bluuebunny/crossref_metadata_2025_split huggingface dataset:
Germanene/2D-AlP van der Waals heterostructure: Tunable structural and electronic properties
Authors: Mojumder Md. Rayid Hasan , Islam Md. Sherajul , Park Jeongwon 
Published: January 2021

Developing van der Waals heterostructures (vdWHs) utilizing vertical mounting of diverse two-dimensional (2D) materials is an efficient way of achieving favorable characteristics. Using first-principles calculations, we demonstrated the geometric configurations and electronic properties of germanene/2D-AlP vdWHs. We considered four high symmetric patterns that show a bandgap opening in the heterostructures of 200 meV–460 meV. The incorporation of spin-orbital coupling reduces the bandgap by 20 meV–90 meV. Both direct and indirect bandgaps were found from these high symmetric patterns, depending on the structural patterns. The charge density distribution and the partial density of states confirmed that germanene was the property builder of the heterostructure, in which 2D-AlP could be a decent substrate. The heterostructure bandgap can be widely tuned in the range 0 meV–500 meV by changing the interlayer separation between the two monolayers. The application of strain and external electric fields also significantly tailored the electronic structures of the heterostructures. Intriguingly, an exceptionally high carrier mobility of more than 1.5 × 105 cm2 V−1 s−1 was observed, which outperforms compared to other studies on germanene heterostructures. All these promising properties make the germanene/2D-AlP heterostructure a viable candidate for FETs, strain sensors, nanoelectronics, and spintronic devices.
Rashba coupling and spin switching through surface states of Dirac semimetals
Authors: Baba Yuriko , Domínguez-Adame Francisco , Platero Gloria , Molina Rafael A 
Published: January 2021

Abstract
We study the effect of the Rashba spin–orbit coupling on the Fermi arcs of topological Dirac semimetals. The Rashba coupling is induced by breaking the inversion symmetry at the surface. Remarkably, this coupling could be enhanced by the interaction with the substrate and controlled by an external electric field. We study analytically and numerically the rotation of the spin of the surface states as a function of the electron’s momentum and the coupling strength. Furthermore, a detailed analysis of the spin-dependent two-terminal conductance is presented in the clean limit and with the addition of a random distribution of impurities. Depending on the magnitude of the quadratic terms in the Hamiltonian, the spin-flip conductance may become dominant, thus showing the potential of the system for spintronic applications, since the effect is robust even in the presence of disorder.
Tunable bandpass plasmonic filter based on graphene as the nonlinear Kerr material
Authors: Kokabi Mohsen , Ghorbani Saeed , Moayed Seyed Hossein 
Published: January 2021

Abstract
In this paper, a band-pass plasmonic filter is introduced based on metal–insulator–metal waveguide coupled with two narrow slabs. Our reported plasmonic structure is investigated using the numerical solution of finite element method. The filter performance is analyzed for two cases of linear and nonlinear. The selected Kerr nonlinear material is a single graphene layer. The simulation results show that, we can tune the resonant wavelength by considering the Kerr effect of the graphene layer, performance and by adjusting the incident light signal without changing the physical characteristics of the structure. The simplicity of the structure and a compact size are the advantages of the proposed nonlinear plasmonic filter which make that suitable to design the integrated all-optical circuits.
Management of Distress in Patients with Cancer—Are We Doing the Right Thing?
Authors: Dekker Joost , Graves Kristi D , Badger Terry A , Diefenbach Michael A 
Published: January 2021

Abstract

Background
Screening for distress and referral for the provision of psychosocial care is currently the preferred approach to the management of distress in patients with cancer. To date, this approach has shown a limited effect on the reduction of distress. Recent commentaries have argued that the implementation of distress screening should be improved. On the other hand, the underlying assumption that a referral for psychosocial care is required for distressed patients can be questioned. This has led to the development of an alternative approach, called emotional support and case finding.

Purpose
In the context of finding innovative solutions to tomorrow’s health challenges, we explore ways to optimize distress management in patients with cancer.

Methods and Results
We discuss three different approaches: (i) optimization of screening and referral, (ii) provision of emotional support and case finding, and (iii) a hybrid approach with multiple assessments, using mobile technology.

