bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of growth pattern, condition factor, gonadosomatic index of Manggabai (Glosogobius giuris) and Payangka (Ophieleotris aporos) in Limboto Lake, Gorontalo, Indonesia
Authors: Hasim Hasim , Tuheteru Jali , Fazrin Dewi Nuryanti
Published: June 2021

Abstract. Hasim, Tuheteru J, Fazrin DN. 2021. Comparison of growth pattern, condition factor, gonadosomatic index of Manggabai (Glosogobius giuris) and Payangka (Ophieleotris aporos) in Limboto Lake, Gorontalo, Indonesia. Biodiversitas 22: 3388-3393. Manggabai and Payangka are endangered native fishes in Limboto Lake due to continuous degradation in the lake. In addition, silting lake along with its area that continues to narrow can threaten the life of both fishes although the government has stipulated restoration of Limboto Lake as the ecosystem of the fishes. However, the current information on the fishes remains considerably limited in terms of making it as a conservation strategy. This study aims to analyze the relationship between the total length and weight of Payangka and Manggabai. Furthermore, it analyzes the condition factors and the gonadosomatic index of the two fishes. The research method integrates survey and laboratory techniques. The fishes are collected by using trap made of bamboo and motorcycle tires that are installed for three days and the catches are 60 fishes including 30 Manggabai and 30 Payangka. Then the total length and weight of the fish and their gonad weight were measured. Data analysis used mathematical formulation of the relationship between total weight and length, condition factor, and gonadosomatic index. The result of the analysis shows that the growth pattern of the Manggabai was negative allometric whereas the Payangka was positive allometric. The condition factor for both types is generally less than 1.7. The gonadosomatic index of Manggabai ranges from 4.10-20.00% and Payangka ranges from 0.05-1.98%. These conditions indicate that differences in growth pattern, condition factor, and gonadosomatic index are different forms of response to environmental conditions and in the spawning season of both types of fish.
Sponge community (Porifera) in coral reef ecosystem in Sabang, Aceh Province, Indonesia
Authors: Aulia Elsa Dianita , Hadi Tri Aryono , Utama Rizkie Satria
Published: June 2021

Abstract. Aulia ED, Hadi TA, Utama RS. 2021. Sponge community (Porifera) in coral reef ecosystem in Sabang, Aceh Province, Indonesia. Biodiversitas 22: 3394-3402. Sponges are one of the most influential benthic organisms in coral reef ecosystems. Many studies about sponge communities have been carried out globally, from tropical to temperate regions. In Indonesia, however, sponge communities have not been adequately observed, especially their diversity and interaction with habitats. Sabang, a developing city located in the northwest of Indonesia, has a lack of information about benthic communities and no reports about sponges. This study investigated the sponge community (species richness, coverage, and morphological characters) and the interactions, both within sponges and with corals and substrates, in Sabang. The study found that the sponge richness (species and morphology) and coverage are categorized as poor, having only 24 species with seven morphologies, and coverage of 1.79 ± 1.03% (SE). The interaction analyses showed significant relationships occur among sponge variables but not between sponges and corals, nor between sponges and their substrates. These results could be attributed to the hydrodynamic-related stresses in Sabang, which are likely influenced by exposure to the open ocean, a condition that is less favorable to diversity and interaction. It is necessary to regularly monitor the condition of benthic communities in Sabang in order to better understand their stable state and detect any change over time.
Diversity and potential contribution of wild edible plants to sustainable food security in North Wollo, Ethiopia
Authors: Hassen Ahmed
Published: June 2021

Hassen A. 2021. Diversity and potential contribution of wild edible plants to sustainable food security in North Wollo, Ethiopia. Biodiversitas 22: 2501-2510. Rural communities in different parts of the world use WEPs as supplementary food to increase dietary diversity. The findings of this study showed that 40.7% of the participants were food insecure in the study area. They are significantly dependent on WEPs when sudden drought exists. There were no significant studies conducted about ethnobotany in the study area. Therefore, this study was the first attempt to survey the perception of local people towards the potential resources of WEPs for sustainable food security, and conservation and management trends in North Wollo. Data was collected using semi-structured interviews (135 participants), tour-guided field observation, and focus group discussion (45 participants) to get relevant and adequate data. Descriptive statistics, one-way ANOVA, and preference ranking were used to analyze and interpret the quantitative data. A total of 66 locally available WEPs belong to 30 families found in the study area. Respondents’ preference revealed that O. ficus-indica, Z.spina-christ, C. spinarum, F. sur, and U. sinesis were ranked first, second, third, fourth, and fifth, respectively. Hence, this study will provide relevant information for policy-makers and managers to combat food insecurity in the study area.
Generating bursts of femtosecond laser pulses with a tunable delay and envelope in a folded Michelson interferometer
Authors: Zhou Boyang , Cheng He , Soileau M. J. , Yu Xiaoming
Published: June 2021

