bluuebunny/crossref_metadata_2025 huggingface dataset:
Complete Genome Sequence of Ebrios, a Novel T7virus Isolated from the Ebrie Lagoon in Abidjan, Côte d’Ivoire
Authors: Ngazoa-Kakou Solange , Philippe Cécile , Tremblay Denise M. , Loignon Stéphanie , Koudou Aristide , Abole Ahmed , Ngolo Coulibaly David , Kan Kouassi Stéphane , Kouamé Sina Mireille , Aoussi Serge , Dosso Mireille , Moineau Sylvain
Published: June 2018

The lytic
Escherichia coli
phage Ebrios was isolated from a water sample collected in Ebrie Lagoon on the Adiopodoumé River in Abidjan (Republic of Côte d’Ivoire, West Africa). The linear genome of this
Podoviridae
family member contains 39,752 bp, has a G+C content of 52.9%, is composed of 53 open reading frames, and is related to the
Stenotrophomonas maltophilia
phage IME15.
Draft Genome Sequence of Dyella sp. Strain C11, Isolated from a Malaysian Tropical Peat Swamp Forest
Authors: Too Chin Chin , Ong Kuan Shion , Lee Sui Mae , Yule Catherine M. , Keller Alexander
Published: June 2018

We report here the draft genome sequences of a bacterial isolate,
Dyella
sp. strain C11, which was isolated from a Malaysian tropical peat swamp forest. The putative genes for the biogeochemical processes were annotated, and the genome was deposited in an online database.
Draft Genome Sequence of a Clinical Isolate of Fusarium fujikuroi Isolated from a Male Patient with Acute Myeloid Leukemia
Authors: Urbaniak Camilla , Dadwal Sanjeet , Bagramyan Karine , Venkateswaran Kasthuri
Published: June 2018

Here, we present the draft whole-genome sequence of a clinical isolate of
Fusarium fujikuroi
cultured from a patient undergoing chemotherapy for refractory acute myeloid leukemia.
Whole-Genome Sequencing and Annotation of a Drug-Resistant Extrapulmonary Clinical Isolate of Beijing Genotype Mycobacterium tuberculosis from Pune, India
Authors: Hatolkar Swarupa M. , Misra Rabindra N. , Mahato Rajesh , Jadhav Savita
Published: June 2018

Whole-genome sequencing has emerged as a powerful tool to map genetic diversity among
Mycobacterium tuberculosis
isolates and identify the genomic signatures associated with drug resistance, pathogenesis, and disease transmission. Isolate LJ319 of the
Mycobacterium tuberculosis
complex (MTC)-Beijing genotype circulating in Maharashtra, India, which was obtained from the cerebrospinal fluid (CSF) of an immunocompetent patient, was subjected to whole-genome sequencing.
First Whole-Genome Characterization of Avian Nephritis Virus 2 of Broiler Chicken from Pará, Brazil
Authors: Castro Ceyla Maria Oeiras , Chagas Elaine Hellen Nunes , Bezerra Delana Andreza Melo , da Silva Sandro Patroca , Cruz Ana Cecília Ribeiro , Sousa Júnior Edivaldo Costa , Silva René Ribeiro , Resque Hugo Reis , Gabbay Yvone Benchimol , Mascarenhas Joana D’Arc Pereira
Published: June 2018

Our results show the first full-genome characterization of avian nephritis virus 2 recovered from stools of broiler chickens at a commercial farm located in Benevides, Pará, Brazil. Nucleotide analyses of whole-genome sequences showed the isolate to be a strain of
Avastrovirus 2
in the family
Astroviridae
.
Complete Genome Sequence of Bacillus subtilis Strain MH1, Which Has a High Level of Bacteriocin-Like Activity, Isolated from Soil in Bangladesh
Authors: Hossain Mohammad Shahnoor , Akhter Marufa Zerin , Hossain Muhammad Maqsud , Shishir M. Asaduzzaman , Khan Shakila Nargis , Hoq M. Mozammel
Published: June 2018

Bacillus subtilis
MH1 demonstrates a high level of bacteriocin activity against several pathogenic bacteria. We announce here the full-genome sequence of strain MH1, isolated from soil in Bangladesh. This genome length is 4,094,053 bp, with 43.5% GC content, 4,217 coding sequences (CDS), 10 rRNA, 84 tRNA, and 1 transfer-messenger RNA (tmRNA).
Complete Genome Sequence of Bacillus subtilis Strain DKU_NT_03, Isolated from a Traditional Korean Food Using Soybean (Chung-gook-jang) for High-Quality Nattokinase Activity
Authors: Jeong Hee-Won , Bang Man-Seok , Lee Yea-jin , Lee Su Ji , Lee Sang-Cheol , Shin Jang-In , Oh Chung-Hun
Published: June 2018

We present here the complete genome sequence of
Bacillus subtilis
strain DKU_NT_03 isolated from the traditional Korean food chung-gook-jang, which is made from soybeans. This strain was chosen to identify genetic factors with high-quality nattokinase activity.
Genome Sequence of Bacillus megaterium Strain YC4-R4, a Plant Growth-Promoting Rhizobacterium Isolated from a High-Salinity Environment
Authors: Vílchez Juan Ignacio , Tang Qiming , Kaushal Richa , Wang Wei , Lv Suhui , He Danxia , Chu Zhaoqing , Zhang Heng , Liu Renyi , Zhang Huiming
Published: June 2018

