bluuebunny/crossref_metadata_2025 huggingface dataset:
Determination of Aliphatic and Polycyclic Aromatic Hydrocarbons in Marine Core Sediments off Johor, Malaysia
Authors: Ruzani Raihanah Na Ilah , Suratman Suhaimi , Fadzil Muhammad Fais , Yun Pang Swee , Rozmi Nur Shahirah , Tahir Norhayati Mohd
Published: September 2021

Aliphatic hydrocarbons and polycyclic aromatic hydrocarbons (PAHs) were studied in two sediment cores of southern South China Sea off Johor coastal area. The concentrations of the total identified resolved aliphatic hydrocarbons (TiRAHs) in the coastal station (STC104) ranged from 0.35 to 2.07 µg/g while the offshore station (STC100) varied from 0.05 to 14.7 µg/g. The concentrations of total PAHs were varied from not detected to 33.9 ng/g. The nalkanes distribution in STC104 were predominant in short chain carbons from marine productivity, petroleum mixture and minor higher plant input, while STC100 exhibited a bimodal distribution with mixed input of marine and terrestrial origin. PAHs isomer ratios cross-plot have showed mixed input of pyrogenic and petrogenic inputs while perylene was dominated in STC100 followed by fossil fuels and pyrogenic source. Presence of perylene in both cores suggesting the contribution of biogenic sources. Principal component analysis was used to cluster the relationship of the hydrocarbons at both sediment cores.
Green Synthesis of Co3O4 Nanoparticles using Mappia Foetida Leaf Extract and its Antimicrobial Potential
Authors: Patil Jayashri B , Takate Sushma J , Moharekar Sanjay T , Zaware Bhaskar H , Moharekar Shubhangi S
Published: September 2021

In this paper the novel green synthesis of cobalt oxide nanoparticles (Co3O4NPs) from cobalt chloride (CoCl2) using Mappia foetida leaf extract was investigated. The characterization of the Co3O4NPs was done by using UV – Vis spectroscopy, EDX, XRD and SEM analysis techniques. Comparative antibacterial study was done against gram positive and gram negative bacteria by well diffusion method in which results revealed that the biologically synthesized Co3O4NPs showed relatively similar antibacterial potential as chemically synthesized Co3O4NPs and higher antibacterial potential than that of positive control.
Proximate Analysis, Antoxidant Property and Cytotoxicity Assessment for Pseuderanthemum Reticulatum Leaves
Authors: Sheela S. Margrat , Vimala J. Rosaline
Published: September 2021

The bioactive constituents derived from plants attract the attention of researchers due to their potential applications in the medicinal field. In this regard, the proximate analysis and the cytotoxicity study of the plant materials play an important role in the phytochemical research. In the present work, estimation of total ash, moisture content, fiber content, crude protein, and carbohydrate were carried out under proximate analysis and the antioxidant activity of the anthocyanin present in the plant material was evaluated by DPPH (2,2-diphenyl-1-picrylhydrazyl) method. The separation of anthocyanin pigment from the plant material was done by paper chromatography (PC) technique and they are characterized by UV spectrum, chemical test and the Rf values obtained from paper chromatography. This study also investigated the in vitro cytotoxicity of Pseuderanthemum reticulatum leaves by means of MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide)) assay PBMC (Peripheral Blood Mononuclear Cell). The results of the proximate analysis showed that the plant material contains 7.6% of moisture content, 16.6 % of total ash, 5.6% of crude protein, 23.0% of crude fiber, 3.82% of crude fat and 23.64 % of carbohydrate. The free radical scavenging ability of the separated anthocyanin was found to be 72.58% at 10 µg/mL. The cytotoxicity investigation showed that the aqueous extract possess the IC50 value of 161.5μg/mL. The High percentage of radical scavenging activity and low toxicity of the plant suggest that it can be extensively used for the investigation of the bioactive constituents and its applications.
Scoping Review of Prospective Clinical Studies, Projects, and Clinical Study Protocol for Korean Medicine Treatment on Dementia
Authors: Kim Je-Beom , Lee Dong-Yoon , Ha Da-Jung , Kwon Chan-Young
Published: September 2021

Objectives: The aim of this study is to review and analyze the trends in prospective clinical research (PCR), project, clinical study protocol of Korean medicine (KM) for dementia. Methods: We searched PCRs of KM on dementia in six electronical databases, up to January 28, 2021. Moreover, the clinical research protocol and projects of KM for dementia were searched. Results: Total eight PCRs, nine projects, and three clinical study protocols were included. In the PCRs, there were one randomized controlled trial, five before and after study, and two comparative group before-after studies. Four of them used herbal medicine, two used acupuncture, one study used both herbal medicine and acupuncture, and the other one used moxibustion. Jowiseungchung-tang was the most frequently used herbal medicine. BL62, KI6 were used in electro-acupuncture, auricular-Shenmen in auricular acupuncture, and GV20 in moxibustion. The most frequent outcome was Korean-Dementia Rating Scale (K-DRS). One reported significant increase in K-DRS score, one reported 60% improvement, and the other studies mostly reported no significant difference. In the projects including 20 clinical studies of dementia, herbal medicine, integrative medicine and acupuncture were mainly used. In the protocols, herbal medicine, complex KM intervention, and integrative medicine were used. Conclusions: Currently, the number of PCRs of KM for dementia is very scarce. Therefore, the researcher's interest in this field and national research support should be made more, and the quality of clinical research in the future can be further improved by supplementing the limitations of previously published clinical research.
Review of Latest Traditional Chinese Medicine Clinical Studies on Pediatric Tic Disorder with Tuina Treatment
Authors: Park Jem Ma
Published: September 2021