Bursts of 16 femtosecond laser pulses are generated in a fourfold
Michelson interferometer with a tunable delay and envelope. Solutions
are given to solve the “forward problem” (bursts from a given
parameter set) and “inverse problem” (obtain parameter set from a
given burst). Three types of bursts are generated experimentally with
envelopes suitable for applications in laser materials processing and
the generation of terahertz radiation.
Bubble optics: Leonardo’s cross revisited—Part 3, nonparaxial analytical methods
Authors: Lock James A. , Selmke Markus
Published: June 2021

In about 1508, Leonardo da Vinci first noted and sketched a cross-shaped caustic produced by a plane wave diagonally incident on the circularly symmetric meniscus surrounding a bubble on the surface of a water-filled container. This caustic was analyzed in two companion papers using a numerical ray theory spot diagram approach, and paraxial analytical methods. In this study we employ nonparaxial analytical methods, which are necessary when the outer bubble meniscus rises high above the ambient water surface. We also use a simple exactly soluble approximation to the outer meniscus shape, and obtain a distorted astroid caustic. We show that one of the refraction astroid cusp points is blocked by an aperture effect for steeply diagonally incident light, and the missing cusp is approximately replaced by a new cusp due to light transmitted through the bubble into the water, and reflecting from the underside of the outer meniscus.
3D face imaging with the spatial-temporal
correlation method using a rotary speckle projector
Authors: Zhou Pei , Zhu Jiangping , Xiong Wei , Zhang Jianwei
Published: June 2021

In this paper, a compact, cost-effective, and fast rotary speckle
projector (RSP) is designed and manufactured for high-precision
three-dimensional (3D) face data acquisition. Compared with the common
speckle projectors, RSP uses a simple speckle pattern design method
and has a good performance in high-speed projection and compact
structure, which allows a flexible balance between measurement
accuracy and time cost in a real acquisition task. Using a carefully
designed rotation angle of the speckle mask, temporally and spatially
non-correlative speckle patterns in the measurement volume can be
generated. The rotation angle of the speckle mask is carefully checked
and optimally selected via detailed theoretical analysis, simulation,
and experiments to ensure 3D reconstruction accuracy across the
reconstruction area. Subsequently, a binocular 3D face imaging system
composed of the RSP and two cameras is constructed. With captured
stereo speckle image pairs, we adopted our previously well-established
spatial-temporal correlation method to determine the disparity. The
accuracy of the 3D face imaging system was verified by using a real
face mask, which is standardized by a certified, high-precision
industrial 3D scanner. The real face data collection under various
expressions has demonstrated that the proposed system also has a good
performance for 3D face imaging in dynamic scenes.
Atomic transitions for adaptive optics
Authors: Yang Rui , Hellemeier Joschua , Hickson Paul
Published: June 2021

Adaptive optics systems using sodium laser guide stars are widely
employed at major astronomical observatories. It is natural to ask
whether other atomic species might offer advantages. In this paper, we
review all abundant atoms and ions in the upper atmosphere, including
Na, Fe,

M

g

+

,

S

i

+

,

C

a

+

, and K and also the non-metallic
species N,

N

+

, O, and H, considering their
potential for adaptive optics. Return fluxes for all transitions that
can be excited using either one or two wavelengths were computed. We
also considered multi-wavelength emission, comparing the performance
of different transitions for polychromatic laser guide star (PLGS)
adaptive optics. We find that of all the mesospheric metals, Na is the
most suitable for both monochromatic laser guide stars and PLGSs,
providing about six times more return flux than the best transitions
in Fe. For high-altitude observatories, excitation at 330 nm in Na
should give the highest PLGS performance. Atomic O, N, and

N

+

have strong transitions and very high
abundances in the mesosphere. This makes them potential candidates for
the generation of intense laser guide stars by amplified spontaneous
emission, if a suitable excitation process can be demonstrated. Direct
excitation by CW lasers is impractical, as all transitions from the
ground state are beyond the atmospheric cutoff. Nevertheless, it may
be possible using high-power pulsed lasers.
Self-supporting, ultra-thin and highly transparent conducting nickel grids for extremely flexible and stretchable electrochromic devices
Authors: Zhao Shi-Qing , Jiang Zhou-Ying , Chen Lin-Sen , Huang Wenbin , Liu Yan-Hua
Published: June 2021

It has been a great challenge to design an extremely flexible and stretchable electrochromic device (ECD), due to the physical deformation and fracture of the conductive materials and supporting substrates after plenty of bending. To solve the aforementioned shortcoming of ECDs, in this paper, a self-supporting metal Ni gird electrode is mentioned, which discarded solid or flexible polymeric substrates, having outstanding features of extremely foldability (bending radius lower 50 μm), stretchability (stretching to 117.6%), excellent conductivity (sheet resistance lower 0.4 Ω/sq), high transmittance (about 90% in full spectra), and ultra-thin thickness (3.7 μm). By assembling the metal electrode, the electrochromic material and the hydrogel, a paper-thin, ultra-flexible, and stretchable ECD with an overall thickness of 113 μm was prepared, which could be attached to the manifold and undulating surface of things and be stretched without compromising the dynamic bleaching and coloration performance. The triple-layered and substrate-free ECD with excellent flexibility and wearability could serve as futuristic electronics used for multiple purposes, like flexible displays, camouflage wearables and medical monitoring, etc.
Position correlation enabled quantum imaging with undetected photons
Authors: Viswanathan Balakrishnan , Barreto Lemos Gabriela , Lahiri Mayukh
Published: June 2021