Here, we report the complete genome sequence for
Bacillus megaterium
strain YC4-R4, a highly salt-tolerant rhizobacterium that promotes growth in plants. The sequencing process was performed by combining pyrosequencing and single-molecule sequencing techniques. The complete genome is estimated to be approximately 5.44 Mb, containing a total of 5,673 predicted protein-coding DNA sequences (CDSs).
Complete Genome Sequence of Lychnis Mottle Virus Isolated in Japan
Authors: Fujimoto Yuji , Nijo Takamichi , Hosoe Naoi , Watanabe Kiyoto , Maejima Kensaku , Yamaji Yasuyuki , Namba Shigetou
Published: June 2018

We report here the first complete genome sequence of a Japanese isolate of lychnis mottle virus (LycMoV-J). The genome segments of LycMoV-J have a unique structure in their 3′ untranslated regions, and the encoded proteins have the same structure as that of an isolate reported from South Korea.
Genome Sequence of Listeria monocytogenes 2542, a Serotype 4b Strain from a Cheese-Related Outbreak in Portugal
Authors: Ferreira Vânia , Magalhães Rui , Almeida Gonçalo , Cabanes Didier , Fritzenwanker Moritz , Chakraborty Trinad , Hain Torsten , Teixeira Paula
Published: June 2018

We report here the draft genome sequence of
Listeria monocytogenes
2542, a serotype 4b clinical strain recovered from a placental sample during a cheese-related listeriosis outbreak in Portugal.
Draft Genome Sequence of Paraburkholderia sp. Strain C35, Isolated from a Malaysian Tropical Peat Swamp Forest
Authors: Too Chin Chin , Ong Kuan Shion , Ankenbrand Markus J. , Lee Sui Mae , Yule Catherine M. , Keller Alexander
Published: June 2018

We report the draft genome sequence of a bacterial isolate,
Paraburkholderia
sp. strain C35, which was isolated from a Malaysian tropical peat swamp forest. The putative genes for the biogeochemical processes were annotated and are publicly available in the online databases.
Draft Genome Sequence of Roseomonas aestuarii Strain JR1/69-1-13 Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia
Authors: Grouzdev Denis S. , Babich Tamara L. , Tourova Tatiyana P. , Sokolova Diyana S. , Abdullin Ruslan R. , Poltaraus Andrey B. , Schevchenko Margarita A. , Toshchakov Stepan V. , Nazina Tamara N.
Published: June 2018

The draft genome sequence of
Roseomonas aestuarii
strain JR1/69-1-13, an aerobic chemoorganotrophic bacterium isolated from nitrate- and radionuclide-contaminated groundwater in Russia, is presented here. The genome was annotated to elucidate the genomic basis for the strain’s adaptation to the environment and its resistance to nitrate, heavy metals, and metalloids.
Genome Sequences for Three Strains of Kocuria rosea, Including the Type Strain
Authors: Trachtenberg Ariel M. , Goen Abigail E. , MacLea Kyle S.
Published: June 2018

Genomes from three strains of
Kocuria rosea
were sequenced.
K. rosea
ATCC 186, the type strain, was 3,958,612 bp in length with a total G+C content of 72.70%. When assembled,
K. rosea
ATCC 516 was 3,862,128 bp with a 72.82% G+C content.
K. rosea
ATCC 49321 was 4,018,783 bp in size with a 72.49% G+C content.
Stress-Induced, Highly Efficient, Donor Cell-Dependent Cell-to-Cell Natural Transformation in Bacillus subtilis
Authors: Zhang Xiaoming , Jin Tingting , Deng Liping , Wang Chao , Zhang Yuhua , Chen Xiangdong
Published: June 2018

Because DNA is easily prepared, studies of bacterial natural genetic transformation traditionally focus on recipient cells. However, such laboratory artifacts cannot explain how this process occurs in nature. In most cases, competence is only transient and involves approximately 20 to 50 genes, and it is unreasonable for bacteria to spend so many genetic resources on unpredictable and uncertain environmental DNA. Here, we characterized a donor cell-dependent CTCNT process in
B. subtilis
and related species that was almost completely resistant to DNase treatment and was more efficient than classical natural transformation using naked DNA as a donor, i.e., DNA-to-cell transformation, suggesting that DNA donor cells were also important in the transformation process in natural environments.
Signatures of Selection at Drug Resistance Loci in Mycobacterium tuberculosis
Authors: Mortimer Tatum D. , Weber Alexandra M. , Pepperell Caitlin S.
Published: June 2018

Mycobacterium tuberculosis
, the causative agent of tuberculosis (TB), is a significant burden on global health. Antibiotic treatment imposes strong selective pressure on
M. tuberculosis
populations. Identifying the mutations that cause drug resistance in
M. tuberculosis
is important for guiding TB treatment and halting the spread of drug resistance. Whole-genome sequencing (WGS) of
M. tuberculosis
isolates can be used to identify novel mutations mediating drug resistance and to predict resistance patterns faster than traditional methods of drug susceptibility testing. We have used WGS from natural populations of drug-resistant
M. tuberculosis
to characterize effects of selection for advantageous mutations on patterns of diversity at genes involved in drug resistance. The methods developed here can be used to identify novel advantageous mutations, including new resistance loci, in
M. tuberculosis
and other clonal pathogens.
Morphological and topographical appearance of microaneurysms on optical coherence tomography angiography
Authors: Schreur Vivian , Domanian Artin , Liefers Bart , Venhuizen Freerk G , Klevering B Jeroen , Hoyng Carel B , de Jong Eiko K , Theelen Thomas
Published: June 2018

Aims

To investigate retinal microaneurysms in patients with diabetic macular oedema (DME) by optical coherence tomography angiography (OCTA) according to their location and morphology in relationship to their clinical properties, leakage on fundus fluorescein angiography (FFA) and retinal thickening on structural OCT.

