bluuebunny/crossref_metadata_2025 huggingface dataset:
Implementation of infectious diseases rapid molecular diagnostic tests and antimicrobial stewardship program involvement in acute-care hospitals
Authors: Kondo Maiko , Simon Matthew S. , Westblade Lars F. , Jenkins Stephen G. , Babady N. Esther , Loo Angela S. , Calfee David P.
Published: October 2020

A survey of acute-care hospitals found that rapid molecular diagnostic tests (RMDTs) have been widely adopted. Although many hospitals use their antimicrobial stewardship team and/or guidelines to help clinicians interpret results and optimize treatment, opportunities to more fully achieve the potential benefits of RMDTs remain.
Transformation of aqueous protein attenuated total reflectance infra-red absorbance spectroscopy to transmission
Authors: Rodger Alison , Steel Michael J. , Goodchild Sophia C. , Chmel Nikola P. , Reason Andrew
Published: October 2020

Infrared (IR) spectroscopy is increasingly being used to probe the secondary structure of proteins, especially for high-concentration samples and biopharmaceuticals in complex formulation vehicles. However, the small path lengths required for aqueous protein transmission experiments, due to high water absorbance in the amide I region of the spectrum, means that the path length is not accurately known, so only the shape of the band is ever considered. This throws away a dimension of information. Attenuated total reflectance (ATR) IR spectroscopy is much easier to implement than transmission IR spectroscopy and, for a given instrument and sample, gives reproducible spectra. However, the ATR-absorbance spectrum varies with sample concentration and instrument configuration, and its wavenumber dependence differs significantly from that observed in transmission spectroscopy. In this paper, we determine, for the first time, how to transform water and aqueous protein ATR spectra into the corresponding transmission spectra with appropriate spectral shapes and intensities. The approach is illustrated by application to water, concanavalin A, haemoglobin and lysozyme. The transformation is only as good as the available water refractive index data. A hybrid of literature data provides the best results. The transformation also allows the angle of incidence of an ATR crystal to be determined. This opens the way to using both spectral shape and spectra intensity for protein structure fitting.
Getting and spending in London and Yorkshire: a young musician’s account book for 1799–1800
Authors: Baldwin Olive , Wilson Thelma
Published: October 2020

In March 1799 John White was 20 years old and already an experienced professional violinist and cellist. He kept a detailed account book between March 1799 and March 1800 that provides much information about the economic and professional life of a young musician at the very end of the eighteenth century. White had showed early musical promise, and when he was 15 he attracted the patronage of the future Lord Harewood, who enabled him to take lessons from leading musical figures and appointed him as his director of music. White lived at Harewood House, near Leeds, but he spent some months of the London season each year with the Harewood family in their house in Hanover Square. The accounts show how White earned money in London by playing at private and public concerts and deputising at almost every place of musical entertainment in the capital. In Yorkshire he led orchestras in concerts and oratorio performances, took on pupils and visited Scarborough. White’s meticulous lists of his income and expenditure, from an expensive violin, a harp and harp lessons to silk stockings, waistcoats and hair ribbon, paint a fascinating picture of a young man making his way in the musical profession.
Input spacing in second language classroom settings: Replications of Bird (2010) and Serrano (2011)
Authors: Rogers John
Published: October 2020

This paper proposes the replication of Bird's (2010) and Serrano's (2011) studies, which examined distribution of practice effects in second language acquisition (SLA). These studies, which took place in authentic classroom contexts, produced conflicting results regarding the degree to which the learning of a second language (L2) benefited from distributed instruction. In the first part of the paper, I discuss the distribution of practice research in the learning and teaching of L2s. I then describe Bird's (2010) and Serrano's (2011) work, and highlight the strengths and limitations of the approaches of these studies. Finally, a number of approaches to approximate replications are suggested for each study in order to assess the reliability, internal validity, and generalizability of the original findings
Status and short-term environmental changes of lakes in the area of Devil's Bay, Vega Island, Antarctic Peninsula
Authors: Kavan Jan , Nedbalová Linda , Nývlt Daniel , Čejka Tomáš , Lirio Juan Manuel
Published: October 2020

Climate change affects various components of the polar environment, including lacustrine systems in many regions of the Antarctic Peninsula. However, the recent status of these life-preserving habitats remains poorly known. We performed field geomorphological mapping and limnological characterization of lakes distributed across Devil's Bay in the northern area of Vega Island, James Ross Archipelago, and described some significant changes in their physical and chemical properties during the 2013 summer season. Fifty lakes were described in the area, even though the area is relatively small (~12 km2). Six major lake types were distinguished based on their geomorphological settings and their origins, and their hydrochemical properties were compared with the neighbouring lake districts. The geomorphic characteristics of the lakes range from stable lakes on till plains (21 out of 50 lakes), to kettle lakes on fresh moraines with an unstable shoreline, to very dynamic ice-contact lakes with fluctuating water levels and inundated areas. The ice-contact lake dynamics were observed using ‘Lake Payer’ as an example. At the interface between hydrology and geosciences, this study provides new and original data from a yet largely unexplored region and emphasizes the importance of cross-disciplinary research in polar sciences.
Consumption of breast milk, formula and other non-human milk by children aged under 2 years: analysis of eighty-six low- and middle-income countries
Authors: Neves Paulo AR , Barros Aluísio JD , Baker Phillip , Piwoz Ellen , Santos Thiago M , Gatica-Domínguez Giovanna , Vaz Juliana S , Rollins Nigel , Victora Cesar G
Published: October 2020

Objective:

To investigate the prevalence and socio-economic inequalities in breast milk, breast milk substitutes (BMS) and other non-human milk consumption, by children under 2 years in low- and middle-income countries (LMIC).