Conclusions
We suggest continued research on the screening and referral approach, to broaden the evidence-base on improving emotional support and case finding, and to evaluate the utility of multiple assessments of distress with new interactive mobile tools. Lessons learned from these efforts can be applied to other disease areas, such as cardiovascular disease or diabetes.
Angry in America: Psychophysiological Responses to Unfair Treatment
Authors: Thayer Julian F , Carnevali Luca , Sgoifo Andrea , Williams DeWayne P 
Published: January 2021

Abstract

Background
African Americans have the highest rates of hypertension-related disease of any ethnic group in the USA. Importantly, racism and discrimination have been linked to these higher rates of morbidity and mortality. Discrimination is deleterious not only to those that are the recipients of this unfair treatment but also to the partners and family members of those affected as well to those that perpetrate this bias.

Purpose
In this paper, we identify a unique pattern of physiological response to unfair treatment, we have called the “cardiovascular conundrum.” This pattern is characterized by greater heart rate variability and greater total peripheral resistance in African Americans compared to their European American counterparts.

Methods and Results
We review the evidence supporting the existence of this pattern and propose several physiological and psychological factors that might underpin it. We also propose a number of factors that might help to mitigate the deleterious effects associated with it.

Conclusions
Whereas the context of the current review is on Black/White disparities the framework we propose may be relevant to others exposed to unfair treatment. Ultimately, the systemic factors that perpetuate these inequalities will require that we first acknowledge and then face the challenges they present if we are to address the wealth and health disparities in our country.
The Association Between Psychological Distress and Cancer Mortality in the United States: Results from the 1997–2014 NHIS-NDI Record Linkage Study
Authors: Lee Hyunjung , Singh Gopal K 
Published: January 2021

Abstract

Background/Purpose
Psychological distress can influence cancer mortality through socioeconomic disadvantage, health-risk behaviors, or reduced access to care. These disadvantages can result in higher risks of cancer occurrence, a delayed cancer diagnosis, hamper adherence to treatment, and provoke inflammatory responses leading to cancer. Previous studies have linked psychological distress to cancer mortality. However, studies are lacking for the U.S. population.

Methods
This study examines the Kessler six-item psychological distress scale as a risk factor for U.S. cancer mortality using the pooled 1997–2014 data from the National Health Interview Survey (NHIS) linked to National Death Index (NDI) (N = 513,012). Cox proportional hazards regression was used to model survival time as a function of psychological distress and sociodemographic and behavioral covariates.

Results
In Cox models with 18 years of mortality follow-up, the cancer mortality risk was 80% higher (hazard ratio [HR] = 1.80; 95% CI = 1.64, 1.97) controlling for age; 61% higher (HR = 1.61; 95% CI = 1.46, 1.76) in the SES-adjusted model, and 33% higher (HR = 1.33; 95% CI = 1.21, 1.46) in the fully-adjusted model among adults with serious psychological distress (SPD), compared with adults without psychological distress. Males, non-Hispanic Whites, and adults with incomes at or above 400% of the federal poverty level had greater cancer mortality risk associated with SPD. Using an 8 years of mortality follow-up, those with SPD had 108% increased adjusted risks of mortality from breast cancer.

Conclusion
Our study findings underscore the significance of addressing psychological well-being in the population as a strategy for reducing cancer mortality.
HSP70gene expression responses to the temperature stress in pufferfish (Takifugu rubripes)
Authors: Fan Kun-peng , Hua Xin-tong , Liu Ya-fang , Zhang Zhi-qiang , Li Xiao-hao , Liu Ying , Liu Peng-fei 
Published: January 2021

ABSTRACTIn this study, we isolated and characterized HSP70 cDNA from pufferfish (Takifugu rubripes). The 3053 bp full-length TrHSP70 sequence consisted of a 167 bp 5′-UTR (untranslated region), a 2535 bp open reading frame, and a 351 bp 3′-UTR. BLAST analysis revealed that the TrHSP70 shared high similarity with HSP70 sequences in other species. In our study, we set 3 experimental groups as H1 group (20 °C), H2 group (24 °C), and H3 group (28 °C) for checking the expression level of TrHSP70 in T. rubripes. Tissue-specific gene expression results showed that TrHSP70 had higher expression in the intestines than other tissues of the T. rubripes by RT-qPCR. In the experimental group, we found that the expression of TrHSP70 was upregulated in different tissues in the H3 group. The results show that TrHSP70 is a constitutively expressed gene, which plays an important role in maintaining normal physiological function and coping with stress.
Testing the niche differentiation hypothesis in wild capuchin monkeys with polymorphic color vision
Authors: DePasquale Allegra N , Webb Shasta E , Williamson Rachel E , Fedigan Linda M , Melin Amanda D 
Published: January 2021

