje Keith F , Leekha Surbhi , Harris Anthony D 
Published: May 2020

Abstract

Background
Quantifying the amount and diversity of antibiotic use in United States hospitals assists antibiotic stewardship efforts but is hampered by limited national surveillance. Our study aimed to address this knowledge gap by examining adult antibiotic use across 576 hospitals and nearly 12 million encounters in 2016–2017.

Methods
We conducted a retrospective study of patients aged ≥ 18 years discharged from hospitals in the Premier Healthcare Database between 1 January 2016 and 31 December 2017. Using daily antibiotic charge data, we mapped antibiotics to mutually exclusive classes and to spectrum of activity categories. We evaluated relationships between facility and case-mix characteristics and antibiotic use in negative binomial regression models.

Results
The study included 11 701 326 admissions, totaling 64 064 632 patient-days, across 576 hospitals. Overall, patients received antibiotics in 65% of hospitalizations, at a crude rate of 870 days of therapy (DOT) per 1000 patient-days. By class, use was highest among β-lactam/β-lactamase inhibitor combinations, third- and fourth-generation cephalosporins, and glycopeptides. Teaching hospitals averaged lower rates of total antibiotic use than nonteaching hospitals (834 vs 957 DOT per 1000 patient-days; P &lt; .001). In adjusted models, teaching hospitals remained associated with lower use of third- and fourth-generation cephalosporins and antipseudomonal agents (adjusted incidence rate ratio [95% confidence interval], 0.92 [.86–.97] and 0.91 [.85–.98], respectively). Significant regional differences in total and class-specific antibiotic use also persisted in adjusted models.

Conclusions
Adult inpatient antibiotic use remains high, driven predominantly by broad-spectrum agents. Better understanding reasons for interhospital usage differences, including by region and teaching status, may inform efforts to reduce inappropriate antibiotic prescribing.
Cell-free DNA as a marker for the outcome of end-stage renal disease patients on haemodialysis
Authors: Coimbra Susana , Rocha Susana , Nascimento Henrique , Valente Maria João , Catarino Cristina , Rocha-Pereira Petronila , Sameiro-Faria Maria , Oliveira José Gerardo , Madureira José , Fernandes João Carlos , Miranda Vasco , Belo Luís , Bronze-da-Rocha Elsa , Santos-Silva Alice 
Published: May 2020

AbstractBackgroundDNA damage and inflammation are common in end-stage renal disease (ESRD). Our aim was to evaluate the levels of circulating cell-free DNA (cfDNA) and the relationship with inflammation, anaemia, oxidative stress and haemostatic disturbances in ESRD patients on dialysis. By performing a 1-year follow-up study, we also aimed to evaluate the predictive value of cfDNA for the outcome of ESRD patients.MethodsA total of 289 ESRD patients on dialysis were enrolled in the study: we evaluated cfDNA, haemogram, serum iron, hepcidin, inflammatory and oxidative stress markers, and haemostasis. Events and causes of deaths were recorded throughout the follow-up period.ResultsESRD patients, as compared with controls, presented significantly higher levels of cfDNA, hepcidin, and inflammatory and oxidative stress markers, and significantly lower values of iron and anaemia-related haemogram parameters. The all-cause mortality rate was 9.7%; compared with alive patients, deceased patients (n = 28) were older and presented significantly higher values of inflammatory markers and of cfDNA, which was almost 2-fold higher. Furthermore, cfDNA was the best predictor of all-cause mortality and cardiovascular mortality in ESRD patients, in both unadjusted and adjusted models for basic confounding factors in dialysis.ConclusionsOur data show cfDNA to be a valuable predictive marker of prognosis in ESRD patients on dialysis treatment; high levels of cfDNA were associated with a poor outcome.
Seasonal Population Dynamics of Potato Psyllid (Hemiptera: Triozidae) in the Columbia River Basin
Authors: Cohen Abigail L , Wohleb Carrie H , Rondon Silvia I , Swisher Grimm Kylie D , Cueva Isabel , Munyaneza Joseph E , Jones Vincent P , Crowder David W 
Published: May 2020