Design:

We analysed the prevalence of continued breast-feeding at 1 and 2 years and frequency of formula and other non-human milk consumption by age in months. Indicators were estimated through 24-h dietary recall. Absolute and relative wealth indicators were used to describe within- and between-country socio-economic inequalities.

Setting:

Nationally representative surveys from 2010 onwards from eighty-six LMIC.

Participants:

394 977 children aged under 2 years.

Results:

Breast-feeding declined sharply as children became older in all LMIC, especially in upper-middle-income countries. BMS consumption peaked at 6 months of age in low/lower-middle-income countries and at around 12 months in upper-middle-income countries. Irrespective of country, BMS consumption was higher in children from wealthier families, and breast-feeding in children from poorer families. Multilevel linear regression analysis showed that BMS consumption was positively associated with absolute income, and breast-feeding negatively associated. Findings for other non-human milk consumption were less straightforward. Unmeasured factors at country level explained a substantial proportion of overall variability in BMS consumption and breast-feeding.

Conclusions:

Breast-feeding falls sharply as children become older, especially in wealthier families in upper-middle-income countries; this same group also consumes more BMS at any age. Country-level factors play an important role in explaining BMS consumption by all family wealth groups, suggesting that BMS marketing at national level might be partly responsible for the observed differences.
Psychische Störungen bei Vorschulkindern
Authors: Hussong Justine , Overs Cornelia , Paulus Frank W. , Bolten Margarete , In-Albon Tina , Equit Monika , Gontard Alexander von
Published: October 2020

Zusammenfassung. Um psychische Störungen bei jungen Kindern zu erfassen, wurde das Klassifikationssystem DC: 0 – 5 entwickelt. Das Ziel dieser Studie war es, Diagnosen nach DC: 0 – 5 und ICD-10 zu vergleichen. Bei 176 konsekutiv vorgestellten Kindern (70,5 % Jungen) mit einem mittleren Alter von 3,96 Jahren wurden Diagnosen nach ICD-10 und DC: 0 – 5 vergeben. 78,4 % der Kinder hatten eine Diagnose nach ICD-10, 88,1 % der Kinder nach DC: 0 – 5. Die häufigste ICD-10 Diagnose war Störung des Sozialverhaltens mit oppositionellem Verhalten (ODD; 28,4 %), gefolgt von Schlafstörungen (21,0 %), ADHS (14,8 %) und Angststörungen (6,8 %). Die häufigsten DC: 0 – 5 Diagnosen waren ADHS (30,7 %) und die Dysregulierte Ärger- und Aggressionsstörung (31,3 %), gefolgt von Schlaf-‍, Angst-‍, Ess- und Traumafolgestörungen. Zusammengefasst ist die DC: 0 – 5 das spezifischste Klassifikationssystem zur Diagnose psychischer Störungen bei jungen Kindern. Es hat sich in Kombination mit der ICD-10 in der klinischen Praxis bewährt. Wünschenswert wäre die weitere Verwendung und Überprüfung der DC: 0 – 5 in klinischen Studien.
Kindliche narrative Kohärenz als Prädiktor für spätere soziale Kompetenz und positive Peerbeziehungen
Authors: Stadelmann Stephanie , Stadelmann Stephanie , Netzl Johanna , Dähne Verena , White Lars Otto , Klein Annette Maria , Klitzing Kai von , Döhnert Mirko , Döhnert Mirko
Published: October 2020

Zusammenfassung. Die Studie untersucht den prädiktiven Wert sozialer Kompetenz-Themen und narrativer Kohärenz, erfasst in einem Spielnarrativ-Verfahren, für soziale Kompetenz und Peerbeziehungen von Kindern, eingeschätzt durch die Eltern. Untersucht wurden 97 8- bis 14-Jährige mit/ohne psychische Störungen zu zwei Zeitpunkten ( t1/ t2). Das Spielnarrativ-Verfahren wurde zu t1 durchgeführt. Eltern schätzten soziale Kompetenzen und Peerbeziehungen zu t1 und t2 ein. Multivariate Analysen zeigten, dass höhere narrative Kohärenz in den Spielnarrativen (nicht aber soziale Kompetenz-Themen) quer- und längsschnittlich mit höheren sozialen Kompetenzen, positiveren Peerbeziehungen, weniger sozialen Problemen und sozialem Rückzug im Elternurteil zusammenhing. Höhere narrative Kohärenz sagte auch den Zuwachs positiver Peerbeziehungen und die Verminderung sozialen Rückzugs 1,5 Jahre später voraus. Die Befunde belegen die Bedeutung narrativer Kohärenz für die kindliche sozioemotionale Entwicklung.
What Controls Giant Subduction Earthquakes?
Authors: Waldron Patricia
Published: October 2020

Subduction zones with a low dipping angle and thick sediments can produce giant earthquakes; this finding lets researchers estimate worst-case scenarios for coastlines around the world.
Forcing From Lower Thermosphere and Quiet Time Scintillation Longitudinal Dependence
Authors: Yizengaw Endawoke , Groves Keith
Published: October 2020