Objectives: The purpose of this review is to investigate the latest traditional Chinese medicine clinical studies on pediatric tic disorder with Tuina treatment and propose the directions of future studies and clinical applications. Methods: To obtain data from CNKI, set the field by ‘中醫學’, ‘中藥’, ‘中西醫結合’ and used keywords ‘抽动障碍’, ‘抽動 穢語綜合’, ‘小兒抽动’, ‘兒童抽动’ and ‘推拿’, ‘導引’, ‘按摩’, ‘Tuina’, ‘massage’ in cross combination way. Results: 12 clinical studies were selected. These studies were analyzed by author & year, subjects, diagnostic criterion, evaluation criterion, syndrome differentiation, treatment period, methods& results, frequent acupoints and assessment of the quality of studies. All of reports achieved effective therapeutic results on the pediatric tic disorder with Tuina treatment. Conclusion: Tuina treatment has a positive effect and are easily accepted by children who have fear and rejection to traditional Korean Medicine such as acupuncture and Herbal remedy. It is also safe and simple to operate. So the Tuina treatment is worthy to disseminate potential for further development in the treatment of pediatric tic disorders.
A Systematic Review of effect on Heat-sensitive Moxibustion for Benign Prostatic Hyperplasia
Authors: Kim MinSeok , Ju HongMin , Kim MinHwa , Park SunYoung , Yun YoungJu , Park SeongHa
Published: September 2021

Objectives: The aim of this study is to investigate the effect of Heat-sensitive Moxibustion on Benign Prostatic Hyperplasia Methods: We searched articles from Academic Journals(CAJ) online databases, Oriental Medicine Advanced Searching Integrated System (OASIS), Searching key words were ‘前列腺增生’, ‘熱敏灸’ and ‘열민구’, ‘전립선비대’. The search range included randomized controlled trials (RCTs). Among the articles published to 2020, 10 articles were found. After review the title, abstract and original, 3 articles were selected finally to rule out treatment combined with completely different treatments. Result: The Heat-sensitive moxibustion at acupoints in the treatment of Benign prostatic hyperplasia were significantly superior to control group after treatment in the symptoms of patients, IPSS, QOL, PVR and Qmax(P<0.05). The Heat-sensitive moxibustion can significantly reduce the incidence of temporary urinary incontinence after Transurethral resection of the prostate(TURP) and improve life quality and satisfaction of patients(P<0.05). The individualized desensitization saturated time and amount of Heat-sensitive moxibustion is superior effective to general amount and time of traditional moxibustion in the total effective rate, IPSS, Ru and Qmax(P<0.01) for Benign prostatic hyperplasia. Conclusion: Heat sensitive moxibustion directly transfer heat to the source of a disease. So it can be considered as a good treatment for Benign prostate hypertrophy. It was also shown a better effect on BPH compared to traditional moxibustion, According to the thermo principles of tumor, if the tumor cell's death temperature of 43°C is reached, that can cause tumor degeneration. Therefore I think Heat sensitive moxibustion can be applied to various tumor disease. The results of this study could be applied to clinical treatment of BPH. However, additional large-scale clinical researches should be conducted.
Effects of Korean Medicine Treatment focusing on Acupotomy of headache: A Case Report of Four Patients
Authors: Lee Joohyun , Chu Hongmin , Kang Kyungho , Moon Ju-hyeon , Kim Jongchul , Park Jeongsu , Chae Hyocheong , Jung Sehun , Kim Jaehyo , Ryu Myungseok
Published: September 2021

Background: The aim of this study was to report the effect of acupotomy for patients with headache. Methods: Four patients with headache were treated with acupotomy. The improvement of symptoms was evaluated by numeric rating scale(NRS), Headache impact test-6(HIT-6) and headache attack frequency. Results: The numeric rating scale score and headache attack frequency decreased throughout the treatment period. No side effects were observed during treatment. Conclusion: Acupotomy had shown a positive clinical effect in the treatment of a headache in this case series. Further studies are required for its application on various headache.
Influence of collimator aberrations on the instrument line shape of a Fourier transform spectrometer
Authors: Wawrzyniuk Leszek
Published: September 2021

The influence of the aberrations of a collimator optical system on the instrument line shape (ILS) of a Fourier transform spectrometer was studied. By analyzing the wave propagation in the spectrometer, numerical distributions of intensity in images of source points visible at different angles from the center of the collimator were modeled. Thus, the shape of the function describing the angular distribution of the intensity in the interferometer was obtained. Then, the ILS of the spectrometer was derived. The influence of the aberration on the ILS was analyzed by determining the shifts of the line positions for different values of third-order aberrations and parameters of the device (field of view and diameter of the aperture). Conclusions concerning the influence of the particular aberrations are presented.
Registration of 3D point clouds using a local descriptor based on grid point normal
Authors: Wang Jiang , Wu Bin , Kang Jiehu
Published: September 2021

