bluuebunny/crossref_metadata_2025 huggingface dataset:
Cisplatin resistance reversal in lung cancer by tumor acidity-activable vesicular nanoreactorsviatumor oxidative stress amplification
Authors: Mukerabigwi Jean Felix , Han Yu , Lu Nannan , Ke Wendong , Wang Yuheng , Zhou Qinghao , Mohammed Fathelrahman , Ibrahim Alhadi , Zheng Bin , Ge Zhishen
Published: January 2021

A vesicular therapeutic nanoreactor coloading glucose oxidase and cisplatin is engineered to effectively inhibit cisplatin-resistant tumor growth through the amplification of intracellular oxidative stress and activation of pro-apoptotic pathways.
Nanoparticle-mediated tumor vaccines for personalized therapy: preparing tumor antigensin vivoorex vivo?
Authors: Li Qian , Li Jia , Song Sha , Chen Wujun , Shen Xin , Li Suming , Xing Dongming
Published: January 2021

Tumor vaccines, focusing on tailoring individual tumor antigens, have gained much attention in personalized tumor therapy.
Acid and alkali-resistant Dy4coordination clusters: synthesis, structure and slow magnetic relaxation behaviors
Authors: Yu Shui , Hu Huancheng , Chen Yunkai , Chen Zilu , Zhang Zhanyun , Ding Man-Man , Zhang Yi-Quan , Liu Dongcheng , Liang Yuning , Liang Fupei
Published: January 2021

Two Dy4coordination clusters with different skeletons exhibit slow magnetic relaxation behaviours and high stabilities in water and common organic solvents, as well as in acid and base solutions.
Critical effect of the bottom electrode on the ferroelectricity of epitaxial Hf0.5Zr0.5O2thin films
Authors: Estandía Saúl , Gàzquez Jaume , Varela María , Dix Nico , Qian Mengdi , Solanas Raúl , Fina Ignasi , Sánchez Florencio
Published: January 2021

Comparison of a set of perovskite electrodes shows that La1−x(Ca,Sr)xMnO3is critical to stabilize the ferroelectric orthorhombic phase in epitaxial films. The stabilization is favored if the La content in the manganite is high.
Correction: In vitro vascularization of tissue engineered constructs by non-viral delivery of pro-angiogenic genes
Authors: Moreira Helena R. , Raftery Rosanne M. , da Silva Lucília P. , Cerqueira Mariana T. , Reis Rui L. , Marques Alexandra P. , O'Brien Fergal J.
Published: January 2021

Correction for ‘In vitro vascularization of tissue engineered constructs by non-viral delivery of pro-angiogenic genes’ by Helena R. Moreira et al., Biomater. Sci., 2021, DOI: 10.1039/d0bm01560a.
Combined computational and intracellular peptide library screening: towards a potent and selective Fra1 inhibitor
Authors: Yu Miao , Ghamsari Lila , Rotolo Jim A. , Kappel Barry J. , Mason Jody M.
Published: January 2021

Here we describe library design coupled with computational and intracellular screening as an effective methodology to derive an antagonist that is selective for Fra1 relative to Jun counterparts.
A cerium oxide@metal–organic framework nanoenzyme as a tandem catalyst for enhanced photodynamic therapy
Authors: Liu Jintong , Ye Lin Yao , Xiong Wei Hong , Liu Tianrui , Yang Hong , Lei Jianping
Published: January 2021

An all-in-one CeOx@metal–organic framework hybrid has been developed for oxygen-promoted photodynamic therapy with self-feedback through tandem homogeneous catalysis.
Associations Between Speech Perception, Vocabulary, and Phonological Awareness Skill in School-Aged Children With Speech Sound Disorders
Authors: Benway Nina R. , Garcia Kelly , Hitchcock Elaine , McAllister Tara , Leece Megan C. , Wang Qiu , Preston Jonathan L.
Published: January 2021

Purpose

Prior studies report conflicting descriptions of the relationships between phonological awareness (PA), vocabulary, and speech perception in preschoolers with speech disorders. This study sought to determine the nature of these relationships in a sample of school-aged children with residual speech sound errors affecting /ɹ/.

Method

Participants included 110 children aged 7;0–17;4 (years;months) with residual errors impacting /ɹ/. Data on perceptual acuity and perceptual bias in an /ɹ/ identification task, receptive vocabulary, and PA were obtained. A theoretically and empirically motivated path model was constructed with vocabulary mediating the relationship between two measures of speech perception and PA. Model parameters were determined through maximum likelihood estimation with standard errors that were robust to nonnormality. Monte Carlo simulation was used to examine achieved power at the current sample size.

Results

The saturated path model explained 19% of the variance in PA. The direct path between age-adjusted perceptual acuity and PA was significant, as was the direct path between vocabulary and PA. Contrary to our hypothesis, there was no evidence in the current sample that vocabulary skill mediated the relationship between speech perception and PA. Each individual path was adequately powered at the current sample size.

Conclusions

The overall model provided evidence for a continued relationship between speech perception, measured by perceptual acuity of the sound in error, and PA in school-aged children with residual speech errors. Thus, measures of speech perception remain relevant to the assessment of school-aged children and adolescents in this population.