The quiet time ionospheric plasma bubbles that occur almost every day become a significant threat for radio frequency (RF) signal degradation that affects communication and navigation systems. We have analyzed multi‐instrument observations to determine the driving mechanism for quiet time bubbles and to answer the longstanding problem, what controls the longitudinal and seasonal dependence of ionospheric irregularity occurrence rate? While VHF scintillation and GNSS ROTI are used to characterize irregularity occurrence, the vertical drifts from JRO and IVM onboard C/NOFS, as well as gravity waves (GWs) amplitudes, extracted SABER temperature profiles, are utilized to identify the potential driving mechanism for the generation of small‐scale plasma density irregularities. We demonstrated that the postsunset vertical drift enhancement may not always be a requirement for the generation of equatorial plasma bubbles. The tropospheric GWs with a vertical wavelength (4 km < λv < 30 km) can also penetrate to higher altitudes and provide enough seeding to the bottom side ionosphere and elicit density irregularity. This paper, using a one‐to‐one comparison between GWs amplitudes and irregularity occurrence distributions, also demonstrated that the GWs seeding plays a critical role in modulating the longitudinal dependence of equatorial density irregularities. Thus, it is becoming increasingly clear that understanding the forcing from a lower thermosphere is critically essential for the modeling community to predict and forecast the day‐to‐day and longitudinal variabilities of ionospheric irregularities and scintillations.
Efficacy and safety profile of deep responders to carfilzomib-based therapy: a subgroup analysis from ASPIRE and ENDEAVOR
Authors: Weisel Katja , Mateos Maria-Victoria , Gay Francesca , Delforge Michel , Cook Gordon , Szabo Zsolt , Desgraz Renaud , DeCosta Lucy , Moreau Philippe
Published: October 2020

To understand the profile of best responders (complete response or better [≥CR]) to carfilzomib, we described the characteristics, progression-free survival (PFS), overall survival (OS) data, and the safety of patients who achieved ≥CR to carfilzomib-based treatment in ASPIRE and ENDEAVOR. In post hoc analyses from ASPIRE and ENDEAVOR, median PFS and OS were longer for ≥CR patients versus those who achieved a very good partial response or partial response (VGPR/PR). In the carfilzomib arm of ASPIRE, median PFS was 50.4 months for ≥CR versus 22.1 months for VGPR/PR; median OS was 67.0 versus 44.2 months, respectively. In the carfilzomib arm of ENDEAVOR, median PFS was 34.0 for ≥CR versus 20.4 months for VGPR/PR; median OS was non-estimable. Despite the longer treatment duration, fewer patients with ≥CR versus VGPR/PR experienced treatment-emergent adverse events that led to discontinuation of carfilzomib-based treatment in ASPIRE or ENDEAVOR. Low serum lactate dehydrogenase was the only factor associated with achieving ≥CR vs patients not achieving CR in ASPIRE in multivariate regression analyses. No association was found between cytogenetic risk status and reaching ≥CR. Carfilzomib treatment may lead to rapid and deep responses, irrespective of most patient characteristics.
Genomic and kinetic analysis of novel Nitrospinae enriched by cell sorting
Authors: Mueller Anna J , Jung Man-Young , Strachan Cameron R , Herbold Craig W , Kirkegaard Rasmus H , Wagner Michael , Daims Holger
Published: October 2020

Chemolithoautotrophic nitrite-oxidizing bacteria (NOB) are key players in global nitrogen and carbon cycling. Members of the phylum Nitrospinae are the most abundant, known NOB in the oceans. To date, only two closely affiliated Nitrospinae species have been isolated, which are only distantly related to the environmentally abundant uncultured Nitrospinae clades. Here, we applied live cell sorting, activity screening, and subcultivation on marine nitrite-oxidizing enrichments to obtain novel marine Nitrospinae. Two binary cultures were obtained, each containing one Nitrospinae strain and one alphaproteobacterial heterotroph. The Nitrospinae strains represent two new genera, and one strain is more closely related to environmentally abundant Nitrospinae than previously cultured NOB. With an apparent half-saturation constant of 8.7 ± 2.5 µM, this strain has the highest affinity for nitrite among characterized marine NOB, while the other strain (16.2 ± 1.6 µM) and Nitrospina gracilis (20.1 ± 2.1 µM) displayed slightly lower nitrite affinities. The new strains and N. gracilis share core metabolic pathways for nitrite oxidation and CO2 fixation but differ remarkably in their genomic repertoires of terminal oxidases, use of organic N sources, alternative energy metabolisms, osmotic stress and phage defense. The new strains, tentatively named “Candidatus Nitrohelix vancouverensis” and “Candidatus Nitronauta litoralis”, shed light on the niche differentiation and potential ecological roles of Nitrospinae.
Correction: Potent and specific MTH1 inhibitors targeting gastric cancer
Authors: Zhou Wenjuan , Ma Liying , Yang Jing , Qiao Hui , Li Lingyu , Guo Qian , Ma Jinlian , Zhao Lijuan , Wang Junwei , Jiang Guozhong , Wan Xiangbin , Goscinski Mariusz Adam , Ding Lina , Zheng Yichao , Li Wencai , Liu Hongmin , Suo Zhenhe , Zhao Wen
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
High resolution spectral metrology leveraging topologically enhanced optical activity in fibers
Authors: Greenberg Aaron P. , Prabhakar Gautam , Ramachandran Siddharth
Published: October 2020

Optical rotation, a form of optical activity, is a phenomenon employed in various metrological applications and industries including chemical, food, and pharmaceutical. In naturally-occurring, as well as structured media, the integrated effect is, however, typically small. Here, we demonstrate that, by exploiting the inherent and stable spin-orbit interaction of orbital angular momentum fiber modes, giant, scalable optical activity can be obtained, and that we can use this effect to realize a new type of wavemeter by exploiting its optical rotary dispersion. The device we construct provides for an instantaneous wavelength-measurement technique with high resolving power R = 3.4 × 106 (i.e., resolution < 0.3 pm at 1-μm wavelengths) and can also detect spectral bandwidths of known lineshapes with high sensitivity.
Structure of inhibitor-bound mammalian complex I
Authors: Bridges Hannah R. , Fedor Justin G. , Blaza James N. , Di Luca Andrea , Jussupow Alexander , Jarman Owen D. , Wright John J. , Agip Ahmed-Noor A. , Gamiz-Hernandez Ana P. , Roessler Maxie M. , Kaila Ville R. I. , Hirst Judy
Published: October 2020