Methods

OCTA and FFA images of 31 eyes of 24 subjects were graded for the presence of microaneurysms. The topographical and morphological appearance of microaneurysms on OCTA was evaluated and classified. For each microaneurysm, the presence of focal leakage on FFA and associated retinal thickening on OCT was determined.

Results

Of all microaneurysms flagged on FFA, 295 out of 513 (58%) were also visible on OCTA. Microaneurysms with focal leakage and located in a thickened retinal area were more likely to be detected on OCTA than not leaking microaneurysms in non-thickened retinal areas (p=0.001). Most microaneurysms on OCTA were seen in the intermediate (23%) and deep capillary plexus (22%). Of all microaneurysms visualised on OCTA, saccular microaneurysms were detected most often (31%), as opposed to pedunculated microaneurysms (9%). Irregular, fusiform and mixed fusiform/saccular-shaped microaneurysms had the highest likeliness to leak and to be located in thickened retinal areas (p<0.001, p<0.001 and p=0.001).

Conclusions

Retinal microaneurysms in DME could be classified topographically and morphologically by OCTA. OCTA detected less microaneurysms than FFA, and this appeared to be dependent on leakage activity and retinal thickening. Morphological appearance of microaneurysms (irregular, fusiform and mixed saccular/fusiform) was associated with increased leakage activity and retinal thickening.
Dysnatremia among runners in a half marathon performed under warm and humid conditions
Authors: Martinez-Cano Juan Pablo , Cortes-Castillo Valeria , Martinez-Villa Juliana , Ramos Juan Carlos , Uribe Juan Pablo
Published: June 2018

Background

Dysnatremia has been associated with sports activity, especially long-distance running and endurance sports. High fluid intake is associated with hyponatremia. This study aims to evaluate dysnatremia and risk factors in half-marathon runners under warm and humid environmental conditions. 

Methods

A cross-sectional study was performed among randomly selected runners in the 2017 Cali half marathon. Runners on diuretic therapy or with a known history of kidney disease were excluded. Participants went through a 2-day assessment. Previous medical history, training history, body mass index and running history were determined in the first assessment. Symptoms of dysnatremia and level of fluid consumption during the race were registered during the second assessment and post-run blood sampling for serum [Na+] was also undertaken. 

Results

130 runners were included in the study. The complete 2-day assessment was performed on 81 participants (62%) that were included in the final analysis. No cases of hyponatremia were found; instead, there were six cases of asymptomatic hypernatremia (7.4%). This hypernatremia had a statistically significant association with lower frequency (p=0.01) and volume of fluid intake during the race (water: p=0.02, Gatorade: p=0.04). 

Conclusion

Hyponatremia has been associated with high fluid intake in races performed under cool weather, such as the Boston Marathon during spring. In contrast, hypernatremia was found in a half marathon in warm and humid weather, which was associated with lower volume and frequency of fluid intake, suggesting that under warm and humid conditions, a median fluid intake of 900 mL during the race could prevent this event.
Use of routinely captured echocardiographic data in the diagnosis of severe aortic stenosis
Authors: Bradley Steven M , Foag Katie , Monteagudo Khua , Rush Pam , Strauss Craig E , Gössl Mario , Sorajja Paul
Published: June 2018

Objective

To determine the implications of applying guideline-recommended definitions of aortic stenosis to echocardiographic data captured in routine clinical care.

Methods

Retrospective observational study of 213 174 patients who underwent transthoracic echocardiographic imaging within Allina Health between January 2013 and October 2017. The sensitivity, specificity, positive predictive value, negative predictive value and accuracy of echocardiographic measures for severe aortic stenosis were determined relative to the documented interpretation of severe aortic stenosis.

Results

Among 77 067 patients with complete assessment of the aortic valve, 1219 (1.6%) patients were categorised as having severe aortic stenosis by the echocardiographic reader. Relative to the documented interpretation, aortic valve area (AVA) as a measure of severe aortic stenosis had the high sensitivity (94.1%) but a low positive predictive value (37.5%). Aortic valve peak velocity and mean gradient were specific (>99%), but less sensitive (<70%). A measure incorporating peak velocity, mean gradient and dimensionless index (either by velocity time integral or peak velocity ratio) achieved a balance of sensitivity (92%) and specificity (99%) with little detriment in accuracy relative to peak velocity and mean gradient alone (98.9% vs 99.3%). Using all available data, the proportion of patients whose echocardiogram could be assessed for aortic stenosis was 79.8% as compared with 52.7% by documented interpretation alone.

Conclusion

A measure that used dimensionless index in place of AVA addressed discrepancies between quantitative echocardiographic data and the documented interpretation of severe aortic stenosis. These findings highlight the importance of understanding the limitations of clinical data as it relates to quality improvement efforts and pragmatic research design.
Mortality in adult patients with fluid overload evaluated by BIVA upon admission to the emergency department
Authors: Kammar-García Ashuin , Pérez-Morales Ziv , Castillo-Martinez Lilia , Villanueva-Juárez José Luis , Bernal-Ceballos Fernanda , Rocha-González Héctor Isaac , Remolina-Schlig Miguel , Hernández-Gilsoul Thierry
Published: June 2018

Purpose of the study

The aim of this study was to investigate the association of fluid overload, measured by bioelectrical impedance vector analysis (BIVA) and also by accumulated fluid balance, with 30-day mortality rates in patients admitted to the emergency department (ED).