Supplemental Material

https://doi.org/10.23641/asha.13641275
The Case for Holistic Review in Communication Sciences and Disorders Admissions
Authors: Mandulak Kerry Callahan
Published: January 2021

Purpose:

The purpose of this article is to review the foundational tenets and current evidence regarding holistic review for graduate admissions that can be applied specifically to the field of communication sciences and disorders (CSD). Holistic review represents a paradigm shift from expecting the
best students
as those with the highest academic metrics to those who are a
best fit
with the mission, values, and goals of any program. This shift may be challenging for widespread adoption by the CSD field. It requires reconsideration of long-standing traditions and beliefs about admissions criteria, and a strong definition of what makes a successful student and future practitioner.

Conclusions:

A comprehensive exploration of current knowledge around holistic review and faculty perceptions or hesitations could inform future policies, create a unified effort across the fields of speech-language pathology and audiology, and inspire collaborative work among graduate programs. We have the opportunity to facilitate changes that will ultimately result in a workforce that reflects the world in which we live and the populations we serve. Graduate CSD programs must be training students who are both academically successful and who provide culturally sensitive, responsive, and competent clinical care.
Metallicities and ages for 35 star clusters and their surrounding fields in the Small Magellanic Cloud
Authors: Narloch W. , Pietrzyński G. , Gieren W. , Piatti A. E. , Górski M. , Karczmarek P. , Graczyk D. , Suchomska K. , Zgirski B. , Wielgórski P. , Pilecki B. , Taormina M. , Kałuszyński M. , Pych W. , Hajdu G. , Rojas García G.
Published: January 2021

Aims. In this work we study 35 stellar clusters in the Small Magellanic Cloud (SMC) in order to provide their mean metallicities and ages. We also provide mean metallicities of the fields surrounding the clusters.

Methods. We used Strömgren photometry obtained with the 4.1 m SOAR telescope and take advantage of (b − y) and m1 colors for which there is a metallicity calibration presented in the literature.

Results. The spatial metallicity and age distributions of clusters across the SMC are investigated using the results obtained by Strömgren photometry. We confirm earlier observations that younger, more metal-rich star clusters are concentrated in the central regions of the galaxy, while older, more metal-poor clusters are located farther from the SMC center. We construct the age–metallicity relation for the studied clusters and find good agreement with theoretical models of chemical enrichment, and with other literature age and metallicity values for those clusters. We also provide the mean metallicities for old and young populations of the field stars surrounding the clusters, and find the latter to be in good agreement with recent studies of the SMC Cepheid population. Finally, the Strömgren photometry obtained for this study is made publicly available.
It’s all about the brand: place brand credibility, place attachment, and consumer loyalty
Authors: Reitsamer Bernd F. , Brunner-Sperdin Alexandra
Published: January 2021

Despite the growing attention brand credibility attracts in recent marketing literature, little is known about the credibility of place brands and their relationship with consumers’ loyalty. The present study builds on brand signalling and attachment theory to investigate whether credible place brands affect consumers’ attachment formation, their subsequent word of mouth (WOM) and intention to return. Survey data from an Alpine winter sport destination reveal that place brand credibility is a key antecedent of consumers’ attachment. Moreover, consistent with brand signalling theory, credible place brands exert a particularly strong direct effect on consumers’ WOM. A positive effect on their intention to return, however, will result only if they feel attached with the place brand beforehand. Implications for marketing scholars and brand managers are offered.
Crystallographic and morphological sensitivity of N2 activation over ruthenium
Authors: Lin Hao , Liu Jin-xun , Fan Hong-jun , Li Wei-xue
Published: January 2021

Ruthenium (Ru) serves as a promising catalyst for ammonia synthesis via the Haber-Bosch process, identification of the structure sensitivity to improve the activity of Ru is important but not fully explored yet. We present here density functional theory calculations combined with micro-kinetic simulations on nitrogen molecule activation, a crucial step in ammonia synthesis, over a variety of hexagonal close-packed (hcp) and face-center cubic (fcc) Ru facets. Hcp {213¯0} facet exhibits the highest activity toward N2 dissociation in hcp Ru, followed by the (0001) monatomic step sites. The other hcp Ru facets have N2 dissociation rates at least three orders lower. Fcc {211} facet shows the best performance for N2 activation in fcc Ru, followed by {311}, which indicates stepped surfaces make great contributions to the overall reactivity. Although hcp Ru {213¯0} facet and (0001) monatomic step sites have lower or comparable activation barriers compared with fcc Ru {211} facet, fcc Ru is proposed to be more active than hcp Ru for N2 conversion due to the exposure of the more favorable active sites over step surfaces in fcc Ru. This work provides new insights into the crystal structure sensitivity of N2 activation for mechanistic understanding and rational design of ammonia synthesis over Ru catalysts.
Photodissociation dynamics of CS2 near 204 nm: The
S(3PJ)+CS(X1Σ+)
channels
Authors: Zhao Min , Li Zhen-xing , Xie Ting , Chang Yao , Wu Fu-yan , Wang Qin , Chen Wen-tao , Wang Tao , Wang Xing-an , Yuan Kai-jun , Yang Xue-ming
Published: January 2021

