bluuebunny/crossref_metadata_2025 huggingface dataset:
Emerging zoonotic diseases originating in mammals: a systematic review of effects of anthropogenic land‐use change
Authors: White Rebekah J. , Razgour Orly
Published: June 2020

Zoonotic pathogens and parasites that are transmitted from vertebrates to humans are a major public health risk with high associated global economic costs. The spread of these pathogens and risk of transmission accelerate with recent anthropogenic land‐use changes (LUC) such as deforestation, urbanisation, and agricultural intensification, factors that are expected to increase in the future due to human population expansion and increasing demand for resources.

We systematically review the literature on anthropogenic LUC and zoonotic diseases, highlighting the most prominent mammalian reservoirs and pathogens, and identifying avenues for future research.

The majority of studies were global reviews that did not focus on specific taxa. South America and Asia were the most‐studied regions, while the most‐studied LUC was urbanisation. Livestock were studied more within the context of agricultural intensification, carnivores with urbanisation and helminths, bats with deforestation and viruses, and primates with habitat fragmentation and protozoa.

Research into specific animal reservoirs has improved our understanding of how the spread of zoonotic diseases is affected by LUC. The behaviour of hosts can be altered when their habitats are changed, impacting the pathogens they carry and the probability of disease spreading to humans. Understanding this has enabled the identification of factors that alter the risk of emergence (such as virulence, pathogen diversity, and ease of transmission). Yet, many pathogens and impacts of LUC other than urbanisation have been understudied.

Predicting how zoonotic diseases emerge and spread in response to anthropogenic LUC requires more empirical and data synthesis studies that link host ecology and responses with pathogen ecology and disease spread. The link between anthropogenic impacts on the natural environment and the recent COVID‐19 pandemic highlights the urgent need to understand how anthropogenic LUC affects the risk of spillover to humans and spread of zoonotic diseases originating in mammals.
The majority of the matrix protein TapA is dispensable for Bacillus subtilis colony biofilm architecture
Authors: Earl Chris , Arnaouteli Sofia , Bamford Natalie C. , Porter Michael , Sukhodub Tetyana , MacPhee Cait E. , Stanley‐Wall Nicola R.
Published: June 2020

Biofilm formation is a co‐operative behaviour, where microbial cells become embedded in an extracellular matrix. This biomolecular matrix helps manifest the beneficial or detrimental outcome mediated by the collective of cells. Bacillus subtilis is an important bacterium for understanding the principles of biofilm formation. The protein components of the B. subtilis matrix include the secreted proteins BslA, which forms a hydrophobic coat over the biofilm, and TasA, which forms protease‐resistant fibres needed for structuring. TapA is a secreted protein also needed for biofilm formation and helps in vivo TasA‐fibre formation but is dispensable for in vitro TasA‐fibre assembly. We show that TapA is subjected to proteolytic cleavage in the colony biofilm and that only the first 57 amino acids of the 253‐amino acid protein are required for colony biofilm architecture. Through the construction of a strain which lacks all eight extracellular proteases, we show that proteolytic cleavage by these enzymes is not a prerequisite for TapA function. It remains unknown why TapA is synthesised at 253 amino acids when the first 57 are sufficient for colony biofilm structuring; the findings do not exclude the core conserved region of TapA having a second role beyond structuring the B. subtilis colony biofilm.
Relationship between the location of ligamentum flavum hypertrophy and its stress in finite element analysis
Authors: Peng Yong‐xing , Zheng Zhen‐yu , Wang, MD Wei‐guo , Liu Lin , Chen, MD Feng , Xu, MD Hong‐tao , Zhang Zhong‐min
Published: June 2020

Objective

To quantitatively describe the stress of the ligamentum flavum (LF) using the finite element method and to compare the stress at different parts of the healthy LF.

Methods

Based on the high resolution computed tomography imaging data of a healthy 22‐year‐old man, three‐dimensional nonlinear L4–5 lumbar finite element model (FEM) representing intact condition was developed. The LF, as the object of the present research, was incorporated into the spinal model in the form of solid three‐dimensional structure. The model’s validity is verified by comparing its biomechanical indices, such as range of motion and axial compression pressure displacement, with published results under specific loading conditions. To authenticate the accuracy of the solid LF, the lamina attachments, the central cross‐section, and other anatomy indicators were compared with figures in the published literature. After the average and maximum von Mises stress on the surface of LF under various working conditions were measured using ANSYS and AutoCAD software, the surface stress difference in the LF between the ventral and dorsal sides as well as the lateral and lamina parts were determined.

Results

The FEM predicted a similar tendency for biomechanical indices as shown in previous studies. The lamina attachments, the central cross‐section, and the height as well as the width of the LF in the healthy FEM were in accordance with published results. In the healthy model, the average and maximum von Mises stress in the shallow layer of the LF were, respectively, 1.40, 2.28, 1.76, 1.48, 1.38 and 1.79, 2.41, 1.46, 1.42, 1.71 times that in the deep layer under a compressive preload of 500 N incorporated with flexion, extension, and lateral and rotational moments (10 Nm). The most conspicuous difference in surface stress was observed with the flexion motion, with a nearly 241% difference in the maximum stress and a 228% difference in the average stress compared to those in other states. As far as the whole dorsal side of the LF was concerned, the maximum surface stress was almost all concentrated in the dorsal neighboring facet joint portion. In addition, the maximum and average stress were, respectively, 77%, 72%, 15%, 11%, 71% and 153%, 39%, 54%, 200%, 212% higher in the lateral part than in the lamina part.

