bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome‐wide identification of U‐box genes and protein ubiquitination under PEG‐induced drought stress in potato
Authors: Tang Xun , Ghimire Shantwana , Liu Weigang , Fu Xue , Zhang Huanhuan , Sun Fujun , Zhang Ning , Si Huaijun
Published: June 2021

Protein ubiquitination is one of the most important posttranslational modifications in eukaryotic cells, and it is involved in a variety of biological processes, including abiotic stress response. The ubiquitination modification is highly specific, which depends on the accurate recognition of substrate proteins by ubiquitin ligase. Plant U‐box (PUB) proteins are a class of ubiquitin ligases, multiple members of which have shown to participate in water‐deficit stress in Arabidopsis and rice. U‐box gene family and large‐scale profiling of the ubiquitome in potato has not been reported to date, although it is one of the most important food crops. The identified 66 U‐box genes from the potato genome database were unevenly distributed on 10 chromosomes. These StPUBs have a large number of tandem repeat sequences. Analysis of gene expression characteristics revealed that many StPUBs responded to abiotic stress. Three hundred and fourteen lys modification sites were identified under PEG‐induced drought stress, which were distributed on 200 proteins, with 25 differential ubiquitination modification sites, most of which were up‐regulated. The ubiquitination modification in potato protein was enhanced under PEG‐induced drought stress, and U‐box ubiquitin ligase was involved. This study provides an overall strategy and rich data set to clarify the effects of ubiquitination on potatoes under PEG‐induced drought stress and the ubiquitination modification involved in potato U‐box genes in response to PEG‐induced drought stress.
PD components and distractor inhibition in visual search: New evidence for the signal suppression hypothesis
Authors: Drisdelle Brandi Lee , Eimer Martin
Published: June 2021

The hypothesis that salient distractors in visual search are actively suppressed is supported by the fact that these objects elicit PD components believed to be associated with inhibition. This account was challenged by researchers who found that a PD to lateral color singleton distractors was followed by a contralateral negativity, which they interpreted as an N2pc indicative of attentional capture. As this would be at odds with successful distractor suppression, they proposed an alternative lateral‐first serial scanning hypothesis, which assumes that the PD might actually be an N2pc elicited when a lateral context item is selected. We tested this hypothesis by measuring lateralized ERP components to search displays with two lateral and two vertical midline items, including a color singleton and a shape‐defined target. Color singletons triggered PD components not only in blocks where attention was unfocused because target location was unpredictable, but critically also in blocks where targets only appeared on the midline and participants had no reason to attend to lateral items. This is inconsistent with the serial scanning hypothesis and supports the idea that the PD reflects signal suppression. PD components to singleton distractors were followed by a contralateral negativity, which we interpreted as a second PD elicited by nonsalient distractors on the opposite side. Our sequential inhibition account reconciles conflicting results of recent studies and emphasizes the role of inhibitory processes during attentional target selection in visual search.
Criteria for the recognition of clastic halite: The modern Dead Sea shoreline
Authors: Lowenstein Tim K. , Weldeghebriel Mebrahtu F. , Sirota Ido , Eyal Haggai , Mor Ziv , Lensky Nadav G.
Published: June 2021

Sedimentological studies of modern halites have focused on shallow water to subaerially‐exposed saline pans, where in‐place crystal growth, dissolution and cementation textures dominate. Clastic halite transported and deposited by waves and unidirectional currents as bedload is poorly known. This paper: (i) describes and interprets the diagnostic sedimentary features of clastic halite from a modern outcrop exposed along the north‐western coastline of the Dead Sea; and (ii) provides criteria for recognition of clastic halite in the rock record. The 2 m thick halite unit at Nahal Og was deposited within the last four decades at water depths <30 m as Dead Sea levels fell ca 30 m. Clastic halites consist of frameworks of sorted crystals with point contacts and no preferred growth fabrics. Halite cumulates, deposited as suspended load, precipitated in the water column and sank to the brine bottom. The excellent sorting and purity of halite crystal layers are unique to cumulates. Small‐scale ripple cross‐stratified thin beds and intraclast conglomerates were deposited from bedload. Halite bedload deposits (composed of halite flat pebbles, ooids, rafts, single clear crystals, cumulate crystals, mud intraclasts and rounded mudballs, foraminifera, gypsum) reflect wave transport and deposition via oscillatory flow above wave base, or by unidirectional flow in the breaker and surf zones. In addition, waves on the Dead Sea coast generate longshore currents. Thin beds produced by wave‐influenced oscillatory transport of halite are symmetrical in cross‐section. Less common cross‐stratified units with asymmetrical cross‐sections indicate unidirectional currents. Clastic halite, especially as a bedload deposit, has rarely been identified in ancient evaporites. Shoreline deposits from ancient halites, however, must contain wave‐reworked and current‐reworked layers and should be common in saline giants, given their enormous size and potential for generating waves and currents. Documentation of modern clastic halite may lead to a better understanding of ancient hypersaline environments on Earth.
Dynamic connectedness and spillovers across sectors: Evidence from the Indian stock market
Authors: Chatziantoniou Ioannis , Gabauer David , Marfatia Hardik A.
Published: June 2021