Respiratory complex I (NADH:ubiquinone oxidoreductase) captures the free energy from oxidising NADH and reducing ubiquinone to drive protons across the mitochondrial inner membrane and power oxidative phosphorylation. Recent cryo-EM analyses have produced near-complete models of the mammalian complex, but leave the molecular principles of its long-range energy coupling mechanism open to debate. Here, we describe the 3.0-Å resolution cryo-EM structure of complex I from mouse heart mitochondria with a substrate-like inhibitor, piericidin A, bound in the ubiquinone-binding active site. We combine our structural analyses with both functional and computational studies to demonstrate competitive inhibitor binding poses and provide evidence that two inhibitor molecules bind end-to-end in the long substrate binding channel. Our findings reveal information about the mechanisms of inhibition and substrate reduction that are central for understanding the principles of energy transduction in mammalian complex I.
Understanding and managing new risks on the Nile with the Grand Ethiopian Renaissance Dam
Authors: Wheeler Kevin G. , Jeuland Marc , Hall Jim W. , Zagona Edith , Whittington Dale
Published: October 2020

When construction of the Grand Ethiopian Renaissance Dam (GERD) is completed, the Nile will have two of the world’s largest dams—the High Aswan Dam (HAD) and the GERD—in two different countries (Egypt and Ethiopia). There is not yet agreement on how these dams will operate to manage scarce water resources. We elucidate the potential risks and opportunities to Egypt, Sudan and Ethiopia by simulating the filling period of the reservoir; a new normal period after the reservoir fills; and a severe multi-year drought after the filling. Our analysis illustrates how during filling the HAD reservoir could fall to levels not seen in recent decades, although the risk of water shortage in Egypt is relatively low. The new normal will benefit Ethiopia and Sudan without significantly affecting water users in Egypt. Management of multi-year droughts will require careful coordination if risks of harmful impacts are to be minimized.
Metformin enhances anti-mycobacterial responses by educating CD8+ T-cell immunometabolic circuits
Authors: Böhme Julia , Martinez Nuria , Li Shamin , Lee Andrea , Marzuki Mardiana , Tizazu Anteneh Mehari , Ackart David , Frenkel Jessica Haugen , Todd Alexandra , Lachmandas Ekta , Lum Josephine , Shihui Foo , Ng Tze Pin , Lee Bernett , Larbi Anis , Netea Mihai G. , Basaraba Randall , van Crevel Reinout , Newell Evan , Kornfeld Hardy , Singhal Amit
Published: October 2020

Patients with type 2 diabetes (T2D) have a lower risk of Mycobacterium tuberculosis infection, progression from infection to tuberculosis (TB) disease, TB morality and TB recurrence, when being treated with metformin. However, a detailed mechanistic understanding of these protective effects is lacking. Here, we use mass cytometry to show that metformin treatment expands a population of memory-like antigen-inexperienced CD8+CXCR3+ T cells in naive mice, and in healthy individuals and patients with T2D. Metformin-educated CD8+ T cells have increased (i) mitochondrial mass, oxidative phosphorylation, and fatty acid oxidation; (ii) survival capacity; and (iii) anti-mycobacterial properties. CD8+ T cells from Cxcr3−/− mice do not exhibit this metformin-mediated metabolic programming. In BCG-vaccinated mice and guinea pigs, metformin enhances immunogenicity and protective efficacy against M. tuberculosis challenge. Collectively, these results demonstrate an important function of CD8+ T cells in metformin-derived host metabolic-fitness towards M. tuberculosis infection.
ATP hydrolysis by yeast Hsp104 determines protein aggregate dissolution and size in vivo
Authors: Sathyanarayanan Udhayabhaskar , Musa Marina , Bou Dib Peter , Raimundo Nuno , Milosevic Ira , Krisko Anita
Published: October 2020

Signs of proteostasis failure often entwine with those of metabolic stress at the cellular level. Here, we study protein sequestration during glucose deprivation-induced ATP decline in Saccharomyces cerevisiae. Using live-cell imaging, we find that sequestration of misfolded proteins and nascent polypeptides into two distinct compartments, stress granules, and Q-bodies, is triggered by the exhaustion of ATP. Both compartments readily dissolve in a PKA-dependent manner within minutes of glucose reintroduction and ATP level restoration. We identify the ATP hydrolase activity of Hsp104 disaggregase as the critical ATP-consuming process determining compartments abundance and size, even in optimal conditions. Sequestration of proteins into distinct compartments during acute metabolic stress and their retrieval during the recovery phase provide a competitive fitness advantage, likely promoting cell survival during stress.
Spectroscopic capture of a low-spin Mn(IV)-oxo species in Ni–Mn3O4 nanoparticles during water oxidation catalysis
Authors: Park Sunghak , Jin Kyoungsuk , Lim Hyung Kyu , Kim Jin , Cho Kang Hee , Choi Seungwoo , Seo Hongmin , Lee Moo Young , Lee Yoon Ho , Yoon Sangmoon , Kim Miyoung , Kim Hyungjun , Kim Sun Hee , Nam Ki Tae
Published: October 2020

