bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantum parametric mode sorting: a case study on small angle scattering
Authors: Zhu Shenyu , Sua Yong Meng , Hu Yongxiang , Weimer Carl , Ma Zhaohui , Zheng Zipei , Rehain Patrick , Stamnes Knut , Zhou Yingzhen , Lee Jennifer H. , Huang Yu-Ping
Published: July 2021

Quantum parametric mode sorting has been shown to enable photon counting with precise time gating and exceptional noise rejection that significantly exceeds what is possible with linear filters. While previous experimental demonstrations were in a collinear optical configuration, its response to off-axis scattering must be understood to apply it more broadly in remote sensing missions. To evaluate this prospect, we use a laboratory testbed to examine its performance for detecting photons at small angles, along both forward and backward directions, after passing through strongly scattering media. Our results find no measurable degradation in detecting noncollinear photons along both directions. This finding indicates that the key intra-pulse coherence essential to quantum parametric mode sorting is maintained at a small scattering angle, permitting its applications on a moving platform.
Effect of loss on linear optical quantum logic gates
Authors: Davis James E. , Güney Durdu Ö.
Published: July 2021

Linear optical quantum gates have been proposed as a possible implementation for quantum computers. Most experimental linear optical quantum gates are constructed with free-space optical components with negligible loss. In this work, we analyze symmetric and asymmetric partially polarizing lossy beam splitters. Using the generalized beam splitter equations, we study the effects of loss on two linear optical quantum gates: the first is a commonly used CNOT gate, and the second is a W state expansion gate. Envisioning inherent loss in plasmonics and metamaterials as a new degree of freedom and those materials systems as a route for miniaturization, we reconsider the requirements of the lossy CNOT gate and show it is possible to simplify the three-beam-splitter design to a single beam splitter without sacrificing success probability.
Broadband and switchable terahertz polarization converter based on graphene metasurfaces
Authors: Zhang Rui , You Bing , Wang Shengchuan , Han Kui , Shen Xiaopeng , Wang Weihua
Published: July 2021

In this work, we propose broadband and switchable terahertz (THz) polarization converters based on either graphene patch metasurface (GPMS) or its complementary structure (graphene hole metasurface, GHMS). The patch and hole are simply cross-shaped, composed of two orthogonal arms, along which plasmonic resonances mediated by Fabry-Perot cavity play a key role in polarization conversion (PC). An incidence of linear polarization will be converted to its cross-polarization (LTL) or circular polarization (LTC), as the reflected wave in the direction of two arms owning the same amplitude and π phase difference (LTL), or ±π/2 phase difference (LTC). Such requirements can be met by optimizing the width and length of two arms, thickness of dielectric layer, and Fermi level EF of graphene. By using GPMS, LTL PC of polarization conversion ratio (PCR) over 90% is achieved in the frequency range of 2.92 THz to 6.26 THz, and by using GHMS, LTC PC of ellipticity χ ≤ −0.9 at the frequencies from 4.45 THz to 6.47 THz. By varying the Fermi level, the operating frequency can be actively tuned, and the functionality can be switched without structural modulation; for instance, GPMS supports LTL PC as EF = 0.6 eV and LTC PC of χ ≥ 0.9 as EF = 1.0 eV, in the frequency range of 2.69 THz to 4.19 THz. Moreover, GHMS can be optimized to sustain LTL PC and LTC PC of |χ| ≥ 0.9, in the frequency range of 4.96 THz to 6.52 THz, which indicates that the handedness of circular polarization can be further specified. The proposed polarization converters of broad bandwidth, active tunability, and switchable functionality will essentially make a significant progress in THz technology and device applications, and can be widely utilized in THz communications, sensing and spectroscopy.
Large-tuning-range frequency stabilization of an ultraviolet laser by an open-loop piezoelectric ceramic controlled Fabry–Pérot cavity
Authors: Zheng Yong-Xiang , Cui Jin-Ming , Ai Ming-Zhong , Qian Zhong-hua , Cao Huan , Huang Yun-Feng , Jia Xiao-Jun , Li Chuan-Feng , Guo Guang-Can
Published: July 2021

We demonstrate a laser frequency stabilization method with large tuning range to stabilize a UV laser by installing piezoelectric ceramic actuators into a Fabry–Pérot cavity with an ultra-low expansion spacer. To suppress piezoelectric drift, a two-layer symmetrical structure is adopted for the piezoelectric actuator, and a 14.7 GHz tuning range is achieved. The short-term drift of the piezoelectric ceramics caused by temperature and creep is eliminated, and the long-term drift is 0.268 MHz/h when the Fabry–Pérot cavity is sealed in a chamber without a vacuum environment. The long-term frequency drift is mainly caused by stress release and is eliminated by compensating the cavity voltage with an open loop. Without the need for an external reference or a vacuum environment, the laser frequency stabilization system is greatly simplified, and it can be extended to wavelengths ranging from ultraviolet to infrared. Owing to its simplicity, stability, and large tuning range, it is applicable in cold atom and trapped ion experiments.
Observation of rotational coherence in an excited state of CO+
Authors: Wan Y. X. , Fu B. T. , Xie H. Q. , Yu S. P. , Lei H. B. , Zhang F. B. , Zhang Z. H. , Qiao L. L. , Li G. H. , Zhao J. , Zhao Z. X. , Yao J. P. , Cheng Y.
Published: July 2021

The vacuum ultraviolet (VUV) radiation is generated in the strong-field-ionized CO molecules through