We investigate stock market sectoral connectedness in India utilizing a time‐varying parameter vector autoregressive connectedness approach. Results show that stock market sectoral connectedness varies across time. Connectedness is strongest during the 2008 crisis, the double‐digit inflation and stock market crash of 2011, following the national elections of 2014, and the demonetization of 2016. Among sectors, consumers' spending, industry, finance, and basic materials are net transmitters of shocks, while information technology, fast‐moving consumer goods, health care, and telecommunications are net receivers. Findings can help formulate policies that alleviate sectoral imbalances and promote balanced growth. They are also useful for devising optimal portfolio diversification strategies.
Behavior genetics research on personality: Moving beyond traits to examine characteristic adaptations
Authors: Nguyen Phuong Linh L. , Syed Moin , McGue Matt
Published: June 2021

This study argues that behavior genetics research on personality should expand beyond universal traits to include characteristic adaptations. Trait research examines broad, decontextualized, and universal domains such as the Five‐Factor Model. Characteristic adaptations are more contextualized than traits, such as goals and life strategies as responses to specific life demands. The study is organized into three sections: (1) a review of the abundance of behavior genetics research on personality traits, which has reached a convergent point at which few further findings are reported beyond the classic distribution of high genetic and non‐shared environmental influences with little to no shared environmental effect; (2) a review of existing behavior genetics research on characteristic adaptations that, although limited in volume, has demonstrated patterns far less consistent than traits; and (3) a discussion on future directions and important limitations to consider in conducting and interpreting behavior genetics research on non‐trait personality. The connection between characteristic adaptations and contextualized life outcomes, the preponderance of homogenous findings on traits, and the sparse yet promising findings of characteristic adaptations, all support the need for behavior genetics research on personality to expand beyond the broad trait level to characteristic adaptations and beyond.
An Advanced Fairy‐Tale Course: Text Selection, Assignments, and Student Feedback
Authors: Schenker Theresa
Published: June 2021

This article describes an advanced German course focusing on the German fairy‐tale tradition. Course components are summarized and the themes and selected fairy tales for each unit are outlined. Additionally, 12 creative assignments are explained that were designed to foster students’ engagement with the language and content of the fairy tales. The article also presents results from a feedback survey in which students summarized their reasons for taking the course, evaluated the individual course components, provided their perceptions of the assignments and course topics, and discussed the assignments’ perceived effects on the development of their advanced German skills. The student feedback can help instructors who are interested in creating a course on fairy tales understand students’ preferences for themes and assignments that best support student learning.
Fairy Tales and the Transmission of Prejudice
Authors: Helfer Martha B.
Published: June 2021

“Fairy Tales and the Transmission of Prejudice” is a unit in a lecture course on fairy tales that draws on research on anti‐Semitism in 18th‐ and 19th‐century German literature and culture, mapping questions raised in 18th‐ and 19th‐century tales onto contemporary issues: The unit traces a trajectory from the Enlightenment to the present, and from Germany to the United States, analyzing a variety of texts, including Lessing's drama Nathan the Wise (1779), the three Grimms’ tales about Jews – “The Clear Sun Will Bring it to Light” (1815), “The Jew in Thorns” (1815), and “The Good Bargain” (1819) –, Spiegelman's graphic Holocaust narrative Maus (1980), and Sendak's illustrations for Wilhelm Grimm's Dear Mili (Grimm & Sendak, 1988). This article outlines the course, its background, and how the texts and their contexts are implemented in class. Throughout the course unit, the discussion of anti‐Semitism in the fairy tales is broadened to one of prejudice in general. The article concludes with a brief discussion of student reactions to this unit.
A Conformable Two-Dimensional Resistance Temperature Detector for Measuring Average Skin Temperature
Authors: Namisnak Laura H. , Khoshnevis Sepideh , Diller Kenneth R.
Published: June 2021

Thermoregulation research and various medical procedures are accomplished by manipulating skin temperature in a nonuniform pattern. Skin temperature monitoring is essential to assess conformance to protocol specifications and to prevent thermal injury. Existing solutions for skin temperature monitoring include single point sensors, such as thermocouples, and two-dimensional methods of sensing surface temperature, such as infrared thermography, and wearable technology. Single point sensors cannot detect the average temperature and consequently their measurements cannot be representative of average surface temperature in a nonuniform temperature field. Infrared thermography requires optical access, and existing ambulatory sensors may require complex manufacturing processes and impede the heat exchange with a source by including a structural substrate layer. Our solution is a two-dimensional resistance temperature detector (two-dimensional (2D) RTD) created by knitting copper magnet wire into custom shapes. The 2D RTDs were calibrated, compared to one-dimensional sensors and wearable sensors, and analyzed for hysteresis, repeatability, and surface area conformation. Resistance and temperature were correlated with an R2 of 0.99. The 2D RTD proved to be a superior device for measuring average skin temperature over a defined area exposed to a nonuniform temperature boundary in the absence of optical access such as when a full body thermal control garment is worn.
Impact of Approximations in Operating History Data on Spent Fuel Properties With Serpent 2
Authors: Häkkinen Silja
Published: June 2021

In this work, the effect of averaging operating history parameters such as power history, boron concentration and coolant density, and temperature on spent nuclear fuel properties was investigated. The examined properties were assembly activity, decay heat, photon emission rate, spontaneous fission rate, and the concentration of some mobile nuclides and fissile nuclides. Calculations were performed on two similar VVER-440 fuel assemblies irradiated in different positions of the core using Serpent 2. Averaging power history over the entire irradiation history had a significant effect on assembly activity, decay heat, and photon emission rate overestimating these properties approximately 70% right after irradiation. However, the effect quickly died out and after 10 years of cooling, the effect was less than 1%. If the last cycle (third cycle) was modeled accurately and the power density of only the first two cycles was averaged, the differences remained always below 1%. The effect of operating history approximations on spontaneous fission rate and the nuclide concentrations was much smaller remaining mostly below 1.5%. The sensitivity of nuclide concentrations to approximations in individual operating history parameters was dependent on the nuclide in question and no trend applying to all studied nuclides could be observed.
Flow and Heat Transfer Simulation in a Complete Pressurized Water Reactor Fuel Assembly Using Wall-Modeled RANS
Authors: Mikuž B. , Roelofs F.
Published: June 2021