The coarse-to-fine method is the prime technology for point cloud registration in 3D reconstruction. Aimed at the problem of low accuracy of coarse registration for the partially overlapping point clouds, a novel, to the best of our knowledge, 3D local feature descriptor named grid normals deviation angles statistics (GNDAS) for aligning roughly pairwise point clouds is proposed in this paper. The descriptor is designed by first dividing evenly the local surface into some grids along the

x

axis and

y

axis of the local reference frame, then making the statistics of the deviation angles of normals at grid points. Based on the correspondences generated by matching descriptors and a transformation estimation method, the initial registration result is obtained. The coarse registration result is used as the initial value of the iterative closest point algorithm to achieve the refinement of the registration result. Experimental comparisons on two public datasets demonstrate that our GNDAS descriptor has high descriptiveness and strong robustness to noise at low level and varying mesh resolution. The registration results also confirm the superiority of our registration approach over previous versions in accuracy and efficiency.
Fiber source of femtosecond pulses at 910–940  nm based on a Mamyshev pulse oscillator and wavelength conversion in a photonic crystal fiber
Authors: Liaugminas Gustas , Želudevičius Julijanas , Regelskis Kęstutis
Published: September 2021

In this work, we present a fiber-based setup for femtosecond pulse generation at

∼
910
−
940

n
m

wavelength. Pump pulses from a Mamyshev oscillator with center wavelength at 1036 nm 1 ps duration are amplified and coupled into a photonic crystal fiber forming a soliton at 1051 nm. Due to the nonlinear four-wave mixing process, soliton pulses are converted to 910–940 nm with a few hundred femtosecond pulses with energy up to 0.7 nJ. The proposed design utilizes features of the Mamyshev oscillator, enabling a robust way of generating femtosecond pulses at

∼
910
−
940

n
m

.
Artificial neural networks used to retrieve effective properties of metamaterials
Authors: Repän Taavi , Venkitakrishnan Ramakrishna , Rockstuhl Carsten
Published: September 2021

We propose using deep neural networks for the fast retrieval of effective properties of metamaterials based on their angular-dependent reflection and transmission spectra from thin slabs. While we noticed that non-uniqueness is an issue for a successful application, we propose as a solution an automatic algorithm to subdivide the entire parameter space. Then, in each sub-space, the mapping between the optical response (complex reflection and transmission coefficients) and the corresponding material parameters (dielectric permittivity and permeability) is unique. We show that we can easily train one neural network per sub-space. For the final parameter retrieval, predictions from the different sub-networks are compared, and the one with the smallest error expresses the desired effective properties. Our approach allows a significant reduction in run-time, compared to more traditional least-squares fitting. Using deep neural networks to retrieve effective properties of metamaterials is a significant showcase for the application of AI technology to nanophotonic problems. Once trained, the nets can be applied to retrieve properties of a larger number of different metamaterials.
Impact of nonlinear effects in Si towards integrated microwave-photonic applications
Authors: Bass Jake , Tran Huong , Du Wei , Soref Richard , Yu Shui-Qing
Published: September 2021

As one of major integrated microwave photonics (IMWP) platforms, Si photonics exhibits the intensity-dependent Kerr effect and two-photon absorption (TPA) with associated free carrier effects (FCE). At the commonly used 1.55 µm, TPA losses and the associated FCE would eventually limit the dynamic range of Si photonic links. Resonating structures such as ring resonators (RRs) experience enhanced nonlinear effects due to significant intensity buildup. According to the bandgap characteristics of Si, TPA can be eliminated at and beyond 2.2 µm. In this work, a systemic simulation of straight waveguides and RRs is performed at wavelengths from 1.55 to 2.2 µm where the wavelength-dependent TPA loss is investigated. Moreover, the Kerr effect leads to unwanted change of refractive index, which shifts the RR resonant wavelength at both 1.55 and 2.2 µm, thus needing shift compensation. Compensated RRs operating at 2.2 µm could open a new venue for Si photonics towards IMWP applications.
High-speed object detection with a single-photon time-of-flight image sensor
Authors: Mora-Martín Germán , Turpin Alex , Ruget Alice , Halimi Abderrahim , Henderson Robert , Leach Jonathan , Gyongy Istvan
Published: September 2021

3D time-of-flight (ToF) imaging is used in a variety of applications such as augmented reality (AR), computer interfaces, robotics and autonomous systems. Single-photon avalanche diodes (SPADs) are one of the enabling technologies providing accurate depth data even over long ranges. By developing SPADs in array format with integrated processing combined with pulsed, flood-type illumination, high-speed 3D capture is possible. However, array sizes tend to be relatively small, limiting the lateral resolution of the resulting depth maps and, consequently, the information that can be extracted from the image for applications such as object detection. In this paper, we demonstrate that these limitations can be overcome through the use of convolutional neural networks (CNNs) for high-performance object detection. We present outdoor results from a portable SPAD camera system that outputs 16-bin photon timing histograms with 64×32 spatial resolution, with each histogram containing thousands of photons. The results, obtained with exposure times down to 2 ms (equivalent to 500 FPS) and in signal-to-background (SBR) ratios as low as 0.05, point to the advantages of providing the CNN with full histogram data rather than point clouds alone. Alternatively, a combination of point cloud and active intensity data may be used as input, for a similar level of performance. In either case, the GPU-accelerated processing time is less than 1 ms per frame, leading to an overall latency (image acquisition plus processing) in the millisecond range, making the results relevant for safety-critical computer vision applications which would benefit from faster than human reaction times.
Spatio-temporal continuous gesture recognition under degraded environments: performance comparison between 3D integral imaging (InIm) and RGB-D sensors
Authors: Krishnan Gokul , Huang Yinuo , Joshi Rakesh , O’Connor Timothy , Javidi Bahram
Published: September 2021