Conclusion

Based on the predisposition of LF hypertrophy in the human spine and the stress distribution of this study, the positive correlation between LF hypertrophy and its stress was confirmed.
When the Other‐Mind Skepticism Encounters the Happy Fish
Authors: Hou Richard W. T. , Wang Linton
Published: June 2020

In this paper, we reconstruct the debate between Zhuangzi 莊子 and Hui Shi 惠施 that took place on the bridge over the Hao River 濠水 as a substantive debate concerning the epistemic other‐mind skepticism according to which no one mind knows the mental states of the other. We demonstrate how this reconstruction leads to substantive conclusions of the viability of Hui Shi’s position in particular and of the other‐mind skepticism in general. This demonstration is accomplished by means of the contemporary philosophical development regarding, for example, whether asserting a proposition implies that the asserter knows the proposition, whether the closure principle of epistemic logic should be held, and whether knowing something is a mental state. We hold that this debate’s resolution is substantively entangled with contemporary philosophical concerns.
The potential for Fusarium oxysporum f. sp. fragariae, cause of fusarium wilt of strawberry, to colonize organic matter in soil and persist through anaerobic soil disinfestation
Authors: Henry Peter M. , Haugland Megan , Lopez Lia , Munji Mariel , Watson Dean C. , Gordon Thomas R.
Published: June 2020

Fusarium wilt of strawberry, caused by Fusarium oxysporum f. sp. fragariae, is a disease of primary concern for strawberry production in many countries. Crop rotation and anaerobic soil disinfestation (ASD) have gained recent interest for their potential to contribute to management of this disease. Both techniques involve incorporation of organic matter into soil, which may be utilized by strains of Fusarium that are competitive saprophytes. We show that F. oxysporum f. sp. fragariae can colonize strawberry, lettuce, raspberry, and broccoli leaf tissues, which are sources of organic matter generated during crop rotation. This pathogen increased in soil population density during ASD treatments that did not become anaerobic, possibly as a result of growth on the organic amendment. However, significant population decreases were observed after ASD treatment when at least 100,000 cumulative reduced mV hours occurred in a 14‐day experiment. Post‐ASD abundance of F. oxysporum f. sp. fragariae in soil was negatively correlated with cumulative reduced mV hours. The only treatment that consistently caused disinfestation was exposed to a maximum temperature of 22 °C, which indicates there is potential for developing effective ASD treatments in the cool climates where strawberries are grown. Awareness that F. oxysporum f. sp. fragariae can act as a competitive soil saprophyte should be further investigated for its potential to alter disease outcomes where organic amendments are applied.
Neurodevelopmental findings in children 20‐30 months of age with postnatal Zika infection at 1‐12 months of age, Colombia, September‐November 2017
Authors: Pacheco Oscar , Newton Suzanne M. , Daza Marcela , Cates Jordan E. , Reales Javier Alberto Madero , Burkel Veronica K. , Mercado Marcela , Godfred‐Cato Shana , Gonzalez Maritza , Anderson Kayla N. , Woodworth Kate R. , Valencia Diana , Tong Van T. , Gilboa Suzanne M. , Osorio May Bibiana , Rodríguez Dora Yurany Sánchez , Prieto‐Alvarado Franklyn Edwin , Moore Cynthia A. , Honein Margaret A. , Ospina Martínez Martha L.
Published: June 2020

Background

Zika virus (ZIKV) infection during pregnancy can cause infant brain and eye abnormalities and has been associated with adverse neurodevelopmental outcomes in exposed infants. Evidence is limited on ZIKV’s effects on children infected postnatally within the first year of life.

Objective

To determine whether any adverse neurodevelopmental outcomes occurred in early childhood for children infected postnatally with ZIKV during infancy, given the neurotoxicity of ZIKV infection and the rapid brain development that occurs in infancy and early childhood.

Methods

The Colombia Instituto Nacional de Salud (INS) conducted health and developmental screenings between September and November 2017 to evaluate 60 children at ages 20‐30 months who had laboratory‐confirmed symptomatic postnatal ZIKV infection at ages 1‐12 months. We examined the frequency of adverse neurologic, hearing, eye, and developmental outcomes as well as the relationship between age at Zika symptom onset and developmental outcomes.

Results

Nine of the 60 (15.0%) children had adverse outcomes on the neurologic, hearing, or eye examination. Six of the 47 (12.8%) children without these adverse findings, and who received a valid developmental screening, had an alert score in the hearing‐language domain which signals the need for additional developmental evaluation.

Conclusion

Neurologic, hearing, eye, and developmental findings suggest reassuring results. Since the full spectrum of neurodevelopmental outcomes in children postnatally infected with ZIKV remains unknown, routine paediatric care is advised to monitor the development of these children to ensure early identification of any adverse neurodevelopmental outcomes.
Non‐uniform distribution of passive muscle stiffness within hamstring
Authors: Miyamoto Naokazu , Kimura Noriko , Hirata Kosuke
Published: June 2020