Reproduction of turbulent flow and heat transfer inside a pressurized water reactor (PWR) fuel assembly is a challenging task due to the complex geometry and the huge computational domain. Capability of a wall-modeled Reynolds-averaged Navier–Stokes (RANS) simulation approach has been examined, which had already been validated against the measurements of the MATiS-H experiment. The method is here expanded to a larger computational domain aiming to reproduce flow and thermal field in the entire PWR fuel assembly. Namely, in the first part of this study, wall-modeled RANS is performed in a relatively short section of the representative PWR fuel assembly containing one single mixing grid with an array of 15 × 15 fuel rods. Linear and nonlinear eddy-viscosity turbulence models have been applied; however no significant difference is observed in the predicted pressure drop in the fuel assembly. The obtained predictions revealed an interesting pattern of swirl flow as well as diagonal cross flow downstream the mixing grid, which is driven by the applied design of split-type mixing vanes. In the second part, the computational model is extended to a domain representative of a complete PWR fuel assembly with ten mixing grids, inlet and outlet sections. Pressure drop and flow field are analyzed together with the predicted temperature and potential hot spots. In spite of a relatively coarse spatial resolution of the applied approach, the wall-modeled RANS provided promising results at least for the qualitative prediction of the pressure, flow field, and location of hot spots.
Fabrication of Carbon Nanotube Gas Sensor Using Stepwise Dielectrophoretic Deposition Onto Interdigitated Pyrolyzed Carbon Electrodes
Authors: Singleton Taajza , Kulinsky Lawrence
Published: June 2021

Carbon nanotubes (CNTs) have been implemented in the creation of many micro- and nanodevices due to their physical properties such as large volume-to-surface area as well as their high thermal and electrical conductivity. The paper describes a novel dielectrophoretic stepwise deposition of CNTs (that alternates deposition of CNTs and drying steps) between the interdigitated fingers of carbon electrodes. Multiphysics simulation illustrates the physics of CNT alignment along the electrical field lines that forms a basis for dielectrophoretic deposition of CNTs. This fabrication methodology resulted in creation of proof-of-concept nitrogen gas sensor.
Aerodynamic Optimization of a Swept Horizontal Axis Wind Turbine Blade
Authors: Kaya Mehmet Numan , Köse Faruk , Uzol Oğuz , Ingham Derek , Ma Lin , Pourkashanian Mohamed
Published: June 2021

The aerodynamic shapes of the blades are still of high importance and various aerodynamic designs have been developed in order to increase the amount of energy production. In this study, a swept horizontal axis wind turbine blade has been optimized to increase the aerodynamic efficiency using the computational fluid dynamics method. To illustrate the technique, a wind turbine with a rotor diameter of 0.94 m has been used as the baseline turbine, and the most appropriate swept blade design parameters, namely the sweep start-up section, tip displacement, and mode of the sweep have been investigated to obtain the maximum power coefficient at the design tip speed ratio. At this stage, a new equation that allows all three swept blade design parameters to be changed independently has been used to design swept blades, and the response surface method has been used to find out the optimum swept blade parameters. According to the results obtained, a significant increase of 4.28% in the power coefficient was achieved at the design tip speed ratio with the newly designed optimum swept wind turbine blade. Finally, baseline and optimum swept blades have been compared in terms of power coefficients at different tip speed ratios, force distributions, pressure distributions, and tip vortices.
Fundamentals of CANDU Reactor Physics
Authors: Shen Wei , Rouben Benjamin
Published: June 2021

Nuclear Engineering and Technology for the 21st Century - Monograph Series

Jovica Riznic, Series Editor

With more than 75 years of combined working experience in the area of reactor physics and safety, the intention of the authors of this monograph is to provide a practical book on reactor physics, particularly for the safe operation of aged CANDU reactors, with minimal mathematics or equations. The book gives a glimpse of first principles and their engineering application in reactor physics, for those who are interested in or are working in the Canadian nuclear industry. The book is also ideal as a reference for physicists, operators, regulatory staff, and for those who need to interact with reactor physicists at CANDU sites, nuclear laboratories, institutes, universities, or engineering companies.

This book assumes prior knowledge of nuclear physics offered at the secondary level. As very few equations appear in the monograph, it is not considered suitable for specialists whose focus is only on calculations or on the development of software on reactor physics. Such readers should refer to the books listed in the bibliography at the end of the monograph.
Neutron Kinetics and Reactor Control
Authors: Shen Wei , Rouben Benjamin
Published: June 2021

A nuclear reactor is designed to achieve the very delicate balance between neutron “production” (release) in fission reactions and neutron loss by absorption and leakage. A given neutron will be “born” in a fission event and will then usually scatter about the reactor until it meets its eventual “death” either by being absorbed in some material or by leaking out of the reactor. A certain number of these neutrons will be absorbed by fissionable nuclei and induce further fissions, thereby leading to the birth of new fission neutrons, that is, to a new generation of neutrons. The ratio of the number of neutrons born in a fission-neutron generation to the number born in the previous generation is called the effective reactor multiplication factor, keff. The keff characterizes the balance or imbalance in the chain reaction. Alternatively, keff can be defined by the ratio of production rate to loss rate of neutrons in the reactor. These definitions are given below:
Performance and reliability of β-Ga2O3 Schottky barrier diodes at high temperature
Authors: Heinselman Karen , Walker Patrick , Norman Andrew , Parilla Philip , Ginley David , Zakutayev Andriy
Published: June 2021

