bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sox2-Evf2 lncRNA-mediated mechanisms of chromosome topological control in developing forebrain
Authors: Cajigas Ivelisse , Chakraborty Abhijit , Lynam Madison , Swyter Kelsey R. , Bastidas Monique , Collens Linden , Luo Hao , Ay Ferhat , Kohtz Jhumku D. 
Published: February 2021

ABSTRACT
The Evf2 long non-coding RNA directs Dlx5/6 ultraconserved enhancer(UCE)-intrachromosomal interactions, regulating genes across a 27 Mb region on chromosome 6 in mouse developing forebrain. Here, we show that Evf2 long-range gene repression occurs through multi-step mechanisms involving the transcription factor Sox2. Evf2 directly interacts with Sox2, antagonizing Sox2 activation of Dlx5/6UCE, and recruits Sox2 to the Dlx5/6eii shadow enhancer and key Dlx5/6UCE interaction sites. Sox2 directly interacts with Dlx1 and Smarca4, as part of the Evf2 ribonucleoprotein complex, forming spherical subnuclear domains (protein pools, PPs). Evf2 targets Sox2 PPs to one long-range repressed target gene (Rbm28), at the expense of another (Akr1b8). Evf2 and Sox2 shift Dlx5/6UCE interactions towards Rbm28, linking Evf2/Sox2 co-regulated topological control and gene repression. We propose a model that distinguishes Evf2 gene repression mechanisms at Rbm28 (Dlx5/6UCE position) and Akr1b8 (limited Sox2 availability). Genome-wide control of RNPs (Sox2, Dlx and Smarca4) shows that co-recruitment influences Sox2 DNA binding. Together, these data suggest that Evf2 organizes a Sox2 PP subnuclear domain and, through Sox2-RNP sequestration and recruitment, regulates chromosome 6 long-range UCE targeting and activity with genome-wide consequences.
The lysosomotrope GPN mobilises Ca2+ from acidic organelles
Authors: Yuan Yu , Kilpatrick Bethan S. , Gerndt Susanne , Bracher Franz , Grimm Christian , Schapira Anthony H. , Patel Sandip 
Published: February 2021

ABSTRACT
Lysosomes are acidic Ca2+ stores often mobilised in conjunction with endoplasmic reticulum (ER) Ca2+ stores. Glycyl-L-phenylalanine 2-naphthylamide (GPN) is a widely used lysosomotropic agent that evokes cytosolic Ca2+ signals in many cells. However, whether these signals are the result of a primary action on lysosomes is unclear in light of recent evidence showing that GPN mediates direct ER Ca2+ release through changes in cytosolic pH. Here, we show that GPN evoked rapid increases in cytosolic pH but slower Ca2+ signals. NH4Cl evoked comparable changes in pH but failed to affect Ca2+. The V-type ATPase inhibitor, bafilomycin A1, increased lysosomal pH over a period of hours. Acute treatment modestly affected lysosomal pH and potentiated Ca2+ signals evoked by GPN. In contrast, chronic treatment led to more profound changes in luminal pH and selectively inhibited GPN action. GPN blocked Ca2+ responses evoked by the novel nicotinic acid adenine dinucleotide phosphate-like agonist, TPC2-A1-N. Therefore, GPN-evoked Ca2+ signals were better correlated with associated pH changes in the lysosome compared to the cytosol, and were coupled to lysosomal Ca2+ release. We conclude that Ca2+ signals evoked by GPN most likely derive from acidic organelles.
Experience, but not age, is associated with volumetric mushroom body expansion in solitary alkali bees
Authors: Hagadorn Mallory A. , Johnson Makenna M. , Smith Adam R. , Seid Marc A. , Kapheim Karen M. 
Published: February 2021

ABSTRACTIn social insects, changes in behavior are often accompanied by structural changes in the brain. This neuroplasticity may come with experience (experience-dependent) or age (experience-expectant). Yet, the evolutionary relationship between neuroplasticity and sociality is unclear, because we know little about neuroplasticity in the solitary relatives of social species. We used confocal microscopy to measure brain changes in response to age and experience in a solitary halictid bee (Nomia melanderi). First, we compared the volume of individual brain regions among newly emerged females, laboratory females deprived of reproductive and foraging experience, and free-flying, nesting females. Experience, but not age, led to significant expansion of the mushroom bodies – higher-order processing centers associated with learning and memory. Next, we investigated how social experience influences neuroplasticity by comparing the brains of females kept in the laboratory either alone or paired with another female. Paired females had significantly larger olfactory regions of the mushroom bodies. Together, these experimental results indicate that experience-dependent neuroplasticity is common to both solitary and social taxa, whereas experience-expectant neuroplasticity may be an adaptation to life in a social colony. Further, neuroplasticity in response to social chemical signals may have facilitated the evolution of sociality.
Experimenting in Equilibrium
Authors: Wager Stefan , Xu Kuang 
Published: February 2021