In this paper, we introduce a deep learning-based spatio-temporal continuous human gesture recognition algorithm under degraded conditions using three-dimensional (3D) integral imaging. The proposed system is shown as an efficient continuous human gesture recognition system for degraded environments such as partial occlusion. In addition, we compare the performance between the 3D integral imaging-based sensing and RGB-D sensing for continuous gesture recognition under degraded environments. Captured 3D data serves as the input to a You Look Only Once (YOLOv2) neural network for hand detection. Then, a temporal segmentation algorithm is employed to segment the individual gestures from a continuous video sequence. Following segmentation, the output is fed to a convolutional neural network-based bidirectional long short-term memory network (CNN-BiLSTM) for gesture classification. Our experimental results suggest that the proposed deep learning-based spatio-temporal continuous human gesture recognition provides substantial improvement over both RGB-D sensing and conventional 2D imaging system. To the best of our knowledge, this is the first report of 3D integral imaging-based continuous human gesture recognition with deep learning and the first comparison between 3D integral imaging and RGB-D sensors for this task.
Modeling of iterative time-reversed ultrasonically encoded optical focusing in a reflection mode
Authors: Wang Jian , Liang Hanpeng , Luo Jiawei , Ye Bolin , Shen Yuecheng
Published: September 2021

Time-reversed ultrasonically-encoded (TRUE) optical focusing is a promising technique to realize deep-tissue optical focusing by employing ultrasonic guide stars. However, the sizes of the ultrasound-induced optical focus are determined by the wavelengths of the ultrasound, which are typically tens of microns. To satisfy the need for high-resolution imaging and manipulation, iterative TRUE (iTRUE) was proposed to break this limit by triggering repeated interactions between light and ultrasound and compressing the optical focus. However, even for the best result reported to date, the resolutions along the ultrasound axial and lateral direction were merely improved by only 2-fold to 3-fold. This observation leads to doubt whether iTRUE can be effective in reducing the size of the optical focus. In this work, we address this issue by developing a physical model to investigate iTRUE in a reflection mode numerically. Our numerical results show that, under the influence of shot noises, iTRUE can reduce the optical focus to a single speckle within a finite number of iterations. This model also allows numerical investigations of iTRUE in detail. Quantitatively, based on the parameters set, we show that the optical focus can be reduced to a size of 1.6 µm and a peak-to-background ratio over 104 can be realized. It is also shown that iTRUE cannot significantly advance the focusing depth. We anticipate that this work can serve as useful guidance for optimizing iTRUE system for future biomedical applications, including deep-tissue optical imaging, laser surgery, and optogenetics.
Noncontact characterization of microstructured optical fibers coating in real time
Authors: Ermatov Timur , Gnusov Ivan , Skibina Julia , Noskov Roman E. , Gorin Dmitry
Published: September 2021

Functional nanocoatings have allowed hollow-core microstructured
optical fibers (HC-MOFs) to be introduced into biosensing and
photochemistry applications. However, common film characterization
tools cannot evaluate the coating performance in
situ. Here we report the all-optical noncontact
characterization of the HC-MOF coating in real time. Self-assembled
multilayers consisting of inversely charged polyelectrolytes (PEs) are
deposited on the HC-MOF core capillary, and a linear spectral shift in
the position of the fiber transmission minima with increasing the film
thickness is observed as small as

∼

1.5
−
6

n
m

per single PE bilayer. We exemplify
the practical performance of our approach by registering an increase
in the coating thickness from

6

±

1

 to

11

±

1

n
m

per PE bilayer with increasing ionic
strength in the PE solutions from 0.15 to 0.5 M NaCl. Additionally, we
show real-time monitoring of pH-induced coating dissolving. Simplicity
and high sensitivity make our approach a promising tool allowing
noncontact analysis of the HC-MOF coating which is still challenging
for other methods.
Direct femtosecond laser inscription of an IR fluorotellurite fiber Bragg grating
Authors: Liu Lutao , Chen Fengyi , Xiao Xusheng , Li Xingyong , Wang Ruohui , Liu Chengzhen , Guo Haitao
Published: September 2021