Beta-gallium oxide (β-Ga2O3) is an ultrawide bandgap semiconductor that has potential for power electronic applications and devices operating at high temperatures. Particularly important for these applications are its 4.9 eV bandgap, facile electron doping, and the ability to grow β-Ga2O3 crystals from the melt. In this work, vertical β-Ga2O3 Schottky barrier diodes were fabricated using Pt Schottky and Ti-based Ohmic contacts and Au contact pads on unintentionally doped n-type, (2¯01)-oriented single crystal substrates. The diode’s temperature-dependent electrical properties up to 400 °C were investigated, and the Pt/Ga2O3 Schottky barrier height was determined to be close to 1.2 eV. The degradation of the contacts over multiple cycles up to 400 °C was observed, resulting in a significant increase in series resistance of the diodes by 1000× at ambient temperature after they were cycled. According to electron microscopy measurements, this degradation is likely due in part to the migration and oxidation of Ti at the top surface of the Au contact pads. This degradation highlights the need for further research and development to ensure stable Ohmic and Schottky contacts to Ga2O3 at temperatures above 400 °C.
State and Trait Fatigue and Energy Predictors of Postural Control and Gait
Authors: Kowalski Katie L. , Boolani Ali , Christie Anita D.
Published: June 2021

Compromised attentional resources during perceived fatigue has been suggested to alter motor control. The authors determined if measures of postural control and gait are predicted by state and trait physical and mental fatigue and energy, and how these relationships are modified by sex, sleep quality, and physical activity. Young adults (n = 119) completed the Modified Clinical Test of Sensory Integration, overground walking, and questionnaires to quantify fatigue and energy, sleep quality, and physical activity. Regression models indicated that trait fatigue, trait energy, and sleep quality were predictors of postural control (p ≤ .02, R2 ≥ .04). State fatigue, state energy, and sex were predictors of gait (p ≤ .05, R2 ≥ .03). While the variance explained was low (3–13%), the results demonstrate perceptions of fatigue and energy may influence posture and gait.
Molecular-scale spatio-chemical control of the activating-inhibitory signal integration in NK cells
Authors: Toledo Esti , Le Saux Guillaume , Edri Avishay , Li Long , Rosenberg Maor , Keidar Yossi , Bhingardive Viraj , Radinsky Olga , Hadad Uzi , Di Primo Carmelo , Buffeteau Thierry , Smith Ana-Sunčana , Porgador Angel , Schvartzman Mark
Published: June 2021

Molecular devices for the spatial control of activating and inhibitory receptors help in their signal integration.
Childhood cross-ethnic exposure predicts political behavior seven decades later: Evidence from linked administrative data
Authors: Brown Jacob R. , Enos Ryan D. , Feigenbaum James , Mazumder Soumyajit
Published: June 2021

Big data show that the liberalizing effect of racial diversity in childhood persists throughout a lifetime and even into old age.
Unlocking big data doubled the accuracy in predicting the grain yield in hybrid wheat
Authors: Zhao Yusheng , Thorwarth Patrick , Jiang Yong , Philipp Norman , Schulthess Albert W. , Gils Mario , Boeven Philipp H. G. , Longin C. Friedrich H. , Schacht Johannes , Ebmeyer Erhard , Korzun Viktor , Mirdita Vilson , Dörnte Jost , Avenhaus Ulrike , Horbach Ralf , Cöster Hilmar , Holzapfel Josef , Ramgraber Ludwig , Kühnle Simon , Varenne Pierrick , Starke Anne , Schürmann Friederike , Beier Sebastian , Scholz Uwe , Liu Fang , Schmidt Renate H. , Reif Jochen C.
Published: June 2021

Capitalizing on big data for wheat doubled the accuracy in predicting grain yield compared with current medium-sized datasets.
An inside look at a biofilm:
Pseudomonas aeruginosa
flagella biotracking
Authors: Ozer Eden , Yaniv Karin , Chetrit Einat , Boyarski Anastasya , Meijler Michael M. , Berkovich Ronen , Kushmaro Ariel , Alfonta Lital
Published: June 2021

P. aeruginosa
flagella are recorded across the entire biofilm life cycle as likely biofilm structural scaffolds.
Aztreonam-Avibactam Susceptibility Testing Program for Metallo-Beta-Lactamase-Producing
Enterobacterales
in the Antibiotic Resistance Laboratory Network, March 2019 to December 2020
Authors: Bhatnagar Amelia , Boyd Sandra , Sabour Sarah , Bodnar Janine , Nazarian Elizabeth , Peinovich Nadine , Wagner Christine , Craft Bradley , Snippes Vagnone Paula , Simpson Justin , Stone Victoria N. , Therrien Michelle , Bateman Allen , Lower Danielle , Huang Jennifer Y. , Gumbis Stephanie , Lonsway David , Lutgring Joseph D. , Karlsson Maria , Brown Allison C.
Published: June 2021