2

+

1

resonance excitation with two-color femtosecond laser pulses. When scanning the relative delay between two pump pulses, the rotational-resolved VUV radiations show periodic oscillations lasting as long as 500 ps. Fourier analysis reveals that these oscillations correspond to rotational beat frequencies of the

A

2

Π

i

state of

C
O

+

, which is the result of multi-channel interference during the resonant excitation process. High resolution of Fourier transform spectra up to

0.067

c
m

−
1

allows us to obtain the fine energy levels of the

A

2

Π

i

state. The theoretical calculation is in good agreement with the experimental observation. This work reveals the rotational coherence of the ionic excited state and shows the prospect of rotational coherence spectroscopy in measuring fine structures of molecular ions.
Role of frequency dependence of the nonlinearity on a soliton’s evolution in photonic crystal fibers
Authors: Bose Surajit , Melchert Oliver , Willms Stephanie , Babushkin Ihar , Morgner Uwe , Demircan Ayhan , Agrawal Govind P.
Published: July 2021

We reveal the crucial role played by the frequency dependence of the nonlinear parameter on the evolution of femtosecond solitons inside photonic crystal fibers (PCFs). We show that the conventional approach based on the self-steepening effect is not appropriate when such fibers have two zero-dispersion wavelengths, and several higher-order nonlinear terms must be included for realistic modeling of the nonlinear phenomena in PCFs. These terms affect not only the Raman-induced wavelength shift of a soliton but also impact its shedding of dispersive radiation.
Generation and transmission of phase-stable coherent multi-band linear frequency modulated signals
Authors: Li Baiyu , Wang Xi , Wei Wei , Xie Weilin , Dong Yi
Published: July 2021

We present a coherent multi-band linear frequency modulated (LFM) signal generation and transmission system based on dual optical frequency combs (OFCs). In the proposed scheme, the two OFCs are phase-locked to ensure high coherence of the generated multi-band LFM signals. A round-trip phase correction is adopted to stabilize the time delay of the fiber transmission and enable the system to resist temperature variation. In the demonstration experiment, the generated multi-band LFM signals across L, S, and C frequency bands has a bandwidth of 200 MHz in each band. The root-mean-square (RMS) phase deviation of the multi-band signal is below

4
×

10

−
3

r
a
d

after 1.2 km fiber transmission. During 1°C temperature variation, the RMS phase drift is suppressed from 1 rad to 0.1 rad. The high signal coherence between different bands and the capability of resisting temperature variation are highly desired for a multi-band distributed radar system.
Speckle filtering through nonlinear wave mixing
Authors: Rocha J. C. A. , Pires D. G. , Neto J. G. M. N. , Jesus-Silva A. J. , Litchinitser N. M. , Fonseca E. J. S.
Published: July 2021

Light scattering by disordered media is a ubiquitous effect. After passing through them, the light acquires a random phase, masking or destroying associated information. Filtering this random phase is of paramount importance to many applications, such as sensing, imaging, and optical communication, to cite a few, and it is commonly achieved through computationally extensive post-processing using statistical correlation. In this work, we show that mixing noisy optical modes of various complexity in a second-order nonlinear medium can be used for efficient and straightforward filtering of a random wavefront under sum-frequency generation processes without utilizing correlation-based calculations.
Comparative advantages of a type-II superlattice barrier over an AlGaSb barrier for enhanced performance of InAs/GaSb LWIR nBn photodetectors
Authors: Lee Hyun-Jin , Jang Ahreum , Kim Young Ho , Jung Han , Bidenko Pavlo , Kim Sanghyeon , Kim Minje , Nah Junghyo
Published: July 2021

The barrier layer in InAs/GaSb LWIR nBn detector is usually composed of AlGaSb alloy, which has a non-negligible valence band offset and is sensitive to chemical solutions. In this work, we investigated a type-II superlattice (T2SL) barrier that is homogeneous with the T2SL absorber layer in order to resolve these drawbacks of the AlGaSb barrier. The lattice mismatch of the T2SL barrier was smaller than that of the AlGaSb barrier. At

−

70

m
V

and 80 K, the dark current density and the noise equivalent temperature difference of the nBn devices with the T2SL barrier were

4.4

×

1

0

−
6

A

/

c
m

2

and 33 mK, respectively.
Viral dynamics of acute SARS-CoV-2 infection and applications to diagnostic and public health strategies
Authors: Kissler Stephen M. , Fauver Joseph R. , Mack Christina , Olesen Scott W. , Tai Caroline , Shiue Kristin Y. , Kalinich Chaney C. , Jednak Sarah , Ott Isabel M. , Vogels Chantal B. F. , Wohlgemuth Jay , Weisberger James , DiFiori John , Anderson Deverick J. , Mancell Jimmie , Ho David D. , Grubaugh Nathan D. , Grad Yonatan H.
Published: July 2021