Abstract
The polymorphic color vision system present in most North, Central, and South American monkeys is a textbook case of balancing selection, yet the mechanism behind it remains poorly understood. Previous work has established task-specific foraging advantages to different color vision phenotypes: dichromats (red-green colorblind) are more efficient foraging for invertebrates, while trichromats (color “normal” relative to humans) are more efficient foraging for “reddish” ripe fruit, suggesting that niche differentiation may underlie the maintenance of color vision variation. We explore a prediction of the niche differentiation hypothesis by asking whether dichromatic and trichromatic capuchin monkeys (Cebus imitator) diverge in their foraging activity budget, specifically testing whether dichromats forage more frequently for invertebrates and trichromats forage more frequently for “reddish” ripe fruit. To assess this, we analyze a large data set of behavioral scan samples (n = 21 984) from 48 wild adult female capuchins of known color vision genotype, dominance rank, and reproductive status, together with models of food conspicuity. We find no significant differences between dichromats and trichromats in the frequency of scans spent foraging for different food types but do find that nursing females forage less overall than cycling females. Our results suggest that the potential for color-vision-based niche differentiation in foraging time may be curtailed by the energetic requirements of reproduction, behavioral synchrony caused by group living, and/or individual preferences. While niche differentiation in activity budgets by color vision type is not apparent, fine-scale niche differentiation may be occurring. This research enhances our understanding of the evolutionary processes maintaining sensory polymorphisms.
PhenoTagger: a hybrid method for phenotype concept recognition using human phenotype ontology
Authors: Luo Ling , Yan Shankai , Lai Po-Ting , Veltri Daniel , Oler Andrew , Xirasagar Sandhya , Ghosh Rajarshi , Similuk Morgan , Robinson Peter N , Lu Zhiyong 
Published: January 2021

Abstract

Motivation
Automatic phenotype concept recognition from unstructured text remains a challenging task in biomedical text mining research. Previous works that address the task typically use dictionary-based matching methods, which can achieve high precision but suffer from lower recall. Recently, machine learning-based methods have been proposed to identify biomedical concepts, which can recognize more unseen concept synonyms by automatic feature learning. However, most methods require large corpora of manually annotated data for model training, which is difficult to obtain due to the high cost of human annotation.

Results
In this article, we propose PhenoTagger, a hybrid method that combines both dictionary and machine learning-based methods to recognize Human Phenotype Ontology (HPO) concepts in unstructured biomedical text. We first use all concepts and synonyms in HPO to construct a dictionary, which is then used to automatically build a distantly supervised training dataset for machine learning. Next, a cutting-edge deep learning model is trained to classify each candidate phrase (n-gram from input sentence) into a corresponding concept label. Finally, the dictionary and machine learning-based prediction results are combined for improved performance. Our method is validated with two HPO corpora, and the results show that PhenoTagger compares favorably to previous methods. In addition, to demonstrate the generalizability of our method, we retrained PhenoTagger using the disease ontology MEDIC for disease concept recognition to investigate the effect of training on different ontologies. Experimental results on the NCBI disease corpus show that PhenoTagger without requiring manually annotated training data achieves competitive performance as compared with state-of-the-art supervised methods.

Availabilityand implementation
The source code, API information and data for PhenoTagger are freely available at https://github.com/ncbi-nlp/PhenoTagger.