Classical approaches to experimental design assume that intervening on one unit does not affect other units. There are many important settings, however, where this noninterference assumption does not hold, as when running experiments on supply-side incentives on a ride-sharing platform or subsidies in an energy marketplace. In this paper, we introduce a new approach to experimental design in large-scale stochastic systems with considerable cross-unit interference, under an assumption that the interference is structured enough that it can be captured via mean-field modeling. Our approach enables us to accurately estimate the effect of small changes to system parameters by combining unobtrusive randomization with lightweight modeling, all while remaining in equilibrium. We can then use these estimates to optimize the system by gradient descent. Concretely, we focus on the problem of a platform that seeks to optimize supply-side payments [Formula: see text] in a centralized marketplace where different suppliers interact via their effects on the overall supply-demand equilibrium, and we show that our approach enables the platform to optimize [Formula: see text] in large systems using vanishingly small perturbations. This paper was accepted by Hamid Nazerzadeh, big data analytics.
Assessment of preschool children's sleep habits in relation to the time spent watching television
Authors: Matziou Theodora , Perdikaris Pantelis , Vlachioti Efrosini , Konstantaki Evanthia , Koumpagioti Despoina , Boutopoulou Varvara , Nteli Charalampia , Matziou Vasiliki 
Published: February 2021

Aims To assess preschool children's sleep habits and television viewing habits, parents' perceptions about TV viewing and any correlation between the two. Methods The study was conducted between March and June 2018 in randomly selected kindergartens of a large city in Greece. A total of 100 pre-school children and their parents participated in the study. Two questionnaires, the Children's Sleep Habits Questionnaire (CSHQ) and the Children's Television-Viewing Habits Questionnaire (CTVQ), were validated in Greek and used for this study. Results Children's age (P=0.001), parents' educational level (P<0.001) and number of siblings (P<0.001) were found to significantly affect the time children spent watching TV daily. Fathers' age (P=0.004), number of siblings (P=0.001) and time children spent watching TV daily (P=0.007) were negatively correlated with CSHQ score. Conclusions Pre-school aged children spend a large amount of time watching TV, which results in altered sleep patterns, despite parents encouraging them to participate in other activities. Healthcare professionals should provide parents, teachers and children with evidence-based information and advice in order to lower the incidence of sleep disorders resulting from excessive time spent watching TV.
Returns to Workplace Training for Male and Female Employees and Implications for the Gender Wage gap: A Quantile Regression Analysis
Authors: Icardi Rossella 
Published: February 2021

Context: Existing studies have explored the association between workplace training and wages suggesting that training participation may have a positive association with wages. However, we still know very little about whether this association varies between men and women. Through its potential positive association with wages, training may balance wage differences between men and women. In addition, the gender wage gap varies across the wage distribution. Differences in the association between training participation and wages for men and women across the earnings spectrum may offer an explanation as to why the discrepancy in female/male earnings is larger at some point of the wage distribution compared to others. Approach: Using data from the Programme for International Assessment of Adult Competencies (PIAAC) and unconditional quantile regression, this paper examines whether the association between workplace training and wages differs between men and women at different points of the wage distribution across 14 European countries. To partly control for endogeneity in training participation, detailed measures of cognitive skills have been included in the models. Findings: Findings show gender differences in the association between training and wages across the wage distribution. In most countries, results indicate larger training coefficients for women than men at the lower end of the wage spectrum whereas they are larger for men at the top. This pattern holds across most countries with the only exception of Liberal ones, where women benefit less than men across the entire wage spectrum.Conclusions: The findings of this work reveal that distributional variations in returns to workplace training follow a similar pattern across industrialized countries, despite their different institutional settings. Moreover, differences in training coefficients of men and women at different parts of the wage distribution suggest that training could reduce gender wage differences among low earners and potentially widen the gap in wages among individuals at the top of the wage distribution.
Long-range optical coherence tomography with extended depth-of-focus: a
visual feedback system for smart laser osteotomy
Authors: Hamidi Arsham , Bayhaqi Yakub A. , Canbaz Ferda , Navarini Alexander A. , Cattin Philippe C. , Zam Azhar 
Published: February 2021