SARS-CoV-2 infections are characterized by viral proliferation and clearance phases and can be followed by low-level persistent viral RNA shedding. The dynamics of viral RNA concentration, particularly in the early stages of infection, can inform clinical measures and interventions such as test-based screening. We used prospective longitudinal quantitative reverse transcription PCR testing to measure the viral RNA trajectories for 68 individuals during the resumption of the 2019–2020 National Basketball Association season. For 46 individuals with acute infections, we inferred the peak viral concentration and the duration of the viral proliferation and clearance phases. According to our mathematical model, we found that viral RNA concentrations peaked an average of 3.3 days (95% credible interval [CI] 2.5, 4.2) after first possible detectability at a cycle threshold value of 22.3 (95% CI 20.5, 23.9). The viral clearance phase lasted longer for symptomatic individuals (10.9 days [95% CI 7.9, 14.4]) than for asymptomatic individuals (7.8 days [95% CI 6.1, 9.7]). A second test within 2 days after an initial positive PCR test substantially improves certainty about a patient’s infection stage. The effective sensitivity of a test intended to identify infectious individuals declines substantially with test turnaround time. These findings indicate that SARS-CoV-2 viral concentrations peak rapidly regardless of symptoms. Sequential tests can help reveal a patient’s progress through infection stages. Frequent, rapid-turnaround testing is needed to effectively screen individuals before they become infectious.
Quantitative mapping of mRNA 3’ ends in Pseudomonas aeruginosa reveals a pervasive role for premature 3’ end formation in response to azithromycin
Authors: Konikkat Salini , Scribner Michelle R. , Eutsey Rory , Hiller N. Luisa , Cooper Vaughn S. , McManus Joel
Published: July 2021

Pseudomonas aeruginosa produces serious chronic infections in hospitalized patients and immunocompromised individuals, including patients with cystic fibrosis. The molecular mechanisms by which P. aeruginosa responds to antibiotics and other stresses to promote persistent infections may provide new avenues for therapeutic intervention. Azithromycin (AZM), an antibiotic frequently used in cystic fibrosis treatment, is thought to improve clinical outcomes through a number of mechanisms including impaired biofilm growth and quorum sensing (QS). The mechanisms underlying the transcriptional response to AZM remain unclear. Here, we interrogated the P. aeruginosa transcriptional response to AZM using a fast, cost-effective genome-wide approach to quantitate RNA 3’ ends (3pMap). We also identified hundreds of P. aeruginosa genes with high incidence of premature 3’ end formation indicative of riboregulation in their transcript leaders using 3pMap. AZM treatment of planktonic and biofilm cultures alters the expression of hundreds of genes, including those involved in QS, biofilm formation, and virulence. Strikingly, most genes downregulated by AZM in biofilms had increased levels of intragenic 3’ ends indicating premature transcription termination, transcriptional pausing, or accumulation of stable intermediates resulting from the action of nucleases. Reciprocally, AZM reduced premature intragenic 3’ end termini in many upregulated genes. Most notably, reduced termination accompanied robust induction of obgE, a GTPase involved in persister formation in P. aeruginosa. Our results support a model in which AZM-induced changes in 3’ end formation alter the expression of central regulators which in turn impairs the expression of QS, biofilm formation and stress response genes, while upregulating genes associated with persistence.
Clinical manifestations and health outcomes associated with Zika virus infections in adults: A systematic review
Authors: Halani Sheliza , Tombindo Panashe E. , O’Reilly Ryan , Miranda Rafael N. , Erdman Laura K. , Whitehead Clare , Bielecki Joanna M. , Ramsay Lauren , Ximenes Raphael , Boyle Justin , Krueger Carsten , Willmott Shannon , Morris Shaun K. , Murphy Kellie E. , Sander Beate
Published: July 2021

Background

Zika virus (ZIKV) has generated global interest in the last five years mostly due to its resurgence in the Americas between 2015 and 2016. It was previously thought to be a self-limiting infection causing febrile illness in less than one quarter of those infected. However, a rise in birth defects amongst children born to infected pregnant women, as well as increases in neurological manifestations in adults has been demonstrated. We systemically reviewed the literature to understand clinical manifestations and health outcomes in adults globally.

Methods

This review was registered prospectively with PROPSERO (CRD 42018096558). We systematically searched for studies in six databases from inception to the end of September 2020. There were no language restrictions. Critical appraisal was completed using the Joanna Briggs Institute Critical Appraisal Tools.

Findings

We identified 73 studies globally that reported clinical outcomes in ZIKV-infected adults, of which 55 studies were from the Americas. For further analysis, we considered studies that met 70% of critical appraisal criteria and described subjects with confirmed ZIKV. The most common symptoms included: exanthema (5,456/6,129; 89%), arthralgia (3,809/6,093; 63%), fever (3,787/6,124; 62%), conjunctivitis (2,738/3,283; 45%), myalgia (2,498/5,192; 48%), headache (2,165/4,722; 46%), and diarrhea (337/2,622; 13%). 36/14,335 (0.3%) of infected cases developed neurologic sequelae, of which 75% were Guillain-Barré Syndrome (GBS). Several subjects reported recovery from peak of neurological complications, though some endured chronic disability. Mortality was rare (0.1%) and hospitalization (11%) was often associated with co-morbidities or GBS.

Conclusions

The ZIKV literature in adults was predominantly from the Americas. The most common systemic symptoms were exanthema, fever, arthralgia, and conjunctivitis; GBS was the most prevalent neurological complication. Future ZIKV studies are warranted with standardization of testing and case definitions, consistent co-infection testing, reporting of laboratory abnormalities, separation of adult and pediatric outcomes, and assessing for causation between ZIKV and neurological sequelae.
Enantiospecific antitrypanosomal in vitro activity of eflornithine
Authors: Boberg Mikael , Cal Monica , Kaiser Marcel , Jansson-Löfmark Rasmus , Mäser Pascal , Ashton Michael
Published: July 2021