Quantum imaging with undetected photons (QIUP) is a unique imaging technique that does not require the detection of the light used for illuminating the object. This technique requires a correlated pair of photons. In the existing implementations of QIUP, the imaging is enabled by the momentum correlation between the twin photons. We investigate the complementary scenario in which the imaging is instead enabled by the position correlation between the two photons. We present a general theory and show that the properties of the images obtained in these two cases are significantly distinct.
High-spectral-resolution lidar for measuring tropospheric temperature profiles by means of Rayleigh–Brillouin scattering
Authors: Xu Jiaqi , Witschas Benjamin , Kabelka Pau Gomez , Liang Kun
Published: June 2021

A novel high-spectral-resolution lidar receiver based on a Fizeau interferometer and a photomultiplier tube array for tropospheric temperature profiling is introduced. Compared to other temperature lidars, an imaging approach is used to resolve the entire Rayleigh–Brillouin (RB) spectrum without applying frequency scanning techniques. The functionality of the system is demonstrated by means of a nighttime measurement. Atmospheric temperature is retrieved from 4.0 km to 9.2 km by analyzing the measured RB spectra with the Tenti S6 line shape model. The systematic error of the retrieved temperatures is determined to be smaller than 3 K, and the corresponding random error varies between 1.7 K (4.0 km) and 2.3 K (9.2 km) for an observation time of 5 min and a vertical resolution of 0.3 km. Considering the short averaging time and the stable arrangement of the system, the suggested approach is also attractive for future airborne applications.
Sub-bandgap absorption and photo-response of molybdenum heavily doped black silicon fabricated by a femtosecond laser
Authors: Yang Yang , Zhao Ji-Hong , Li Chao , Chen Qi-Dai , Chen Zhan-Guo , Sun Hong-Bo
Published: June 2021

Molybdenum (Mo)-doped black silicon (Si) is obtained by using femtosecond laser irradiation. The concentration of Mo atoms at the depth from 10 to 200 nm has exceeded

10

19

c
m

−
3

. In contrast, the carrier concentration in the Mo-doped layer is lower than

10

15

c
m

−
3

. The surface morphologies with ripple and conical spike microstructures are formed by changing the pulsed laser fluences. The Mo-doped Si samples exhibit a sub-bandgap (

1100

∼

2500

n
m

) absorptance of more than 60% at a wavelength of 1310 nm. A Mo-doped Si photodetector is made, and the responsivity of the device for 1310 nm is up to 76 mA/W at a

−

10

V

bias.
Liquid crystal microlenses based on binary surface alignment controlled by focused ion beam treatment
Authors: Palto Serguei P. , Geivandov Artur R. , Kasyanova Irina V. , Simdyankin Ivan V. , Artemov Vladimir V. , Gorkunov Maxim V.
Published: June 2021

We report the formation of high optical power microlenses in the near-surface region of the liquid crystal layer. Such microlenses, possessing a very small focal length

f

at a rather large aperture A (

f

/

A

∼

2

), are able to focus the light into spots of a characteristic size comparable with the wavelength. Using numerical modeling, a specific patterning profile of a liquid crystal (LC) alignment surface by an ion beam is proposed to provide the aligning properties necessary for the formation of an array of microlenses with a focal length comparable to the LC cell thickness. The proposed microlens arrays are produced, and their optical properties are discussed.
Planar GeSn lateral p-i-n resonant-cavity-enhanced photodetectors for short-wave infrared integrated photonics
Authors: Chang Chen-Yang , Bansal Radhika , Lee Kuo-Chih , Sun Greg , Soref Richard , Cheng H. H. , Chang Guo-En
Published: June 2021

We report normal-incidence planar GeSn resonant-cavity-enhanced photodetectors (RCE-PDs) with a lateralp-i-nhomojunction configuration on a silicon-on-insulator (SOI) platform for short-wave infrared (SWIR) integrated photonics. The buried oxide of the SOI platform and the depositedSiO2layer serve as the bottom and top reflectors, respectively, creating a vertical cavity for enhancing the optical responsivity. The planarp-i-ndiode structure is favorable for complementary-metal-oxide-semiconductor-compatible, large-scale integration. With the bandgap reduction enabled by the 4.2% Sn incorporation into the GeSn active layer, the photodetection range extends to 1960 nm. The promising results demonstrate that the developed planar GeSn RCE-PDs are potential candidates for SWIR integrated photonics.
Fractional orbital angular momentum conversion in second-harmonic generation with an asymmetric perfect vortex beam
Authors: Dai Kunjian , Miller J. Keith , Li Wenzhe , Watkins Richard J. , Johnson Eric G.
Published: June 2021