High-valent metal-oxo moieties have been implicated as key intermediates preceding various oxidation processes. The critical O–O bond formation step in the Kok cycle that is presumed to generate molecular oxygen occurs through the high-valent Mn-oxo species of the water oxidation complex, i.e., the Mn4Ca cluster in photosystem II. Here, we report the spectroscopic characterization of new intermediates during the water oxidation reaction of manganese-based heterogeneous catalysts and assign them as low-spin Mn(IV)-oxo species. Recently, the effects of the spin state in transition metal catalysts on catalytic reactivity have been intensely studied; however, no detailed characterization of a low-spin Mn(IV)-oxo intermediate species currently exists. We demonstrate that a low-spin configuration of Mn(IV), S = 1/2, is stably present in a heterogeneous electrocatalyst of Ni-doped monodisperse 10-nm Mn3O4 nanoparticles via oxo-ligand field engineering. An unprecedented signal (g = 1.83) is found to evolve in the electron paramagnetic resonance spectrum during the stepwise transition from the Jahn–Teller-distorted Mn(III). In-situ Raman analysis directly provides the evidence for Mn(IV)-oxo species as the active intermediate species. Computational analysis confirmed that the substituted nickel species induces the formation of a z-axis-compressed octahedral C4v crystal field that stabilizes the low-spin Mn(IV)-oxo intermediates.
Author Correction: Superconductivity mediated by polar modes in ferroelectric metals
Authors: Enderlein C. , de Oliveira J. Ferreira , Tompsett D. A. , Saitovitch E. Baggio , Saxena S. S. , Lonzarich G. G. , Rowley S. E.
Published: October 2020

An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Identifying human body states by using a flexible integrated sensor
Authors: Jin Ying , Chen Guoning , Lao Kete , Li Songhui , Lu Yong , Gan Yufeng , Li Zhundong , Hu Jiajia , Huang Jingcheng , Wen Jinxiu , Deng Honggui , Yang Min , Chen Zhiming , Hu Xiaoyan , Liang Baowen , Luo Jianyi
Published: October 2020

Flexible sensors are required to be lightweight, compatible with the skin, sufficiently sensitive, and easily integrated to extract various kinds of body vital signs during continuous healthcare monitoring in daily life. For this, a simple and low-cost flexible temperature and force sensor that uses only two carbon fiber beams as the sensing layer is reported in this work. This simple, flexible sensor can not only monitor skin temperature changes in real time but can also extract most pulse waves, including venous waves, from most parts of the human body. A pulse diagnostic glove containing three such flexible sensors was designed to simulate pulse diagnostic methods used in traditional Chinese medicine. Wearable equipment was also designed in which four flexible sensors were fixed onto different body parts (neck, chest, armpit, and fingertip) to simultaneously monitor body temperature, carotid pulse, fingertip artery pulse, and respiratory rate. Four important physiological indicators—body temperature (BT), blood pressure (BP), heart rate (HR), and respiratory rate (RR)—were extracted by the wearable equipment and analyzed to identify exercise, excited, tired, angry, and frightened body states.
Revealing the growth kinetics of atmospheric corrosion pitting in aluminum via in situ microtomography
Authors: Noell Philip J. , Schindelholz Eric J. , Melia Michael A.
Published: October 2020

Understanding the mechanistic relationship between the environment, microstructure, and local kinetics of atmospheric corrosion damage remains a central challenge. To address this challenge, this study used laboratory-based X-ray tomography to directly observe attack in-operando over an extended period, enabling insights into the evolving growth kinetics and morphology of individual pits over months of exposure. Damage progression associated with nine pits in a 99.9% pure aluminum wire exposed to chloride salts in humid air was characterized. Most pits grew at a nominally linear rate up until pit death, which occurred within 12–24 h of nucleation. Exceptions to this were observed, with three pits exhibiting bimodal growth kinetics and growing for 40 or more hours. This was explained by secondary droplets that formed near the pits, increasing the cathode area. A corrosion-driven drying mechanism likely contributed to pit death in both cases. Pits first grew into the material followed by lateral expansion.
Precise programmable quantum simulations with optical lattices
Authors: Qiu Xingze , Zou Jie , Qi Xiaodong , Li Xiaopeng
Published: October 2020

We present an efficient approach to precisely simulate tight binding models with optical lattices, based on programmable digital-micromirror-device (DMD) techniques. Our approach consists of a subroutine of Wegner-flow enabled precise extraction of a tight-binding model for a given optical potential, and a reverse engineering step of adjusting the potential for a targeting model, for both of which we develop classical algorithms to achieve high precision and high efficiency. With renormalization of Wannier functions and high band effects systematically calibrated in our protocol, we show the tight-binding models with programmable onsite energies and tunnelings can be precisely simulated with optical lattices integrated with the DMD techniques. With numerical simulation, we demonstrate that our approach would facilitate quantum simulation of localization physics with adequate programmability and atom-based boson sampling for illustration of quantum computational advantage. We expect this approach would pave a way towards large-scale and precise programmable quantum simulations based on optical lattices.
Proclivities for prevalence and treatment of antibiotics in the ambient water: a review
Authors: Bhagat Chandrashekhar , Kumar Manish , Tyagi Vinay Kumar , Mohapatra Pranab Kumar
Published: October 2020