Aztreonam-avibactam is a drug combination pending phase 3 clinical trials and is suggested for treatment of severe infections caused by metallo-beta-lactamase (MBL)-producing
Enterobacterales
by combining ceftazidime-avibactam and aztreonam. Beginning in 2019, four Antibiotic Resistance Laboratory Network regional laboratories offered aztreonam-avibactam susceptibility testing by broth microdilution.
Trichoderma reesei
ACE4, a Novel Transcriptional Activator Involved in the Regulation of Cellulase Genes during Growth on Cellulose
Authors: Chen Yumeng , Lin Aibo , Liu Pei , Fan Xingjia , Wu Chuan , Li Ni , Wei Liujing , Wang Wei , Wei Dongzhi
Published: June 2021

T. reesei
is commonly utilized in industry to produce cellulases, enzymes that degrade lignocellulosic biomass for the production of bioethanol and bio-based products.
T. reesei
is capable of rapidly initiating the biosynthesis of cellulases in the presence of cellulose, which has made it useful as a model fungus for studying gene expression in eukaryotes. Cellulase gene expression is controlled through multiple transcription factors at the transcriptional level.
Molecular Insights into the Copper-Sensitive Operon Repressor in Acidithiobacillus caldus
Authors: Hou Shaoxiang , Tong Yanjun , Yang Hailin , Feng Shoushuai
Published: June 2021

Research on copper resistance among various species has attracted considerable interest. However, due to the lack of effective and reproducible genetic tools, few studies regarding copper resistance have been reported for
A. caldus
.
Functional Analysis of Deoxyhexose Sugar Utilization in Escherichia coli Reveals Fermentative Metabolism under Aerobic Conditions
Authors: Millard Pierre , Pérochon Julien , Létisse Fabien
Published: June 2021

E. coli
’s ability to survive in, grow in, and colonize the gastrointestinal tract stems from its use of partially digested food and hydrolyzed glycosylated proteins (mucins) from the intestinal mucus layer as substrates. These include
l
-fucose and
l
-rhamnose, two 6-deoxyhexose sugars, whose catabolic pathways have been established by genetic and biochemical studies.
Practical Guidance for Clinical Microbiology Laboratories: Diagnosis of Ocular Infections
Authors: Leal Sixto M. , Rodino Kyle G. , Fowler W. Craig , Gilligan Peter H.
Published: June 2021

The variety and complexity of ocular infections have increased significantly in the last decade since the publication ofCumitech 13B,Laboratory Diagnosis of Ocular Infections(L. D. Gray, P. H. Gilligan, and W. C. Fowler,Cumitech 13B,Laboratory Diagnosis of Ocular Infections, 2010). The purpose of this practical guidance document is to review, for individuals working in clinical microbiology laboratories, current tools used in the laboratory diagnosis of ocular infections.
Mobile Oxazolidinone Resistance Genes in Gram-Positive and Gram-Negative Bacteria
Authors: Schwarz Stefan , Zhang Wanjiang , Du Xiang-Dang , Krüger Henrike , Feßler Andrea T. , Ma Shizhen , Zhu Yao , Wu Congming , Shen Jianzhong , Wang Yang
Published: June 2021

Seven mobile oxazolidinone resistance genes, including
cfr
,
cfr
(B),
cfr
(C),
cfr
(D),
cfr
(E),
optrA
, and
poxtA
, have been identified to date. The
cfr
genes code for 23S rRNA methylases, which confer a multiresistance phenotype that includes resistance to phenicols, lincosamides, oxazolidinones, pleuromutilins, and streptogramin A compounds. The
optrA
and
poxtA
genes code for ABC-F proteins that protect the bacterial ribosomes from the inhibitory effects of oxazolidinones.
Framing Bacterial Genomics for Public Health (Care)
Authors: Halpin Alison Laufer , McDonald L. Clifford , Elkins Christopher A.
Published: June 2021

Advancements in comparative genomics have generated significant interest in defining applications for health care-associated pathogens. Clinical microbiology, however, relies on increasingly automated platforms to quickly identify pathogens, resistance mechanisms, and therapy options within Clinical Laboratory Improvement Amendments (CLIA)- and FDA-approved frameworks.
Evaluation of the Diagnostic Performance of a Semiquantitative Cryptococcal Antigen Point-of-Care Assay among HIV-Infected Persons with Cryptococcal Meningitis
Authors: Tadeo Kiiza Kandole , Nimwesiga Audrey , Kwizera Richard , Apeduno Lucy , Martyn Emily , Okirwoth Michael , Nalintya Elizabeth , Rajasingham Radha , Williams Darlisha A. , Rhein Joshua , Meya David B. , Kafufu Bosco , Boulware David R. , Skipper Caleb P.
Published: June 2021

A newly developed cryptococcal antigen (CrAg) semiquantitative (SQ) lateral flow assay (LFA) provides a semiquantitative result in a rapid one-step test instead of performing serial dilutions to determine CrAg titer. We prospectively compared the diagnostic performance of the CrAgSQ assay (IMMY) with the CrAg LFA (IMMY) on cerebrospinal fluid (CSF) samples collected from persons with HIV-associated meningitis.
Tree Shrew Cells Transduced with Human CD4 and CCR5 Support Early Steps of HIV-1 Replication, but Viral Infectivity Is Restricted by APOBEC3
Authors: Luo Meng-Ting , Mu Dan , Yang Xiang , Luo Rong-Hua , Zheng Hong-Yi , Chen Min , Guo Ying-Qi , Zheng Yong-Tang
Published: June 2021