This study proposes a novel, to the best of our knowledge, development of fluorotellurite glass fiber Bragg gratings (FBGs). Shell-like morphology was achieved using a single femtosecond laser pulse illuminated through the fiber’s polymer coating. Different FBG fabrication methods and parameters were systematically studied to optimize performance. The fluorotellurite FBG exhibited a high sensitivity to writing laser power and reflectivity saturation effect in repetitive writing. A low-insertion-loss fluorotellurite FBG with a reflectivity of over 99% and bandwidth of less than 1 nm was successfully inscribed. The flexible inscription methods can write an FBG at any wavelength in the fluorotellurite glass transparent window, and are applicable to infrared fiber lasers or sensors.
Study on the difference in exciton generation processes for a single host and exciplex-type co-host
Authors: Xu Huiwen , Lin Jinyu , Jiang Xinyan , Jin Yu , Lin Zhili , Zhang Xining , Li Xiaoyan , Yang Huishan , Wu Zhijun
Published: September 2021

We distinctly reveal the difference in the exciton generation processes in phosphorescent organic light-emitting devices with an exciplex-type co-host and a single host. Excitons in the co-host consisting of 4,4,4-tris(N-carbazolyl)-triphenylamine and 1,3,5-tris(N-phenylbenzimidazol-2-yl)benzene are created via efficient energy transfer from the exciplex to the phosphorescent dopant. In contrast, excitons in the single host of 4,4,4-tris(N-carbazolyl)-triphenylamine are formed by the combination of holes and electrons trapped by the phosphorescent dopants. The optimized device utilizing the co-host system exhibits highly superior performance relative to the single-host device. The maximum external quantum efficiency and maximum luminance are 14.88% and

90,700

c
d

/

m

2

for the co-host device, being 1.6 times and 3.6 times the maximum external efficiency and maximum luminance for the single-host device, respectively. Significantly, the critical current density, evaluating the device efficiency roll-off characteristic, is as high as

327.8

m
A

/

c
m

2

, which is highly superior to

120.8

m
A

/

c
m

2

for the single-host device, indicating the notable alleviation in efficiency roll-off for the co-host device. The significant improvement in device performance is attributed to eliminating the exciton quenching resulting from the captured holes and the efficient energy transfer from the exciplex-type co-host to the phosphorescent emitter incurred by the reverse intersystem crossing process.
Mutually induced soliton polarization instability in a bidirectional ultrafast fiber laser
Authors: Yang Kai , Li Ti-Jian , Li Xing-Di , Chen Ji-Xiang , Liu Meng , Cui Hu , Luo Ai-Ping , Xu Wen-Cheng , Luo Zhi-Chao
Published: September 2021

The bidirectional ultrafast fiber laser is a promising light source for dual-comb applications. The counter-propagating geometry could lead to soliton interaction through gain sharing, as well as the possible outcome of polarization instability. However, the polarization dynamics hidden behind the soliton interaction process in bidirectional fiber lasers were rarely investigated. Herein, we report on the polarization instability induced by the mutual soliton interactions through fiber gain in a bidirectional mode-locked fiber laser. Depending on the adjustment of the intracavity birefringence, the polarization states of two counter-propagating solitons can exhibit similar periodical polarization switching behaviors with a polarization-rotating transition state. The successive interactions of the bidirectional solitons mediated by the polarization cross-saturation effect of gain fiber could be responsible for the soliton polarization instability. These findings, in addition to the fundamental interest of the soliton nonlinear dynamics in dissipative optical systems, also open up new possibilities for creating dynamical control of the soliton polarization state and performance improvement in bidirectional ultrafast fiber lasers.
Basis profile curve identification to understand electrical stimulation effects in human brain networks
Authors: Miller Kai J. , Müller Klaus-Robert , Hermes Dora
Published: September 2021

Brain networks can be explored by delivering brief pulses of electrical current in one area while measuring voltage responses in other areas. We propose a convergent paradigm to study brain dynamics, focusing on a single brain site to observe the average effect of stimulating each of many other brain sites. Viewed in this manner, visually-apparent motifs in the temporal response shape emerge from adjacent stimulation sites. This work constructs and illustrates a data-driven approach to determine characteristic spatiotemporal structure in these response shapes, summarized by a set of unique “basis profile curves” (BPCs). Each BPC may be mapped back to underlying anatomy in a natural way, quantifying projection strength from each stimulation site using simple metrics. Our technique is demonstrated for an array of implanted brain surface electrodes in a human patient. This framework enables straightforward interpretation of single-pulse brain stimulation data, and can be applied generically to explore the diverse milieu of interactions that comprise the connectome.
PopART-IBM, a highly efficient stochastic individual-based simulation model of generalised HIV epidemics developed in the context of the HPTN 071 (PopART) trial
Authors: Pickles Michael , Cori Anne , Probert William J. M. , Sauter Rafael , Hinch Robert , Fidler Sarah , Ayles Helen , Bock Peter , Donnell Deborah , Wilson Ethan , Piwowar-Manning Estelle , Floyd Sian , Hayes Richard J. , Fraser Christophe ,   HPTN 071 (PopART) Study Team
Published: September 2021