The polyamine synthesis inhibitor eflornithine is a recommended treatment for the neglected tropical disease Gambian human African trypanosomiasis in late stage. This parasitic disease, transmitted by the tsetse fly, is lethal unless treated. Eflornithine is administered by repeated intravenous infusions as a racemic mixture of L-eflornithine and D-eflornithine. The study compared thein vitroantitrypanosomal activity of the two enantiomers with the racemic mixture against threeTrypanosoma brucei gambiensestrains. Antitrypanosomalin vitroactivity at varying drug concentrations was analysed by non-linear mixed effects modelling. For all three strains, L-eflornithine was more potent than D-eflornithine. Estimated 50% inhibitory concentrations of the three strains combined were 9.1 μM (95% confidence interval [8.1; 10]), 5.5 μM [4.5; 6.6], and 50 μM [42; 57] for racemic eflornithine, L-eflornithine and D-eflornithine, respectively. The higherin vitropotency of L-eflornithine warrants further studies to assess its potential for improving the treatment of late-stage Gambian human African trypanosomiasis.
Are indigenous territories effective natural climate solutions? A neotropical analysis using matching methods and geographic discontinuity designs
Authors: Alejo Camilo , Meyer Chris , Walker Wayne S. , Gorelik Seth R. , Josse Carmen , Aragon-Osejo Jose Luis , Rios Sandra , Augusto Cicero , Llanos Andres , Coomes Oliver T. , Potvin Catherine
Published: July 2021

Indigenous Territories (ITs) with less centralized forest governance than Protected Areas (PAs) may represent cost-effective natural climate solutions to meet the Paris agreement. However, the literature has been limited to examining the effect of ITs on deforestation, despite the influence of anthropogenic degradation. Thus, little is known about the temporal and spatial effect of allocating ITs on carbon stocks dynamics that account for losses from deforestation and degradation. Using Amazon Basin countries and Panama, this study aims to estimate the temporal and spatial effects of ITs and PAs on carbon stocks. To estimate the temporal effects, we use annual carbon density maps, matching analysis, and linear mixed models. Furthermore, we explore the spatial heterogeneity of these estimates through geographic discontinuity designs, allowing us to assess the spatial effect of ITs and PAs boundaries on carbon stocks. The temporal effects highlight that allocating ITs preserves carbon stocks and buffer losses as well as allocating PAs in Panama and Amazon Basin countries. The geographic discontinuity designs reveal that ITs’ boundaries secure more extensive carbon stocks than their surroundings, and this difference tends to increase towards the least accessible areas, suggesting that indigenous land use in neotropical forests may have a temporarily and spatially stable impact on carbon stocks. Our findings imply that ITs in neotropical forests support Nationally Determined Contributions (NDCs) under the Paris Agreement. Thus, Indigenous peoples must become recipients of countries’ results-based payments.
A meta-analysis of effects of dietary seaweed on beef and dairy cattle performance and methane yield
Authors: Lean Ian J. , Golder Helen M. , Grant Tianna M. D. , Moate Peter J.
Published: July 2021

There has been considerable interest in the use of red seaweed, and in particular Asparagopsis taxiformis, to increase production of cattle and to reduce greenhouse gas emissions. We hypothesized that feeding seaweed or seaweed derived products would increase beef or dairy cattle performance as indicated by average daily gain (ADG), feed efficiency measures, milk production, and milk constituents, and reduce methane emissions. We used meta-analytical methods to evaluate these hypotheses. A comprehensive search of Google Scholar, Pubmed and ISI Web of Science produced 14 experiments from which 23 comparisons of treatment effects could be evaluated. Red seaweed (Asparagopsis taxiformis) and brown seaweed (Ascophyllum nodosum) were the dominant seaweeds used. There were no effects of treatment on ADG or dry matter intake (DMI). While there was an increase in efficiency for feed to gain by 0.38 kg per kg [standardized mean difference (SMD) = 0.56; P = 0.001] on DerSimonian and Laird (D&L) evaluation, neither outcome was significant using the more rigorous robust regression analysis (P >0.06). The type of seaweed used was not a significant covariable for ADG and DMI, but A. nodosum fed cattle had lesser feed to gains efficiency compared to those fed A. taxiformis. Milk production was increased with treatment on weighted mean difference (WMD; 1.35 ± 0.44 kg/d; P <0.001); however, the SMD of 0.45 was not significant (P = 0.111). Extremely limited data suggest the possibility of increased percentages of milk fat (P = 0.040) and milk protein (P = 0.001) on (D&L) WMD evaluation. The limited data available indicate dietary supplementation with seaweed produced a significant and substantial reduction in methane yield by 5.28 ± 3.5 g/kg DMI (P = 0.003) on D&L WMD evaluation and a D&L SMD of −1.70 (P = 0.001); however, there was marked heterogeneity in the results (I2 > 80%). In one comparison, methane yield was reduced by 97%. We conclude that while there was evidence of potential for benefit from seaweed use to improve production and reduce methane yield more in vivo experiments are required to strengthen the evidence of effect and identify sources of heterogeneity in methane response, while practical applications and potential risks are evaluated for seaweed use.
Identification and engraftment of new bacterial strains by shotgun metagenomic sequence analysis in patients with recurrent Clostridioides difficile infection before and after fecal microbiota transplantation and in healthy human subjects
Authors: Verma Sandeep , Dutta Sudhir K. , Firnberg Elad , Phillips Laila , Vinayek Rakesh , Nair Padmanabhan P.
Published: July 2021

Background

Recurrent Clostridioides diffícile infection (RCDI) is associated with major bacterial dysbiosis and colitis. Fecal microbiota transplantation (FMT) is a highly effective therapeutic modality for RCDI. While several studies have identified bacterial species associated with resolution of symptoms in patients, characterization of the fecal microbiome at the bacterial strain level in RCDI patients before and after FMT and healthy donors, has been lacking. The aim of this study was to examine the ability of bacterial strains from healthy donors to engraft in the gastrointestinal tract of patients with RCDI following FMT.