Design

We conducted a prospective observational study of fluid overload using BIVA, taking measures using a multiple-frequency whole-body tetrapolar equipment. Accumulated fluid balances were obtained at 24, 48 and 72 hours from ED admission and its association with 30-day mortality.

Patients

109 patients admitted to the ED classified as fluid overloaded by both methods.

Results

According to BIVA, 71.6% (n=78) of patients had fluid overload on ED admission. These patients were older and had higher Sequential Organ Failure Assessment scores. During a median follow-up period of 30 days, 32.1% (n=25) of patients with fluid overload evaluated by BIVA died versus none with normovolaemia (p=0.001). There was no statistically significant difference in mortality between patients with and without fluid overload as assessed by accumulated fluid balance (p=0.81).

Conclusions

Fluid overload on admission evaluated by BIVA was significantly related to mortality in patients admitted to the ED.
A Stock Model with Varying Stock Diffusion for Uncertain Market
Authors: Li Shengguo , Peng Jin , Zhang Bo
Published: June 2018

The option-pricing problem is an important topic in modern finance. In this paper, we propose a stock model with varying stock diffusion based on uncertainty theory. The European option pricing formulas are derived from the proposed uncertain stock model, and some mathematical properties of these formulas are investigated. Moreover, extended uncertain stock models are introduced and discussed. Finally, numerical examples are given to illustrate the proposed model.
Two-Dimensional Frictionless Contact of a Coated Half-Plane Based on Couple Stress Theory
Authors: Song Hongxiaia , Ke Liaoliang , Wang Yuesheng , Yang Jie , Jiang Han
Published: June 2018

Based on the couple stress theory, the size-dependent frictionless contact problem between a rigid punch and a homogeneous coated half-plane is investigated in this paper. This theory describes the size effect that emerges from the material microstructures by introducing the characteristic material length. With the aid of the Fourier transform method, the size-dependent contact problem of the rigid flat, cylindrical, parabolic and wedge punches is reduced to a Cauchy singular integral equation of the first kind. Subsequently, it is transformed into algebraic ones and solved numerically by using Gauss–Chebyshev integration formulas. Numerical results for the normal and in-plane contact stresses, contact width and indentation depth are given. The effect of the length scale parameters on the contact stress and indentation is predicted by the couple stress elasticity, which shows a strong dependence on the characteristic material length.
Order Flows and Limit Order Book Resiliency on the Meso-Scale
Authors: Bechler Kyle , Ludkovski Mike
Published: June 2018

We investigate the behavior of limit order books (LOBs) on the meso-scale motivated by order execution scheduling algorithms. To do so, we carry out empirical analysis of the order flows from market and limit order submissions, aggregated from tick-by-tick data via volume-based bucketing, as well as various LOB depth and shape metrics. We document a nonlinear relationship between trade imbalance and price change, which however can be converted into a linear link by considering a weighted average of market and limit order flows. We also document a hockey-stick dependence between trade imbalance and one-sided limit order flows, highlighting numerous asymmetric effects between the active and passive sides of the LOB. To address the phenomenological features of price formation, we construct regression models to identify the most significant predictors, confirming the predictive power of limit order flows. Another finding is that the deeper LOB shape, rather than just the book imbalance, is more relevant on this timescale. The empirical results are based on analysis of six large-tick assets from Nasdaq.
Performance-Based Design of Perforated-Wall Caisson Breakwaters
Authors: Suh Kyung-Duck , Kim Nam-Hoon , Oh Sang-Ho , Ji Chang-Hwan , Kim Dong Hyawn
Published: June 2018

In this study, the performance-based design method developed for a conventional solid-wall caisson breakwater is extended to a perforated-wall caisson breakwater. First, to verify the mathematical model to calculate the sliding distance of a perforated-wall caisson, hydraulic experiment is conducted. A good agreement is shown between the model and experimental results. The developed performance-based design method is then compared with the conventional deterministic method in different water depths. Both the expected sliding distance and the exceedance percentage of total sliding distance during the structure lifetime decrease shorewards outside the surf zone, but they increase again toward the shore inside the surf zone. The performance-based design method is either more economical or less economical than the deterministic method depending on which design criterion is used. If the criterion for expected sliding distance or exceedance percentage is used in the ultimate limit state, the former method is less economical than the latter outside the surf zone, whereas the two methods are equally economical inside the surf zone. However, if the breakwater is designed to satisfy the criterion for exceedance percentage in the repairable limit state, the former method is more economical than the latter in all water depths.
DO BANKS GAME ON DYNAMIC PROVISIONING?
Authors: CARBO-VALVERDE SANTIAGO , RODRIGUEZ-FERNANDEZ FRANCISCO
Published: June 2018

Reducing credit procyclicality represents one of the key challenges on the regulatory agenda to reform the financial system architecture. Some early experiences may provide some insights on how countercyclical regulations may be effective. The Spanish dynamic provisions scheme implemented in 2000 is one of the main reference points in this context. We analyze the effects of dynamic provisions on managerial accounting discretion and ex-ante risk-taking behavior by banks. We empirically examine a sample of Spanish banks using quarterly information from 1995Q1 to 2013Q4. Our findings suggest that the counter-cyclicality of provisions has been reduced over time, as it has also been the case of managerial discretion (income smoothing and profit signaling). However, the results suggest that banks game on dynamic provisions by taking an ex-ante riskier behavior once the dynamic provisioning scheme is adopted.
Digital Human Models in Human Factors and Ergonomics Evaluation of Gesture Interfaces
Authors: Aromaa Susanna , Frangakis Nikos , Tedone Domenico , Viitaniemi Juhani , Aaltonen Iina
Published: June 2018