Abstract
Understanding factors that affect the population dynamics of insect pest species is key for developing integrated pest management strategies in agroecosystems. Most insect pest populations are strongly regulated by abiotic factors such as temperature and precipitation, and assessing relationships between abiotic conditions and pest dynamics can aid decision-making. However, many pests are also managed with insecticides, which can confound relationships between abiotic factors and pest dynamics. Here we used data from a regional monitoring network in the Pacific Northwest United States to explore effects of abiotic factors on populations of an intensively managed potato pest, the potato psyllid (Bactericera cockerelli Šulc), which can vector Candidatus Liberibacter psyllaurus, a bacterial pathogen of potatoes. We assessed effects of temperature on psyllid populations, and show psyllid population growth followed predictable patterns within each year, but there was considerable variation across years in psyllid abundance. Examination of seasonal weather patterns suggested that in 2017, when psyllid populations were less abundant by several orders of magnitude than other years, a particularly long and cold period of winter weather may have harmed overwintering populations and limited population growth. The rate of degree-day accumulation over time, as well as total degree-day accumulation also affected trap catch abundance, likely by mediating the number of psyllid generations per season. Our findings indicate that growers can reliably infer the potential magnitude of risk from potato psyllids using monitoring data, date of first detection, seasonal weather patterns, and population size early in the growing season.
Delayed Mating with Multiple Partners Decreases Indexes of Mating in Female and Male Spodoptera litura (Lepidoptera: Noctuidae)
Authors: Di Xueyuan , Liu Jianfeng , Wu Chengxu , Yan Bin , Yu Xiaofei , Yang Maofa 
Published: May 2020

Abstract
Delayed mating is an effective strategy that can decrease the fecundity of a pest by reducing the time that females have to mate. This disruption does not completely inhibit mating and may lead to multiple matings. The effects of delayed mating with multiple partners on different indexes of mating in female and male Spodoptera litura (Fabricius) (Lepidoptera: Noctuidae) were determined in this study. The delay in mating significantly decreased the number of matings and the mating success of both sexes and the male contribution to reproduction. Compared with the effect on female fecundity, the delayed mating with multiple partners had a greater effect on the male mate contribution to fecundity. The longevity of females and males increased significantly with a 72 h delay in mating. Linear regression analysis showed negative relationships between delayed mating and fecundity and number of matings in both sexes. Thus, delayed mating with multiple partners can disrupt the mating and reproductive potential of S. litura.
The use of echo density to quantify pulmonary right-to-left shunt in transthoracic contrast echocardiography
Authors: Kroon Steven , Van Thor Mitch C J , Vorselaars Veerle M M , Hosman Anna E , Swaans Martin J , Snijder Repke J , Mager Hans-Jurgen , Post Marco C 
Published: May 2020

Abstract

Aims
Transthoracic contrast echocardiography (TTCE) is the recommended screening tool to detect pulmonary right-to-left shunt (RLS) caused by pulmonary arteriovenous malformations (PAVMs). We assessed a novel method to quantify the RLS using the change in echo density (ED) following contrast injection.

Methods and results
An analysis of 437 consecutive patients [58% female, 47 years, interquartile range (IQR) 33–60] who underwent TTCE for the detection of a pulmonary RLS. Using ImageJ (National Institutes of Health), the change in ED was measured for each patient. This method was strongly correlated (Spearman’s ρ = 0.89; P &lt; 0.0001) with our standard method based on a four-point grading scale (no, mild, moderate, and severe RLS). In patients without a history of embolotherapy (n = 334), a PAVM was detected with chest computed tomography (CT) in 66 and embolotherapy was judged possible in 35 of these patients. The median increase in ED was higher in the latter: +20.1% (IQR 12.3–34.0) compared to non-treatable PAVM +0.2% (IQR −0.2 to 1.1). The specificity to detect treatable PAVMs increased from 87% to 90% when using the novel method without affecting the sensitivity (of 100%). Using the optimal cut-off value of +4.5% increase in ED, 8/74 (11%) needed chest CT-scans—individuals with a moderate or severe RLS—were no longer required without missing any treatable PAVM.

Conclusions
The use of ED quantification for pulmonary RLS is promising; resulting in a substantial decrease in the number of chest CT scans needed. However, this method and the threshold should be validated in an independent study population.