In the intial two decades of the twenty-first century, antibiotic (AB) resistance in human pathogens has emerged as a major challenge for water, sanitation, and public health. Considering these challenges, we critically reviewed AB-related studies with particular emphasis on their (i) patterns of consumption, (ii) pathway prevalences and environmental implications in ambient waters, and (iii) benefits and limitations of existing AB removal/purging techniques. We found that lifestyle, land use, urbanization, the ease of availability, and the tendency of the medical practitioners to recommend ABs are the key factors governing the AB use pathway and enrichment in the environment. In the developing world, the most prevalent group of ABs is quinolone, whereas in the developed world, older-generation AB groups are most prevalent. Further, enormous variability in the consumption of ABs around the globe is explicitly highlighted in this study. Ciprofloxacin has been reported in the highest concentration among all the ABs with 28–31 mg L−1 in the raw wastewater of the Indian subcontinent. We found that adsorption may be one of the most efficient AB removal techniques, and NaOH-activated carbon prepared from Macadamia nut shells is the most effective adsorbent identified to date. The literature showed that the Langmuir isotherm and pseudo-second-order kinetic model explain the AB adsorption mechanism most effectively. The future challenge lies in developing advanced protocols and markers to prioritize the strategy and simulate the ecotoxicities of the individual and a mixture of ABs.
HARDI-ZOOMit protocol improves specificity to microstructural changes in presymptomatic myelopathy
Authors: Labounek René , Valošek Jan , Horák Tomáš , Svátková Alena , Bednařík Petr , Vojtíšek Lubomír , Horáková Magda , Nestrašil Igor , Lenglet Christophe , Cohen-Adad Julien , Bednařík Josef , Hluštík Petr
Published: October 2020

Diffusion magnetic resonance imaging (dMRI) proved promising in patients with non-myelopathic degenerative cervical cord compression (NMDCCC), i.e., without clinically manifested myelopathy. Aim of the study is to present a fast multi-shell HARDI-ZOOMit dMRI protocol and validate its usability to detect microstructural myelopathy in NMDCCC patients. In 7 young healthy volunteers, 13 age-comparable healthy controls, 18 patients with mild NMDCCC and 15 patients with severe NMDCCC, the protocol provided higher signal-to-noise ratio, enhanced visualization of white/gray matter structures in microstructural maps, improved dMRI metric reproducibility, preserved sensitivity (SE = 87.88%) and increased specificity (SP = 92.31%) of control-patient group differences when compared to DTI-RESOLVE protocol (SE = 87.88%, SP = 76.92%). Of the 56 tested microstructural parameters, HARDI-ZOOMit yielded significant patient-control differences in 19 parameters, whereas in DTI-RESOLVE data, differences were observed in 10 parameters, with mostly lower robustness. Novel marker the white-gray matter diffusivity gradient demonstrated the highest separation. HARDI-ZOOMit protocol detected larger number of crossing fibers (5–15% of voxels) with physiologically plausible orientations than DTI-RESOLVE protocol (0–8% of voxels). Crossings were detected in areas of dorsal horns and anterior white commissure. HARDI-ZOOMit protocol proved to be a sensitive and practical tool for clinical quantitative spinal cord imaging.
Seven decades of chemotherapy clinical trials: a pan-cancer social network analysis
Authors: Li Xuanyi , Sigworth Elizabeth A. , Wu Adrianne H. , Behrens Jess , Etemad Shervin A. , Nagpal Seema , Go Ronald S. , Wuichet Kristin , Chen Eddy J. , Rubinstein Samuel M. , Venepalli Neeta K. , Tillman Benjamin F. , Cowan Andrew J. , Schoen Martin W. , Malty Andrew , Greer John P. , Fernandes Hermina D. , Seifter Ari , Chen Qingxia , Chowdhery Rozina A. , Mohan Sanjay R. , Dewdney Summer B. , Osterman Travis , Ambinder Edward P. , Buchbinder Elizabeth I. , Schwartz Candice , Abraham Ivy , Rioth Matthew J. , Singh Naina , Sharma Sanjai , Gibson Michael K. , Yang Peter C. , Warner Jeremy L.
Published: October 2020

Clinical trials establish the standard of cancer care, yet the evolution and characteristics of the social dynamics between the people conducting this work remain understudied. We performed a social network analysis of authors publishing chemotherapy-based prospective trials from 1946 to 2018 to understand how social influences, including the role of gender, have influenced the growth and development of this network, which has expanded exponentially from fewer than 50 authors in 1946 to 29,197 in 2018. While 99.4% of authors were directly or indirectly connected by 2018, our results indicate a tendency to predominantly connect with others in the same or similar fields, as well as an increasing disparity in author impact and number of connections. Scale-free effects were evident, with small numbers of individuals having disproportionate impact. Women were under-represented and likelier to have lower impact, shorter productive periods (P < 0.001 for both comparisons), less centrality, and a greater proportion of co-authors in their same subspecialty. The past 30 years were characterized by a trend towards increased authorship by women, with new author parity anticipated in 2032. The network of cancer clinical trialists is best characterized as strategic or mixed-motive, with cooperative and competitive elements influencing its appearance. Network effects such as low centrality, which may limit access to high-profile individuals, likely contribute to the observed disparities.
Plasmonically enhanced mid-IR light source based on tunable spectrally and directionally selective thermal emission from nanopatterned graphene
Authors: Shabbir Muhammad Waqas , Leuenberger Michael N.
Published: October 2020

We present a proof of concept for a spectrally selective thermal mid-IR source based on nanopatterned graphene (NPG) with a typical mobility of CVD-grown graphene (up to 3000 $$\hbox {cm}^2\,\hbox {V}^{-1}\,\hbox {s}^{-1}$$

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-
1

), ensuring scalability to large areas. For that, we solve the electrostatic problem of a conducting hyperboloid with an elliptical wormhole in the presence of an in-plane electric field. The localized surface plasmons (LSPs) on the NPG sheet, partially hybridized with graphene phonons and surface phonons of the neighboring materials, allow for the control and tuning of the thermal emission spectrum in the wavelength regime from $$\lambda =3$$

λ
=
3

to 12 $$\upmu$$
μ
m by adjusting the size of and distance between the circular holes in a hexagonal or square lattice structure. Most importantly, the LSPs along with an optical cavity increase the emittance of graphene from about 2.3% for pristine graphene to 80% for NPG, thereby outperforming state-of-the-art pristine graphene light sources operating in the near-infrared by at least a factor of 100. According to our COMSOL calculations, a maximum emission power per area of $$11\times 10^3$$