Gesture-based interfaces are becoming a widely used interaction modality in many industrial applications. Therefore, it is important to guarantee usable and ergonomic interfaces for workers. The purpose of this study was to investigate whether the use of digital human models (DHMs) by human factors/ergonomics (HFE) experts can complement the user evaluation of gesture interface prototypes. Two case studies were conducted, in which gesture-based systems for remote robot control were evaluated. The results indicate that the use of DHMs supports the findings from self-reported HFE evaluations. However, digital human modeling still has some limitations. For example, in this study, it was not possible to evaluate small muscle groups (e.g. fingers). We argue that adaptation of the DHMs could be a rapid and simple alternative for supporting the HFE design of gestures.
XD-AR
Authors: Speicher Maximilian , Hall Brian D. , Yu Ao , Zhang Bowen , Zhang Haihua , Nebeling Janet , Nebeling Michael
Published: June 2018

Augmented Reality (AR) developers face a proliferation of new platforms, devices, and frameworks. This often leads to applications being limited to a single platform and makes it hard to support collaborative AR scenarios involving multiple different devices. This paper presents XD-AR, a cross-device AR application development framework designed to unify input and output across hand-held, head-worn, and projective AR displays. XD-AR's design was informed by challenging scenarios for AR applications, a technical review of existing AR platforms, and a survey of 30 AR designers, developers, and users. Based on the results, we developed a taxonomy of AR system components and identified key challenges and opportunities in making them work together. We discuss how our taxonomy can guide the design of future AR platforms and applications and how cross-device interaction challenges could be addressed. We illustrate this when using XD-AR to implement two challenging AR applications from the literature in a device-agnostic way.
Djnn/Smala
Authors: Magnaudet Mathieu , Chatty Stéphane , Conversy Stéphane , Leriche Sébastien , Picard Celia , Prun Daniel
Published: June 2018

The persistent difficulty to develop and maintain interactive software has unveiled the inadequacy of traditional imperative programming languages. In the recent years, several solutions have been proposed to enrich the existing languages with constructs dedicated to interaction. In this paper, we propose a different approach that takes interaction as the primary concern to build a new programming language. We present Djnn, a conceptual framework based on the concepts of process and process activation, then we introduce Smala a programming language derived from this framework. We propose a solution for the unification of the concepts of event and data-flow, and for the derivation of complex control structures from a small set of basic ones. We detail the syntax and the semantics of Smala. Finally, we illustrate through a real-size application how it enables building all parts of an interactive software. Djnn and Smala may offer designers and programmers usable means to think of interactions and translate them into running code.
Metabolic Regulation of Transcription and Chromatin
Authors: Conaway Ronald C.
Published: June 2018

Although cell metabolism has been established as a major regulator of eukaryotic gene expression, the mechanisms underlying this regulation are still being uncovered. Recent years have seen great advances in our understanding of biochemical mechanisms of metabolic regulation of transcription and chromatin. Prime examples include insights into how nutrients and cellular energy status regulate synthesis of ribosomal RNAs by RNA polymerases I and III during ribosome biogenesis and how a variety of enzymes that catalyze modifications of histones in chromatin are regulated by the levels of certain metabolites. This volume of the Annual Review of Biochemistry includes a set of reviews describing these and other advances in understanding aspects of the metabolic regulation of RNA polymerases I and III transcription and chromatin.
Protein Quality Control Degradation in the Nucleus
Authors: Enam Charisma , Geffen Yifat , Ravid Tommer , Gardner Richard G.
Published: June 2018

Nuclear proteins participate in diverse cellular processes, many of which are essential for cell survival and viability. To maintain optimal nuclear physiology, the cell employs the ubiquitin-proteasome system to eliminate damaged and misfolded proteins in the nucleus that could otherwise harm the cell. In this review, we highlight the current knowledge about the major ubiquitin-protein ligases involved in protein quality control degradation (PQCD) in the nucleus and how they orchestrate their functions to eliminate misfolded proteins in different nuclear subcompartments. Many human disorders are causally linked to protein misfolding in the nucleus, hence we discuss major concepts that still need to be clarified to better understand the basis of the nuclear misfolded proteins’ toxic effects. Additionally, we touch upon potential strategies for manipulating nuclear PQCD pathways to ameliorate diseases associated with protein misfolding and aggregation in the nucleus.
Novel hemodynamic structures in the human glomerulus
Authors: Neal Christopher R. , Arkill Kenton P. , Bell James S. , Betteridge Kai B. , Bates David O. , Winlove C. Peter , Salmon Andrew H. J. , Harper Steven J.
Published: June 2018