The development of animal models is critical for studying human diseases and their pathogenesis and for evaluating drug and vaccine efficacy. For improved AIDS research, the ideal animal model of HIV-1 infection should be a small laboratory mammal that closely mimics virus replication in humans.
Genome Scale Analysis Reveals IscR Directly and Indirectly Regulates Virulence Factor Genes in Pathogenic
Yersinia
Authors: Balderas David , Mettert Erin , Lam Hanh N. , Banerjee Rajdeep , Gverzdys Tomas , Alvarez Pablo , Saarunya Geetha , Tanner Natasha , Zoubedi Adam , Wei Yahan , Kiley Patricia J. , Auerbuch Victoria
Published: June 2021

How bacteria adapt to the changing environment within the host is critical for their ability to survive and cause disease. For example, the mammalian host severely restricts iron availability to limit bacterial growth, referred to as nutritional immunity.
Obesity-Related Gut Microbiota Aggravates Alveolar Bone Destruction in Experimental Periodontitis through Elevation of Uric Acid
Authors: Sato Keisuke , Yamazaki Kyoko , Kato Tamotsu , Nakanishi Yumiko , Tsuzuno Takahiro , Yokoji-Takeuchi Mai , Yamada-Hara Miki , Miura Nobuaki , Okuda Shujiro , Ohno Hiroshi , Yamazaki Kazuhisa
Published: June 2021

Obesity is an epidemic health issue with a rapid increase worldwide. It increases the risk of various diseases, including periodontal disease, an oral chronic infectious disease.
Bioenergetic Heterogeneity in Mycobacterium tuberculosis Residing in Different Subcellular Niches
Authors: Akela Ajit Kumar , Kumar Ashwani
Published: June 2021

ATP/ADP levels guide bacterial cells, whether to replicate or to enter nonreplicating persistence. However, tools for measuring ATP/ADP levels with spatiotemporal resolution are lacking.
A Prevalent Focused Human Antibody Response to the Influenza Virus Hemagglutinin Head Interface
Authors: McCarthy Kevin R. , Lee Jiwon , Watanabe Akiko , Kuraoka Masayuki , Robinson-McCarthy Lindsey R. , Georgiou George , Kelsoe Garnett , Harrison Stephen C.
Published: June 2021

The rapid appearance of mutations in circulating human influenza viruses and selection for escape from herd immunity require prediction of likely variants for an annual updating of influenza vaccines. The identification of human antibodies that recognize conserved surfaces on the influenza virus hemagglutinin (HA) has prompted efforts to design immunogens that might selectively elicit such antibodies.
GP96 Drives Exacerbation of Secondary Bacterial Pneumonia following Influenza A Virus Infection
Authors: Sumitomo Tomoko , Nakata Masanobu , Nagase Satoshi , Takahara Yuki , Honda-Ogawa Mariko , Mori Yasushi , Akamatsu Yukako , Yamaguchi Masaya , Okamoto Shigefumi , Kawabata Shigetada
Published: June 2021

Secondary bacterial pneumonia following an influenza A virus (IAV) infection is a major cause of morbidity and mortality. Although it is generally accepted that preceding IAV infection leads to increased susceptibility to secondary bacterial infection, details regarding the pathogenic mechanism during the early stage of superinfection remain elusive.
Human Gut Faecalibacterium prausnitzii Deploys a Highly Efficient Conserved System To Cross-Feed on β-Mannan-Derived Oligosaccharides
Authors: Lindstad Lars J. , Lo Galiana , Leivers Shaun , Lu Zijia , Michalak Leszek , Pereira Gabriel V. , Røhr Åsmund K. , Martens Eric C. , McKee Lauren S. , Louis Petra , Duncan Sylvia H. , Westereng Bjørge , Pope Phillip B. , La Rosa Sabina Leanti
Published: June 2021

Commensal butyrate-producing bacteria belonging to the
Firmicutes
phylum are abundant in the human gut and are crucial for maintaining health. Currently, insight is lacking into how they target otherwise indigestible dietary fibers and into the trophic interactions they establish with other glycan degraders in the competitive gut environment.
Closing Clostridium botulinum Group III Genomes Using Long-Read Sequencing
Authors: Woudstra Cedric , Mäklin Tommi , Derman Yagmur , Bano Luca , Skarin Hanna , Mazuet Christelle , Honkela Antti , Lindström Miia
Published: June 2021

Clostridium botulinum
group III is the anaerobic Gram-positive bacteria producing the deadly neurotoxin responsible for animal botulism. Here, we used long-read sequencing to produce four complete genomes from
Clostridium botulinum
group III neurotoxin types C, D, C/D, and D/C. The protocol to obtain high-molecular-weight DNA from
C. botulinum
group III is described.
Transcription Repressor Protein ZBTB25 Associates with HDAC1-Sin3a Complex in Mycobacterium tuberculosis-Infected Macrophages, and Its Inhibition Clears Pathogen by Autophagy
Authors: Madhavan Aravind , Arun K. B. , Pushparajan Akhil Raj , Balaji M. , Kumar Ramakrishnan Ajay
Published: June 2021

Following infection with
M. tuberculosis
, levels of HDAC1 go up in macrophages, and it is recruited to the promoter of
IL-12B
where it hypoacetylates histone H3, leading to the downregulation of the gene. Here, we show that host transcriptional repressor protein ZBTB25 and transcriptional corepressor Sin3a associate with HDAC1 in the silencing complex.
First IncHI2 Plasmid Carrying
mcr-9.1
,
bla
VIM-1
, and Double Copies of
bla
KPC-3
in a Multidrug-Resistant Escherichia coli Human Isolate
Authors: Simoni Serena , Mingoia Marina , Brenciani Andrea , Carelli Maria , Lleò Maria M. , Malerba Giovanni , Vignaroli Carla
Published: June 2021