11
×

10
3

W/$$\hbox {m}^2$$

m
2

at $$T=2000$$

T
=
2000

K for a bias voltage of $$V=23$$

V
=
23

V is achieved by controlling the temperature of the hot electrons through the Joule heating. By generalizing Planck’s theory to any grey body and deriving the completely general nonlocal fluctuation-dissipation theorem with nonlocal response of surface plasmons in the random phase approximation, we show that the coherence length of the graphene plasmons and the thermally emitted photons can be as large as 13 $$\upmu$$
μ
m and 150 $$\upmu$$
μ
m, respectively, providing the opportunity to create phased arrays made of nanoantennas represented by the holes in NPG. The spatial phase variation of the coherence allows for beamsteering of the thermal emission in the range between $$12^\circ$$

12
∘

and $$80^\circ$$

80
∘

by tuning the Fermi energy between $$E_F=1.0$$

E
F

=
1.0

eV and $$E_F=0.25$$

E
F

=
0.25

eV through the gate voltage. Our analysis of the nonlocal hydrodynamic response leads to the conjecture that the diffusion length and viscosity in graphene are frequency-dependent. Using finite-difference time domain calculations, coupled mode theory, and RPA, we develop the model of a mid-IR light source based on NPG, which will pave the way to graphene-based optical mid-IR communication, mid-IR color displays, mid-IR spectroscopy, and virus detection.
Higher cytolytic score correlates with an immunosuppressive tumor microenvironment and reduced survival in glioblastoma
Authors: Haddad Alexander F. , Chen Jia-Shu , Oh Taemin , Pereira Matheus P. , Joshi Rushikesh S. , Aghi Manish K.
Published: October 2020

Cytolytic score (CYT), calculated from mRNA expression levels of granzyme and perforin, positively correlates with CD8+ T cell infiltration/activity in a variety of cancers. Unlike other cancers, higher CYT has been associated with worse prognosis in glioblastoma (GBM). To address this discrepancy, we sought to investigate the relationship between CYT and immune checkpoint gene score (ICGscore), as well as their correlation with patient survival and tumor immune cell infiltration. Clinical and RNA-sequencing data for patients with newly diagnosed GBM were obtained from The Cancer Genome Atlas. Maximally-selected rank statistics was used to dichotomize subgroups. CIBERSORT was used to estimate abudence of immune cell-types. Spearman correlation was used to characterize the relationship between CYT and ICGscore. Kaplan–Meier curves were generated for survival analysis. Overall, 28/151 patients had high CYT. High CYT was associated with a mesenchymal subtype (p < 0.001) and worse survival (7.45 vs. 12.2 months, p < 0.001). There were no differences in patient demographics, IDH/MGMT mutation status, or treatment. On subgroup analysis, patients with high CYT/ICGscore had significantly increased CD8+ infiltration (p < 0.001), as expected, and worse survival (HR 0.445, p < 0.01). Furthermore, CYT strongly correlated with ICGscore (RS = 0.675, p < 0.001). The high CYT/ICGscore subgroup was associated with greater infiltration of M2 macrophages (p = 0.011) and neutrophils (p = 0.055). Our study highlights a multidimensional immunosuppressive GBM microenvironment in patients with higher CYT and potentially identifies patients with high CYT/ICGscore as a subgroup that may particularly benefit from multi-faceted immunotherapies, given their already elevated tumor CD8+ T cell levels.
Protein conformational entropy is not slaved to water
Authors: Marques Bryan S. , Stetz Matthew A. , Jorge Christine , Valentine Kathleen G. , Wand A. Joshua , Nucci Nathaniel V.
Published: October 2020

Conformational entropy can be an important element of the thermodynamics of protein functions such as the binding of ligands. The observed role for conformational entropy in modulating molecular recognition by proteins is in opposition to an often-invoked theory for the interaction of protein molecules with solvent water. The “solvent slaving” model predicts that protein motion is strongly coupled to various aspects of water such as bulk solvent viscosity and local hydration shell dynamics. Changes in conformational entropy are manifested in alterations of fast internal side chain motion that is detectable by NMR relaxation. We show here that the fast-internal side chain dynamics of several proteins are unaffected by changes to the hydration layer and bulk water. These observations indicate that the participation of conformational entropy in protein function is not dictated by the interaction of protein molecules and solvent water under the range of conditions normally encountered.
Floquet-engineered quantum walks
Authors: Katayama Haruna , Hatakenaka Noriyuki , Fujii Toshiyuki
Published: October 2020

The quantum walk is the quantum-mechanical analogue of the classical random walk, which offers an advanced tool for both simulating highly complex quantum systems and building quantum algorithms in a wide range of research areas. One prominent application is in computational models capable of performing any quantum computation, in which precisely controlled state transfer is required. It is, however, generally difficult to control the behavior of quantum walks due to stochastic processes. Here we unveil the walking mechanism based on its particle-wave duality and then present tailoring quantum walks using the walking mechanism (Floquet oscillations) under designed time-dependent coins, to manipulate the desired state on demand, as in universal quantum computation primitives. Our results open the path towards control of quantum walks.
Pore-scale experimental investigation of oil recovery enhancement in oil-wet carbonates using carbonaceous nanofluids
Authors: Zhang Bingjun , Mohamed Abdelhalim I. A. , Goual Lamia , Piri Mohammad
Published: October 2020