Limited information is available on whether stiffness is different within and between the constituents of the hamstring, that is, the biceps femoris long head (BFlh), semitendinosus (ST), and semimembranosus (SM). Therefore, understanding of hamstring injuries and stretching effect on hamstring stiffness is difficult. The present study primarily aimed to identify whether passive muscle stiffness differs between the BFlh, ST, and SM and between the proximal, middle, and distal sites within each muscle. Secondly, the effect of stretching exercise on the heterogeneity in passive muscle stiffness was examined. In the lengthened hamstring positions by extending the knee joint or flexing the hip joint, passive muscle shear modulus (a measure of stiffness) at the proximal, middle, and distal sites of the BFlh, ST, and SM was measured by using ultrasound shear wave elastography. Furthermore, before and after five repetitions of 90‐seconds static stretching for the hamstring, passive muscle shear modulus at the proximal and distal sites of the SM was measured. The shear modulus was significantly higher in the SM than in the BFlh and ST and higher at the distal site than the proximal site in all muscles. After the stretching, the higher shear modulus at the distal site of the SM compared to the proximal site was still observed (pre‐stretching: +80%, post‐stretching: +81%). These findings indicate that passive muscle stiffness varies within the hamstring regardless of performing stretching exercise and that passive muscle stiffness is not highest at the proximal site of the SM where a stretching‐type hamstring strain typically occurs.
The epidemiology of kicking injuries in professional Rugby Union: A 15‐season prospective study
Authors: Lazarczuk Stephanie L. , Love Thomas , Cross Matthew J. , Stokes Keith A. , Williams Sean , Taylor Aileen E. , Fuller Colin W. , Brooks John H. M. , Kemp Simon P. T. , Bezodis Neil E.
Published: June 2020

Purpose

While kicking in Rugby Union can be influential to match outcome, the epidemiology of kicking injuries remains unknown. This study therefore aimed to investigate the epidemiology of injuries attributed to kicking in professional rugby, including playing position‐specific effects and differences in kicking volumes and kick types.

Methods

Fifteen seasons of injury surveillance data and two seasons of match kicking characteristics from professional rugby players were analyzed. Incidence, propensity, and severity of kicking‐related injuries were calculated together with the locations and types of these injuries. Position‐related differences in match kicking types and volumes were also established.

Results

Seventy‐seven match and 55 training acute‐onset kicking injuries were identified. The match kicking injury incidence for backs was 1.4/1000 player‐match‐hours. Across all playing positions, the propensity for match kicking injury was 0.57 injuries/1000 kicks. Fly‐halves sustained the greatest proportion of match kicking injuries (47%) and performed the greatest proportion of match kicks (46%); an average propensity for match kicking injury (0.58/1000 kicks). Scrum‐halves executed 27% of match‐related kicks but had a very low propensity for match kicking injury (0.17/1000 kicks). All other positional groups executed a small proportion of match‐related kicks but a high propensity for match kicking injury. Ninety‐two percent of match kicking injuries occurred in the pelvis or lower limb, with the majority sustained by the kicking limb. 21% of all match kicking injuries were associated with the rectus femoris muscle.

Conclusion

Match kicking profiles and kicking injuries sustained are position‐dependent, which provides valuable insight for developing player‐specific conditioning and rehabilitation protocols.
Multi‐subject stochastic blockmodels with mixed effects for adaptive analysis of individual differences in human brain network cluster structure
Authors: Pavlović Dragana M. , Guillaume Bryan R.L. , Afyouni Soroosh , Nichols Thomas E.
Published: June 2020

Recently, there has been a renewed interest in the class of stochastic blockmodels (SBM) and their applications to multi‐subject brain networks. In our most recent work, we have considered an extension of the classical SBM, termed heterogeneous SBM (Het‐SBM), that models subject variability in the cluster‐connectivity profiles through the addition of a logistic regression model with subject‐specific covariates on the level of each block. Although this model has proved to be useful in both the clustering and inference aspects of multi‐subject brain network data, including fleshing out differences in connectivity between patients and controls, it does not account for dependencies that may exist within subjects. To overcome this limitation, we propose an extension of Het‐SBM, termed Het‐Mixed‐SBM, in which we model the within‐subject dependencies by adding subject‐ and block‐level random intercepts in the embedded logistic regression model. Using synthetic data, we investigate the accuracy of the partitions estimated by our proposed model as well as the validity of inference procedures based on the Wald and permutation tests. Finally, we illustrate the model by analyzing the resting‐state fMRI networks of 99 healthy volunteers from the Human Connectome Project (HCP) using covariates like age, gender, and IQ to explain the clustering patterns observed in the data.
Does lymph node morphology using ultrasound reflect aetiology? A pictorial essay, part I
Authors: Trenker Corinna , Görg Christian , Hollerweger Alois , Jenssen Christian , Dong Yi , Cui Xin-Wu , Dietrich Christoph F
Published: June 2020

The evaluation of lymph nodes (LNs) using ultrasound requires a high level of clinical and sonographic competence. This “pictorial essay” is intended to illustrate eye-catching examples of relevant “clinical-sonographic visual diagnoses” of LNs. We provide typical images and take-home messages of eye-catching features to illustrate the featured publications.The first part includes “important differential diagnoses of eye-catching features of suspected lymphadenopathy” and “benign lymphadenopathy”. The second part will include “Eye-catching features of malignant lymphadenopathy, both carcinoma and lymphoma”
Comparison of macroscopic and microscopic emission characteristics of large area field emitters based on carbon nanotubes and graphene
Authors: Popov Eugeni O. , Kolosko Anatoly G. , Filippov Sergey V. , Terukov Evgeny I. , Ryazanov Roman M. , Kitsyuk Evgeny P.
Published: June 2020

Nanostructured multitip surfaces have sufficient potential to obtain the high emission currents necessary to develop stable and noninertial sources of free electrons with increased levels of permissible currents. The key to understanding the processes of formation and stability of macroscopic emission currents from these large area field emitters (LAFEs) is assessing the local characteristics of individual emission sites. Herein, a method for determining the local emission characteristics of nanoscale emission sites is developed via processing the glow pattern data and a system for rapidly recording the current–voltage characteristics of LAFEs.
Anti-twinning in nanoscale tungsten
Authors: Wang Jiangwei , Zeng Zhi , Wen Minru , Wang Qiannan , Chen Dengke , Zhang Yin , Wang Peng , Wang Hongtao , Zhang Ze , Mao Scott X. , Zhu Ting
Published: June 2020