Methods

Fecal samples were collected from 22 patients with RCDI before and after FMT and their corresponding healthy donors. Total DNA was extracted from each sample and analyzed by shotgun metagenomic sequencing. The Cosmos-ID analysis platform was used for taxonomic assignment of sequences and calculation of the relative abundance (RA) of bacterial species and strains. From these data, the total number of bacterial strains (BSI), Shannon diversity index, dysbiosis index (DI), and bacterial engraftment factor, were calculated for each strain.

Findings

A marked reduction (p<0·0001) in the RA of total and specific bacterial strains, especially from phylum Firmicutes, was observed in RCDI patients prior to FMT. This change was associated with an increase in the DI (p<0·0001) and in pathobiont bacterial strains from phylum Proteobacteria, such as Escherichia coli O157:H7 and Klebsiella pneumoniae UCI 34. BSI was significantly lower in this group of patients as compared to healthy donors and correlated with the Shannon Index. (p<0·0001). Identification and engraftment of bacterial strains from healthy donors revealed a greater diversity and higher relative abundance of short-chain fatty acid (SCFA)-producing bacterial strains, including Lachnospiraceae bacterium 5_1_63FAA_u_t, Dorea formicigenerans ATCC 27755, Anaerostipes hadrusand others, in RCDI patients after FMT.

Interpretation

These observations identify a group of SCFA-producing bacterial strains from healthy donors that engraft well in patients with RCDI following FMT and are associated with complete resolution of clinical symptoms and bacterial dysbiosis.
Prognostic model for nephrotoxicity among HIV-positive Zambian adults receiving tenofovir disoproxil fumarate-based antiretroviral therapy
Authors: Chabala Freeman W. , Siew Edward D. , Mutale Wilbroad , Mulenga Lloyd , Mweemba Aggrey , Goma Fastone , Banda Njeleka , Kaonga Patrick , Wester William C. , Heimburger Douglas C. , Aliyu Muktar H. , Munkombwe Derick
Published: July 2021

Persons living with HIV (PLWH) receiving tenofovir disoproxil fumarate (TDF)-based antiretroviral therapy (ART) risk suffering TDF-associated nephrotoxicity (TDFAN). TDFAN can result in short- and long-term morbidity, including permanent loss of kidney function, chronic kidney disease (CKD), and end-stage kidney disease (ESKD) requiring dialysis. Currently, there is no model to predict this risk or discern which patients to initiate TDF-based therapy. Consequently, some patients suffer TDFAN within the first few months of initiating therapy before switching to another suitable antiretroviral or a lower dose of TDF. In a prospective observational cohort study of adult Zambian PLWH, we modelled the risk for TDFAN before initiating therapy to identify individuals at high risk for experiencing AKI after initiating TDF-based therapy. We enrolled 205 HIV-positive, ART-naïve adults initiating TDF-based therapy followed for a median of 3.4 months for TDFAN at the Adult Infectious Disease Research Centre (AIDC) in Lusaka, Zambia. We defined TDFAN as meeting any of these acute kidney disease (AKD) criteria: 1) An episode of estimated glomerular filtration rate (eGFR)< 60ml/ min/1.73m2 within 3 months, 2) reduced eGFR by> 35% within 3 months or 3) increased serum creatinine by> 50% within 3 months. A total of 45 participants (22%) developed acute kidney disease (AKD) after TDF-based therapy. The development of AKD within the first 3 months of commencing TDF-based therapy was associated with an increase in baseline serum creatinine, age, baseline eGFR and female sex. We concluded that baseline characteristics and baseline renal function biomarkers predicted the risk for AKD within the first 3-months of TDF-based therapy.
Histological and biomechanical properties of systemic arteries in young and old Warmblood horses
Authors: Vera Lisse , Muylle Sofie , Van Steenkiste Glenn , Segers Patrick , Decloedt Annelies , Chiers Koen , van Loon Gunther
Published: July 2021

Arterial rupture is a well-recognized cause of sudden death in horses, which mainly affects older horses. The arterial wall is known to stiffen with age, although the underlying age-related histological and biomechanical changes remain unclear. The purpose of this study was to investigate the effect of aging by histological analysis of the arterial wall and examination of the arterial wall biomechanical properties using an inflation-extension test. Entire circular samples of the proximal and distal aorta, cranial and caudal common carotid, external iliac, femoral and median artery were collected from 6 young (6 years) and 14 old horses (≥15 years). Samples of all arteries were histologically examined and intima media thickness as well as area % of elastin, smooth muscle actin and collagen type I and III were determined. Older horses had a significantly larger intima media thickness and a significantly higher area % of smooth muscle actin compared to young horses. Samples of the proximal and distal aorta, the caudal common carotid and the external iliac artery were mechanically assessed using an in-house developed inflation-extension device with ultrasound analysis. Rupture occurred in a minority of arteries (8/78) at high pressures (between 250–300 mmHg), and mostly occurred in older horses (7/8). Pressure-area, pressure-compliance and pressure-distensibility curves were constructed. A significant difference in the pressure-area curves of the distal aorta, common carotid artery and external iliac artery, the pressure-compliance curves of the proximal aorta and carotid artery and the pressure-distensibility curve of the proximal aorta was observed between young and old horses. Results demonstrate an effect of age on the histological and biomechanical properties of the arterial wall, which might explain why arterial rupture occurs more often in older horses.
BCDnet: Parallel heterogeneous eight-class classification model of breast pathology
Authors: He Qingfang , Cheng Guang , Ju Huimin
Published: July 2021