To investigate human glomerular structure under conditions of physiological perfusion, we have analyzed fresh and perfusion-fixed normal human glomeruli at physiological hydrostatic and oncotic pressures using serial resin section reconstruction, confocal, multiphoton, and electron microscope imaging. Afferent and efferent arterioles (21.5 ± 1.2 µm and 15.9 ± 1.2 µm diameter), recognized from vascular origins, lead into previously undescribed wider regions (43.2 ± 2.8 µm and 38.4 ± 4.9 µm diameter) we have termed vascular chambers (VCs) embedded in the mesangium of the vascular pole. Afferent VC (AVC) volume was 1.6-fold greater than efferent VC (EVC) volume. From the AVC, long nonbranching high-capacity conduit vessels ( n = 7) (Con; 15.9 ± 0.7 µm diameter) led to the glomerular edge, where branching was more frequent. Conduit vessels have fewer podocytes than filtration capillaries. VCs were confirmed in fixed and unfixed specimens with a layer of banded collagen identified in AVC walls by multiphoton and electron microscopy. Thirteen highly branched efferent first-order vessels (E1; 9.9 ± 0.4 µm diameter) converge on the EVC, draining into the efferent arteriole (15.9 ± 1.2 µm diameter). Banded collagen was scarce around EVCs. This previously undescribed branching topology does not conform to the branching of minimum energy expenditure (Murray’s law), suggesting that even distribution of pressure/flow to the filtration capillaries is more important than maintaining the minimum work required for blood flow. We propose that AVCs act as plenum manifolds possibly aided by vortical flow in distributing and balancing blood flow/pressure to conduit vessels supplying glomerular lobules. These major adaptations to glomerular capillary structure could regulate hemodynamic pressure and flow in human glomerular capillaries.
Interhemispheric dominance switching in a neural network model for birdsong
Authors: Galvis Daniel , Wu Wei , Hyson Richard L. , Johnson Frank , Bertram Richard
Published: June 2018

Male zebra finches produce a sequence-invariant set of syllables, separated by short inspiratory gaps. These songs are learned from an adult tutor and maintained throughout life, making them a tractable model system for learned, sequentially ordered behaviors, particularly speech production. Moreover, much is known about the cortical, thalamic, and brain stem areas involved in producing this behavior, with the premotor cortical nucleus HVC (proper name) being of primary importance. In a previous study, our group developed a behavioral neural network model for birdsong constrained by the structural connectivity of the song system, the signaling properties of individual neurons and circuits, and circuit-breaking behavioral studies. Here we describe a more computationally tractable model and use it to explain the behavioral effects of unilateral cooling and electrical stimulations of HVC on song production. The model demonstrates that interhemispheric switching of song control is sufficient to explain these results, consistent with the hypotheses proposed when the experiments were initially conducted. Finally, we use the model to make testable predictions that can be used to validate the model framework and explain the effects of other perturbations of the song system, such as unilateral ablations of the primary input and output nuclei of HVC.

NEW & NOTEWORTHY In this report, we propose a two-hemisphere neural network model for the bilaterally symmetrical song system underlying birdsong in the male zebra finch. This model captures the behavioral effects of unilateral cooling and electrical stimulations of the premotor cortical nucleus HVC during song production, supporting the hypothesis of interhemispheric switching of song control. We use the model to make testable predictions regarding the behavioral effects of other unilateral perturbations to the song system.
Natural echolocation sequences evoke echo-delay selectivity in the auditory midbrain of the FM bat, Eptesicus fuscus
Authors: Macías Silvio , Luo Jinhong , Moss Cynthia F.
Published: June 2018

Echolocating bats must process temporal streams of sonar sounds to represent objects along the range axis. Neuronal echo-delay tuning, the putative mechanism of sonar ranging, has been characterized in the inferior colliculus (IC) of the mustached bat, an insectivorous species that produces echolocation calls consisting of constant frequency and frequency modulated (FM) components, but not in species that use FM signals alone. This raises questions about the mechanisms that give rise to echo-delay tuning in insectivorous bats that use different signal designs. To investigate whether stimulus context may account for species differences in echo-delay selectivity, we characterized single-unit responses in the IC of awake passively listening FM bats, Eptesicus fuscus, to broadcasts of natural sonar call-echo sequences, which contained dynamic changes in signal duration, interval, spectrotemporal structure, and echo-delay. In E. fuscus, neural selectivity to call-echo delay emerges in a population of IC neurons when stimulated with call-echo pairs presented at intervals mimicking those in a natural sonar sequence. To determine whether echo-delay selectivity also depends on the spectrotemporal features of individual sounds within natural sonar sequences, we studied responses to computer-generated echolocation signals that controlled for call interval, duration, bandwidth, sweep rate, and echo-delay. A subpopulation of IC neurons responded selectively to the combination of the spectrotemporal structure of natural call-echo pairs and their temporal patterning within a dynamic sonar sequence. These new findings suggest that the FM bat’s fine control over biosonar signal parameters may modulate IC neuronal selectivity to the dimension of echo-delay.

NEW & NOTEWORTHY Echolocating bats perform precise auditory temporal computations to estimate their distance to objects. Here, we report that response selectivity of neurons in the inferior colliculus of a frequency modulated bat to call-echo delay, or target range tuning, depends on the temporal patterning and spectrotemporal features of sound elements in a natural echolocation sequence. We suggest that echo responses to objects at different distances are gated by the bat’s active control over the spectrotemporal patterning of its sonar emissions.
Long-term effects of direct current are reproduced by intermittent depolarization of myelinated nerve fibers
Authors: Bączyk M. , Jankowska E.
Published: June 2018