Tungsten nanowires showed an unexpected anti-twinning phenomenon, which is strongly size-dependent.
Beneficial metabolic role of β-arrestin-1 expressed by AgRP neurons
Authors: Pydi Sai P. , Cui Zhenzhong , He Zhenyan , Barella Luiz F. , Pham Jonathan , Cui Yinghong , Oberlin Douglas J. , Egritag Hale Ergin , Urs Nikhil , Gavrilova Oksana , Schwartz Gary J. , Buettner Christoph , Williams Kevin W. , Wess Jürgen
Published: June 2020

This study suggests that agents able to enhance the activity of β-arrestin-1 in AgRP neurons may be useful as antidiabetic drugs.
Remote heteroepitaxy of GaN microrod heterostructures for deformable light-emitting diodes and wafer recycle
Authors: Jeong Junseok , Wang Qingxiao , Cha Janghwan , Jin Dae Kwon , Shin Dong Hoon , Kwon Sunah , Kang Bong Kyun , Jang Jun Hyuk , Yang Woo Seok , Choi Yong Seok , Yoo Jinkyoung , Kim Jong Kyu , Lee Chul-Ho , Lee Sang Wook , Zakhidov Anvar , Hong Suklyun , Kim Moon J. , Hong Young Joon
Published: June 2020

Remote epitaxy enables to fabricate flexible GaN micro-LED sticker releasable from wafer.
Phospholipid distribution in the cytoplasmic membrane of Gram-negative bacteria is highly asymmetric, dynamic, and cell shape-dependent
Authors: Bogdanov Mikhail , Pyrshev Kyrylo , Yesylevskyy Semen , Ryabichko Sergey , Boiko Vitalii , Ivanchenko Pavlo , Kiyamova Ramziya , Guan Ziqiang , Ramseyer Christophe , Dowhan William
Published: June 2020

The cell shape of Gram-negative bacteria is maintained metabolically by asymmetric lipid distribution in biogenic plasma membrane.
The effect of moiré superstructures on topological edge states in twisted bismuthene homojunctions
Authors: Gou Jian , Kong Longjuan , He Xiaoyue , Huang Yu Li , Sun Jiatao , Meng Sheng , Wu Kehui , Chen Lan , Wee Andrew Thye Shen
Published: June 2020

Moiré superstructure–induced edge state modulation has been observed in bismuthene homojunctions.
Early isotopic evidence for maize as a staple grain in the Americas
Authors: Kennett Douglas J. , Prufer Keith M. , Culleton Brendan J. , George Richard J. , Robinson Mark , Trask Willa R. , Buckley Gina M. , Moes Emily , Kate Emily J. , Harper Thomas K. , O’Donnell Lexi , Ray Erin E. , Hill Ethan C. , Alsgaard Asia , Merriman Christopher , Meredith Clayton , Edgar Heather J. H. , Awe Jaime J. , Gutierrez Said M.
Published: June 2020

We use carbon isotopes in human bone as the earliest direct evidence for maize as a staple grain in the Americas.
Calcium isotopic evidence for the mantle sources of carbonatites
Authors: Amsellem Elsa , Moynier Frédéric , Bertrand Hervé , Bouyon Amaury , Mata João , Tappe Sebastian , Day James M. D.
Published: June 2020

Melting of recycled carbonate in the mantle explains the origin of carbonatitic magmas.
White nanolight source for optical nanoimaging
Authors: Umakoshi Takayuki , Tanaka Misaki , Saito Yuika , Verma Prabhat
Published: June 2020

We created a nanoscale white light source, which realized a unique optical imaging and showed great potential for nanoscicence.
Immune landscapes predict chemotherapy resistance and immunotherapy response in acute myeloid leukemia
Authors: Vadakekolathu Jayakumar , Minden Mark D. , Hood Tressa , Church Sarah E. , Reeder Stephen , Altmann Heidi , Sullivan Amy H. , Viboch Elena J. , Patel Tasleema , Ibrahimova Narmin , Warren Sarah E. , Arruda Andrea , Liang Yan , Smith Thomas H. , Foulds Gemma A. , Bailey Michael D. , Gowen-MacDonald James , Muth John , Schmitz Marc , Cesano Alessandra , Pockley A. Graham , Valk Peter J. M. , Löwenberg Bob , Bornhäuser Martin , Tasian Sarah K. , Rettig Michael P. , Davidson-Moncada Jan K. , DiPersio John F. , Rutella Sergio
Published: June 2020

Dissecting the immune architecture of AML and its influence on therapeutic response identifies patients for whom immunotherapy will be most beneficial.
Following the rules to foil Gram-negative infections
Authors: Baca Justin T.
Published: June 2020

Molecular design principles increase accumulation of an antibiotic in multidrug resistant Gram-negative bacteria.
Filoviruses Use the HOPS Complex and UVRAG To Traffic to Niemann-Pick C1 Compartments during Viral Entry
Authors: Bo Yuxia , Qiu Shirley , Mulloy Rory P. , Côté Marceline
Published: June 2020