We report a novel IncHI2 plasmid coharboring
bla
VIM-1
, two copies of
bla
KPC-3
and
mcr-9.1
resistance genes in a human
Escherichia coli
of the new serogroup O188. The
bla
VIM-1
gene was included in a class 1 integron,
mcr-9.1
in a cassette bracketed by IS
903
and ΔIS1R, and
bla
KPC-3
in two copies within a new composite Tn
4401
-like transposon. The emergence of carbapenem and colistin resistance genes in a single plasmid is of great concern for upcoming clinical therapies.
The
higBA-
Type Toxin-Antitoxin System in IncC Plasmids Is a Mobilizable Ciprofloxacin-Inducible System
Authors: Qi Qin , Kamruzzaman Muhammad , Iredell Jonathan R.
Published: June 2021

Toxin-antitoxin (TA) systems play vital roles in maintaining plasmids in bacteria. Plasmids with incompatibility group C are large plasmids that disseminate via conjugation and carry high-profile antibiotic resistance genes.
Temporal Changes of Virus-Like Particle Abundance and Metagenomic Comparison of Viral Communities in Cropland and Prairie Soils
Authors: Cornell Carolyn R. , Zhang Ya , Van Nostrand Joy D. , Wagle Pradeep , Xiao Xiangming , Zhou Jizhong
Published: June 2021

Conversion of land alters the physiochemical and biological environments by not only changing the aboveground community, but also modifying the soil environment for viruses and microbes. Soil microbial communities are critical to nutrient cycling, carbon mineralization, and soil quality; and viruses are known for influencing microbial abundance, community structure, and evolution.
Chromatin-Associated Protein Complexes Link DNA Base J and Transcription Termination in
Leishmania
Authors: Jensen Bryan C. , Phan Isabelle Q. , McDonald Jacquelyn R. , Sur Aakash , Gillespie Mark A. , Ranish Jeffrey A. , Parsons Marilyn , Myler Peter J.
Published: June 2021

Leishmania
parasites cause a variety of serious human diseases, with no effective vaccine and emerging resistance to current drug therapy. We have previously shown that a novel DNA base called J is critical for transcription termination at the ends of the polycistronic gene clusters that are a hallmark of
Leishmania
and related trypanosomatids.
Genomic Determinants Encode the Reactivity and Regioselectivity of Flavin-Dependent Halogenases in Bacterial Genomes and Metagenomes
Authors: Jeon Jehyun , Lee Jaehee , Jung Se-Min , Shin Jae Hong , Song Woon Ju , Rho Mina
Published: June 2021

Halogenases are playing an important role as tailoring enzymes in biosynthetic pathways. Flavin-dependent tryptophan halogenases (Trp-FDHs) are among the enzymes that have broad substrate scope and high selectivity.
Microbiome Aggregated Traits and Assembly Are More Sensitive to Soil Management than Diversity
Authors: Neal Andrew L. , Hughes David , Clark Ian M. , Jansson Janet K. , Hirsch Penny R.
Published: June 2021

Changes in soil microbiome diversity and function brought about by land management are predicted to influence a range of environmental services provided by soil, including provision of food and clean water. However, opportunities to compare the long-term effects of combinations of stresses imposed by different management approaches are limited.
Supplemental Material: Anoxic depositional overprinting of 238U/235U in calcite: When do carbonates tell black shale tales?
Authors: Chen Xinming , al. et
Published: June 2021

Details of methods and a data summary.
Supplemental Material: Phanerozoic record of mantle-dominated arc magmatic surges in the Zealandia Cordillera
Authors: Ringwood Mary , Schwartz Joshua J. , al. et
Published: June 2021

Detailed analytical methods and U-Pb zircon geochronology results, zircon cathodoluminescence images, Tera-Wasserburg plots, and tables containing igneous and detrital zircon data and volume addition rate calculations.
Transmission of Microwaves through the Composite Material with Fe–Si–Nb–Cu–B Alloy Particles
Authors: Rinkevich A. B. , Ryabkov Yu. I. , Perov D. V. , Pakhomov Ya. A. , Kuznetsov E. A.
Published: June 2021

The transmission of electromagnetic waves through the samples of the composite material containing Fe–Si–Nb–Cu–B alloy particles with a size of up to 50 µm was studied. The dependences of the transmission and reflection ratio on the magnetic field were measured at frequencies from 12 to 38 GHz. The dependence of the effective magnetic permeability on the magnetic field was determined, and the complex refractive index was calculated. The frequency dependence of maximum values was investigated for the real and imaginary parts of this index.
Functional Diversity of Morphologically Similar Digestive Organs in Muroidea Species
Authors: Naumova E. I. , Chistova T. Yu. , Varshavskii A. A. , Zharova G. K.
Published: June 2021

We examine possible ways of functional adjustment of morphologically similar alimentary tracts in rodents with different dietary specializations. We study the structure of stomach and gut epithelial surface as well as the features of its colonization with microorganisms in five gerbil species:Psammomys obesus, Meriones crassus, Gerbillus henleyi, G. andersoni, andG. dasyurus. Data on the morphological diversity of mucosa-associated microbiota have been obtained and confirmed by the results of previous microbiology studies. Species differences in chymus acidity associated with dietary specialization have been determined. Variations in the activity of the endoglucanase microbial enzyme, which is crucial for rodents fed on cellulose-containing food, have also been detected. The importance of microbiota for functional adaptations to various food types in rodents with morphologically similar digestive tracts has been evaluated.
Image-guided intervention in the management of chronic patellar tendinopathy with calcification: a three-pronged approach
Authors: Butt Aqeel , Umaskanth Neelan , Sahu Ajay
Published: June 2021