Mathematical models are powerful tools in HIV epidemiology, producing quantitative projections of key indicators such as HIV incidence and prevalence. In order to improve the accuracy of predictions, such models need to incorporate a number of behavioural and biological heterogeneities, especially those related to the sexual network within which HIV transmission occurs. An individual-based model, which explicitly models sexual partnerships, is thus often the most natural type of model to choose. In this paper we present PopART-IBM, a computationally efficient individual-based model capable of simulating 50 years of an HIV epidemic in a large, high-prevalence community in under a minute. We show how the model calibrates within a Bayesian inference framework to detailed age- and sex-stratified data from multiple sources on HIV prevalence, awareness of HIV status, ART status, and viral suppression for an HPTN 071 (PopART) study community in Zambia, and present future projections of HIV prevalence and incidence for this community in the absence of trial intervention.
The genetic consequences of dog breed formation—Accumulation of deleterious genetic variation and fixation of mutations associated with myxomatous mitral valve disease in cavalier King Charles spaniels
Authors: Axelsson Erik , Ljungvall Ingrid , Bhoumik Priyasma , Conn Laura Bas , Muren Eva , Ohlsson Åsa , Olsen Lisbeth Høier , Engdahl Karolina , Hagman Ragnvi , Hanson Jeanette , Kryvokhyzha Dmytro , Pettersson Mats , Grenet Olivier , Moggs Jonathan , Del Rio-Espinola Alberto , Epe Christian , Taillon Bruce , Tawari Nilesh , Mane Shrinivas , Hawkins Troy , Hedhammar Åke , Gruet Philippe , Häggström Jens , Lindblad-Toh Kerstin
Published: September 2021

Selective breeding for desirable traits in strictly controlled populations has generated an extraordinary diversity in canine morphology and behaviour, but has also led to loss of genetic variation and random entrapment of disease alleles. As a consequence, specific diseases are now prevalent in certain breeds, but whether the recent breeding practice led to an overall increase in genetic load remains unclear. Here we generate whole genome sequencing (WGS) data from 20 dogs per breed from eight breeds and document a ~10% rise in the number of derived alleles per genome at evolutionarily conserved sites in the heavily bottlenecked cavalier King Charles spaniel breed (cKCs) relative to in most breeds studied here. Our finding represents the first clear indication of a relative increase in levels of deleterious genetic variation in a specific breed, arguing that recent breeding practices probably were associated with an accumulation of genetic load in dogs. We then use the WGS data to identify candidate risk alleles for the most common cause for veterinary care in cKCs–the heart disease myxomatous mitral valve disease (MMVD). We verify a potential link to MMVD for candidate variants near the heart specificNEBLgene in a dachshund population and show that two of theNEBLcandidate variants have regulatory potential in heart-derived cell lines and are associated with reducedNEBLisoform nebulette expression in papillary muscle (but not in mitral valve, nor in left ventricular wall). Alleles linked to reduced nebulette expression may hence predispose cKCs and other breeds to MMVD via loss of papillary muscle integrity.
Bacterial persistence is essential for susceptible cell survival in indirect resistance, mainly for lower cell densities
Authors: Rebelo João S. , Domingues Célia P. F. , Monteiro Francisca , Nogueira Teresa , Dionisio Francisco
Published: September 2021

Antibiotic-susceptible bacteria may survive bactericidal antibiotics if other co-inhabiting bacteria detoxify the medium through antibiotic degradation or modification, a phenomenon denominated as indirect resistance. However, it is unclear how susceptible cells survive while the medium is still toxic. One explanation relies on the speed of detoxification, and another, non-exclusive explanation, relies on persistence, a state of bacterial dormancy where cells with low metabolic activity and growth rates are phenotypically tolerant to antibiotics and other cytotoxic substances. Here we simulated the fate of susceptible cells in laboratory experiments in the context of indirect resistance to understand whether persistence is necessary to explain the survival of susceptible cells. Depending on the strain and experimental conditions, the decay of persister populations may follow an exponential or a power-law distribution. Therefore, we studied the impact of both distributions in the simulations. Moreover, we studied the impact of considering that persister cells have a mechanism to sense the presence of a toxic substance–a mechanism that would enable cells to leave the dormant state when the medium becomes nontoxic. The simulations show that surviving susceptible cells under indirect resistance may originate both from persister and non-persister populations if the density of detoxifying cells is high. However, persistence was necessary when the initial density of detoxifying cells was low, although persister cells remained in that dormancy state for just a few hours. Finally, the results of our simulations are consistent both with exponential and power-law decay of the persistence population. Whether indirect resistance involves persistence should impact antibiotic treatments.
Examining sex differences in neurodevelopmental and psychiatric genetic risk in anxiety and depression
Authors: Martin Joanna , Asjadi Kimiya , Hubbard Leon , Kendall Kimberley , Pardiñas Antonio F. , Jermy Bradley , Lewis Cathryn M. , Baune Bernhard T. , Boomsma Dorret I. , Hamilton Steven P. , Lucae Susanne , Magnusson Patrik K. , Martin Nicholas G. , McIntosh Andrew M. , Mehta Divya , Mors Ole , Mullins Niamh , Penninx Brenda W. J. H. , Preisig Martin , Rietschel Marcella , Jones Ian , Walters James T. R. , Rice Frances , Thapar Anita , O’Donovan Michael ,   Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium
Published: September 2021