We study the photodissociation dynamics of CS2 in the ultraviolet region using the time-sliced velocity map ion imaging technique. The S(3PJ)+CS(X1Σ+) product channels were observed and identified at four wavelengths of 201.36, 203.10, 204.85 and 206.61 nm. In the measured images of S(3PJ=2,1,0), the vibrational states of the CS(X1Σ+) co-products were partially resolved and the vibrational state distributions were determined. Moreover, the product total kinetic energy releases and the anisotropic parameters were derived. The relatively small anisotropic parameter values indicate that the S(3PJ=2,1,0)+CS(X1Σ+) channels are very likely formed via the indirect predissociation process of CS2. The study of the S(3PJ=2,1,0)+CS(X1Σ+) channels, which come from the spin-orbit coupling dissociation process of CS2, shows that nonadiabatic process plays a role in the ultraviolet photodissociation of CS2.
Theoretical studies on the reaction kinetics of methyl 2-furoate with hydroxyl radical
Authors: He Wei , Lu Jing , Zhang Li-dong , Liu Jing , Wei Li-xia
Published: January 2021

Methyl 2-furoate (FAME2) is a model for the potential renewable biofuel of dimethyl furan-2,5-dicarboxylate, with the development of its new synthesis method. The potential energy surfaces of H-abstractions and OH-additions between FAME2 and hydroxyl radical (OH) were studied using CCSD(T)/CBS//M062X/cc-pVTZ. The subsequent isomerization and decomposition reactions were also determined for the primary radicals produced. The results showed that H-abstraction on the branched methyl group was the dominant channel and that the OH-addition reactions on the furan ring had a significant pressure dependency. The rate coefficients presented here provide important kinetic data to support future improvement of the combustion mechanism of FAME2, and present a sound basis for further research into practical fuels.
Surface, size and thermal effects in alkali metal with core-electron binding-energy shifts
Authors: Zhu Wen-huan , Huang Zhong-kai , Bo Mao-lin , Huang Jin , Peng Cheng , Liu Hai
Published: January 2021

Consistency between density functional theory calculations and X-ray photoelectron spectroscopy measurements confirms our predications on the undercoordination-induced local bond relaxation and core level shift of alkali metal, which determine the surface, size and thermal properties of materials. Zone-resolved photoelectron spectroscopy analysis method and bond order-length-strength theory can be utilized to quantify the physical parameters regarding bonding identities and electronic property of metal surfaces, which allows for the study of the core-electron binding-energy shifts in alkali metals. By employing these methods and first principle calculation in this work, we can obtain the information of bond and atomic cohesive energy of under-coordinated atoms at the alkali metal surface. In addition, the effect of size and temperature towards the binding-energy in the surface region can be seen from the view point of Hamiltonian perturbation by atomic relaxation with atomic bonding.
A new experimental method for investigations on microstructure of liquid-vapor interface
Authors: Li Ziyuan , Chen Ziwei , Hu Jie , Li Hao , Tian Shan Xi
Published: January 2021

Many physical, chemical, and biological processes happen in liquid-vapor interface and are profoundly influenced with the local microstructures. In contrast to the liquid bulk, molecular orientation is the remarkable one of asymmetric structural features of the interface. Here we report an experimental method, namely, electron-impact time-delayed mass spectrometry and give a brief review about our recent progresses. This brand-new method not only enables us to have more insights into the interfacial structures, as done with small-angle X-ray and neutron scatterings and vibrational sum frequency generation spectroscopy, but also provides opportunity to explore the electron-driven chemical reactions therein.
Agenda-setting in a social media age
Authors: Carazo-Barrantes Carolina
Published: January 2021

This paper analyzes the role of social media in electoral processes and contemporary political life. We analyze Costa Rica’s 2018 presidential election from an agenda-setting perspective, studying the media, the political and the public agendas, and their relationships. We explore whether social media, Facebook specifically, can convey an agenda-setting effect; if social media public agenda differs from the traditional MIP public agenda; and what agenda-setting methodologies can benefit from new approaches in the social media context. The study revealed that social media agendas are complex and dynamic and, in this case, did not present an agenda-setting effect. We not only found that the social media public agenda does not correlate with the conventional MIP public agenda, but that neither does the media online agenda and the media’s agenda on Facebook. Our exploration of more contemporary methods like big data, social network analysis (SNA), and social media mining point to them as necessary complements to the traditional methodological proposal of agenda-setting theory which have become insufficient to explain the current media environment.
Der Einfluss der akademischen Interaktionen auf die Auflagen- und Wirkungsgeschichte von Hermann PaulsPrinzipien
Authors: Chen Beijia
Published: January 2021

Trotz der zahlreichen Untersuchungen zu den modernen Sprachideen in Hermann PaulsPrinzipiensowie deren Einfluss auf die Sprachwissenschaftsgeschichte wurde die reichliche Auflagen- und Wirkungsgeschichte dieses Werkes nur selten in der linguistischen Historiographie thematisiert. Durch Rekonstruierung der Wechselbeziehungen zwischen Paul und den Rezipienten derPrinzipienbeleuchtet der vorliegende Beitrag aus einer wissenschaftssoziologischen Perspektive einige bisher unbemerkte Details bezüglich der Auflagen- und Wirkungsgeschichte derPrinzipienunter dem Einfluss der akademischen Interaktionen, bei denen Pauls Aussagen in diesem Werk teils fixiert, teils zugespitzt, teils abgeschwächt wurden und die Sprachwissenschaft gewissermaßen mit in die Moderne gesteuert wurde.
Father Iakinf Bičurin’s theory of mental inflection in Chinese
Authors: Koža Ksenija
Published: January 2021

