bluuebunny/crossref_metadata_2025 huggingface dataset:
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.
Multi-aperture system approach for snapshot multispectral imaging applications
Authors: Hubold Martin , Montag Elisabeth , Berlich René , Brunner Robert , Brüning Robert
Published: February 2021

We present an ultra-compact system approach for snapshot, multispectral imaging. It is based on a slanted linear variable spectral filter mounted in close proximity to the entrance pupil of a micro-optical, multi-aperture imaging system. A compact demonstration setup with a size of only 60 × 60 × 28 mm3 is developed, which enables the acquisition of 66 spectral channels in a single shot and offers a linear spectral sampling of approximately six nanometers over an extended wavelength range of 450-850 nm. The spatial sampling of each channel covers up to 400 × 400 pixels. First, the concept, the optical design and the fabrication are detailed. After the optical performance characterization, a comprehensive calibration strategy is developed and applied. An experimental demonstration is performed by acquiring the spatial and the spectral information of an imaged test scene.
Neural-adjoint method for the inverse design of all-dielectric metasurfaces
Authors: Deng Yang , Ren Simiao , Fan Kebin , Malof Jordan M. , Padilla Willie J.
Published: February 2021

All-dielectric metasurfaces exhibit exotic electromagnetic responses, similar to those obtained with metal-based metamaterials. Research in all-dielectric metasurfaces currently uses relatively simple unit-cell designs, but increased geometrical complexity may yield even greater scattering states. Although machine learning has recently been applied to the design of metasurfaces with impressive results, the much more challenging task of finding a geometry that yields a desired spectra remains largely unsolved. We propose and demonstrate a method capable of finding accurate solutions to ill-posed inverse problems, where the conditions of existence and uniqueness are violated. A specific example of finding the metasurface geometry which yields a radiant exitance matching the external quantum efficiency of gallium antimonide is demonstrated. We also show how the neural-adjoint method can intelligently grow the design search space to include designs that increasingly and accurately approximate the desired scattering response. The neural-adjoint method is not restricted to the case demonstrated and may be applied to plasmonics, photonic crystal, and other artificial electromagnetic materials.
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.
Direct generation of relativistic isolated attosecond pulses in transmission from laser-driven plasmas
Authors: Jiang Yan , Chen Zi-Yu , Liu Zhanjun , Cao Lihua , Zheng Chunyang , Xie Rui , Chao Yue , He Xiantu
Published: February 2021

Isolated attosecond pulses are useful to perform pump–probe experiments at a high temporal resolution, and provide a new tool for ultrafast metrology. However, it is still a challenging task to generate such pulses of high intensity, even for a few-cycle laser. Through particle-in-cell simulations, we show that it is possible to directly generate a giant isolated attosecond pulse in the transmission direction from relativistic laser-driven plasmas. Compared to attosecond pulse generation in the reflection direction, no further spectral filtering is needed. The underlying radiation mechanism is coherent synchrotron emission, and the transmitted isolated attosecond pulse can reach relativistic intensity. This provides a promising alternative to generate intense isolated attosecond pulses for ultrafast studies.
Optimum design of NOLM-driven mode-locked fiber lasers
Authors: Malfondet A. , Parriaux A. , Krupa K. , Millot G. , Tchofo-Dinda P.
Published: February 2021

Most of the saturable absorbers commonly used to perform mode locking in laser cavities affect the trigger conditions of laser oscillation, which requires manually forcing the laser start-up by various means such as polarization controllers. We present a procedure for designing a laser cavity driven by a nonlinear optical loop mirror, which allows the laser to operate optimally without interfering with the oscillation triggering conditions, thus opening up possibilities for integration of this type of laser.
The protease corin regulates electrolyte homeostasis in eccrine sweat glands
Authors: He Meiling , Zhou Tiantian , Niu Yayan , Feng Wansheng , Gu Xiabing , Xu Wenting , Zhang Shengnan , Wang Zhiting , Zhang Yue , Wang Can , Dong Liang , Liu Meng , Dong Ningzheng , Wu Qingyu
Published: February 2021