This Letter demonstrates the nonlinear conversion of asymmetric perfect
vortex (APV) beams with fractional orbital angular momentum (OAM). By
controlling the amplitude and phase of the fundamental light field, we
create APVs whose global OAM demonstrates a one-to-one correspondence
of the charge numbers for fractional OAM values. The results show that
the OAM of the second-harmonic generation fields follow the OAM
conservation law. The nonlinear interactions of multiple OAM beams
with the APVs are also investigated as they relate to the nonlinear
frequency conversion and are shown to exhibit unique frequencies as a
result of the Doppler frequency tagged OAM values.
Self-starting triple-wavelength vector dark soliton with a bismuth-doped fiber saturable absorber
Authors: Zhang Pei , Nizamani Bilal , Najm Mustafa Mohammed , Dimyati Kaharudin , Yasin Moh , Harun Sulaiman Wadi
Published: June 2021

We report on the generation of a triple-wavelength vector dark soliton in an all-fiber ring cavity of erbium-doped fiber laser mode-locked with a bismuth-doped fiber saturable absorber. The formation of the triple-wavelength vector dark soliton is due to the cross-phase coupling derived from the cavity birefringence. The mode-locked laser operated at a 1.89 MHz repetition rate with a 335 ns pulse width, and its robustness is confirmed.
Kilowatt level Raman amplifier based on 100  µm core diameter multimode GRIN fiber with M2 = 1.6
Authors: Fan Chenchen , Xiao Hu , Yao Tianfu , Xu Jiangming , Chen Yizhu , Leng Jinyong , Zhou Pu
Published: June 2021

In this Letter, we demonstrate a high-power Raman fiber amplifier with excellent beam quality based on graded-index fiber. The Yb-doped fiber laser (YDFL) and bandwidth-tunable amplified spontaneous emission (ASE) source are employed as the pump source to compare the laser performance separately. When the ASE with a bandwidth of 8 nm is employed, a maximum power of 943 W at 1130 nm is achieved, which is twice that pumped by YDFL. The beam quality factor

M

2

at maximum output power is 1.6, with a brightness enhancement (BE) factor of 27. To the best of our knowledge, this is the best beam quality and BE factor based on pure Raman gain with output power of over 100 W.
Rapid microstructural plasticity in the cortical semantic network following a short language learning session
Authors: Vukovic Nikola , Hansen Brian , Lund Torben Ellegaard , Jespersen Sune , Shtyrov Yury
Published: June 2021

Despite the clear importance of language in our life, our vital ability to quickly and effectively learn new words and meanings is neurobiologically poorly understood. Conventional knowledge maintains that language learning—especially in adulthood—is slow and laborious. Furthermore, its structural basis remains unclear. Even though behavioural manifestations of learning are evident near instantly, previous neuroimaging work across a range of semantic categories has largely studied neural changes associated with months or years of practice. Here, we address rapid neuroanatomical plasticity accompanying new lexicon acquisition, specifically focussing on the learning of action-related language, which has been linked to the brain’s motor systems. Our results show that it is possible to measure and to externally modulate (using transcranial magnetic stimulation (TMS) of motor cortex) cortical microanatomic reorganisation after mere minutes of new word learning. Learning-induced microstructural changes, as measured by diffusion kurtosis imaging (DKI) and machine learning-based analysis, were evident in prefrontal, temporal, and parietal neocortical sites, likely reflecting integrative lexico-semantic processing and formation of new memory circuits immediately during the learning tasks. These results suggest a structural basis for the rapid neocortical word encoding mechanism and reveal the causally interactive relationship of modal and associative brain regions in supporting learning and word acquisition.
RNA-directed DNA methylation prevents rapid and heritable reversal of transposon silencing under heat stress in Zea mays
Authors: Guo Wei , Wang Dafang , Lisch Damon
Published: June 2021

In large complex plant genomes, RNA-directed DNA methylation (RdDM) ensures that epigenetic silencing is maintained at the boundary between genes and flanking transposable elements. In maize, RdDM is dependent on Mediator of Paramutation1 (Mop1), a gene encoding a putative RNA dependent RNA polymerase. Here we show that although RdDM is essential for the maintenance of DNA methylation of a silenced MuDR transposon in maize, a loss of that methylation does not result in a restoration of activity. Instead, heritable maintenance of silencing is maintained by histone modifications. At one terminal inverted repeat (TIR) of this element, heritable silencing is mediated via histone H3 lysine 9 dimethylation (H3K9me2), and histone H3 lysine 27 dimethylation (H3K27me2), even in the absence of DNA methylation. At the second TIR, heritable silencing is mediated by histone H3 lysine 27 trimethylation (H3K27me3), a mark normally associated with somatically inherited gene silencing. We find that a brief exposure of high temperature in a mop1 mutant rapidly reverses both of these modifications in conjunction with a loss of transcriptional silencing. These reversals are heritable, even in mop1 wild-type progeny in which methylation is restored at both TIRs. These observations suggest that DNA methylation is neither necessary to maintain silencing, nor is it sufficient to initiate silencing once has been reversed. However, given that heritable reactivation only occurs in a mop1 mutant background, these observations suggest that DNA methylation is required to buffer the effects of environmental stress on transposable elements.
RIOK2 phosphorylation by RSK promotes synthesis of the human small ribosomal subunit
Authors: Cerezo Emilie L. , Houles Thibault , Lié Oriane , Sarthou Marie-Kerguelen , Audoynaud Charlotte , Lavoie Geneviève , Halladjian Maral , Cantaloube Sylvain , Froment Carine , Burlet-Schiltz Odile , Henry Yves , Roux Philippe P. , Henras Anthony K. , Romeo Yves
Published: June 2021