The article deals with the highly original idea of mental inflection [умственное словоизменение] in Chinese put
forward by the prominent nineteenth-century Russian sinologist Nikita (比丘林, Father Iakinf or Hyacinthus) Bičurin (1777–1853) in his Kitajskaja Grammatika (1835)
and other language-related works. The concept refers to the internal features of Chinese morphology which compensate for the
absence of common grammatical inflection. Fostered in an Humboldtian spirit, the theory established a link between covert
categories and their surface representations a century before functional syntax appeared on the linguistic stage.
Furor over the Fed: A President’s Tweets and Central Bank Independence
Authors: Camous Antoine , Matveev Dmitry
Published: January 2021

We illustrate how financial market data are informative about the interactions between monetary and fiscal policy. Federal funds futures are private contracts that reflect investor’s expectations about future monetary policy decisions. By relating price movements of these contracts with President Trump’s tweets on monetary policy, we explore how financial market participants have perceived attempts by the President to influence monetary policy decisions. Our results indicate that market participants expected the Federal Reserve Bank to adjust monetary policy in the direction suggested by President Trump. (JEL codes: E44, E52, and E58)
Forward-Secure Edge Authentication for Graphs
Authors: Zhu Fei , Yi Xun , Abuadbba Alsharif , Khalil Ibrahim , Nepal Surya , Huang Xinyi
Published: January 2021

The edge authentication of graphs has been studied in the literature because graphs are one of the most widely used data organization structures. The majority of such schemes cannot be used to authenticate general directed graphs (GDGs); other schemes cannot be used for addressing either the issue of dynamic update or the issue of information leakage (such as the existence of nodes/edges and structural relationship of the graph). Also, all the existing schemes do not consider the forward security: if the signer’s secret key has been compromised, all previously generated signatures remain valid. This property provides high-level security protection for authentication schemes. To address these issues, in this work, we propose a forward-secure edge authentication scheme for GDGs. Observe that existing such schemes can only give a proof such that ‘there is an edge between nodes $u$ and $v$’. Our scheme, however, can directly give a proof such that ‘there is no edge between nodes $u$ and $v$’, which makes the function of edge authentication schemes more diverse. Moreover, our proposed scheme is proven to be secure against an adaptive chosen-message adversary in the random oracle model. To show its desirable performance, we analyze the computational costs of our scheme and compare it with other related schemes in terms of features.
Age-Related Changes in Presynaptic Inhibition During Gait Initiation
Authors: Filho Solival Santos , Coelho Daniel Boari , Ugrinowitsch Carlos , de Souza Caroline Ribeiro , Magalhães Fernando Henrique , de Lima-Pardini Andrea Cristina , de Oliveira Éden Marcos Braga , Mattos Eugenia , Teixeira Luis Augusto , Silva-Batista Carla
Published: January 2021

Age-related changes in presynaptic inhibition (PSI) have not been observed during gait initiation, which requires anticipatory postural adjustment (APA). As APA is centrally modulated and is impaired in older compared to young adults, here we aimed to study the presynaptic control and co-contraction levels in the ankle muscles during gait initiation in older compared to young adults. Fifteen older (age range 65–80 years) and 15 young adults (age range 19–30 years) performed a gait initiation task on a force platform under 3 conditions: (i) without electrical stimulation; (ii) test Hoffman reflex (H-reflex); and (iii) conditioned H-reflex. H-reflexes were evoked on the soleus muscle when the APA amplitude exceeded 10%–20% of the average baseline mediolateral force. Participants also performed quiet stance as a control task. Results showed that both age groups presented similar PSI levels during quiet stance (p = .941), while in the gait initiation older adults presented higher PSI levels, longer duration, and lower amplitude of APA than young adults (p < .05). Older adults presented higher co-contraction ratio in both tasks than young adults (p < .05). Correlations between the PSI levels and the APA amplitude (r = −0.61, p = .008), and between the PSI levels and the co-contraction ratio during gait initiation (r = −0.64, p = .005) were found for older adults only. APA amplitude explained 49% of the variance of the PSI levels (p = .003). Our findings suggest that older compared to young adults have increased presynaptic control to compensate for the decreased supraspinal modulation on impaired APAs during gait initiation.
Quality indicators for hospital antimicrobial stewardship programmes: a systematic review
Authors: O’Riordan F , Shiely F , Byrne S , Fleming A
Published: January 2021

Background

Measuring the quality and effectiveness of antimicrobial stewardship (AMS) programmes with quality indicators (QIs) is an area of increasing interest. We conducted a systematic review to identify QIs of AMS programmes in the hospital setting and critically appraise their methodological quality.

Methods

We searched the Cochrane Library, PubMed, MEDLINE, EMBASE, CINAHL, Scopus/web of science databases and the grey literature for studies that defined and/or described the development process and characteristics of the QIs developed. The Appraisal of Indicators through Research and Evaluation (AIRE) instrument was used to critically appraise the methodological quality of the QI sets.

Results

We identified 16 studies of QI sets consisting of 229 QIs. The QI sets addressed a broad range of areas of AMS in the hospital setting and consisted of 75% process indicators, 24% structural indicators and 1% outcome indicators. There was a wide variation in the information and level of detail presented describing the methodological characteristics of the QI sets identified.