Ebola viruses (EBOV) and other filoviruses cause sporadic and unpredictable outbreaks of highly lethal diseases. The lack of FDA-approved therapeutics, particularly ones with panfiloviral specificity, highlights the need for continued research efforts to understand aspects of the viral life cycle that are common to all filoviruses. As such, viral entry is of particular interest, as all filoviruses must reach cellular compartments containing the viral receptor Niemann-Pick C1 to enter cells. Here, we present an inducible CRISPR/Cas9 method to rapidly and efficiently generate knockout cells in order to interrogate the roles of a broad range of host factors in viral entry. Using this approach, we showed that EBOV entry depends on both the homotypic fusion and protein sorting (HOPS) tethering complex in coordination with UV radiation resistance-associated gene (UVRAG). Importantly, we demonstrate that the HOPS complex and UVRAG are required by all pathogenic filoviruses, representing potential targets for panfiloviral therapeutics.
Ebola Virus Inclusion Body Formation and RNA Synthesis Are Controlled by a Novel Domain of Nucleoprotein Interacting with VP35
Authors: Miyake Tsuyoshi , Farley Charlotte M. , Neubauer Benjamin E. , Beddow Thomas P. , Hoenen Thomas , Engel Daniel A.
Published: June 2020

Inclusion bodies (IBs) are cytoplasmic sites of RNA synthesis for a variety of negative-sense RNA viruses, including Ebola virus. In addition to housing important steps in the viral life cycle, IBs protect new viral RNA from innate immune attack and contain specific host proteins whose function is under study. A key viral factor in Ebola virus IB formation is the nucleoprotein, NP, which also is important in RNA encapsidation and synthesis. In this study, we have identified two domains of NP that control inclusion body formation. One of these, the central domain (CD), interacts with viral protein VP35 to control both inclusion body formation and RNA synthesis. The other is the NP C-terminal domain (NP-Ct), whose function has not previously been reported. These findings contribute to a model in which NP and its interactions with VP35 link the establishment of IBs to the synthesis of viral RNA.
Draft Genome Sequence of the Astaxanthin-Producing Microalga Haematococcus lacustris Strain NIES-144
Authors: Morimoto Daichi , Yoshida Takashi , Sawayama Shigeki
Published: June 2020

Haematococcus lacustris
is an industrially important eukaryotic microalga that is thought to be a great source of natural astaxanthin with strong antioxidant activity. Here, we report the draft assembly and annotation results of the genome of
H. lacustris
NIES-144. These data will expand our knowledge of the molecular biological features of this microalga.
Draft Genome Sequence of an Escherichia coli Sequence Type 420 Isolate from a Patient with Urinary Tract Infection in Northern California
Authors: Matsui Yusuke , Hu Yuan , Tarlton Nicole J. , Riley Lee W.
Published: June 2020

The genome sequence of a uropathogenic
Escherichia coli
sequence type 420 strain isolated from a patient with urinary tract infection in northern California is described here. The draft genome sequence includes a 4.8-Mb chromosome, accompanied by a 114-kb plasmid containing IncFIB/IncFII/Col156 and a 35-kb plasmid containing IncN3.
Draft Genome Sequence of Actinomyces neuii UMB1295, Isolated from the Female Urinary Tract
Authors: Markovic Tijana , Miller-Ensminger Taylor , Voukadinova Adelina , Wolfe Alan J. , Putonti Catherine
Published: June 2020

Actinomyces neuii
is an opportunistic pathogen. Within the urogenital tract, it has been associated with bacterial vaginosis and overactive bladder symptoms. Here, we investigate a draft genome sequence of
A. neuii
UMB1295, which was isolated from a catheterized urine sample from a woman with a urinary tract infection.
Draft Genome Sequence of Lactobacillus crispatus UMB1163, Isolated from the Female Urinary Tract
Authors: Khan Fabeiha , Miller-Ensminger Taylor , Voukadinova Adelina , Wolfe Alan J. , Putonti Catherine
Published: June 2020

Lactobacillus crispatus
is a Gram-positive bacterium shown to protect against urinary and vaginal infections. Here, we report the draft genome sequence of
L. crispatus
UMB1163, isolated from the female urinary tract.
Draft Genome Sequence of Staphylococcus epidermidis UMB8493, Isolated from the Female Urinary Tract
Authors: Truckenbrod Anthony , Miller-Ensminger Taylor , Voukadinova Adelina , Wolfe Alan J. , Putonti Catherine
Published: June 2020

Staphylococcus epidermidis
is a native member of the human microbiota. Here, we report the draft genome sequence of
S. epidermidis
UMB8493, an isolate from a catheterized urine sample from a female with overactive bladder symptoms. The 2.54-Mbp draft genome encodes genes associated with beta-lactam and fosfomycin resistance.
Draft Genome Sequence of Escherichia coli UMB9246, Isolated from the Bladder of a Woman with Recurrent Urinary Tract Infection
Authors: Belmonte Mikalina , Miller-Ensminger Taylor , Voukadinova Adelina , Wolfe Alan J. , Putonti Catherine
Published: June 2020

Escherichia coli
is a Gram-negative, motile, rod-shaped bacterium that causes the majority of uncomplicated urinary tract infections (UTIs). Here, we report the draft genome of
E. coli
strain UMB9246, an isolate from a woman with recurrent UTI.
Identification of a Divergent Isolate of Ryegrass Mosaic Virus in Ohio Wheat
Authors: Hodge B. A. , Paul P. A. , Stewart L. R.
Published: June 2020