Ribosome biogenesis lies at the nexus of various signaling pathways coordinating protein synthesis with cell growth and proliferation. This process is regulated by well-described transcriptional mechanisms, but a growing body of evidence indicates that other levels of regulation exist. Here we show that the Ras/mitogen-activated protein kinase (MAPK) pathway stimulates post-transcriptional stages of human ribosome synthesis. We identify RIOK2, a pre-40S particle assembly factor, as a new target of the MAPK-activated kinase RSK. RIOK2 phosphorylation by RSK stimulates cytoplasmic maturation of late pre-40S particles, which is required for optimal protein synthesis and cell proliferation. RIOK2 phosphorylation facilitates its release from pre-40S particles and its nuclear re-import, prior to completion of small ribosomal subunits. Our results bring a detailed mechanistic link between the Ras/MAPK pathway and the maturation of human pre-40S particles, which opens a hitherto poorly explored area of ribosome biogenesis.
Diagnostic accuracy of GeneXpert MTB/RIF assay for detection of tubercular pleural effusion
Authors: Jain Jyoti , Jadhao Pooja , Banait Shashank , Salunkhe Preetam
Published: June 2021

India has been engaged in tuberculosis (TB) control activities for over 50 years and yet TB continues to remain India’s important public health problem. The present study was conducted to compare the performance of GeneXpert MTB/RIF (GXpert) assay with composite reference standard in diagnosing cases of tubercular pleural effusion (TPE) and to evaluate the reliability of rifampicin resistance. A cross-sectional study was performed in a Department of Medicine of a rural teaching tertiary care hospital in central India. In all consecutive patients with pleural effusion on chest radiograph presenting to Department of Medicine, GXpert assay and composite reference standard was performed to evaluate the diagnostic accuracy of GXpert assay for detecting TPE in comparison to composite reference standard. Standard formulae were used to calculate the sensitivity, specificity, positive predictive values (PPV), negative predictive values (NPV), positive likelihood ratios (LR+) and negative likelihood ratios (LR-). Mc-Nemar’s test was applied to compare variables. All comparisons were two-tailed. We considered the difference to be statistically significant if the P value was less than 0.05. The sensitivity of the GXpert assay in diagnosing TPE was 16.6% among 158 study participants, the specificity was 100% and diagnostic accuracy was 52.5% which was statistically significant (p value < 0.05). It had a PPV of 100% (95%CI: 88.3% - 100%) and a NPV of 47.5% (95%CI: 39.3% - 55.7%). The LR+ and LR-were 23.5 (95%CI: 1.43–38.6) and 0.83 (95%CI: 0.76–0.91) respectively. GXpert assay has a very high specificity in diagnosing TPE but has a low sensitivity. In comparison to composite reference standard Thus its clinical utility is limited when used as a standalone test. A physician’s clinical acumen in combination with routine pleural fluid analysis should be the key factor in the diagnosis of TPE in clinically and radiologically suspected patients, especially in high TB burden countries.
Early mortality in tuberculosis patients initially lost to follow up following diagnosis in provincial hospitals and primary health care facilities in Western Cape, South Africa
Authors: Osman Muhammad , Meehan Sue-Ann , von Delft Arne , Du Preez Karen , Dunbar Rory , Marx Florian M. , Boulle Andrew , Welte Alex , Naidoo Pren , Hesseling Anneke C.
Published: June 2021

In South Africa, low tuberculosis (TB) treatment coverage and high TB case fatality remain important challenges. Following TB diagnosis, patients must link with a primary health care (PHC) facility for initiation or continuation of antituberculosis treatment and TB registration. We aimed to evaluate mortality among TB patients who did not link to a TB treatment facility for TB treatment within 30 days of their TB diagnosis, i.e. who were “initial loss to follow-up (ILTFU)” in Cape Town, South Africa. We prospectively included all patients with a routine laboratory or clinical diagnosis of TB made at PHC or hospital level in Khayelitsha and Tygerberg sub-districts in Cape Town, using routine TB data from an integrated provincial health data centre between October 2018 and March 2020. Overall, 74% (10,208/13,736) of TB patients were diagnosed at PHC facilities and ILTFU was 20.0% (2,742/13,736). Of ILTFU patients, 17.1% (468/2,742) died, with 69.7% (326/468) of deaths occurring within 30 days of diagnosis. Most ILTFU deaths (85.5%; 400/468) occurred in patients diagnosed in hospital. Multivariable logistic regression identified increasing age, HIV positive status, and hospital-based TB diagnosis (higher in the absence of TB treatment initiation and being ILTFU) as predictors of mortality. Although hospitals account for a modest proportion of diagnosed TB patients they have high TB-associated mortality. A hospital-based TB diagnosis is a critical opportunity to identify those at high risk of early and overall mortality. Interventions to diagnose TB before hospital admission, improve linkage to TB treatment following diagnosis, and reduce mortality in hospital-diagnosed TB patients should be prioritised.
Deep learning for discovering pathological continuum of crypts and evaluating therapeutic effects: An implication for in vivo preclinical study
Authors: Shan Dechao , Zheng Jie , Klimowicz Alexander , Panzenbeck Mark , Liu Zheng , Feng Di
Published: June 2021