Breast cancer is the cancer with the highest incidence of malignant tumors in women, which seriously endangers women’s health. With the help of computer vision technology, it has important application value to automatically classify pathological tissue images to assist doctors in rapid and accurate diagnosis. Breast pathological tissue images have complex and diverse characteristics, and the medical data set of breast pathological tissue images is small, which makes it difficult to automatically classify breast pathological tissues. In recent years, most of the researches have focused on the simple binary classification of benign and malignant, which cannot meet the actual needs for classification of pathological tissues. Therefore, based on deep convolutional neural network, model ensembleing, transfer learning, feature fusion technology, this paper designs an eight-class classification breast pathology diagnosis model BCDnet. A user inputs the patient’s breast pathological tissue image, and the model can automatically determine what the disease is (Adenosis, Fibroadenoma, Tubular Adenoma, Phyllodes Tumor, Ductal Carcinoma, Lobular Carcinoma, Mucinous Carcinoma or Papillary Carcinoma). The model uses the VGG16 convolution base and Resnet50 convolution base as the parallel convolution base of the model. Two convolutional bases (VGG16 convolutional base and Resnet50 convolutional base) obtain breast tissue image features from different fields of view. After the information output by the fully connected layer of the two convolutional bases is fused, it is classified and output by the SoftMax function. The model experiment uses the publicly available BreaKHis data set. The number of samples of each class in the data set is extremely unevenly distributed. Compared with the binary classification, the number of samples in each class of the eight-class classification is also smaller. Therefore, the image segmentation method is used to expand the data set and the non-repeated random cropping method is used to balance the data set. Based on the balanced data set and the unbalanced data set, the BCDnet model, the pre-trained model Resnet50+ fine-tuning, and the pre-trained model VGG16+ fine-tuning are used for multiple comparison experiments. In the comparison experiment, the BCDnet model performed outstandingly, and the correct recognition rate of the eight-class classification model is higher than 98%. The results show that the model proposed in this paper and the method of improving the data set are reasonable and effective.
A quantitative assessment of the indirect impacts of human-elephant conflict
Authors: Sampson Christie , Rodriguez S. L. , Leimgruber Peter , Huang Qiongyu , Tonkyn David
Published: July 2021

Human-wildlife conflict has direct and indirect consequences for human communities. Understanding how both types of conflict affect communities is crucial to developing comprehensive and sustainable mitigation strategies. We conducted an interview survey of 381 participants in two rural areas in Myanmar where communities were exposed to human-elephant conflict (HEC). In addition to documenting and quantifying the types of direct and indirect impacts experienced by participants, we evaluated how HEC influences people’s attitudes towards elephant conservation. We found that 99% of participants suffered from some type of indirect impact from HEC, including fear for personal and family safety from elephants and fear that elephants will destroy their home. Despite experiencing moderate levels of indirect impacts from HEC at the community level, participants expressed attitudes consistent with supporting future elephant conservation programs.
A novel high-throughput screen for identifying lipids that stabilise membrane proteins in detergent based solution
Authors: Cecchetti Cristina , Strauss Jannik , Stohrer Claudia , Naylor Claire , Pryor Edward , Hobbs Jeanette , Tanley Simon , Goldman Adrian , Byrne Bernadette
Published: July 2021

Membrane proteins have a range of crucial biological functions and are the target of about 60% of all prescribed drugs. For most studies, they need to be extracted out of the lipid-bilayer, e.g. by detergent solubilisation, leading to the loss of native lipids, which may disturb important protein-lipid/bilayer interactions and thus functional and structural integrity. Relipidation of membrane proteins has proven extremely successful for studying challenging targets, but the identification of suitable lipids can be expensive and laborious. Therefore, we developed a screen to aid the high-throughput identification of beneficial lipids. The screen covers a large lipid space and was designed to be suitable for a range of stability assessment methods. Here, we demonstrate its use as a tool for identifying stabilising lipids for three membrane proteins: a bacterial pyrophosphatase (Tm-PPase), a fungal purine transporter (UapA) and a human GPCR (A2AR). A2AR is stabilised by cholesteryl hemisuccinate, a lipid well known to stabilise GPCRs, validating the approach. Additionally, our screen also identified a range of new lipids which stabilised our test proteins, providing a starting point for further investigation and demonstrating its value as a novel tool for membrane protein research. The pre-dispensed screen will be made commercially available to the scientific community in future and has a number of potential applications in the field.
Correlated color temperature and light intensity: Complementary features in non-visual light field
Authors: Arguelles-Prieto Raquel , Madrid Juan Antonio , Rol Maria Angeles , Bonmati-Carrion Maria Angeles
Published: July 2021