This study investigates the pore-scale displacement mechanisms of crude oil in aged carbonate rocks using novel engineered carbon nanosheets (E-CNS) derived from sub-bituminous coal. The nanosheets, synthesized by a simple top-down technique, were stable in brine without any additional chemicals. Owing to their amphiphilic nature and nano-size, they exhibited dual properties of surfactants and nanoparticles and reduced the oil/brine interfacial tension (IFT) from 14.6 to 5.5 mN/m. X-ray micro-computed tomography coupled with miniature core-flooding was used to evaluate their ability to enhance oil recovery. Pore-scale displacement mechanisms were investigated using in-situ contact angle measurements, oil ganglia distribution analysis, and three-dimensional visualization of fluid occupancy maps in pores of different sizes. Analysis of these maps at the end of various flooding stages revealed that the nanofluid invaded into medium and small pores that were inaccessible to base brine. IFT reduction was identified as the main displacement mechanism responsible for oil recovery during 1 to 8 pore volumes (PVs) of nanofluid injection. Subsequently, wettability alteration was the dominant mechanism during the injection of 8 and 32 PVs, decreasing the average contact angle from 134° (oil wet) to 85° (neutral wet). In-situ saturation data reveals that flooding with only 0.1 wt% of E-CNS in brine resulted in incremental oil production of 20%, highlighting the significant potential of this nanofluid as a recovery agent.
Magnetic resonance fingerprinting of the pancreas at 1.5 T and 3.0 T
Authors: Serrao Eva M. , Kessler Dimitri A. , Carmo Bruno , Beer Lucian , Brindle Kevin M. , Buonincontri Guido , Gallagher Ferdia A. , Gilbert Fiona J. , Godfrey Edmund , Graves Martin J. , McLean Mary A. , Sala Evis , Schulte Rolf F. , Kaggie Joshua D.
Published: October 2020

Magnetic resonance imaging of the pancreas is increasingly used as an important diagnostic modality for characterisation of pancreatic lesions. Pancreatic MRI protocols are mostly qualitative due to time constraints and motion sensitivity. MR Fingerprinting is an innovative acquisition technique that provides qualitative data and quantitative parameter maps from a single free‐breathing acquisition with the potential to reduce exam times. This work investigates the feasibility of MRF parameter mapping for pancreatic imaging in the presence of free-breathing exam. Sixteen healthy participants were prospectively imaged using MRF framework. Regions-of-interest were drawn in multiple solid organs including the pancreas and T1and T2 values determined. MRF T1and T2mapping was performed successfully in all participants (acquisition time:2.4–3.6 min). Mean pancreatic T1values were 37–43% lower than those of the muscle, spleen, and kidney at both 1.5 and 3.0 T. For these organs, the mean pancreatic T2values were nearly 40% at 1.5 T and < 12% at 3.0 T. The feasibility of MRF at 1.5 T and 3 T was demonstrated in the pancreas. By enabling fast and free-breathing quantitation, MRF has the potential to add value during the clinical characterisation and grading of pathological conditions, such as pancreatitis or cancer.
Population genomics in two cave-obligate invertebrates confirms extremely limited dispersal between caves
Authors: Balogh Andras , Ngo Lam , Zigler Kirk S. , Dixon Groves
Published: October 2020

Caves offer selective pressures that are distinct from the surface. Organisms that have evolved to exist under these pressures typically exhibit a suite of convergent characteristics, including a loss or reduction of eyes and pigmentation. As a result, cave-obligate taxa, termed troglobionts, are no longer viable on the surface. This circumstance has led to an understanding of highly constrained dispersal capabilities, and the prediction that, in the absence of subterranean connections, extreme genetic divergence between cave populations. An effective test of this model would involve (1) common troglobionts from (2) nearby caves in a cave-dense region, (3) good sample sizes per cave, (4) multiple taxa, and (5) genome-wide characterization. With these criteria in mind, we used RAD-seq to genotype an average of ten individuals of the troglobiotic spider Nesticus barri and the troglobiotic beetle Ptomaphagus hatchi, each from four closely located caves (ranging from 3 to 13 km apart) in the cave-rich southern Cumberland Plateau of Tennessee, USA. Consistent with the hypothesis of highly restricted dispersal, we find that populations from separate caves are indeed highly genetically isolated. Our results support the idea of caves as natural laboratories for the study of parallel evolutionary processes.
mRNA and miRNA expression profile reveals the role of miR-31 overexpression in neural stem cell
Authors: Li Pengfei , Gao Yuantao , Li Xiao , Tian Feng , Wang Fei , Wang Yali , Zhao Bichun , Zhang Ruxin , Wang Chunfang
Published: October 2020

A detailed understanding of the character and differentiation mechanism of neural stem cells (NSCs) will help us to effectively utilize their transplantation to treat spinal cord injury. In previous studies, we found that compared with motor neurons (MNs), miR-31 was significantly high-expressed in NSCs and might play an important role in the proliferation of NSCs and the differentiation into MNs. To better understand the role of miR-31, we characterized the mRNA and miRNAs expression profiles in the early stage of spinal cord-derived NSCs after miR-31 overexpression. There were 35 mRNAs and 190 miRNAs differentially expressed between the miR-31 overexpression group and the control group. Compared with the control group, both the up-regulated mRNAs and miRNAs were associated with the stemness maintenance of NSCs and inhibited their differentiation, especially to MNs, whereas the down-regulated had the opposite effect. Further analysis of the inhibition of miR-31 in NSCs showed that interfering with miR-31 could increase the expression of MNs-related genes and produce MNs-like cells. All these indicated that miR-31 is a stemness maintenance gene of NSCs and has a negative regulatory role in the differentiation of NSCs into MNs. This study deepens our understanding of the role of miR-31 in NSCs, provides an effective candidate target for effectively inducing the differentiation of NSCs into MNs, and lays a foundation for the effective application of NSCs in clinic.