Conclusions

The QIs identified in this study focused on process and structural indicators with few outcome indicators developed—a major deficiency in this area. Future research should focus on the development of outcome indicators or the use of process or structural indicators linked to outcomes to assess AMS. Testing of the QIs in practice is an essential methodological element of the QI development process and should be included in the QI development study or as planned validation work.
Validation of an internationally derived patient severity phenotype to support COVID-19 analytics from electronic health record data
Authors: Klann Jeffrey G , Estiri Hossein , Weber Griffin M , Moal Bertrand , Avillach Paul , Hong Chuan , Tan Amelia L M , Beaulieu-Jones Brett K , Castro Victor , Maulhardt Thomas , Geva Alon , Malovini Alberto , South Andrew M , Visweswaran Shyam , Morris Michele , Samayamuthu Malarkodi J , Omenn Gilbert S , Ngiam Kee Yuan , Mandl Kenneth D , Boeker Martin , Olson Karen L , Mowery Danielle L , Follett Robert W , Hanauer David A , Bellazzi Riccardo , Moore Jason H , Loh Ne-Hooi Will , Bell Douglas S , Wagholikar Kavishwar B , Chiovato Luca , Tibollo Valentina , Rieg Siegbert , Li Anthony L L J , Jouhet Vianney , Schriver Emily , Xia Zongqi , Hutch Meghan , Luo Yuan , Kohane Isaac S ,   The Consortium for Clinical Characterization of COVID-19 by EHR (4CE) (CONSORTIA AUTHOR), Brat Gabriel A , Murphy Shawn N
Published: January 2021

Objective

The Consortium for Clinical Characterization of COVID-19 by EHR (4CE) is an international collaboration addressing coronavirus disease 2019 (COVID-19) with federated analyses of electronic health record (EHR) data. We sought to develop and validate a computable phenotype for COVID-19 severity.

Materials and Methods

Twelve 4CE sites participated. First, we developed an EHR-based severity phenotype consisting of 6 code classes, and we validated it on patient hospitalization data from the 12 4CE clinical sites against the outcomes of intensive care unit (ICU) admission and/or death. We also piloted an alternative machine learning approach and compared selected predictors of severity with the 4CE phenotype at 1 site.

Results

The full 4CE severity phenotype had pooled sensitivity of 0.73 and specificity 0.83 for the combined outcome of ICU admission and/or death. The sensitivity of individual code categories for acuity had high variability—up to 0.65 across sites. At one pilot site, the expert-derived phenotype had mean area under the curve of 0.903 (95% confidence interval, 0.886-0.921), compared with an area under the curve of 0.956 (95% confidence interval, 0.952-0.959) for the machine learning approach. Billing codes were poor proxies of ICU admission, with as low as 49% precision and recall compared with chart review.

Discussion

We developed a severity phenotype using 6 code classes that proved resilient to coding variability across international institutions. In contrast, machine learning approaches may overfit hospital-specific orders. Manual chart review revealed discrepancies even in the gold-standard outcomes, possibly owing to heterogeneous pandemic conditions.

Conclusions

We developed an EHR-based severity phenotype for COVID-19 in hospitalized patients and validated it at 12 international sites.
Interactions of amino acids and hormones regulate the balance between growth and milk protein synthesis in lactating rats fed diets differing in protein content
Authors: Xu Lianbin , Hanigan Mark D , Lin Xueyan , Li Xiuli , Li Mengmeng , Liu Wei , Hu Zhiyong , Hou Qiuling , Wang Yun , Wang Zhonghua
Published: January 2021

Insulin-like growth factor-I (IGF-I), growth hormone (GH), and prolactin (PRL) play important roles in milk protein synthesis, and their plasma concentrations were reported to be affected by dietary protein intake. To investigate the relationship between circulating amino acid (AA) and concentrations of these hormones, 18 Wistar rats aged 14 wk were assigned to a low (LP; 9% protein), standard (SP; 21% protein), or high-protein (HP; 35% protein) diet from parturition through day 15 of lactation. Plasma, liver, pituitary gland, skeletal muscle, and mammary gland samples were collected at the end of treatment. Circulating and hepatic IGF-I concentrations increased linearly with elevated dietary protein concentrations (P < 0.0001). Rats receiving the HP diet had higher circulating GH (P < 0.01) and pituitary PRL concentrations (P < 0.0001) but lower pituitary GH concentration (P < 0.0001) relative to those in rats receiving the LP and SP diets. Pearson correlation test performed on composed data across treatments showed that several circulating AAs were correlated with circulating and tissue concentrations of IGF-I, GH, and PRL. Multiple linear regression analyses identified Leu, Gln, Ala, Gly, and Arg as the main AAs associated with hormone responses (R2 = 0.37 ~ 0.80; P < 0.05). Rats fed the LP and HP diets had greater Igf1 and Ghr gene expression in skeletal muscle than those fed the SP diets (P < 0.01). However, LP treatment decreased Prlr mRNA abundance in mammary glands as compared with the SP and HP treatments (P < 0.05). The HP diets increased AA transporter expression (P < 0.01) but decreased mammalian target of rapamycin (P < 0.05) and 70 kDa ribosomal protein S6 kinase 1 (P < 0.01) phosphorylation in mammary glands as compared with the LP and SP diets. The results of the present study suggested that several circulating AAs mediated the effects of dietary protein supply on concentrations of IGF-I, GH, and PRL, which in turn altered the metabolism status in peripheral tissues including the lactating mammary glands.
Adaptive Orthogonal Characteristics of Bio-Inspired Neural Networks
Authors: Ishii Naohiro , Deguchi Toshinori , Kawaguchi Masashi , Sasaki Hiroshi , Matsuo Tokuro
Published: January 2021