Applying deep learning to the field of preclinical in vivo studies is a new and exciting prospect with the potential to unlock decades worth of underutilized data. As a proof of concept, we performed a feasibility study on a colitis model treated with Sulfasalazine, a drug used in therapeutic care of inflammatory bowel disease. We aimed to evaluate the colonic mucosa improvement associated with the recovery response of the crypts, a complex histologic structure reflecting tissue homeostasis and repair in response to inflammation. Our approach requires robust image segmentation of objects of interest from whole slide images, a composite low dimensional representation of the typical or novel morphological variants of the segmented objects, and exploration of image features of significance towards biology and treatment efficacy. Both interpretable features (eg. counts, area, distance and angle) as well as statistical texture features calculated using Gray Level Co-Occurance Matrices (GLCMs), are shown to have significance in analysis. Ultimately, this analytic framework of supervised image segmentation, unsupervised learning, and feature analysis can be generally applied to preclinical data. We hope our report will inspire more efforts to utilize deep learning in preclinical in vivo studies and ultimately make the field more innovative and efficient.
Network pharmacology and molecular docking study on the mechanism of colorectal cancer treatment using Xiao-Chai-Hu-Tang
Authors: Jin Jingyun , Chen Bin , Zhan Xiangyang , Zhou Zhiyi , Liu Hui , Dong Yun
Published: June 2021

Background and objective

We aimed to predict the targets and signal pathways of Xiao-Chai-Hu-Tang (XCHT) in the treatment of colorectal cancer (CRC) based on network pharmacology, just as well as to further analyze its anti-CRC material basis and mechanism of action.

Methods

We adopted Traditional Chinese Medicine Systems Pharmacology Database (TCMSP) and Traditional Chinese Medicine Integrated Database (TCMID) databases to screen the active ingredients and potential targets of XCHT. CRC-related targets were retrieved by analyzing published microarray data (accession number GSE110224) from the Gene Expression Omnibus (GEO) database. The common targets were used to construct the “herb-active ingredient-target” network using the Cytoscape 3.8.0 software. Next, we constructed and analyzed protein-to-protein interaction (PPI) using BisoGenet and CytoNCA plug-in in Cytoscape. We then performed Gene Ontology (GO) functional and the Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway enrichment analyses of target genes using the R package of clusterProfiler. Furthermore, we used the AutoDock Tools software to conduct molecular docking studies on the active ingredients and key targets to verify the network pharmacological analysis results.

Results

We identified a total of 71 active XCHT ingredients and 20 potential anti-CRC targets. The network analysis revealed quercetin, stigmasterol, kaempferol, baicalein, and acacetin as potential key compounds, and PTGS2, NR3C2, CA2, and MMP1 as potential key targets. The active ingredients of XCHT interacted with most CRC disease targets. We showed that XCHT’s therapeutic effect was attributed to its synergistic action (multi-compound, multi-target, and multi-pathway). Our GO enrichment analysis showed 46 GO entries, including 20 biological processes, 6 cellular components, and 20 molecular functions. We identified 11 KEGG signaling pathways, including the IL-17, TNF, Toll-like receptor, and NF-kappa B signaling pathways. Our results showed that XCHT could play a role in CRC treatment by regulating different signaling pathways. The molecular docking experiment confirmed the correlation between five core compounds (quercetin, stigmasterol, kaempferol, baicalein, and acacetin) just as well as PTGS2, NR3C2, CA2, and MMP1.

Conclusion

In this study, we described the potential active ingredients, possible targets, and key biological pathways responsible for the efficacy of XCHT in CRC treatment, providing a theoretical basis for further research.
Physiotherapy and related management for childhood obesity: A systematic scoping review
Authors: Truong Kim , Park Sandra , Tsiros Margarita D. , Milne Nikki
Published: June 2021

Introduction

Despite targeted efforts globally to address childhood overweight/obesity, it remains poorly understood and challenging to manage. Physiotherapists have the potential to manage children with obesity as they are experts in movement and physical activity. However, their role remains unclear due to a lack of physiotherapy-specific guidelines. This scoping review aims to explore existing literature, critically appraising and synthesising findings to guide physiotherapists in the evidence-based management of childhood overweight/obesity.

Method

A scoping review was conducted, including literature up to May 2020. A review protocol exists on Open Science Framework athttps://osf.io/fap8g/. Four databases were accessed including PubMed, Embase, CINAHL, Medline via OVID, with grey literature searched through google via “file:pdf”. A descriptive synthesis was undertaken to explore the impact of existing interventions and their efficacy.