This work presents a long-range and extended depth-of-focus optical coherence tomography (OCT) system using a Bessel-like beam (BLB) as a visual feedback system during laser osteotomy. We used a swept-source OCT system (λ
c
= 1310 nm) with an imaging range of 26.2 mm in the air, integrated with a high energy microsecond Er:YAG laser operating at 2.94 µm. We demonstrated that the self-healing characteristics of the BLB could reduce the imaging artifacts that may arise during real-time monitoring of laser ablation. Furthermore, the feasibility of using long-range OCT to monitor a deep laser-induced incision is demonstrated.
2.7 µm band enhancement induced by energy transfer in Er3+/Tm3+ co-doped tellurite glass
Authors: Zhang Yu , Xia Lizhang , Ding Jiale , Li Chengyan , Shen Xinjie , Li Jun , Zhou Yaxun 
Published: February 2021

In this work, the improvement of 2.7 µm band mid-infrared fluorescence of

E
r

3
+

was investigated. When 0.6 mol%

T
m

2

O

3

was incorporated into the tellurite glass doped with 0.5 mol%

E
r

2

O

3

, the 2.7 µm band fluorescence originating from the

E
r

3
+

:

4

I

11

/

2

→

4

I

13

/

2

transition underwent significant enhancement up to 2.3 times under the excitation of an 808 nm laser diode. This enhancement was attributed to the energy transfers between

T
m

3
+

and

E
r

3
+

ions. The energy transfer mechanism was investigated quantitatively by calculating the microparameters and phonon contributions. The obtained result indicated that

E
r

3
+

/

T
m

3
+

co-doped tellurite glass is a promising candidate applied for 2.7 µm band optoelectronic devices.
Thermal and non-thermal intensity dependent optical nonlinearities in ethanol at 800  nm, 1480  nm, and 1560  nm
Authors: Bautista Jessica E. Q. , da Silva-Neto Manoel L. , Campos Cecilia L. A. V. , Maldonado Melissa , de Araújo Cid B. , Gomes Anderson S. L. 
Published: February 2021

Intensity dependent self-action of a continuous wave (CW) or pulsed
optical beam can lead to spatial or spectral effects upon propagation
through a nonlinear medium, which can be described as an intensity
dependence of the refractive index, known as self-phase modulation
(SPM). In this work, we revisit the nonlinear optical propagation of a
CW and a CW mode-locked (CW-ML) high repetition rate [

∼

megahertz (MHz)] laser propagating
through pure ethanol in regions of very low optical absorption
(800 nm) or very high absorption (1480 nm, 1560 nm). Spatial and
spectral SPM and

Z

-scan experiments were performed to
clarify the origin of the third-order nonlinear optical response in
the different optical excitation regimes. From spatial SPM and

Z

-scan at either CW or CW-ML MHz
regime, a thermal nonlinear response was determined to be the origin
of the nonlinearity at 800 nm or 1480 nm, 1560 nm region, with the
nonlinear refractive index response of the order of

10

−
4

−

10

−
9

c
m

2

/

W

. From the spectral SPM, the
non-thermal origin of the nonlinearity, arising from electronic or
nuclear processes in the ethanol, was determined, and values of the
order of

10

−
13

−

10

−
16

c
m

2

/

W

were obtained, depending upon the
spectral region. The results were supported by theoretical
calculations using the nonlinear Schrödinger equation for the spectral
behavior or Fresnel–Kirchhoff integral for the spatial results and
clarify some of the misinterpreted results reported in the literature,
besides complementing other nonlinear refraction data available at
different wavelengths from 355 nm to 1560 nm.
High-performance all-silicon polarizer with 415  nm bandwidth
Authors: Liu Weixi , Dai Daoxin , Shi Yaocheng 
Published: February 2021

On-chip silicon polarizers have been widely used in polarization controllers. However, there is limited research on all-silicon polarizer covering the whole optical communication band due to the strong waveguide dispersion for silicon waveguides. In this Letter, we demonstrated an all-silicon TE polarizer with high polarization extinction ratio and low insertion loss, working for the whole optical communication band. The device is based on a shallow-etched waveguide realized on a silicon-on-insulator (SOI) platform. The optical field of TE polarization is designed to be tightly confined in the shallow-etched silicon waveguide, while that of TM polarization is weakly confined. As a result, TE polarization propagates through the waveguide with low loss, while TM polarization leaks into the substrate and decays finally. The measurements show that a maximum insertion loss