Sweating is a basic skin function in body temperature control. In sweat glands, salt excretion and reabsorption are regulated to avoid electrolyte imbalance. To date, the mechanism underlying such regulation is not fully understood. Corin is a transmembrane protease that activates atrial natriuretic peptide (ANP), a cardiac hormone essential for normal blood volume and pressure. Here, we report an unexpected role of corin in sweat glands to promote sweat and salt excretion in regulating electrolyte homeostasis. In human and mouse eccrine sweat glands, corin and ANP are expressed in the luminal epithelial cells. In corin-deficient mice on normal- and high-salt diets, sweat and salt excretion is reduced. This phenotype is associated with enhanced epithelial sodium channel (ENaC) activity that mediates Na+ and water reabsorption. Treatment of amiloride, an ENaC inhibitor, normalizes sweat and salt excretion in corin-deficient mice. Moreover, treatment of aldosterone decreases sweat and salt excretion in wild-type (WT), but not corin-deficient, mice. These results reveal an important regulatory function of corin in eccrine sweat glands to promote sweat and salt excretion.
Spec2Vec: Improved mass spectral similarity scoring through learning of structural relationships
Authors: Huber Florian , Ridder Lars , Verhoeven Stefan , Spaaks Jurriaan H. , Diblen Faruk , Rogers Simon , van der Hooft Justin J. J.
Published: February 2021

Spectral similarity is used as a proxy for structural similarity in many tandem mass spectrometry (MS/MS) based metabolomics analyses such as library matching and molecular networking. Although weaknesses in the relationship between spectral similarity scores and the true structural similarities have been described, little development of alternative scores has been undertaken. Here, we introduce Spec2Vec, a novel spectral similarity score inspired by a natural language processing algorithm—Word2Vec. Spec2Vec learns fragmental relationships within a large set of spectral data to derive abstract spectral embeddings that can be used to assess spectral similarities. Using data derived from GNPS MS/MS libraries including spectra for nearly 13,000 unique molecules, we show how Spec2Vec scores correlate better with structural similarity than cosine-based scores. We demonstrate the advantages of Spec2Vec in library matching and molecular networking. Spec2Vec is computationally more scalable allowing structural analogue searches in large databases within seconds.
Deep6mA: A deep learning framework for exploring similar patterns in DNA N6-methyladenine sites across different species
Authors: Li Zutan , Jiang Hangjin , Kong Lingpeng , Chen Yuanyuan , Lang Kun , Fan Xiaodan , Zhang Liangyun , Pian Cong
Published: February 2021

N6-methyladenine (6mA) is an important DNA modification form associated with a wide range of biological processes. Identifying accurately 6mA sites on a genomic scale is crucial for under-standing of 6mA’s biological functions. However, the existing experimental techniques for detecting 6mA sites are cost-ineffective, which implies the great need of developing new computational methods for this problem. In this paper, we developed, without requiring any prior knowledge of 6mA and manually crafted sequence features, a deep learning framework named Deep6mA to identify DNA 6mA sites, and its performance is superior to other DNA 6mA prediction tools. Specifically, the 5-fold cross-validation on a benchmark dataset of rice gives the sensitivity and specificity of Deep6mA as 92.96% and 95.06%, respectively, and the overall prediction accuracy is 94%. Importantly, we find that the sequences with 6mA sites share similar patterns across different species. The model trained with rice data predicts well the 6mA sites of other three species:Arabidopsis thaliana,Fragaria vescaandRosa chinensiswith a prediction accuracy over 90%. In addition, we find that (1) 6mA tends to occur at GAGG motifs, which means the sequence near the 6mA site may be conservative; (2) 6mA is enriched in the TATA box of the promoter, which may be the main source of its regulating downstream gene expression.
Genetic loci associated with skin pigmentation in African Americans and their effects on vitamin D deficiency
Authors: Batai Ken , Cui Zuxi , Arora Amit , Shah-Williams Ebony , Hernandez Wenndy , Ruden Maria , Hollowell Courtney M. P. , Hooker Stanley E. , Bathina Madhavi , Murphy Adam B. , Bonilla Carolina , Kittles Rick A.
Published: February 2021