Results

From the initial capture of 1871 articles, 263 intervention-based articles were included. Interventions included qualitative focused physical activity, quantitative focused physical activity and multicomponent interventions. Various outcome measures were utilised including health-, performance- and behaviour-related outcomes. The general trend for physiotherapy involvement with children who are obese appears to favour: 1) multicomponent interventions, implementing more than one component with environmental modification and parental involvement and 2) quantitative physical activity interventions, focusing on the quantity of bodily movement. These approaches most consistently demonstrated desirable changes across behavioural and health-related outcome measures for multicomponent and quantitative physical activity interventions respectively.

Conclusion

When managing children with obesity, physiotherapists should consider multicomponent approaches and increasing the quantity of physical activity, given consistent improvements in various obesity-related outcomes. Such approaches are well suited to the scope of physiotherapists and their expertise in physical activity prescription for the management of childhood obesity. Future research should examine the effect of motor skill interventions and consider the role of environmental modification/parental involvement as factors contributing to intervention success.
The effect of colour on reading performance in children, measured by a sensor hub: From the perspective of gender
Authors: Jakovljević Tamara , Janković Milica M. , Savić Andrej M. , Soldatović Ivan , Mačužić Ivan , Jakulin Tadeja Jere , Papa Gregor , Ković Vanja
Published: June 2021

In recent decades reported findings regarding gender differences in reading achievement, cognitive abilities and maturation process in boys and girls are conflicting. As reading is one of the most important processes in the maturation of an individual, the aim of the study was to better understand gender differences between primary school students. The study evaluates differences in Heart Rate Variability (HRV), Electroencephalography (EEG), Electrodermal Activities (EDA) and eye movement of participants during the reading task. Taking into account that colour may affect reading skills, in that it affects the emotional and physiological state of the body, the research attempts to provide a better understanding of gender differences in reading through examining the effect of colour, as applied to reading content. The physiological responses of 50 children (25 boys and 25 girls) to 12 different background and overlay colours of reading content were measured and summarised during the reading process. Our findings show that boys have shorter reading duration scores and a longer Saccade Count, Saccade Duration Total, and Saccade Duration Average when reading on a coloured background, especially purple, which could be caused by their motivation and by the type of reading task. Also, the boys had higher values for the Delta band and the Whole Range of EEG measurements in comparison to the girls when reading on coloured backgrounds, which could reflect the faster maturation of the girls. Regarding EDA measurements we did not find systematic differences between groups either on white or on coloured/overlay background. We found the most significant differences arose in the HRV parameters, namely (SDNN (ms), STD HR (beats/min), RMSSD (ms), NN50 (beats), pNN50 (%), CVRR) when children read the text on coloured/overlay backgrounds, where the girls showed systematically higher values on HRV measurements in comparison to the boys, mostly with yellow, red, and orange overlay colours.
Production planning of a furniture manufacturing company with random demand and production capacity using stochastic programming
Authors: Gómez-Rocha José Emmanuel , Hernández-Gress Eva Selene , Rivera-Gómez Héctor
Published: June 2021

In this article two multi-stage stochastic linear programming models are developed, one applying the stochastic programming solver integrated by Lingo 17.0 optimization software that utilizes an approximation using an identical conditional sampling and Latin-hyper-square techniques to reduce the sample variance, associating the probability distributions to normal distributions with defined mean and standard deviation; and a second proposed model with a discrete distribution with 3 values and their respective probabilities of occurrence. In both cases, a scenario tree is generated. The models developed are applied to an aggregate production plan (APP) for a furniture manufacturing company located in the state of Hidalgo, Mexico, which has important clients throughout the country. Production capacity and demand are defined as random variables of the model. The main purpose of this research is to determine a feasible solution to the aggregate production plan in a reasonable computational time. The developed models were compared and analyzed. Moreover, this work was complemented with a sensitivity analysis; varying the percentage of service level, also, varying the stochastic parameters (mean and standard deviation) to test how these variations impact in the solution and decision variables.
Differences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers
Authors: Morris Ellen Ruth A. , Boyle Ashley G. , Riihimäki Miia , Aspán Anna , Anis Eman , Hillhouse Andrew E. , Ivanov Ivan , Bordin Angela I. , Pringle John , Cohen Noah D.
Published: June 2021

Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor infects other host mammals or vectors, and infection results in short-lived immunity. Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood. Thus, our objective was to use next-generation sequencing technologies to characterize the genome, methylome, and transcriptome of isolates of SEE from horses with acute clinical strangles and inapparent carrier horses—including isolates recovered from individual horses sampled repeatedly—to assess pathogen-associated changes that might reflect specific adaptions of SEE to the host that contribute to inapparent carriage. The accessory genome elements and methylome of SEE isolates from Sweden and Pennsylvania revealed no significant or consistent differences between acute clinical and inapparent carrier isolates of SEE. RNA sequencing of SEE isolates from Pennsylvania demonstrated no genes that were differentially expressed between acute clinical and inapparent carrier isolates of SEE. The absence of specific, consistent changes in the accessory genomes, methylomes, and transcriptomes of acute clinical and inapparent carrier isolates of SEE indicates that adaptations of SEE to the host are unlikely to explain the carrier state of SEE. Efforts to understand the carrier state of SEE should instead focus on host factors.
Intragenomic sequence variations in the second internal transcribed spacer (ITS2) ribosomal DNA of the malaria vector Anopheles stephensi
Authors: Mishra Shobhna , Sharma Gunjan , Das Manoj K. , Pande Veena , Singh Om P.
Published: June 2021