<

0.25

d
B

and polarization extinction ratio

(

P
E
R

)
>

20

d
B

over an ultrabroad operation band from 1260–1675 nm have been achieved for the proposed polarizer.
Imd pathway-specific immune assays reveal NF-κB stimulation by viral RNA PAMPs in Aedes aegypti Aag2 cells
Authors: Russell Tiffany A. , Ayaz Andalus , Davidson Andrew D. , Fernandez-Sesma Ana , Maringer Kevin 
Published: February 2021

Background
The mosquito Aedes aegypti is a major vector for the arthropod-borne viruses (arboviruses) chikungunya, dengue, yellow fever and Zika viruses. Vector immune responses pose a major barrier to arboviral transmission, and transgenic insects with altered immunity have been proposed as tools for reducing the global public health impact of arboviral diseases. However, a better understanding of virus-immune interactions is needed to progress the development of such transgenic insects. Although the NF-κB-regulated Toll and ‘immunodeficiency’ (Imd) pathways are increasingly thought to be antiviral, relevant pattern recognition receptors (PRRs) and pathogen-associated molecular patterns (PAMPs) remain poorly characterised in A. aegypti.

Methodology/Principle findings
We developed novel RT-qPCR and luciferase reporter assays to measure induction of the Toll and Imd pathways in the commonly used A. aegypti-derived Aag2 cell line. We thus determined that the Toll pathway is not inducible by exogenous stimulation with bacterial, viral or fungal stimuli in Aag2 cells under our experimental conditions. We used our Imd pathway-specific assays to demonstrate that the viral dsRNA mimic poly(I:C) is sensed by the Imd pathway, likely through intracellular and extracellular PRRs. The Imd pathway was also induced during infection with the model insect-specific virus cricket paralysis virus (CrPV).

Conclusions/Significance
Our demonstration that a general PAMP shared by many arboviruses is sensed by the Imd pathway paves the way for future studies to determine how viral RNA is sensed by mosquito PRRs at a molecular level. Our data also suggest that studies measuring inducible immune pathway activation through antimicrobial peptide (AMP) expression in Aag2 cells should be interpreted cautiously given that the Toll pathway is not responsive under all experimental conditions. With no antiviral therapies and few effective vaccines available to treat arboviral diseases, our findings provide new insights relevant to the development of transgenic mosquitoes as a means of reducing arbovirus transmission.
Genomic and RT-qPCR analysis of trimethoprim-sulfamethoxazole and meropenem resistance in Burkholderia pseudomallei clinical isolates
Authors: Schnetterle Marine , Gorgé Olivier , Nolent Flora , Boughammoura Aïda , Sarilar Véronique , Vigier Cécile , Guillier Sophie , Koch Lionel , Degand Nicolas , Ramisse Vincent , Tichadou Xavier , Girleanu Maria , Favier Anne-Laure , Valade Eric , Biot Fabrice , Neulat-Ripoll Fabienne 
Published: February 2021

Background
Melioidosis is an endemic disease in southeast Asia and northern Australia caused by the saprophytic bacteria Burkholderia pseudomallei, with a high mortality rate. The clinical presentation is multifaceted, with symptoms ranging from acute septicemia to multiple chronic abscesses. Here, we report a chronic case of melioidosis in a patient who lived in Malaysia in the 70s and was suspected of contracting tuberculosis. Approximately 40 years later, in 2014, he was diagnosed with pauci-symptomatic melioidosis during a routine examination. Four strains were isolated from a single sample. They showed divergent morphotypes and divergent antibiotic susceptibility, with some strains showing resistance to trimethoprim-sulfamethoxazole and fluoroquinolones. In 2016, clinical samples were still positive for B. pseudomallei, and only one type of strain, showing atypical resistance to meropenem, was isolated.

Principal findings
We performed whole genome sequencing and RT-qPCR analysis on the strains isolated during this study to gain further insights into their differences. We thus identified two types of resistance mechanisms in these clinical strains. The first one was an adaptive and transient mechanism that disappeared during the course of laboratory sub-cultures; the second was a mutation in the efflux pump regulator amrR, associated with the overexpression of the related transporter.