Patellar tendinopathy is a common cause of knee pain and functional impairment in athletes. It is commonly managed using conservative measures such as physiotherapy, but cases that are refractory to such treatment may require a more invasive approach. Various forms of image-guided injection therapy have been described in the literature. We present a case of successful treatment of chronic patellar tendinopathy with calcification with the first reported use of a three-pronged image-guided approach, consisting of dry needling, high volume image-guided injection (but at a reduced dose) and barbotage applied in a single sitting. The patient reported resolution of symptoms persisting to 1 year postprocedure. We suggest that this management option, if supported by further positive research findings, could be used in the future in the management of certain cases of patellar tendinopathy with calcification where conservative measures have failed.
Primary neuroendocrine tumours of the heart: case report and literature review
Authors: Altshuler Ellery , Saker Haneen , Ramnaraign Brian
Published: June 2021

Neuroendocrine tumours occur most frequently in the gastrointestinal tract, lungs, and pancreas. Primary malignant cardiac tumours are uncommon and are usually sarcomas, lymphomas, or, infrequently, mesotheliomas. Primary cardiac neuroendocrine carcinomas are exceedingly rare; only nine have been reported in the literature to date. We report the tenth case of this disorder in a 44-year-old man with a well-differentiated low-grade primary cardiac neuroendocrine carcinoma treated with surgery who remains in remission more than a year later. Our case and review of the literature demonstrate that surgical treatment for well-differentiated primary cardiac neuroendocrine carcinomas can be effective.
Unusual source of recurrent Corynebacterium bacteraemia in an immunocompromised patient
Authors: Bakhsh Abdul Rahim Ali , Lewis Keir Edward
Published: June 2021

We describe a unique case of a patient with acute myeloid leukaemia (AML), with recurring infections during chemotherapy from chronic nasal carriage of non-diphtherial Corynebacterium, who was eventually diagnosed as she presented with neutropaenic sepsis. Identifying (often multiple) sources of infection in immunocompromised patients is crucial but deciding whether multiple organisms, which in health are considered as commensals, are actually pathogenic during vulnerable states—can be clinically difficult. Our case highlights the efforts to correctly identify the actual source of this rare organism and the recognition of its pathogenic potential when other illnesses present. We also review the literature of Corynebacteria in patients with haematological malignancies but believe this is the first case of AML to be infected with Corynebacterium presenting during the COVID-19 pandemic with a probable incidental positive swab for SARS-CoV-2.
Pneumocephalus with meningitis secondary to an old traumatic anterior cranial fossa defect
Authors: Sirur Freston Marc , Daswaney Akash , Raghu Roshini , Khalid Mohammad
Published: June 2021

We report a case of a 30-year-old man who presented with altered mental status, fever, headache and vomiting for 3 days. An initial CT scan of the brain revealed the presence of pneumocephalus with a bony defect in the anterior cranial fossa. The pneumocephalus was not explained initially and the patient was re-examined for any signs of trauma to the face, and a review of the history revealed a series of three traumatic events months prior to this illness. Further laboratory studies revealedStreptococcus pneumoniaein the blood and bacterial meningitis. He was treated with antibiotics and was later taken up for endoscopic repair of the skull base defect. This case highlights the importance of recognising post-traumatic pneumocephalus with superimposed meningitis and sepsis months after a traumatic event to the skull base.
Development of a predictive risk model for all-cause mortality in patients with diabetes in Hong Kong
Authors: Lee Sharen , Zhou Jiandong , Leung Keith Sai Kit , Wu William Ka Kei , Wong Wing Tak , Liu Tong , Wong Ian Chi Kei , Jeevaratnam Kamalan , Zhang Qingpeng , Tse Gary
Published: June 2021

Introduction

Patients with diabetes mellitus are risk of premature death. In this study, we developed a machine learning-driven predictive risk model for all-cause mortality among patients with type 2 diabetes mellitus using multiparametric approach with data from different domains.

Research design and methods

This study used territory-wide data of patients with type 2 diabetes attending public hospitals or their associated ambulatory/outpatient facilities in Hong Kong between January 1, 2009 and December 31, 2009. The primary outcome is all-cause mortality. The association of risk variables and all-cause mortality was assessed using Cox proportional hazards models. Machine and deep learning approaches were used to improve overall survival prediction and were evaluated with fivefold cross validation method.

Results

A total of 273 678 patients (mean age: 65.4±12.7 years, male: 48.2%, median follow-up: 142 (IQR=106–142) months) were included, with 91 155 deaths occurring on follow-up (33.3%; annualized mortality rate: 3.4%/year; 2.7 million patient-years). Multivariate Cox regression found the following significant predictors of all-cause mortality: age, male gender, baseline comorbidities, anemia, mean values of neutrophil-to-lymphocyte ratio, high-density lipoprotein-cholesterol, total cholesterol, triglyceride, HbA1c and fasting blood glucose (FBG), measures of variability of both HbA1c and FBG. The above parameters were incorporated into a score-based predictive risk model that had a c-statistic of 0.73 (95% CI 0.66 to 0.77), which was improved to 0.86 (0.81 to 0.90) and 0.87 (0.84 to 0.91) using random survival forests and deep survival learning models, respectively.

Conclusions

A multiparametric model incorporating variables from different domains predicted all-cause mortality accurately in type 2 diabetes mellitus. The predictive and modeling capabilities of machine/deep learning survival analysis achieved more accurate predictions.