In recent years, neural networks have attracted much attention in the machine learning and the deep learning technologies. Bio-inspired functions and intelligence are also expected to process efficiently and improve existing technologies. In the visual pathway, the prominent features consist of nonlinear characteristics of squaring and rectification functions observed in the retinal and visual cortex networks, respectively. Further, adaptation is an important feature to activate the biological systems, efficiently. Recently, to overcome short-comings of the deep learning techniques, orthogonality for the weights in the networks has been developed for the signal propagation and the efficient optimization of the learning. In this paper, bio-inspired asymmetric networks with nonlinear characteristics are proposed, which are derived from the retinal networks in the biological visual pathway. The asymmetric network proposed here was verified to detect the movement of the object, efficiently in our previous studies. This paper shows a new characteristic of the adaptive orthogonality in the asymmetric networks. First, it is shown that the asymmetric network with nonlinear characteristics is effective for generating orthogonality. Second, the proposed asymmetric network with Gabor filters is compared with the conventional energy model from the point of the orthogonality characteristics. Finally, the asymmetric networks with nonlinear characteristics can generate the extended orthogonal bases in independent subspaces, which are useful for classification and efficient learning.
When Echinococcus granulosus transmigrates from the liver into the pericardium: a case report
Authors: Kuemmerli Christoph , Sánchez-Velázquez Patricia , Tschuor Christoph , Oberkofler Christian , Lachat Mario , Müllhaupt Beat , Clavien Pierre-Alain , Petrowsky Henrik
Published: January 2021

Infection with Echinococcus granulosus is a common helminthic disease worldwide with endemic in a region with high endemic areas in Africa, Asia, Middle East, South America and southern Europe.

We report a rare case of a young patient with cystic echinococcal disease of the liver invading the pericardium. The patient initially presented with life-threatening cardiac tamponade, which resulted in the discovery of the underlying parasitic disease. He successfully underwent en-bloc hepatic pericystectomy and pericardiac resection with closure of the pericardial defect using a xenogeneic patch. After this procedure, he recovered well and had no cardiac complications in the long term. Under treatment with albendazol, the patient showed no signs of recurrent disease.

Cases of complex cystic echinococcosis, which invade adjacent organs or body cavities, often need radical surgery for definitive treatment embedded in a multidisciplinary approach in highly specialized centers.
A highly efficient atomically thin curved PdIr bimetallene electrocatalyst
Authors: Lv Fan , Huang Bolong , Feng Jianrui , Zhang Weiyu , Wang Kai , Li Na , Zhou Jinhui , Zhou Peng , Yang Wenxiu , Du Yaping , Su Dong , Guo Shaojun
Published: January 2021

The multi-metallene with an ultrahigh surface area has great potential in precise tuning of surface heterogeneous d-electronic correlation by surface strain effect for the distinctive surface electronic structure, which is a brand new class of promising 2D electrocatalyst for sustainable energy device application. However, achieving such an atomically thin multi-metallene still presents a great challenge. Herein, we present a new synthetic method for an atomic-level palladium-iridium (PdIr) bimetallene with an average thickness of only ∼1.0 nm for achieving superior catalysis in the hydrogen evolution reaction (HER) and the formic acid oxidation reaction (FAOR). The curved PdIr bimetallene presents a top-ranked high electrochemical active area of 127.5 ± 10.8 m2 gPd+Ir−1 in the reported noble alloy materials, and exhibits a very low overpotential, ultrahigh activity and improved stability for HER and FAOR. DFT calculation reveals that the PdIr bimetallene herein has a unique lattice tangential strain, which can induce surface distortion while concurrently creating a variety of concave-convex featured micro-active regions formed by variously coordinated Pd sites agglomeration. Such a strong strain effect correlates the abnormal on-site active 4d10-t2g-orbital Coulomb correlation potential and directly elevates orbital-electronegativity exposure within these active regions, resulting in a preeminent barrier-free energetic path for significant enhancement of FAOR and HER catalytic performance.
The mechanism of host-induced germination in root parasitic plants
Authors: Nelson David C
Published: January 2021

Chemical signals known as strigolactones (SLs) were discovered more than 50 years ago as host-derived germination stimulants of parasitic plants in the Orobanchaceae. Strigolactone-responsive germination is an essential adaptation of obligate parasites in this family, which depend upon a host for survival. Several species of obligate parasites, including witchweeds (Striga, Alectra spp.) and broomrapes (Orobanche, Phelipanche spp.), are highly destructive agricultural weeds that pose a significant threat to global food security. Understanding how parasites sense SLs and other host-derived stimulants will catalyze the development of innovative chemical and biological control methods. This review synthesizes the recent discoveries of strigolactone receptors in parasitic Orobanchaceae, their signaling mechanism, and key steps in their evolution.
Sleep and cardiometabolic risk: a cluster analysis of actigraphy-derived sleep profiles in adults and children
Authors: Matricciani Lisa , Paquet Catherine , Fraysse François , Grobler Anneke , Wang Yichao , Baur Louise , Juonala Markus , Nguyen Minh Thien , Ranganathan Sarath , Burgner David , Wake Melissa , Olds Tim
Published: January 2021

Study Objectives

Sleep plays an important role in cardiometabolic health. Although the importance of considering sleep as a multidimensional construct is widely appreciated, studies have largely focused on individual sleep characteristics. The association between actigraphy-derived sleep profiles and cardiometabolic health in healthy adults and children has not been examined.