An appropriate exposure to the light-dark cycle, with high irradiances during the day and darkness during the night is essential to keep our physiology on time. However, considering the increasing exposure to artificial light at night and its potential harmful effects on health (i.e. chronodisruption and associated health conditions), it is essential to understand the non-visual effects of light in humans. Melatonin suppression is considered the gold standard for nocturnal light effects, and the activation of intrinsically photosensitive retinal ganglion cells (ipRGCs) through the assessment of pupillary light reflex (PLR) has been recently gaining attention. Also, some theoretical models for melatonin suppression and retinal photoreceptors activation have been proposed. Our aim in this study was to determine the influence of correlated color temperature (CCT) on melatonin suppression and PLR, considering two commercial light sources, as well as to explore the possible correlation between both processes. Also, the contribution of irradiance (associated to CCT) was explored through mathematical modelling on a wider range of light sources. For that, melatonin suppression and PLR were experimentally assessed on 16 healthy and young volunteers under two light conditions (warmer, CCT 3000 K; and cooler, CCT 5700 K, at ~5·1018 photons/cm2/sec). Our experimental results yielded greater post-stimulus constriction under the cooler (5700 K, 13.3 ± 1.9%) than under the warmer light (3000 K, 8.7 ± 1.2%) (p < 0.01), although no significant differences were found between both conditions in terms of melatonin suppression. Interestingly, we failed to demonstrate correlation between PLR and melatonin suppression. Although methodological limitations cannot be discarded, this could be due to the existence of different subpopulations of Type 1 ipRGCs differentially contributing to PLR and melatonin suppression, which opens the way for further research on ipRGCs projection in humans. The application of theoretical modelling suggested that CCT should not be considered separately from irradiance when designing nocturnal/diurnal illumination systems. Further experimental studies on wider ranges of CCTs and light intensities are needed to confirm these conclusions.
Seroprevalence of mycoplasmosis in broiler, layer, and native chickens in Giza, Egypt
Authors: El-Ashram Saeed , Hashad Mahmoud E. , Abdel-Alim G. A. , Abdelhamid Taher , N. Deif Heba
Published: July 2021

We aimed to investigate Mycoplasma infections among chicken flocks (Ross, Lohmann and native) in Giza, Egypt, using serological tests, including the slide plate agglutination (SPA) test, hemagglutination inhibition (HI) test, and enzyme-linked immunosorbent assay (ELISA). The slide plate agglutination examination, a serological test, indicated the prevalence of Mg and Ms infections of 10.9% and 13.2%, respectively. On 91 SPA test positive serum samples for either Mg or Ms, a passive hemagglutination/hemagglutination inhibition (HI) test was performed. The SPA and HI test findings were found to be comparable. On 90 SPA test positive samples, an ELISA was performed using commercial kits for Mg and Ms serodiagnosis. According to the ELISA data, only 83.33% and 18.88% of SPA test positive samples were confirmed as positive for Ms and Mg infections, respectively. The prevalence increased to 84.44% and 77.77%, respectively, when suspected samples were deemed positive.
Vegetables contamination by heavy metals and associated health risk to the population in Koka area of central Ethiopia
Authors: Bayissa Leta Danno , Gebeyehu Hailu Reta
Published: July 2021

Contaminated soil and vegetables have continued to instigate threat to human health globally and specially in developing countries. This study was aimed to determine concentrations of certain heavy metals in soil and vegetables (cabbage and tomato) from Koka area of central Ethiopia using Inductively Coupled Plasma Optical Emission Spectrophotometer (ICP-OES). The amounts of As, Pb, Cd, Zn, Cu, Hg and Co detected in soil samples were found to surpass the reference values for agricultural soil. Similarly, the concentrations of As, Pb, Cd, Cr and Hg obtained in both tomato and cabbage samples have exceeded the recommended values with the mean levels generally ranging from 0.93–6.76, 1.80–7.26, 0.33–1.03, 0.86–5.16 and 3.23–4.36 mg/kg dry weight, respectively. The result obtained have signified that leafy vegetable has hoarded heavy metals more than non-leafy vegetable. The total hazard quote for As and Hg from tomato ingestion and for As, Hg and Co from cabbage ingestion were greater than unity, signifying potential health hazard to the public. The health index (HI) owing to tomato and cabbage ingesting were 5.44 and 14.21, respectively, signifying likely adversative health implication to the population from the ingestion of the vegetables. The Total Cancer Risk (TCR) analysis have uncovered the possible cancer hazard persuaded by Cd, Hg, As and Ni from the ingestion of both vegetables. From the outcomes this study, it can be concluded that the soil and vegetables from Koka areas are possibly contaminated with toxic metals and hence demand strict monitoring to safeguard the public around the study area and beyond.
Maternal dietary practices, dietary diversity, and nutrient composition of diets of lactating mothers in Jimma Zone, Southwest Ethiopia
Authors: Forsido Sirawdink Fikreyesus , Tadesse Frehiwot , Belachew Tefera , Hensel Oliver
Published: July 2021

Background

Optimal nutrition during lactation is essential for the well-being of the mother and the infant. Studies have shown that access to nutrient-rich foods during lactation is critical as minimal stores of nutrients can have adverse effects. This study aimed to investigate the diversity, composition, and nutrient adequacy of diets of lactating mothers in Southwest Ethiopia.

Methods

A community-based cross-sectional survey was carried out in three districts of Jimma Zone, Southwest Ethiopia, in February 2014. A stratified multistage sampling technique was used to select 558 lactating mothers. Data were collected using a pre-tested and structured interviewer-administered questionnaire. Minimum dietary diversity for women (MDD-W) was computed from a single 24-h recall. A cut off value of 5 was used to classify the dietary diversity into achieving MDD-W or not. The proximate, mineral and anti-nutritional compositions of 12 commonly consumed foods were analysed using standard methods. Nutrient adequacy ratio (NAR) and Mean adequacy ratio (MAR) of these foods were estimated.