A recent genome-wide association study (GWAS) in African descent populations identified novel loci associated with skin pigmentation. However, how genomic variations affect skin pigmentation and how these skin pigmentation gene variants affect serum 25(OH) vitamin D variation has not been explored in African Americans (AAs). In order to further understand genetic factors that affect human skin pigmentation and serum 25(OH)D variation, we performed a GWAS for skin pigmentation with 395 AAs and a replication study with 681 AAs. Then, we tested if the identified variants are associated with serum 25(OH) D concentrations in a subset of AAs (n = 591). Skin pigmentation, Melanin Index (M-Index), was measured using a narrow-band reflectometer. Multiple regression analysis was performed to identify variants associated with M-Index and to assess their role in serum 25(OH)D variation adjusting for population stratification and relevant confounding variables. A variant near theSLC24A5gene (rs2675345) showed the strongest signal of association with M-Index (P= 4.0 x 10−30in the pooled dataset). Variants inSLC24A5,SLC45A2andOCA2together account for a large proportion of skin pigmentation variance (11%). The effects of these variants on M-Index was modified by sex (Pfor interaction = 0.009). However, West African Ancestry (WAA) also accounts for a large proportion of M-Index variance (23%). M-Index also varies among AAs with high WAA and high Genetic Score calculated from top variants associated with M-Index, suggesting that other unknown genomic factors related to WAA are likely contributing to skin pigmentation variation. M-Index was not associated with serum 25(OH)D concentrations, but the Genetic Score was significantly associated with vitamin D deficiency (serum 25(OH)D levels less than 12 ng/mL) (OR, 1.30; 95% CI, 1.04–1.64). The findings support the hypothesis suggesting that skin pigmentation evolved responding to increased demand for subcutaneous vitamin D synthesis in high latitude environments.
Split versions of Cleave and Rescue selfish genetic elements for measured self limiting gene drive
Authors: Oberhofer Georg , Ivy Tobin , Hay Bruce A.
Published: February 2021

Gene drive elements promote the spread of linked traits, providing methods for changing the composition or fate of wild populations. Drive mechanisms that are self-limiting are attractive because they allow control over the duration and extent of trait spread in time and space, and are reversible through natural selection as drive wanes. Self-sustainingCleave and Rescue(ClvR) elements include a DNA sequence-modifying enzyme such as Cas9/gRNAs that disrupts endogenous versions of an essential gene, a tightly linked recoded version of the essential gene resistant to cleavage (theRescue), and a Cargo.ClvRspreads by creating loss-of-function (LOF) conditions in which those withoutClvRdie because they lack functional copies of the essential gene. We use modeling to show that when theRescue-Cargo and one or both components required for LOF allele creation (Cas9 and gRNA) reside at different locations (splitClvR), drive ofRescue-Cargo is self-limiting due to a progressive decrease in Cas9 frequency, and thus opportunities for creation of LOF alleles, as spread occurs. Importantly, drive strength and duration can be extended in a measured manner—which is still self-limiting—by moving the two components close enough to each other that they experience some degree of linkage. With linkage, Cas9 transiently experiences drive by hitchhiking withRescue-Cargo until linkage disequilibrium between the two disappears, a function of recombination frequency and number of generations, creating a novel point of control. We implement splitClvRinDrosophila, with key elements on different chromosomes. Cargo/Rescue/gRNAs spreads to high frequency in a Cas9-dependent manner, while the frequency of Cas9 decreases. These observations show that measured, transient drive, coupled with a loss of future drive potential, can be achieved using the simple toolkit that make upClvRelements—Cas9 and gRNAs and aRescue/Cargo.
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.
Heterogeneity in response to serological exposure markers of recent Plasmodium vivax infections in contrasting epidemiological contexts
Authors: Rosado Jason , White Michael T. , Longley Rhea J. , Lacerda Marcus , Monteiro Wuelton , Brewster Jessica , Sattabongkot Jetsumon , Guzman-Guzman Mitchel , Llanos-Cuentas Alejandro , Vinetz Joseph M. , Gamboa Dionicia , Mueller Ivo
Published: February 2021

Background

Antibody responses as serological markers of Plasmodium vivax infection have been shown to correlate with exposure, but little is known about the other factors that affect antibody responses in naturally infected people from endemic settings. To address this question, we studied IgG responses to novel serological exposure markers (SEMs) of P. vivax in three settings with different transmission intensity.