Second Internal Transcribed Spacer (ITS2) ribosomal DNA (rDNA) sequence is a widely used molecular marker for species-identification or -delimitation due to observed concerted evolution which is believed to homogenize rDNA copies in an interbreeding population. However, intra-specific differences in ITS2 ofAnopheles stephensihave been reported. This study reports the presence of intragenomic sequence variation in the ITS2-rDNA ofAn.stephensiand hypothesizes that observed intra-specific differences in this species may have resulted due to ambiguous DNA sequence-chromatogram resulting from intragenomic heterogeneity.Anopheles stephensicollected from different parts of India were sequenced for complete ITS2 and the variable region of 28S-rDNA (d1-d3 domains). Intragenomic variations were found in ITS2 region of allAn.stephensisequenced, but no such variation was observed in d1 to d3 domains of 28S-rDNA. Cloning and sequencing of ITS2 through the d3 domain of the 28S region of rDNA from representative samples from northern, central, and southern India confirmed the presence of intragenomic variation in ITS2 due to transitions at three loci and two bp indel in a di-nucleotide microsatellite locus. Multiple haplotypes were observed in ITS2 raised from such variations. Due to the absence of detectable intragenomic sequence variation in the d1 to d3 domain of 28S rDNA ofAn.stephensi, this region can serve as an ideal reference sequence for taxonomic and phylogenetic studies. The presence of intragenomic variation in rDNA should be carefully examined before using this as a molecular marker for species delimitation or phylogenetic analyses.
Two human antibodies to a meningococcal serogroup B vaccine antigen enhance binding of complement Factor H by stabilizing the Factor H binding site
Authors: Sands Nathaniel A. , Beernink Peter T.
Published: June 2021

Microbial pathogens bind host complement regulatory proteins to evade the immune system. The bacterial pathogen Neisseria meningitidis, or meningococcus, binds several complement regulators, including human Factor H (FH). FH binding protein (FHbp) is a component of two licensed meningococcal vaccines and in mice FHbp elicits antibodies that inhibit binding of FH to FHbp, which defeat the bacterial evasion mechanism. However, humans vaccinated with FHbp develop antibodies that enhance binding of FH to the bacteria, which could limit the effectiveness of the vaccines. In the present study, we show that two vaccine-elicited antibody fragments (Fabs) isolated from different human subjects increase binding of complement FH to meningococcal FHbp by ELISA. The two Fabs have different effects on the kinetics of FH binding to immobilized FHbp as measured by surface plasmon resonance. The 1.7- and 2.0-Å resolution X-ray crystal structures of the Fabs in complexes with FHbp illustrate that the two Fabs bind to similar epitopes on the amino-terminal domain of FHbp, adjacent to the FH binding site. Superposition models of ternary complexes of each Fab with FHbp and FH show that there is likely minimal contact between the Fabs and FH. Collectively, the structures reveal that the Fabs enhance binding of FH to FHbp by altering the conformations and mobilities of two loops adjacent to the FH binding site of FHbp. In addition, the 1.5 Å-resolution structure of one of the isolated Fabs defines the structural rearrangements associated with binding to FHbp. The FH-enhancing human Fabs, which are mirrored in the human polyclonal antibody responses, have important implications for tuning the effectiveness of FHbp-based vaccines.
Conservative production of galactosaminogalactan in Metarhizium is responsible for appressorium mucilage production and topical infection of insect hosts
Authors: Mei Lijuan , Wang Xuewen , Yin Ying , Tang Guirong , Wang Chengshu
Published: June 2021

The exopolysaccharide galactosaminogalactan (GAG) has been well characterized in Aspergilli, especially the human pathogenAspergillus fumigatus. It has been found that a five-gene cluster is responsible for GAG biosynthesis in Aspergilli to mediate fungal adherence, biofilm formation, immunosuppression or induction of host immune defences. Herein, we report the presence of the conserved GAG biosynthetic gene cluster in the insect pathogenic fungusMetarhizium robertsiito mediate either similar or unique biological functions. Deletion of the gene cluster disabled fungal ability to produce GAG on germ tubes, mycelia and appressoria. Relative to the wild type strain, null mutant was impaired in topical infection but not injection of insect hosts. We found that GAG production byMetarhiziumis partially acetylated and could mediate fungal adherence to hydrophobic insect cuticles, biofilm formation, and penetration of insect cuticles. In particular, it was first confirmed that this exopolymer is responsible for the formation of appressorium mucilage, the essential extracellular matrix formed along with the infection structure differentiation to mediate cell attachment and expression of cuticle degrading enzymes. In contrast to its production duringA.fumigatusinvasive growth, GAG is not produced on theMetarhiziumcells harvested from insect hemocoels; however, the polymer can glue germ tubes into aggregates to form mycelium pellets in liquid culture. The results of this study unravel the biosynthesis and unique function of GAG in a fungal system apart from the aspergilli species.