Direct current (DC) potently increases the excitability of myelinated afferent fibers in the dorsal columns, both during DC polarization of these fibers and during a considerable (>1 h) postpolarization period. The aim of the present study was to investigate whether similarly long-lasting changes in the excitability of myelinated nerve fibers in the dorsal columns may be evoked by field potentials following stimulation of peripheral afferents and by subthreshold epidurally applied current pulses. The experiments were performed in deeply anesthetized rats. The effects were monitored by changes in nerve volleys evoked in epidurally stimulated hindlimb afferents and in the synaptic actions of these afferents. Both were found to be facilitated during as well as following stimulation of a skin nerve and during as well as following epidurally applied current pulses of 5- to 10-ms duration. The facilitation occurring ≤2 min after skin nerve stimulation could be linked to both primary afferent depolarization and large dorsal horn field potentials, whereas the subsequent changes (up to 1 h) were attributable to effects of the field potentials. The findings lead to the conclusion that the modulation of spinal activity evoked by DC does not require long-lasting polarization and that relatively short current pulses and intrinsic field potentials may contribute to plasticity in spinal activity. These results suggest the possibility of enhancing the effects of epidural stimulation in human subjects by combining it with polarizing current pulses and peripheral afferent stimulation and not only with continuous DC.

NEW & NOTEWORTHY The aim of this study was to define conditions under which a long-term increase is evoked in the excitability of myelinated nerve fibers. The results demonstrate that a potent and long-lasting increase in the excitability of afferent fibers traversing the dorsal columns may be induced by synaptically evoked intrinsic field as well as by epidurally applied intermittent current pulses. They thus provide a new means for the facilitation of the effects of epidural stimulation.
Emergent coordination with a brain–machine interface: implications for the neural basis of motor learning
Authors: Mangalam Madhur
Published: June 2018

How patterns of covariance in motor output and neural activity emerge over the course of learning is a topic of ongoing investigation. Vaidya et al. (Vaidya M, Balasubramanian K, Southerland J, Badreldin I, Eleryan A, Shattuck K, Gururangan S, Slutzky M, Osborne L, Fagg A, Oweiss K, Hatsopoulos NG. J Neurophysiol 119: 1291–1304, 2018) investigate the emergence of patterns of covariance in the motor output and neural activity in chronically amputated macaques learning reach-to-grasp movements with a brain–machine interface. The authors’ findings have implications for uncovering general principles of how neural coordination unfolds while learning a different motor behavior.
∆E/∆E Measurements of Energetic Ions Using CVD Diamond Detectors
Authors: Alghamdi Ahmed , Heilbronn Lawrence , Castellanos Luis A. , Lukosi Eric
Published: June 2018

Experimental and computational results of a ΔE/ΔE diamond detection system are presented. The ΔE/ΔE detection system was evaluated using energetic proton and iron beams striking thick polyethylene targets at the NASA Space Radiation Laboratory (NSRL) at Brookhaven National Laboratory (BNL). The measured data for diamond sensor A show good agreement with the Geant4 simulation. In addition, simulations have demonstrated the ability to identify hydrogen isotopes using a diamond detection system.
Channel‐Allocation Plan for National and Local T‐DAB Services in VHF Band III
Authors: Ju Sang-Lim , Baek Myung-Sun , Kim Kyung-Seok
Published: June 2018

The digital audio broadcasting (DAB) system is mainly designed for large‐area coverage and is suited for a single‐frequency network (SFN) operating in Very High Frequency (VHF) Band III. To operate successfully, the SFN requires a different network‐planning approach for multiple‐frequency networks and should avoid self‐interference. This paper focuses on nationwide SFN planning and DAB channel‐allocation planning to replace all frequency‐modulation (FM) services with terrestrial DAB services in VHF Band III. In South Korea, VHF Band III has been used for terrestrial digital multimedia broadcasting (T‐DMB) services; thus, available frequencies should be investigated for T‐DAB services and the nationwide SFN. An approach for broadcasting channel‐interference analysis is proposed herein. For the interference analysis, the geographical features and the information for stations of legacy FM radio broadcasting and T‐DMB, such as transmission parameters, are considered. The ratio of the interference area to the coverage is calculated via the channel‐interference analysis. Areas affected by the self‐interference in the nationwide SFN are investigated. The results of this paper provide insights regarding channel‐allocation planning for T‐DAB services and an approach for nationwide SFN planning.
Benign Scrotal Tumor in a Pediatric Patient: Epididymal Cyst
Authors: Fernández-Ibieta María , Villalon-Ferrero Flor , Ramos-García Jose Luis
Published: June 2018

A pediatric patient of 12 years consulted for a left scrotal mass of 2 months of evolution. After suspecting a cystic content due to positive transillumination, on ultrasonography a scrotal cyst separated from the testis, of 5 cm in its maximum length, was confirmed. Due to size, parental anxiety, and the referred short evolution, excision was decided. Given the clinical radiological findings, a scrotal incision was chosen, obtaining complete excision. Biopsy confirmed the diagnosis of simple epididymal cyst (EC). ECs usually present as painless, scrotal swelling in adolescents as a result of dilatation of the efferent epididymal tubules. Many cases (up to 60%) regress spontaneously. In these, average time to involute ranges from 4 to 50 months. Although cases of cyst torsion have been described (with pain derived from ischemia and inflammation), conservative management has been suggested in the majority, both in pediatric and in adult series. Surgery is recommended in some patients, due to testicular pain or increased paratesticular mass, as was our case.
Squamous Cell Carcinoma Arising within Verruca Vulgaris on the Nipple
Authors: Zaesim Araya , Jackson Amanda C. , Lee Sang Wook , Price Shaun A.
Published: June 2018