Methodology

We validated a panel of 34 SEMs in a Peruvian cohort with up to three years’ longitudinal follow-up using a multiplex platform and compared results to data from cohorts in Thailand and Brazil. Linear regression models were used to characterize the association between antibody responses and age, the number of detected blood-stage infections during follow-up, and time since previous infection. Receiver Operating Characteristic (ROC) analysis was used to test the performance of SEMs to identify P. vivax infections in the previous 9 months.

Principal findings

Antibody titers were associated with age, the number of blood-stage infections, and time since previous P. vivax infection in all three study sites. The association between antibody titers and time since previous P. vivax infection was stronger in the low transmission settings of Thailand and Brazil compared to the higher transmission setting in Peru. Of the SEMs tested, antibody responses to RBP2b had the highest performance for classifying recent exposure in all sites, with area under the ROC curve (AUC) = 0.83 in Thailand, AUC = 0.79 in Brazil, and AUC = 0.68 in Peru.

Conclusions

In low transmission settings, P. vivax SEMs can accurately identify individuals with recent blood-stage infections. In higher transmission settings, the accuracy of this approach diminishes substantially. We recommend using P. vivax SEMs in low transmission settings pursuing malaria elimination, but they are likely to be less effective in high transmission settings focused on malaria control.
PI Prob: A risk prediction and clinical guidance system for evaluating patients with recurrent infections
Authors: Rider Nicholas L. , Cahill Gina , Motazedi Tina , Wei Lei , Kurian Ashok , Noroski Lenora M. , Seeborg Filiz O. , Chinn Ivan K. , Roberts Kirk
Published: February 2021

Background

Primary immunodeficiency diseases represent an expanding set of heterogeneous conditions which are difficult to recognize clinically. Diagnostic rates outside of the newborn period have not changed appreciably. This concern underscores a need for novel methods of disease detection.

Objective

We built a Bayesian network to provide real-time risk assessment about primary immunodeficiency and to facilitate prescriptive analytics for initiating the most appropriate diagnostic work up. Our goal is to improve diagnostic rates for primary immunodeficiency and shorten time to diagnosis. We aimed to use readily available health record data and a small training dataset to prove utility in diagnosing patients with relatively rare features.

Methods

We extracted data from the Texas Children’s Hospital electronic health record on a large population of primary immunodeficiency patients (n = 1762) and appropriately-matched set of controls (n = 1698). From the cohorts, clinically relevant prior probabilities were calculated enabling construction of a Bayesian network probabilistic model(PI Prob). Our model was constructed with clinical-immunology domain expertise, trained on a balanced cohort of 100 cases-controls and validated on an unseen balanced cohort of 150 cases-controls. Performance was measured by area under the receiver operator characteristic curve (AUROC). We also compared our network performance to classic machine learning model performance on the same dataset.

Results

PI Prob was accurate in classifying immunodeficiency patients from controls (AUROC = 0.945; p<0.0001) at a risk threshold of ≥6%. Additionally, the model was 89% accurate for categorizing validation cohort members into appropriate International Union of Immunological Societies diagnostic categories. Our network outperformed 3 other machine learning models and provides superior transparency with a prescriptive output element.