A divergent isolate of ryegrass mosaic virus (RGMV) has been identified that is associated with wheat samples collected in Ohio. The complete genome of the virus is 9,570 nucleotides, with a polyprotein open reading frame that shares 77.2% nucleotide sequence identity with the reference ryegrass mosaic virus sequence.
Draft Genome Sequences of Three Isolates of
Golubevia
sp. Basidiomycete Fungi Isolated from Powdery Mildew Pustules
Authors: Russ Lina , Warris Sven , Lombaers-van der Plas Carin , Groenenboom-de Haas Lia H. , Cordewener Jan H. G. , Schijlen Elio , Köhl Jürgen
Published: June 2020

The genomes of three
Golubevia
isolates (BC0812, BC0850, and BC0902) that have been shown to reduce conidiation of
Blumeria graminis
f. sp.
tritici
were sequenced using a dual-platform approach. The assembled genomes will help to elucidate the molecular mechanisms underlying the biocontrol effect of this understudied group.
Genome Sequences of Mycobacteriophages Joselito, Patt, and Tydolla
Authors: Jacob Christina , Alvarez Yunia , Carney Tara , Castro Cynthia , Alvarez Regina , Connors Bernadette J.
Published: June 2020

Mycobacteriophages Joselito, Patt, and Tydolla were isolated from different soil or water samples using
Mycobacterium smegmatis
mc
2
155 as the host. Each was obtained using direct isolation techniques, purified, and then sequenced using the deconvolution of genomes after
en masse
sequencing (DOGEMS) method.
Complete Genome Sequence of Lactobacillus nenjiangensis SH-Y15, Isolated from Sauerkraut
Authors: He Jiale , Liu Yan , Li Fengzi , Wu Hao , Yang Hongyan
Published: June 2020

We isolated a strain of
Lactobacillus nenjiangensis
named SH-Y15 from traditional suan-cai used in northeastern China because it has a high capacity for degrading nitrites at low temperatures. The complete genome of SH-Y15 contains a single circular chromosome and a plasmid. The complete length is 2,249,893 bp, and the G+C content is 39.68%.
Supersymmetric Dirac Hamiltonians in ($$1+1$$) dimensions revisited
Authors: Junker Georg
Published: June 2020

The most general Dirac Hamiltonians in $$(1+1)$$

(
1
+
1
)

dimensions are revisited under the requirement to exhibit a supersymmetric structure. It is found that supersymmetry allows either for a scalar or a pseudo-scalar potential. Their spectral properties are shown to be represented by those of the associated non-relativistic Witten model. The general discussion is extended to include the corresponding relativistic and non-relativistic resolvents. As example, the well-studied relativistic Dirac oscillator is considered and the associated resolved kernel is found in a closed-form expression by utilising the energy-dependent Green’s function of the non-relativistic harmonic oscillator. The supersymmetric quasi-classical approximation for the Witten model is extended to the associated relativistic model.
An Inexact Dual Alternating Direction Method of Multipliers for Image Decomposition and Restoration
Authors: Wang Qingsong , Wang Chengjing , Tang Peipei , Niu Dunbiao
Published: June 2020

In this paper, we apply an inexact dual alternating direction method of multipliers (dADMM) to an image decomposition model. In this model, an image is divided into two meaningful components, i.e., a cartoon part and a texture part. The dADMM presents not only the cartoon part and the texture part of an image but also the restored image (cartoon [Formula: see text] part). We also summarize the global convergence for the algorithm. Numerical experiments demonstrate the efficiency and robustness of the inexact dADMM. Furthermore, we can obtain relatively higher signal-to-noise ratio (SNR) comparing to other algorithms.
Accurate decomposition method and identification technology of drag
Authors: Yu Jia-Lei , Jin Jing , Shao Chun , Zhang Miao , Liu Tie-Jun
Published: June 2020

Aiming at accurate decomposition and identification of drag, the drag prediction technology based on the mid/far-field integral method is developed. The method decomposes the far-field drag into entropy drag and induced drag according to its physical mechanism, and introduces an appropriate entropy correction to eliminate the numerical dissipation by analyzing the influence of the trailing integral section position on the entropy drag calculation. Based on the analysis of thermodynamic reversible processes and irreversible processes, the drag is refined into viscous drag, shock wave drag, induced drag and pseudo-drag. The mid-field integral method is used to calculate the separate contribution of viscous drag, shock wave drag and induced drag by calculating the limited integral domain. Numerical results show that the developed method is feasible in accurately reflecting the physical mechanism and predicting the drag ratio. Thus, it provides a reliable tool for drag reduction of large passenger aircraft.
Shock-induced bubble collapse near a tissue-like material
Authors: Xu Chang , Pan Shu-Cheng
Published: June 2020

In this study, we numerically investigate the shock-induced bubble collapse phenomenon near a tissue-like material. Here, a sharp-interface model is applied to represent a 3-material system containing the liquid, the air and the gelatin. We present the results of the complex interface dynamics and compare them with the experimental data. The goal of this study is to understand the mechanism of the shock wave–bubble interaction near tissues in a more accurate manner with advanced numerical methods.
Simulation of diffusion motion of ionomers using Monte Carlo algorithm
Authors: Xue Kai-Li , Hu Yun-Feng , Yu Xu-Chen , Hou Ji-Xuan
Published: June 2020