Supplementary information
Supplementary data are available at Bioinformatics online.
Nothing in Evolution Makes Sense Except in the Light of Biology
Authors: Reiskind Martha O Burford , Moody Michael L , Bolnick Daniel I , Hanifin Charles T , Farrior Caroline E 
Published: January 2021

Abstract
A key question in biology is the predictability of the evolutionary process. If we can correctly predict the outcome of evolution, we may be better equipped to anticipate and manage species’ adaptation to climate change, habitat loss, invasive species, or emerging infectious diseases, as well as improve our basic understanding of the history of life on Earth. In the present article, we ask the questions when, why, and if the outcome of future evolution is predictable. We first define predictable and then discuss two conflicting views: that evolution is inherently unpredictable and that evolution is predictable given the ability to collect the right data. We identify factors that generate unpredictability, the data that might be required to make predictions at some level of precision or at a specific timescale, and the intellectual and translational value of understanding when prediction is or is not possible.
Growth Hormone Releasing Hormone Reduces Circulating Markers of Immune Activation in Parallel with Effects on Hepatic Immune Pathways in Individuals with HIV-infection and Nonalcoholic Fatty Liver Disease
Authors: Stanley Takara L , Fourman Lindsay T , Wong Lai Ping , Sadreyev Ruslan , Billingsley James M , Feldpausch Meghan N , Zheng Isabel , Pan Chelsea S , Boutin Autumn , Lee Hang , Corey Kathleen E , Torriani Martin , Kleiner David E , Chung Raymond T , Hadigan Colleen M , Grinspoon Steven K 
Published: January 2021

AbstractBackgroundThe growth hormone (GH)/insulin-like growth factor-1 (IGF-1) axis modulates critical metabolic pathways; however, little is known regarding effects of augmenting pulsatile GH secretion on immune function in humans. This study used proteomics and gene set enrichment analysis to assess effects of a GH releasing hormone (GHRH) analog, tesamorelin, on circulating immune markers and liver tissue in people with human immunodeficiency virus (HIV) (PWH) and nonalcoholic fatty liver disease (NAFLD).Methods92 biomarkers associated with immunity, chemotaxis, and metabolism were measured in plasma samples from 61 PWH with NAFLD who participated in a double-blind, randomized trial of tesamorelin versus placebo for 12 months. Gene set enrichment analysis was performed on serial liver biopsies targeted to immune pathways.ResultsTesamorelin, compared to placebo, decreased interconnected proteins related to cytotoxic T-cell and monocyte activation. Circulating concentrations of 13 proteins were significantly decreased, and no proteins increased, by tesamorelin. These included 4 chemokines (CCL3, CCL4, CCL13 [MCP4], IL8 [CXCL8]), 2 cytokines (IL-10 and CSF-1), and 4 T-cell associated molecules (CD8A, CRTAM, GZMA, ADGRG1), as well as ARG1, Gal-9, and HGF. Network analysis indicated close interaction among the gene pathways responsible for these proteins, with imputational analyses suggesting down-regulation of a closely related cluster of immune pathways. Targeted transcriptomics using liver tissue confirmed a significant end-organ signal of down-regulated immune activation pathways.ConclusionsLong-term treatment with a GHRH analog reduced markers of T-cell and monocyte/macrophage activity, suggesting that augmentation of the GH axis may ameliorate immune activation in an HIV population with metabolic dysregulation, systemic and end organ inflammation.Clinical Trials Registration. NCT02196831.
Secondary hyperparathyroidism and adverse health outcomes in adults with chronic kidney disease
Authors: Xu Yang , Evans Marie , Soro Marco , Barany Peter , Carrero Juan Jesus 
Published: January 2021

Abstract

Background
Secondary hyperparathyroidism (sHPT) develops frequently in patients with chronic kidney disease (CKD). However, the burden and long-term impact of sHPT on the risk of adverse health outcomes are not well studied.

Methods
We evaluated all adults receiving nephrologist care in Stockholm during 2006–11 who were not undergoing kidney replacement therapy and had not developed sHPT. Incident sHPT was identified by using clinical diagnoses, initiated medications or two consecutive parathyroid hormone (PTH) measurements ≥130 pg/mL. We characterized sHPT incidence by estimated glomerular filtration rate (eGFR) strata, evaluated clinical predictors and quantified the association between incident sHPT (time-varying exposure) and the risk of fractures, CKD progression, major adverse cardiovascular events (MACEs) and death.