Conclusion

Artificial intelligence methods can classify risk for primary immunodeficiency and guide management. PI Prob enables accurate, objective decision making about risk and guides the user towards the appropriate diagnostic evaluation for patients with recurrent infections. Probabilistic models can be trained with small datasets underscoring their utility for rare disease detection given appropriate domain expertise for feature selection and network construction.
Hematological reference intervals for adult population of Dire Dawa town, East Ethiopia
Authors: Mengistu Sissay Teklay , Tibebu Melatwork , Wasihun Tagesachew , Tsegaye Aster
Published: February 2021

Background

Reference interval (RI) for hematological parameters is used to interpret laboratory test results in the diagnosis, management and monitoring of hematologic disorders. Several factors including sex, age, dietary patterns, pregnancy status, ethnicity and geographic location affect hematological RIs. However, manufacturers derived reference value is currently in use in most developing countries including Ethiopia. This study aimed to establish hematological RIs for adult population living in Dire Dawa town, East Ethiopia.

Methods

In this cross-sectional study, 513 apparently healthy adults of Dire Dawa town were enrolled from January to March 2019. From these, 342 (171 males and 171 non-pregnant females) were aged 18–65 years while 171 were pregnant women aged 15–49 years. After obtaining written informed consent, 5ml fresh whole blood was collected of which 2ml was used for hematologic analysis using Mindray BC-3000plus hematology analyzer and 3ml for serological tests. The 2.5thand 97.5thRI was computed by non-parametric test employing SPSS version 24. P-value <0.05 was considered statistically significant.

Result

Males had significantly higher reference value for most of red cell parameters (Hgb, RBC, HCT, MCH and MCHC) than females (p <0.05), while most of the WBC parameters were significantly higher in females than males. Moreover, non-pregnant women had higher values for most of red cell parameters than pregnant women. Pregnant women had higher WBC parameters than their non-pregnant counterparts.

Conclusion

The hematologic RIs obtained in this study shows variation between genders, between pregnant and non-pregnant women, from the clinical practice currently utilised in Dire Dawa town and from studies conducted in Ethiopia, African countries as well as the Western population. It underscores the need for utilising gender and pregnancy specific, locally derived hematologic RI for better management, diagnosis and monitoring of hematologic disorders for adults of both genders and pregnant women.
Cervical length varies considering different populations and gestational outcomes: Results from a systematic review and meta-analysis
Authors: Bortoletto T. G. , Silva T. V. , Borovac-Pinheiro A. , Pereira C. M. , Silva A. D. , França M. S. , Hatanaka A. R. , Argenton J. P. , Passini R. , Mol B. W. , Cecatti J. G. , Pacagnella R. C.
Published: February 2021

Background

The uterine cervical length is an important risk factor for preterm birth. The aim of this study was to assess cervical length distribution in women with singleton pregnancies, measured by transvaginal ultrasound between 16 and 24 weeks, and its association with population characteristics.

Materials and methods

We searched electronic databases and other sources for studies published from April 1, 1990 to July 21, 2020. Of the 2019 retrieved publications, full-text versions of 137 articles were considered. We included 77 original articles that reported cervical length measurements of 363,431 women. The main aim of this study was to identify the pattern of cervical length in different populations. We collected demographic and clinical data concerning the population, in addition to information regarding the ultrasound examination and cervical length measurement. Regarding study bias, 56 were at low risk of bias and 21 were at medium risk of bias.

Results

The meta-analysis included 57 articles with data from 158,346 women. The mean cervical length was 37.96. mm (95% CI [36.68, 39.24]). Cervical length was shorter in women from Africa and Asia, in those from low-income countries, with a lower body weight, and in those who delivered before 37 gestational weeks. We found that the cervical length from pooled studies is longer than that usually discussed in the literature. Regarding limitations, we had difficulty assessing our main variable because there was no consistent pattern in the way authors reported cervical length measurement. Another limitation was the great heterogeneity between studies.