We present a simple model of ionomers, namely a single polymer chain in a series of fixed attractors. In analogy to ionized bead’s claws of surrounding chains, the set of attractors can affectively slow down the diffusion motion of the target chain. The monomer mean-square displacement of ionomers is studied by using Monte Carlo algorithm, and compared with the prediction of the sticky Rouse model. The diffusion motion properties of ionomers are explored in three aspects, including the chain length of the polymer, the depth of the potential well and the number of ionic groups. The results show that a plateau appears in the monomer diffusion function due to the attraction of the attractors to the claws. However, comparative theoretical predictions and simulation results show that there exists some discrepancy between them. Therefore, the relaxation time distribution of polymer chain motion is explored. The simulation results confirm that the association lifetime is decreasing exponentially, and the expected values of the association lifetime satisfy the Boltzmann distribution as shown by the results. These results perfectly explain the deviation between the simulation data and the theoretical results.
Solitary wave solutions of Kaup–Newell optical fiber model in mathematical physics and its modulation instability
Authors: Arshad Muhammad , Seadawy Aly R. , Lu Dianchen , Ali Farhan
Published: June 2020

Soliton solutions which signify long wave parallel to the magnetic fields of Kaup–Newell optical fiber model are discussed in this paper by two different methods. The improved simple equation method (ISEM) and exp[Formula: see text]-expansion scheme are employed to solve the model to construct the solutions of the model in different cases. The achieved solutions are represented in different and general forms such as logarithmic or exponential function, trigonometric and hyperbolic trigonometric functions, etc. Also, the modulation instability of the model is analyzed which confirms that all obtained exact results are stable. Several solutions from achieved solutions are novel.
A novel method for destabilization of terrorist network
Authors: Singh Saurabh , Verma Shashi Kant , Tiwari Akhilesh
Published: June 2020

Criminal network investigation is an ignited research area nowadays. There are several types of criminal network. Terrorist network is one of them. Exploring terrorist network is a demand of several investigating agencies. Different properties of network can be better considered to probe network properly using multi criteria decision-making methods. Grey Relational Analysis (GRA) method is a structural technique for organizing and analyzing complex decisions based on typical mathematics. This process can be employed for analyzing available datasets and designing useful conclusions. If network is explored and visualized, it can be destabilized efficiently. Identified members can be studied and thus their future actions can be prevented. These generalized designs can be used by government agencies for destabilization of terrorist group. This system is especially useful for countries like India that face a constant threat from various group of terrorists. This generalization can further be used to destabilize various criminal networks and their activities can be prevented. Thus, life and property of individuals can be saved.
An iterative ensemble Kalman method for an inverse scattering problem in acoustics
Authors: Li Zhaoxing
Published: June 2020

This paper studies an inverse problem of reconstructing a sound-soft obstacle from a homogeneous medium. We deal with it in the framework of statistical inversion and adopt an iterative ensemble Kalman algorithm to reconstruct the boundary. Some numerical examples show that the algorithm is effective and it can recover the shape of the boundary using one or several of the incident waves.
Functional Verification of Dynamic Partial Reconfiguration for Software-Defined Radio
Authors: Ahmed Islam , Mohieldin Ahmed Nader , Mostafa Hassan
Published: June 2020

Dynamic Partial Reconfiguration (DPR) on Field Programmable Gate Arrays (FPGAs) allows reconfiguration of some of the logic at runtime while the rest of the logic keeps operating. This feature allows the designers to build complex systems such as Software-Defined Radio (SDR) in a reasonable area. New issues can arise due to usage of DPR technique such as guaranteeing proper connections for the ports of the Reconfigurable Modules (RMs) which share the same Reconfigurable Region (RR) on the FPGA, waiting for running computations on a module before reconfiguring it, isolation of the reconfigurable modules during the reconfiguration process, and initialization of the reconfigurable module after the reconfiguration process is done. Also, the Clock Domain Crossing (CDC) verification of the dynamically reconfigurable systems is a complicated task due to the need to verify all the modes of the designs, and the lack of Computer Aided Design (CAD) tools support for DRS designs. This paper summarizes our previous work to address these verification challenges for DPR. The approaches are demonstrated on a SDR system to show the effectiveness of applying these approaches in the design cycle.
Constraints on light dark matter particles using white dwarf stars
Authors: Panotopoulos Grigoris , Lopes Ilídio
Published: June 2020

We report constraints on the nucleon-dark matter particle cross-section using the internal luminosity of observed white dwarf stars in the globular cluster Messier 4. Our results cover the parameter space corresponding to relatively light dark matter particles, in the sub GeV range, which is known to be very difficult to be probed by direct dark matter searches. The additional luminosity coming from self-annihilations of dark matter particles captured inside the stars must not exceed the observed luminosity. Imposing that condition, we obtain for the spin independent cross-section of light dark matter particles (below 5[Formula: see text]GeV) on baryons [Formula: see text] the upper bound: [Formula: see text].
Generalized Dirac oscillator with κ-Poincaré algebra
Authors: Wu Jing , Long Chao-Yun , Wu Zheng-Xue , Long Zheng-Wen
Published: June 2020

In this paper, the generalized Dirac oscillator with [Formula: see text]-Poincaré algebra is structured by replacing the momentum operator p with [Formula: see text] in [Formula: see text]-deformation Dirac equation. The deformed radial equation is derived for this model. Particularly, by solving the deformed radial equation, the wave functions and energy spectra which depend on deformation parameter [Formula: see text] have been obtained for these quantum systems with [Formula: see text] being a Yukawa-type potential, inverse-square-type singular potential and central fraction power singular potential in two-dimensional space, respectively. The results show that the deformation parameter [Formula: see text] can lead to decreasing of energy levels for the above quantum systems. At the same time, the degeneracy of energy spectra has been discussed and the corresponding conditions of degeneracy have been given for each case.
CONIC CVA AND DVA FOR OPTION PORTFOLIOS
Authors: VAN BAKEL SJOERD , BOROVKOVA SVETLANA , MICHIELON MATTEO
Published: June 2020