Anxiety and depression are common mental health disorders and have a higher prevalence in females. They are modestly heritable, share genetic liability with other psychiatric disorders, and are highly heterogeneous. There is evidence that genetic liability to neurodevelopmental disorders, such as attention deficit hyperactivity disorder (ADHD) is associated with anxiety and depression, particularly in females. We investigated sex differences in family history for neurodevelopmental and psychiatric disorders and neurodevelopmental genetic risk burden (indexed by ADHD polygenic risk scores (PRS) and rare copy number variants; CNVs) in individuals with anxiety and depression, also taking into account age at onset. We used two complementary datasets: 1) participants with a self-reported diagnosis of anxiety or depression (N = 4,178, 65.5% female; mean age = 41.5 years; N = 1,315 with genetic data) from the National Centre for Mental Health (NCMH) cohort and 2) a clinical sample of 13,273 (67.6% female; mean age = 45.2 years) patients with major depressive disorder (MDD) from the Psychiatric Genomics Consortium (PGC). We tested for sex differences in family history of psychiatric problems and presence of rare CNVs (neurodevelopmental and >500kb loci) in NCMH only and for sex differences in ADHD PRS in both datasets. In the NCMH cohort, females were more likely to report family history of neurodevelopmental and psychiatric disorders, but there were no robust sex differences in ADHD PRS or presence of rare CNVs. There was weak evidence of higher ADHD PRS in females compared to males in the PGC MDD sample, particularly in those with an early onset of MDD. These results do not provide strong evidence of sex differences in neurodevelopmental genetic risk burden in adults with anxiety and depression. This indicates that sex may not be a major index of neurodevelopmental genetic heterogeneity, that is captured by ADHD PRS and rare CNV burden, in adults with anxiety and depression.
A security technology of power relay using edge computing
Authors: Sang Zhongqing , Yang Kai , Zhang Rencheng
Published: September 2021

The purposes are to find the techniques suitable for the safety relay protection of intelligent substations and discuss the applicability of edge computing in relay protection. Regarding relay protection in intelligent substations, edge computing and optimized simulated annealing algorithm (OSAA) are combined innovatively to form an edge computing strategy. On this basis, an edge computing model is proposed based on relay fault traveling waves. Under different computing shunt tasks, OSAA can converge after about 1,100 iterations, and its computing time is relatively short. As the global optimal time delay reaches 0.5295, the corresponding computing time is 456.27s, apparently better than the linear search method. The proposed model can reduce the computing time significantly, playing an active role in the safe shunting of power relays. The simulation also finds that the voltage and current waveforms corresponding to the fault state of Phase A are consistent with the actual situations. To sum up, this model provides a reference for improving and optimizing intelligent substation relay protection.
A real-time assay for cell-penetrating peptide-mediated delivery of molecular cargos
Authors: Gentry Schuyler B. , Nowak Scott J. , Ni Xuelei , Hill Stephanie A. , Wade Lydia R. , Clark William R. , Keelaghan Aidan P. , Morris Daniel P. , McMurry Jonathan L.
Published: September 2021

Cell-penetrating peptides (CPPs) are capable of transporting molecules to which they are tethered across cellular membranes. Unsurprisingly, CPPs have attracted attention for their potential drug delivery applications, but several technical hurdles remain to be overcome. Chief among them is the so-called ‘endosomal escape problem,’ i.e. the propensity of CPP-cargo molecules to be endocytosed but remain entrapped in endosomes rather than reaching the cytosol. Previously, a CPP fused to calmodulin that bound calmodulin binding site-containing cargos was shown to efficiently deliver cargos to the cytoplasm, effectively overcoming the endosomal escape problem. The CPP-adaptor, “TAT-CaM,” evinces delivery at nM concentrations and more rapidly than we had previously been able to measure. To better understand the kinetics and mechanism of CPP-adaptor-mediated cargo delivery, a real-time cell penetrating assay was developed in which a flow chamber containing cultured cells was installed on the stage of a confocal microscope to allow for observationab initio. Also examined in this study was an improved CPP-adaptor that utilizes naked mole rat (Heterocephalus glaber) calmodulin in place of human and results in superior internalization, likely due to its lesser net negative charge. Adaptor-cargo complexes were delivered into the flow chamber and fluorescence intensity in the midpoint of baby hamster kidney cells was measured as a function of time. Delivery of 400 nM cargo was observed within seven minutes and fluorescence continued to increase linearly as a function of time. Cargo-only control experiments showed that the minimal uptake which occurred independently of the CPP-adaptor resulted in punctate localization consistent with endosomal entrapment. A distance analysis was performed for cell-penetration experiments in which CPP-adaptor-delivered cargo showing wider dispersions throughout cells as compared to an analogous covalently-bound CPP-cargo. Small molecule endocytosis inhibitors did not have significant effects upon delivery. The real-time assay is an improvement upon static endpoint assays and should be informative in a broad array of applications.
Systematic revision of Gatesona (Crassiclitellata, Lumbricidae), an endemic earthworm genus from the Massif Central (France)
Authors: Marchán Daniel F. , Jiménez Sergio , Decaëns Thibaud , Domínguez Jorge
Published: September 2021