Conclusions

The use of a single cutoff value to define a short cervix diagnosis, an important risk factor for preterm birth, may not be correct and cervical length must be considered according to maternal population characteristics. Future studies should identify different specific curves and cutoff values for cervical length in different populations. This meta-analysis was registered in the PROSPERO database under CRD42017070246 at https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=70246.
The anti-arthritis effect of sulforaphane, an activator of Nrf2, is associated with inhibition of both B cell differentiation and the production of inflammatory cytokines
Authors: Moon Su-Jin , Jhun Jooyeon , Ryu Jaeyoon , Kwon Ji ye , Kim Se-Young , Jung KyoungAh , Cho Mi-La , Min Jun-Ki
Published: February 2021

Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is an important transcription factor that plays a pivotal role in cellular defense against oxidative injury. Nrf2 signaling is involved in attenuating autoimmune disorders such as rheumatoid arthritis (RA). B cells play several roles in the pathogenesis of RA, such as in autoantibody production, antigen presentation, and T-cell activation. We investigated the anti-arthritic mechanisms of sulforaphane, an activator of Nrf2, in terms of its effect on B cells. To investigate the effect of sulforaphane on collagen-induced arthritis (CIA), sulforaphane was administered intraperitoneally after CIA induction. Hematoxylin and eosin-stained sections were scored for inflammation, pannus invasion, and bone and cartilage damage. We assessed the expression levels of inflammation-related factors by real-time PCR and the levels of various IgG subclasses by enzyme-linked immunosorbent assay. Sulforaphane treatment reduced the arthritis score and the severity of histologic inflammation in CIA mice. The joints from sulforaphane-treated CIA mice showed decreased expression of interleukin (IL)-6, IL-17, tumor necrosis factor (TNF)-α, receptor activator of NF-κB ligand, and tartrate-resistant acid phosphatase. Sulforaphane-treated mice showed lower circulating levels of type-II-collagen-specific IgG, IgG1, and IgG2a. In vitro, sulforaphane treatment significantly reduced the differentiation of lipopolysaccharide-stimulated murine splenocytes into plasma B cells and germinal-center B cells. Finally, sulforaphane significantly inhibited the production of IL-6, TNF-α, and IL-17 by human peripheral blood mononuclear cells stimulated with an anti-CD3 monoclonal antibody in a dose-dependent manner. Inhibition of differentiation into plasma B and Germinal Center B cells may be the mechanism underlying the anti-arthritic effect of sulforaphane.
Intimate partner violence by men living with HIV in Cameroon: Prevalence, associated factors and implications for HIV transmission risk (ANRS-12288 EVOLCAM)
Authors: Fiorentino Marion , Sow Abdourahmane , Sagaon-Teyssier Luis , Mora Marion , Mengue Marie-Thérèse , Vidal Laurent , Kuaban Christopher , March Laura , Laurent Christian , Spire Bruno , Boyer Sylvie ,   for the EVOLCam study Group
Published: February 2021

Objectives

Intimate partner violence (IPV) against women is frequent in Central Africa and may be a HIV infection risk factor. More data on HIV-positive men (MLHIV) committing IPV are needed to develop perpetrator-focused IPV and HIV prevention interventions. We investigated the relationship between IPV and HIV transmission risk and IPV-associated factors.

Methods

We used data from the cross-sectional survey EVOLCam which was conducted in Cameroonian outpatient HIV structures in 2014. The study population comprised MLHIV declaring at least one sexual partner in the previous year. Using principal component analysis, we built three variables measuring, respectively, self-reported MLHIV-perpetrated psychological and physical IPV (PPV), severe physical IPV (SPV), and sexual IPV (SV). Ordinal logistic regressions helped investigate: i) the relationship between HIV transmission risk (defined as unstable aviremia and inconsistent condom use) and IPV variables, ii) factors associated with each IPV variable.

Results

PPV, SPV and SV were self-reported by 28, 15 and 11% of the 406 study participants, respectively. IPV perpetrators had a significantly higher risk of transmitting HIV than non-IPV perpetrators. Factors independently associated with IPV variables were: i) socio-demographic, economic and dyadic factors, including younger age (PPV and SPV), lower income (PPV), not being the household head (SPV and SV), living with a main partner (SPV), and having a younger main partner (SPV); ii) sexual behaviors, including ≥2 partners in the previous year (PPV and SPV), lifetime sex with another man (SPV), inconsistent condom use (SV), and >20 partners during lifetime (SV); iii) HIV-related stigma (PPV and SV).