Results
We identified 2556 adults with CKD Stages 1–5 (mean age 66 years, 38% women), of whom 784 developed sHPT during follow-up. The incidence of sHPT increased with advancing CKD: from 57 cases/1000 person-years in CKD Stage G3 to 230 cases/1000 person-years in Stage G5. In multivariable analyses, low eGFR was the strongest sHPT predictor, followed by young age, male sex and diabetes. Incident sHPT was associated with a 1.3-fold (95% confidence interval 1.1–1.8) increased risk of death, a 2.2-fold (1.42–3.28) higher risk of MACEs, a 5.0-fold (3.5–7.2) higher risk of CKD progression and a 1.3-fold (1.5–2.2) higher risk of fractures. Results were consistent in stratified analyses and after excluding early events.

Conclusions
Our findings illustrate the burden of sHPT in advanced CKD and highlight the susceptibility for adverse outcomes of patients developing sHPT. This may inform clinical decisions regarding pre-sHPT risk stratification, PTH monitoring and risk-prevention strategies post-sHPT development.
Development and Validation of Measurement Traceability for In Situ Immunoassays
Authors: Torlakovic Emina E , Sompuram Seshi R , Vani Kodela , Wang Lili , Schaedle Anika K , DeRose Paul C , Bogen Steven A 
Published: January 2021

Abstract

Background
Immunoassays for protein analytes measured in situ support a $2 billion laboratory testing industry that suffers from significant interlaboratory disparities, affecting patient treatment. The root cause is that immunohistochemical testing lacks the generally accepted tools for analytic standardization, including reference standards and traceable units of measure. Until now, the creation of these tools has represented an insoluble technical hurdle.

Methods
We address the need with a new concept in metrology—that is, linked traceability. Rather than calculating analyte concentration directly, which has proven too variable, we calculate concentration by measuring an attached fluorescein, traceable to NIST Standard Reference Material 1934, a fluorescein standard.

Results
For validation, newly developed estrogen receptor (ER) calibrators were deployed in tandem with an array of 80 breast cancer tissue sections in a national external quality assessment program. Laboratory performance was assessed using both the ER standards and the tissue array. Similar to previous studies, the tissue array revealed substantial discrepancies in ER test results among the participating laboratories. The new ER calibrators revealed a broad range of analytic sensitivity, with the lower limits of detection ranging from 7310 to 74 790 molecules of ER. The data demonstrate, for the first time, that the variable test results correlate with analytic sensitivity, which can now be measured quantitatively.

Conclusions
The reference standard enables precise interlaboratory alignment of immunohistochemistry test sensitivity for measuring cellular proteins in situ. The introduction of a reference standard and traceable units of measure for protein expression marks an important milestone.
Physiological responses of gopher tortoises (Gopherus polyphemus) to trapping
Authors: Goessling Jeffrey M , Mendonça Mary T 
Published: January 2021

Abstract
With a growing number of species of conservation concern, understanding the physiological effects of routine sampling of vertebrate species remains a priority to maintain the welfare status of wildlife and ensure such activities are not counter to conservation goals. The gopher tortoise (Gopherus polyphemus) is a species of conservation concern throughout its range and is among the most frequently trapped turtles globally (for both research and conservation activities). Several studies have found equivocal results on the effects of trapping and handling on the glucocorticoid stress response. In this study, we tested how multiple physiological biomarkers (i.e. plasma lactate, corticosterone (cort), heterophil:lymphocyte ratio (HLR) and bactericidal ability (BA)) respond to four different combinations of trapping conditions in comparison to baseline reference sampling. We found that trapping and handling of gopher tortoises yielded a rapid rise in plasma lactate concentration followed by elevations of cort and stress-associated immune changes. In visibly distressed animals that were in traps for fewer than 2 hours, lactate, cort, HLR and BA were all elevated, and generally more so than animals that remained calm in traps for a similar amount of time. Animals that had been trapped and then held for a 3-hour restraint showed similar degrees of physiological alteration as those that showed outward signs of distress. This study demonstrates that trapping may yield physiological disturbances in gopher tortoises, although the intensity of this response is highly variable between individuals and the duration of such alterations remains unknown. This research emphasizes the need for continued work to refine trapping and handling processes in an effort to minimize impacts on individuals and populations.