The Massif Central in France could potentially harbor numerous ancient endemic lineages owing to its long history of continuous geological stability. Several endemic earthworm species inhabit the area, with Allolobophora (Gatesona) chaetophora, Helodrilus (Acystodrilus) and Avelona ligra showing hints of a common evolutionary origin. However, the phylogenetic relationships and taxonomic status of the species remain to be studied through integrative molecular and morphological methods. To this end, eight species including most of the known species and subspecies of All. (Gatesona), Helodrilus (Acystodrilus) musicus, and Avelona ligra were sequenced for a set of five molecular markers. The species were grouped on the basis of the molecular findings in a phylogenetic framework. All. (Gatesona) was included within the same clade as Helodrilus (Acystodrilus) and Avelona, separated from Allolobophora sensu stricto, supporting its status as a good genus. Branch lengths and average pairwise genetic distances suggested the subspecies of All. (Gatesona) chaetophora examined should be considered species-level taxa. Thus, a generic diagnosis for Gatesona stat. nov. is provided, along with redescriptions of Gatesona chaetophora comb. nov., Gatesona rutena comb. nov. stat. nov., Gatesona lablacherensis comb. nov. stat. nov. and Gatesona serninensis comb. nov. stat. nov. The study findings highlight the need for further sampling of earthworm diversity in the Massif Central (and Southern France), in addition to an increased focus on the Eastern European species of Helodrilus.
Spatial equity in the layout of urban public sports facilities in Hangzhou
Authors: Chen Yujuan , Lin Ning , Wu Yangyang , Ding Liang , Pang Jun , Lv Tonghua
Published: September 2021

This paper proposes a framework for a layout evaluation of urban public sports facilities. First, the buffer analysis method is used to measure the service level of public sports facilities. The study findings indicate that the overall service level of public sports facilities presents the spatial characteristics of a central agglomeration, and the value of the service level diffuses outward from high to low. There is evident spatial heterogeneity in the layout of public sports facilities in Hangzhou. Second, the Gini coefficient, Lorenz curve, and location entropy are employed to measure the equity of the distribution among spatial units and the intradistrict disparity. The results show a mismatch between the spatial distribution of the facilities and the distribution of the permanent population. The patterns of distribution of the location entropy classes of Hangzhou can be divided into three types: balanced, alternating, and divergent districts. The method in this paper is effective in measuring spatial equity and visualizing it. it has a certain degree of systemicity, universality and operability. At the same time, this method can compare the diachronic characteristics of the same city and the synchronic characteristics of different cities, which has universal application value.
Basic and complex cognitive functions in Adult ADHD
Authors: Mohamed Saleh M. H. , Butzbach Marah , Fuermaier Anselm B. M , Weisbrod Matthias , Aschenbrenner Steffen , Tucha Lara , Tucha Oliver
Published: September 2021

Background

Many clinical studies reported deficits in basic and complex cognitive functions in adults with Attention-Deficit/Hyperactivity Disorder (ADHD). However, the extent in which deficits in basic functions (i.e., processing speed and distractibility) contribute to complex cognitive impairments (i.e., working memory, planning, cognitive flexibility, memory functions) in adults with ADHD is not well-studied. So far, literature show only one study, revealing that basic functions explain 27–74% of executive dysfunctions. Yet, the authors reported that findings could be affected by the selection of neuropsychological tests. The goal of the present research is to replicate such a finding using a different sample and a different set of neuropsychological tests.

Methods

Forty-eight adult patients with ADHD were compared with 48 healthy controls in basic cognitive functions, namely processing speed and distractibility and more complex cognitive functions, namely selective attention, cognitive flexibility, planning, working memory, verbal fluency, and verbal memory. Basic and complex cognitive functions were assessed using the Vigilance and Sustained Attention, Selective Attention, N-Back, Tower of London, Trail Making Test, Word Fluency, and Verbal Learning and Memory.

Results and conclusion

Logistic regression analyses showed that impairments in complex cognitive functions explained 25% of the variance in ADHD diagnosis. The explained variance dropped from 25% to 9% after considering basic functions of processing speed and distractibility. This 64% reduction highlights the importance of basic functions for impairments in complex functions in patients with ADHD.
phase1RMD: An R package for repeated measures dose-finding designs with novel toxicity and efficacy endpoints
Authors: Yin Jun , Du Yu , Qin Rui , Shen Shihao , Mandrekar Sumithra
Published: September 2021

Traditional dose-finding designs are substantially inefficient for targeted agents and cancer immunotherapies by failing to incorporate efficacy signals, mild and moderate adverse events, and late, cumulative toxicities. However, the lack of user-friendly software is a barrier to the practical use of the novel phase I designs, despite their demonstrated superiority of traditional 3+3 designs. To overcome these barriers, we present an R package, phase1RMD, which provides a comprehensive implementation of novel designs with repeated toxicity measures and early efficacy. A novel phase I repeated measures design that used a continuous toxicity score from multiple treatment cycles was implemented. Furthermore, in studies where preliminary efficacy is evaluated, an adaptive, multi-stage design to identify the most efficacious dose with acceptable toxicity was demonstrated. Functions are provided to recommend the next dose based on the data collected in a phase I trial, as well as to assess trial characteristics given design parameters via simulations. The repeated measure designs accurately estimated both the magnitude and direction of toxicity trends in late treatment cycles, and allocated more patients at therapeutic doses. The R package for implementing these designs is available from the Comprehensive R Archive Network. To our best knowledge, this is the first software that implement novel phase I dose-finding designs that simultaneously accounts for the multiple-grade toxicity events over multiple treatment cycles and a continuous early efficacy outcome. With the software published on CRAN, we will pursue the implementation of these designs in phase I trials in real-life settings.