Conclusion

IPV perpetrators had a higher risk of transmitting HIV and having lifetime and recent risky sexual behaviors. Perpetrating IPV was more frequent in those with socioeconomic vulnerability and self-perceived HIV-related stigma. These findings highlight the need for interventions to prevent IPV by MLHIV and related HIV transmission to their(s) partner(s).
Association of lung diffusion capacity with cardiac remodeling and risk of heart failure: The Framingham heart study
Authors: Yola Ibrahim Musa , Oh Albin , Mitchell Gary F. , O’Connor George , Cheng Susan , Vasan Ramachandran S. , Xanthakis Vanessa
Published: February 2021

Background

Lung function abnormalities are ubiquitous in heart failure (HF). It is unclear, however, if abnormal lung diffusion capacity is associated with cardiac remodeling and antedates HF. We hypothesized that lower lung diffusion capacity for carbon monoxide (DLCO) is associated with worse left ventricular (LV) systolic and diastolic function cross-sectionally, and with higher risk of HF prospectively.

Methods

We evaluated 2423 Framingham Study participants (mean age 66 years, 55% women) free of HF who underwent routine echocardiography and pulmonary function tests. We used multivariable regression models to relate DLCO, forced vital capacity (FVC), and forced expiratory volume in 1 second (FEV1) to left ventricular ejection fraction (LVEF), left atrial (LA) emptying fraction (LAEF), E/e’, E/A, LV mass, and LA diameter (LAD). Multivariable-adjusted Cox proportional hazards regression was used to relate DLCO, FEV1, and FVC to incident HF.

Results

In multivariable-adjusted cross-sectional analyses, DLCO, FEV1, and FVC (dependent variables) were associated positively with LVEF (βDLCO = 0.208, βFEV1 = 0.021, and βFVC = 0.025 per 5% increment in LVEF; p<0.005 for all), and LAEF (βDLCO = 0.707, βFEV1 = 0.058 and βFVC = 0.058 per 5% increment in LAEF; p<0.002 for all). DLCO and FVC were inversely related to E/A (βDLCO = -0.289, βFVC = -0.047 per SD increment in E/A; p<0.001 for all). Additionally, DLCO, FEV1 and FVC were inversely related to HF risk (108 events, median follow-up 9.7 years; multivariable-adjusted hazard ratios per SD increment 0.90, 95% CI 0.86–0.95; 0.42, 95% CI 0.28–0.65, and 0.51, 95% CI 0.36–0.73, respectively). These results remained robust in analyses restricted to non-smokers.

Conclusions

Our large community-based observations are consistent with the concept that lower lung diffusion capacity and expiratory flow rates are associated with cardiac remodeling and may antedate HF. Additional studies are needed to confirm our findings and to evaluate the prognostic utility of pulmonary function testing for predicting HF.
Structural model of corporate social responsibility. An empirical study on Mexican SMEs
Authors: Ríos-Manríquez Martha , Ferrer-Ríos Martha Gabriela , Sánchez-Fernández María Dolores
Published: February 2021

Companies are increasingly aware of their role with regard to social responsibility in its three pillars: economic, social and environmental, with their different stakeholders. Facing the dilemma of choosing the model of social responsibility they should adopt, taking care of their organizational culture and their employees, with a global vision that the business world requires. However, it is not an easy task for small and medium enterprises, mainly because of their economic shortcomings in human resources and knowledge of how to be a socially responsible company. But they are aware that Corporate Social Responsibility (CSR) is an opportunity for development and differentiation in the market. Therefore, the objective of this research is to build, identify and validate a model of Social Responsibility in small and medium enterprises in Guanajuato, Mexico (CSRSMEs), on a sample of 226 SMEs, using as a basis the methodology of the international standard of Ethical and Socially Responsible Management System (SGE21). A quantitative approach was used and, a descriptive analysis, exploratory factor analysis and the structural equation modeling was applied. The results determine that the most relevant variables for being socially responsible are human capital, clients, supply chain, social environment and impact on the community, and organizational governance: Legality and Management System. It is drawn from this work that the flexibility of the so-called Ethical and Socially Responsible Management System has the empirical foundations needed. That is, from the perspective of the company’s management to consider the CSRSMEs model an opportunity to adopt and evaluate the areas of social responsibility management of any business structure in the SMEs in Mexico.
Sensitivity of wild-type and rifampicin-resistant O157 and non-O157 Shiga toxin-producing Escherichia coli to elevated hydrostatic pressure and lactic acid in ground meat and meat homogenate
Authors: Allison Abimbola , Fouladkhah Aliyar Cyrus
Published: February 2021