In this paper, we propose a framework for credit and debit valuation adjustments (CVA and DVA, respectively) for options and option portfolios which is based on conic finance, that is, where the positions are valued at their bid or ask prices depending on whether they are assets or liabilities. This can be achieved by transforming the pricing measure via appropriate distortion functions, depending on (at least) one parameter. We apply our methodology, which is based on the Wang transform, to portfolios of European commodity futures options, and we show that both CVA and DVA are significantly impacted by bid-ask spreads, when compared to their traditional risk-neutral counterparts. In particular, we show that DVA decreases when computed under conic finance settings, which is in line with the regulatory efforts to rein in DVA gains for financial institutions resulting from their own credit quality deterioration. Finally, we investigate the robustness of our approach with respect to the calibrated parameters, and we show that the calibrated distortion parameter is an excellent explanatory variable for the observed bid-ask spreads.
Asia’s Lesser Powers Confront US–China Threat to the Regional Order
Authors: PEMPEL T. J.
Published: June 2020

Tensions between the United States and China have been on the rise under Xi Jinping and Donald Trump, challenging longstanding regional moves to peace and prosperity. In response, a number of less powerful East Asian states have taken steps toward deeper regional economic ties and multilateral institutions. This paper analyzes these competing tensions and their implications for the Asia-Pacific regional order.
Single molecule level studies of reversible ligand binding to metal porphyrins at the solution/solid interface
Authors: Mazur Ursula , Hipps K. W.
Published: June 2020

Ligands bind reversibly to metal porphyrins in processes such as molecular recognition, electron transport and catalysis. These chemically relevant processes are ubiquitous in biology and are important in technological applications. In this article, we focus on the current advances in ligand binding to metal porphyrin receptors noncovalently bound at the solution/solid interface. In particular, we restrict ourselves to studies at the single molecule level. Dynamics of the binding/dissociation process can be monitored by scanning tunneling microscopy (STM) and can yield both qualitative and quantitative information about ligand binding affinity and the energetics that define a particular ligation reaction. Molecular and time dependent imaging can establish whether the process under study is at equilibrium. Ligand-concentration-dependent studies have been used to determine adsorption isotherms and thermodynamic data for processes occurring at the solution/solid interface. In several binding reactions, the solid support acted as an electron-donating fifth coordination site, thereby significantly changing the metal porphyrin receptor’s affinity for exogenous ligands. Supporting calculations provide insight into the metalloporphyrin/support and ligand–metalloporphyrin/support interactions and their energetics.
Linear eigenvalue statistics of random matrices with a variance profile
Authors: Adhikari Kartick , Jana Indrajit , Saha Koushik
Published: June 2020

We give an upper bound on the total variation distance between the linear eigenvalue statistic, properly scaled and centered, of a random matrix with a variance profile and the standard Gaussian random variable. The second-order Poincaré inequality-type result introduced in [S. Chatterjee, Fluctuations of eigenvalues and second order poincaré inequalities, Prob. Theory Rel. Fields 143(1) (2009) 1–40.] is used to establish the bound. Using this bound, we prove central limit theorem for linear eigenvalue statistics of random matrices with different kind of variance profiles. We re-establish some existing results on fluctuations of linear eigenvalue statistics of some well-known random matrix ensembles by choosing appropriate variance profiles.
Spectral Line Registration Backend Based on USRP X300 Software Defined Radio
Authors: Bleiders M. , Antyufeyev O. , Patoka O. , Orbidans A. , Aberfelds A. , Steinbergs J. , Bezrukovs V. , Shmeld I.
Published: June 2020

This paper presents implementation of spectrometer based on off-the-shelf software defined radio (SDR) Ettus Research USRP X300 equipped with TwinRX daughterboard. Parallelized software, employing Fast Fourier Transform (FFT), is developed which allows two channel spectrum processing in real time with bandwidths up to 50[Formula: see text]MHz per channel, sample resolution of 14 bits and FFT lengths up to 32k points. Measured Allan stability time of the spectrometer is at least 750 sin laboratory environment. Software has network server-type interface that allows to conveniently integrate the spectrometer in radio telescope observation control and monitoring system with versatility of SDR allowing to implement various observation modes, for example, total power detection functionality with high frequency selectivity, which allows to carry continuum amplitude calibration in presence of near-by radio frequency interference. Presented spectrometer has been successfully integrated and used at RT-32 and RT-16 radio telescopes of Ventspils International Radio Astronomy Centre.
Tetrahedral Trees
Authors: Fellegara Riccardo , Floriani Leila De , Magillo Paola , Weiss Kenneth
Published: June 2020

We address the problem of performing efficient spatial and topological queries on large tetrahedral meshes with arbitrary topology and complex boundaries. Such meshes arise in several application domains, such as 3D Geographic Information Systems (GISs), scientific visualization, and finite element analysis. To this aim, we propose
Tetrahedral trees
, a family of spatial indexes based on a nested space subdivision (an octree or a kD-tree) and defined by several different subdivision criteria. We provide efficient algorithms for spatial and topological queries on Tetrahedral trees and compare to state-of-the-art approaches. Our results indicate that Tetrahedral trees are an improvement over R
*
-trees for querying tetrahedral meshes; they are more compact, faster in many queries, and stable at variations of construction thresholds. They also support spatial queries on more general domains than topological data structures, which explicitly encode adjacency information for efficient navigation but have difficulties with domains with a non-trivial geometric or topological shape.