Methods

This study used actigraphy-measured sleep data collected between February 2015 and March 2016 in the Child Health CheckPoint study. Participants wore actigraphy monitors (GENEActiv Original, Cambs, UK) on their nondominant wrist for 7 days and sleep characteristics (period, efficiency, timing, and variability) were derived from raw actigraphy data. Actigraphy-derived sleep profiles of 1,043 Australian children aged 11–12 years and 1,337 adults were determined using K-means cluster analysis. The association between cluster membership and biomarkers of cardiometabolic health (blood pressure, body mass index, apolipoproteins, glycoprotein acetyls, composite metabolic syndrome severity score) were assessed using Generalized Estimating Equations, adjusting for geographic clustering, with sex, socioeconomic status, maturity stage (age for adults, pubertal status for children), and season of data collection as covariates.

Results

Four actigraphy-derived sleep profiles were identified in both children and adults: short sleepers, late to bed, long sleepers, and overall good sleepers. The overall good sleeper pattern (characterized by adequate sleep period time, high efficiency, early bedtime, and low day-to-day variability) was associated with better cardiometabolic health in the majority of comparisons (80%).

Conclusion

Actigraphy-derived sleep profiles are associated with cardiometabolic health in adults and children. The overall good sleeper pattern is associated with more favorable cardiometabolic health.
Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood
Authors: Melnick Marko , Gonzales Patrick , LaRocca Thomas J. , Dowell Robin D. , Song Yuping , Wuu Joanne , Benatar Michael , Oskarsson Björn , Petrucelli Leonard , Link Christopher D. , Prudencio Mercedes
Published: January 2021

Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis (ALS) patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq data sets currently being generated.
Long-range allosteric effects - How adenine nucleotides shape the conformational landscape of the Ski2-like RNA helicase, Brr2
Authors: Absmeier Eva , Vester Karen , Ghane Tahereh , Burakovskiy Dmitry , Milon Pohl , Imhof Petra , Rodnina Marina V. , Santos Karine F. , Wahl Markus C.
Published: January 2021

Brr2 is an essential Ski2-like RNA helicase that exhibits a unique structure among the spliceosomal helicases. Brr2 harbors a catalytically active N-terminal helicase cassette and a structurally similar, but enzymatically inactive C-terminal helicase cassette. Both cassettes contain a nucleotide binding pocket. Here we use biophysical and computational methods to delineate the functional connectivity between the cassettes and how occupancy of the nucleotide binding sites may influence each other. Our results show that Brr2 exhibits high specificity for adenine nucleotides with both cassettes binding ADP tighter than ATP. Adenine nucleotide affinity for the inactive C-terminal cassette is more than two orders of magnitude higher than that of the active N-terminal cassette, largely determined by slow nucleotide release. Mutations at the inter-cassette surfaces and in the connecting linker diminish the affinity of adenine nucleotides for both cassettes. Abrogation of nucleotide binding at the C-terminal cassette reduces nucleotide binding at the N-terminal cassette, 70 Å away. Molecular dynamics simulations identified structural communication lines that likely mediate the long-range allosteric effects. Together, our results reveal intricate networks of intra-molecular interactions in the complex Brr2 RNA helicase, which fine-tune its nucleotide affinities and which could be exploited for regulating the enzyme during splicing.
Gene network module changes associated with the vertebrate fin to limb transition
Authors: Fernando Pasan C , Mabee Paula M , Zeng Erliang
Published: January 2021

Evolutionary phenotypic transitions, such as the fin to limb transition in vertebrate evolution, result from changes in associated genes and their interactions, often in response to changing environment. Identifying the associated changes in gene networks is vital to achieve a better understanding of these transitions. Previous experimental studies have been typically limited to manipulating a small number of genes. To expand the number of analyzed genes and hence, biological knowledge, we computationally isolated and compared the gene modules for paired fins (pectoral fin, pelvic fin) of fishes (zebrafish) to those of the paired limbs (forelimb, hindlimb) of mammals (mouse) using quality-enhanced gene networks from zebrafish and mouse. We ranked module genes according to their weighted-degrees and identified the highest-ranking hub genes, which were important for the module stability. Further, we identified genes conserved during the fin to limb transition and investigated the fates of zebrafish-specific and mouse-specific module genes in relation to their involvements in newly emerged or lost anatomical structures during the aquatic to terrestrial vertebrate transition. This paper presents the results of our investigations and demonstrates a general network-based computational workflow to study evolutionary phenotypic transitions involving diverse model organisms and anatomical entities.
Long Reads Capture Simultaneous Enhancer-Promoter Methylation Status for Cell-type Deconvolution
Authors: Margalit Sapir , Abramson Yotam , Sharim Hila , Manber Zohar , Bhattacharya Surajit , Chen Yi-Wen , Vilain Eric , Barseghyan Hayk , Elkon Ran , Sharan Roded , Ebenstein Yuval
Published: January 2021

Motivation

While promoter methylation is associated with reinforcing fundamental tissue identities, the methylation status of distant enhancers was shown by genome-wide association studies to be a powerful determinant of cell-state and cancer. With recent availability of long-reads that report on the methylation status of enhancer-promoter pairs on the same molecule, we hypothesized that probing these pairs on the single-molecule level may serve the basis for detection of rare cancerous transformations in a given cell population. We explore various analysis approaches for deconvolving cell-type mixtures based on their genome-wide enhancer-promoter methylation profiles.