Conclusion
The development of such mechanisms may have a clinical impact on antibiotic treatment. Indeed, their transient nature could lead to an undiagnosed resistance. Efflux overexpression due to mutation leads to an important multiple resistance, reducing the effectiveness of antibiotics during treatment.
Abdominal ultrasound in the diagnostic work-up of visceral leishmaniasis and for detection of complications of spleen aspiration
Authors: Mohammed Rezika , Gebrewold Yonathan , Schuster Angela , Fikre Helina , Mekonnen Tigist , Mulaw Tadele , Bogale Tadfe , Vogt Florian , Diro Ermias , van Griensven Johan 
Published: February 2021

Introduction
Abdominal ultrasound (US) is increasingly used in the diagnostic work-up of infectious diseases, but studies on its diagnostic value in visceral leishmaniasis (VL) are lacking. US could help to identify complications of spleen aspiration (SA). We aimed to assess the diagnostic value of US and the evolution of findings after VL treatment; the incidence and degree of splenic injury; and the pain perceived during SA.

Methodology/result
We conducted a cross-sectional prospective study at the Leishmaniasis Research and Treatment Center, Gondar, Ethiopia between Oct 2017 and Dec 2018. We enrolled VL suspects undergoing tissue aspiration; US were conducted before and after SA, and at the end of VL treatment. Splenic injury was graded using the American association of surgery trauma injury scale (grade 1–4). The pain perceived during SA was graded using a visual analogue scale. Out of 392 VL suspects, 192 (49%) were confirmed VL cases. The median age was 25 years (IQR 21–30). Massive splenomegaly and hepatomegaly were the most common US findings. Splenic nodules were seen in 3.7% of the 190 VL cases and 1.5% of the 197 non-VL cases. Ascites was more common in VL (16.4%) than in non-VL cases (9.1%). The frequency of US abnormalities decreased with treatment. None of the US findings had sufficient sensitivity and specificity to justify its use as a diagnostic test. US detected splenic injury in four of the 318 patients who had post-SA US. All four patients remained clinically stable. Pain was perceived as moderate or severe in 51% of patients.

Conclusion
The diagnostic value of abdominal US for VL was low but found useful to detect subclinical splenic injury. SA caries a risk of splenic injury and was perceived painful by most. Further research on less invasive diagnostic tools is needed.
Comparison of clinical characteristics of Zika and dengue symptomatic infections and other acute illnesses of unidentified origin in Mexico
Authors: Belaunzarán-Zamudio Pablo F. , Mateja Allyson , Guerra-de-Blas Paola del Carmen , Rincón-León Héctor A. , Navarro-Fuentes Karla , Ruiz-Hernández Emilia , Caballero-Sosa Sandra , Camas-Durán Francisco , Priego-Smith Zoila , Nájera-Cancino José G , López-Roblero Alexander , del Carmen Trujillo-Murillo Karina , Powers John H. , Hunsberger Sally , Siddiqui Sophia , Beigel John H. , Valdés-Salgado Raydel , Ruiz-Palacios Guillermo ,   the Mexican Emerging Infectious Diseases Clinical Research Network (LaRed)
Published: February 2021

Background
Our purpose was to provide a detailed clinical description, of symptoms and laboratory abnormalities, and temporality in patients with confirmed Zika and dengue infections, and other acute illnesses of unidentified origin (AIUO).

Methods/ Principal findings
This was a two-year, multicenter, observational, prospective, cohort study. We collected data from patients meeting the Pan American Health Organization’s modified case-definition criteria for probable Zika infection. We identified Zika, dengue chikungunya by RT-PCR in serum and urine. We compared characteristics between patients with confirmed Zika and dengue infections, Zika and AIUO, and Dengue and AIUO at baseline, Days 3,7,28 and 180 of follow-up. Most episodes (67%) consistent with the PAHO definition of probable Zika could not be confirmed as due to any flavivirus and classified as Acute Illnesses of Unidentified Origin (AIUO). Infections by Zika and dengue accounted for 8.4% and 16% of episodes. Dengue patients presented with fever, generalized non-macular rash, arthralgia, and petechiae more frequently than patients with Zika during the first 10 days of symptoms. Dengue patients presented with more laboratory abnormalities (lower neutrophils, lymphocytosis, thrombocytopenia and abnormal liver function tests), with thrombocytopenia lasting for 28 days. Zika patients had conjunctivitis, photophobia and localized macular rash more frequently than others. Few differences persisted longer than 10 days after symptoms initiation: conjunctivitis in Zika infections, and self-reported rash and petechia in dengue infections.

Conclusions
Our study helps characterize the variety and duration of clinical features in patients with Zika, dengue and AIUO. The lack of diagnosis in most patients points to need for better diagnostics to assist clinicians in making specific etiologic diagnoses.