Cutaneous squamous cell carcinoma (SCC) is a common form of skin cancer and often appears as a hard, scaly lump that occasionally ulcerates. It is usually associated with cumulative exposure to ultraviolet light, although prior scarring, chronic wounds, exposure to radiation, HPV infection, and immunosuppression are also associated risk factors. Primary SCC of the nipple is very rare and only a few cases have been reported. We present a case of a 49-year-old female with concerns of a right nipple lesion with erythema and pain. She was initially evaluated for Paget’s disease with an underlying malignancy and cellulitis, but, after biopsy and investigation, she was found to have a well-differentiated SCC arising from a verruca vulgaris. Current literature does not provide distinct guidelines on management of SCC or its variants on the nipple, and the case was managed based off of SCC at other cutaneous sites as well as other cases of SCC on the nipple.
Effects of Iodixanol on Respiratory Functions during Coronary Angiography and the Role of Body Composition
Authors: Guzel Derya , Vural Mustafa Gokhan , Akdemir Ramazan
Published: June 2018

Purpose. The purposes of this study are to assess the acute effects of iodixanol, an iso-osmolar contrast media, on pulmonary functions and to evaluate the body composition in order to find out its role in causing this deterioration. Methods. 35 male and 25 female patients undergoing diagnostic coronary angiography (CA) were enrolled in the study. Before CA, all patients’ body compositions were evaluated by measuring their body mass indexes (BMIs) and waist-to-hip ratios (WHRs). Total body waters (TBWs), fat masses (FMs), fat-free masses (FFMs), and basal metabolism rates (BMRs) were measured via bioimpedance analysis. The CA was performed via radial artery route using iodixanol in every patient. The pulmonary function tests of these patients were performed before, during, and 2 hours after the CA. FEV1∆, FEF25–75%∆, and FVC∆ parameters were calculated by subtracting the measured baseline value from the measurement after the CA. Results. Angiography caused significant reduction in forced expiratory volume in 1 sec (FEV1, from 94.17 ± 18.83 to 84.45 ± 18.31, p<0.0001), forced vital capacity (FVC, from 96.57 ± 15.82 to 88.31 ± 17.96, p<0.0001), and forced expiratory flow at 25–75% (FEF25–75% from 82.54 ± 24.26 to 72.11 ± 25.41, p=0.001) and remained lower after 2 h after CA in male patients, respectively. FEV1 values were 103.40 ± 17.79 to 94.96 ± 17.063 (p=0.004); FVC values were 107.20 ± 19.03 to 99.08 ± 20.56 (p=0.009); and FEF25–75% values were 83.92 ± 24.30 to 73.24 ± 20.45 (p=0.005) before and after CA and remained lower after 2 h after CA in female patients, respectively. FEV1/FVC ratio remained unchanged. FEF25–75%∆ was statistically correlated with FFM, TBW, and WHR (p<0.05; r=−0.344, r=−0.347, and r=0.357, resp.), and FVC∆ was correlated with WHR in male patients (p=0.018, r=397). Conclusions. Our data suggested that diagnostic CA using iodixanol, an iso-osmolar contrast media, leads significant impairment in respiratory functions. Due to the persistence of these reductions even 2 hours after CA, ventilatory functions should be considered especially in patients whose body compositions or hydration levels are not within the desired physiological range.
Experimental Study on the Shear Strength of Cement‐Sand‐Gravel Material
Authors: Yang Jie , Cai Xin , Pang Qiong , Guo Xing-wen , Wu Ying-li , Zhao Jin-lei
Published: June 2018

An experimental study on the shear strength development of cement‐sand‐gravel (CSG) material was carried out using triaxial compression tests. The effects of the cementing agent content, aggregate content, and gradation on the shear strength of CSG material were analyzed. The shear strength remarkably increased with increasing cementing agent content and aggregate content for a given confining pressure. The increase in shear strength with increasing cementing agent content far exceeded that with increasing aggregate content. However, the stress‐strain curves and shear strength changed only slightly when the aggregate gradation for CSG material was adjusted. Based on the test data, a strength criterion for CSG material is proposed as a function of the cementing agent content, aggregate content, and shear strength of the aggregate gradation.
Single File Flow of Biomimetic Beads for Continuous SERS Recording in a Microfluidic Device
Authors: Calzavara Diego , Ferraro Davide , Litti Lucio , Cappozzo Greshia , Mistura Giampaolo , Meneghetti Moreno , Pierno Matteo
Published: June 2018

A major challenge in cancer treatment is the quantification of biomarkers associated with a specific cancer type. Important biomarkers are the circulating tumor cells (CTCs) detached from the main cancer and circulating in the blood. CTCs are very rare and their identification is still an issue. Although CTCs quantification can be estimated by using fluorescent markers, all the fluorescence techniques are strongly limited by the number of emissions (therefore markers) that can be discriminated with one exciting line, by their bleaching characteristics, and by the intrinsic autofluorescence of biological samples. An emerging technique that can overcome these limitations is Surface Enhanced Raman Scattering (SERS). Signals of vibrational origin with intensity similar to those of fluorescence, but narrower bandwidths, can be easily discriminated even by exciting with a single laser line. We recently showed the benefit of this method with cells fixed on a surface. However, this approach is too demanding to be applied in clinical routine. To effectively increase the throughput of the SERS analysis, microfluidics represents a promising tool. We report two different hydrodynamic strategies, based on device geometry and liquids viscosity, to successfully combine a microfluidic design with SERS.