Results

To evaluate our hypothesis we examine long-read optical methylome data for the GM12787 cell line and myoblast cell lines from two donors. We identified over 100,000 enhancer-promoter pairs that co-exist on at least 30 individual DNA molecules per pair. We developed a detailed methodology for mixture deconvolution and applied it to estimate the proportional cell compositions in synthetic mixtures based on analyzing their enhancer-promoter pairwise methylation. We found our methodology to lead to very accurate estimates, outperforming our promoter-based deconvolutions. Moreover, we show that it can be generalized from deconvolving different cell types to subtle scenarios where one wishes to deconvolve different cell populations of the same cell-type.

Availability

The code used in this work to analyze single-molecule Bionano Genomics optical maps is available via the GitHub repositoryhttps://github.com/ebensteinLab/Single_molecule_methylation_in_EP.

Contact

uv@post.tau.ac.il(Y.E),roded@tauex.tau.ac.il(R.S)
The effects of maternal social connectivity and integration on offspring survival in a marmot
Authors: Montero Anita Pilar , Williams Dana M. , Martin Julien G.A. , Blumstein Daniel T.
Published: January 2021

In social species, maternal social relationships, in addition to direct care, impact offspring survival but much of what we know about these effects comes from studies of obligately social and cooperatively breeding species. Yellow-bellied marmots (Marmota flaviventer) are a facultatively social species whose social groups vary in composition, size, and cohesiveness. This natural variation in sociality and cooperative breeding behavior makes yellow-bellied marmots an ideal species within which to study the effects of maternal affiliative and agonistic social behavior on offspring. We used social network analysis to investigate the relationship between maternal social connectivity and integration on offspring summer and yearly survival, with the hypothesis that offspring with more affiliative mothers are more likely to survive than the offspring of more agonistic mothers. However, we found the inverse to be true: pups born to mothers who received more affiliative interactions were less likely to survive while the offspring of mothers who were more highly integrated into agonistic networks had enhanced survival. Overall, maternal social network measures were positively and negatively correlated with offspring survival, indicating that pups are influenced by their mother’s social world, often in contradictory ways. Relative predation risk and colony location also mediated the effects of social relationships on pup survival. This study contributes to a small but growing body of work that demonstrates that specific attributes of sociality have specific consequences and that by adopting an attribute-focused view of sociality we are better able to understand how environmental conditions mediate the costs and benefits of sociality.

Lay Summary

Maternal social relationships can impact offspring survival but much of what we know about these effects comes from studies of obligately social species. In faculatively social yellow-bellied marmots we found that pups born to mothers who received more affiliative interactions were less likely to survive while the offspring of mothers who were more highly integrated into agonistic networks had enhanced survival. Overall, pups are influenced by their mother’s social world, often in contradictory ways.
Genomic and phenotypic biology of novel strains of Dickeya zeae isolated from pineapple and taro in Hawaii: insights into genome plasticity, pathogenicity, and virulence determinants
Authors: Boluk Gamze , Arizala Dario , Dobhal Shefali , Zhang Jingxin , Hu John , Alvarez Anne M. , Arif Mohammad
Published: January 2021

Dickeya zeae, a bacterial plant pathogen in the family Pectobacteriaceae, is responsible for a wide range of diseases on potato, maize, rice, banana, pineapple, taro and ornamentals and significantly reduces crop production; D. zeae causes soft rot of taro (Colocasia esculenta) and heart rot of pineapple (Ananas comosus). In this study, we used Pacific Biosciences to sequence two high quality complete genomes of novel strains of D. zeae: PL65 (size - 4.74997 MB; depth - 701; GC - 53.3%) and A5410 (size - 4.7792 MB; depth - 558; GC - 53.6%) isolated from economically important Hawaiian crops, taro and pineapple, respectively. Additional complete genomes of D. zeae representing two additional hosts (rice and banana), and other species for taxonomic comparison, were retrieved from the NCBI GenBank genome database. The genomic analyses indicated truncated type III and IV secretion systems (T3SS and T4SS) in the taro strain, which only harbors 1 and 2 genes of T3SS and T4SS, respectively, and showed high heterogeneity in the type VI secretion system. Unlike the EC1 strain, neither the PL65 nor the A5410 genome harbors the zeamine biosynthesis gene cluster, which plays a key role in bacterial virulence. The ANI and dDDH percentages between the two genomes were 94.47 and 57.00, respectively. In this study, we compared major virulence factors (plant cell wall-degrading extracellular enzymes and protease) produced by D. zeae strains and virulence ability on taro corms and pineapple. Both strains produced protease, pectate lyases and cellulases but no significant quantitative differences were observed (p>0.05) among the strains. All the strains produced symptoms on taro corms and pineapple leaves. Strain PL65 developed symptoms faster than the others. Our study highlights genetic constituents of pathogenicity determinants and genomic heterogeneity that will help understand the virulence mechanisms and aggressiveness of this plant pathogen.