Results

The mean (±SD) dietary diversity score (DDS) of the study participants was 3.73±1.03. Meeting MDD-W was positively associated with agricultural production diversity (P = 0.001) and educational level of the women (P = 0.04). Conversely, district of the study (P = 0.003) and place of residence (P = 0.019) were negatively associated with meeting MDD-W. The proximate composition (g/100g) of the sampled foods ranged between 24.8–65.6 for moisture, 7.6–19.8 for protein, 2.1–23.1 for crude fat, 2.0–27 for crude fibre, 1.0–21.2 for total ash, and 0.9–45.8 for total carbohydrate content. The calorific value ranged between 124.5–299.6 Kcal/100g. The mineral contents (mg/100g) ranged between 9.5–52.5 for iron, 2.2–4.2 for zinc, 42.6–318.2 for calcium, and 150.7–379.9 for phosphorus. The content of anti-nutritional factors (mg/100g) ranged between 11.1–178.9 for phytate and 3.7–315.9 for tannin. All the commonly consumed maternal foods were not sufficient to meet the energy, fat and protein requirements, (NAR<1). However, all diets provided adequate iron and most of the cereal-based foods provided adequate carbohydrate and minerals. The overall nutrient adequacy was below the cut-off point for all food types.

Conclusions

The diets of lactating mothers in Southwest Ethiopia lack diversity and nutrient adequacy. A community-based nutrition education program on the importance of diet diversity and nutrient intake during lactation based on a multi-sectoral approach is needed.
Lens densitometry for assessment and prediction of cataract progression after pars plana vitrectomy with C3F8-gas for retinal detachment
Authors: Schindler Philipp , Mautone Luca , Bigdon Eileen , Druchkiv Vasyl , Spitzer Martin Stefan , Skevas Christos
Published: July 2021

Purpose

Lens opacification is a common complication after pars plana vitrectomy (PPV) and knowing its progression would facilitate consulting patients. The purpose of this study was to evaluate a quantitative model for lens-status-monitoring after PPV with C3F8 gas. Our model was evaluated in rhegmatogenous retinal detachment (RRD) patients of various age and lens densitometry (LD).

Methods

Data between March 2018 and March 2020 were evaluated retrospectively. LD measurements of the PentacamHR® Nucleus Staging mode (PNS) were used to quantify lens opacification over time. A mixed-effect regression model was designed, to enable LD predictions at any time postoperatively. Calculations were based on patient’s age and baseline LD as dependent variables. Six patients were randomly excluded during model development, to be used for testing its power afterwards.

Results

34 patients (male 19 [55.9%], female 15 [44.1%]) matched the inclusion criteria. Average age was 58.5 years (32–77;±4.3) and average follow-up was 7.2 months (3,4–23.1;±1,8). Mean baseline LD of the treated and fellow eye before surgery were 10.9% (8.7%-14.8%;±0.8) and 10.7% (8.5%-14.1%;±0.6), respectively. Using our prediction model, LD values for the six pre-selected patients closely match the observed data with an average deviation of 1.07%.

Conclusions

Evaluation of age and baseline LD using a mixed-effect regression model might predict cataract progression in RRD patients treated with PPV and C3F8-gas. Such a tool could be considered during cataract surgery consultation in these patients.
Whole genome sequencing identifies novel structural variant in a large Indian family affected with X-linked agammaglobulinemia
Authors: Jain Abhinav , Govindaraj Geeta Madathil , Edavazhippurath Athulya , Faisal Nabeel , Bhoyar Rahul C. , Gupta Vishu , Uppuluri Ramya , Manakkad Shiny Padinjare , Kashyap Atul , Kumar Anoop , Divakar Mohit Kumar , Imran Mohamed , Sawant Sneha , Dalvi Aparna , Chakyar Krishnan , Madkaikar Manisha , Raj Revathi , Sivasubbu Sridhar , Scaria Vinod
Published: July 2021

X—linked agammaglobulinemia (XLA, OMIM #300755) is a primary immunodeficiency disorder caused by pathogenic variations in theBTKgene, characterized by failure of development and maturation of B lymphocytes. The estimated prevalence worldwide is 1 in 190,000 male births. Recently, genome sequencing has been widely used in difficult to diagnose and familial cases. We report a large Indian family suffering from XLA with five affected individuals. We performed complete blood count, immunoglobulin assay, and lymphocyte subset analysis for all patients and analyzed Btk expression for one patient and his mother. Whole exome sequencing (WES) for four patients, and whole genome sequencing (WGS) for two patients have been performed. Carrier screening was done for 17 family members using Multiplex Ligation-dependent Probe Amplification (MLPA) and haplotype ancestry mapping using fineSTRUCTURE was performed. All patients had hypogammaglobulinemia and low CD19+ B cells. One patient who underwent Btk estimation had low expression and his mother showed a mosaic pattern. We could not identify any single nucleotide variants or small insertion/ deletions from the WES dataset that correlates with the clinical feature of the patient. Structural variant analysis through WGS data identifies a novel large deletion of 5,296 bp at loci chrX:100,624,323–100,629,619 encompassing exons 3–5 of theBTKgene. Family screening revealed seven carriers for the deletion. Two patients had a successful HSCT. Haplotype mapping revealed a South Asian ancestry. WGS led to identification of the accurate genetic mutation which could help in early diagnosis leading to improved outcomes, prevention of permanent organ damage and improved quality of life, as well as enabling genetic counselling and prenatal diagnosis in the family.