Various serogroups of Shiga toxin-producingEscherichia colihave been epidemiologically associated with foodborne disease episodes in the United States and around the globe, withE.coliO157: H7 as the dominant serogroup of public health concern. Serogroups other than O157 are currently associated with about 60% of Shiga toxin-producingE.colirelated foodborne illness episodes. Current study evaluated sensitivity of the O157 and epidemiologically important non-O157 serogroups of the pathogen to elevated hydrostatic pressure and 1% lactic acid. Pressure intensity of 250 to 650 MPa were applied for 0 to 7 min for inactivation of strain mixtures of wild-type and rifampicin-resistantE.coliO157, as well as O26, O45, O103, O111, O121, and O145 serogroups and ATCC®43895™strain in ground meat and 10% meat homogenate.E.coliO157 were reduced (p< 0.05) from 6.86 ± 0.2 to 4.56 ± 0.1 log CFU/g when exposed to pressure of 650 MPa for 7 min. Corresponding reductions (p< 0.05) for non-O157E.coliwere from 6.98 ± 0.3 to 4.72 ± 0.1. TheD-values at 650 MPa were 3.71 and 3.47 min for O157 and non-O157 serogroups, respectively. Presence of 1% lactic acid to a great extent augmented (p< 0.05) decontamination efficacy of the treatment in meat homogenate resulting in up to 5.6 and 6.0 log CFU/mL reductions for O157 and non-O157 serogroups, respectively. Among the tested serogroups, the wild-type and rifampicin-resistant phenotypes exhibited (p≥ 0.05) comparable pressure sensitivity. Thus, these two phenotypes could be used interchangeably in validation studies. Our results also illustrate that, application of elevated hydrostatic pressure could be utilized for assuring safety of ground and non-intact meat products against various serogroups of Shiga toxin-producingE.coli. Addition of 1% lactic acid additionally provided industrially appreciable augmentation in efficacy of the pressure-based treatments.
Potential application values of a marine red yeast, Rhodosporidiums sphaerocarpum YLY01, in aquaculture and tail water treatment assessed by the removal of ammonia nitrogen, the inhibition to Vibrio spp., and nutrient composition
Authors: Yun Long , Wang Wei , Li Yingying , Xie Mei , Chen Ting , Hu Chaoqun , Luo Peng , Li Daning
Published: February 2021

In recent years, marine red yeasts have been increasingly used as feed diets for larviculture of aquatic animals mainly due to their rich nutrition and immunopotentiation, however little attention is given to their other probiotic profits. In this study, a marine red yeast strain YLY01 was isolated and purified from farming water and it was identified as a member of Rhodosporidiums sphaerocarpum by the phylogeny based on 18S rDNA sequence. The strain YLY01 could effectively remove ammonia nitrogen from an initial 9.8 mg/L to 1.3 mg/L in 48 h when supplemented with slight yeast extract and glucose in water samples and the removal rate of ammonia nitrogen was up to 86%. Shrimps (Litopenaeus vannamei) in experimental group incubated with the yeast YLY01 exhibited a higher survival rate than those in blank control group and positive control group challenged by Vibrio harveyi, and it manifested that the strain has high biosecurity to at least shrimps. The strain YLY01 could inhibit the growth of Vibrio cells when a small quantity of carbon source was added into farming water. In addition, a nutrition composition assay showed the contents of protein, fatty acids, and total carotenoids of the yeast YLY01 were 30.3%, 3.2%, and 1.2 mg/g of dry cell weight, respectively. All these results indicated that the marine red yeast YLY01 has a great potential to be used as a versatile probiotic in aquaculture and to be developed as a microbial agent for high-ammonia tail water treatment.